Evolutionary Genealogy of Genes: Non-supervised Orthologous Groups
Names
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Evolutionary Genealogy of Genes: Non-supervised Orthologous Groups
metasource: Fairsharing.org
version: FAIRsharing.org: eggNOG; Evolutionary Genealogy of Genes: Non-supervised Orthologous Groups; DOI: https://doi.org/10.25504/FAIRsharing.j1wj7d; Last edited: Jan. 8, 2019, 1:13 p.m.; Last accessed: Jan 03 2022 7:07 p.m.
eggNOG
metasource: Fairsharing.org
version: FAIRsharing.org: eggNOG; Evolutionary Genealogy of Genes: Non-supervised Orthologous Groups; DOI: https://doi.org/10.25504/FAIRsharing.j1wj7d; Last edited: Jan. 8, 2019, 1:13 p.m.; Last accessed: Jan 03 2022 7:07 p.m.
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657
metasource: bio.tools
version: extracted_at: 2022-11-04T11:29:55.005995
eggnog
metasource: bio.tools
version: extracted_at: 2022-11-04T11:29:55.005995
Names
More detailed information about this field from each metasource.
Evolutionary Genealogy of Genes: Non-supervised Orthologous Groups
metasource: Fairsharing.orgversion: FAIRsharing.org: eggNOG; Evolutionary Genealogy of Genes: Non-supervised Orthologous Groups; DOI: https://doi.org/10.25504/FAIRsharing.j1wj7d; Last edited: Jan. 8, 2019, 1:13 p.m.; Last accessed: Jan 03 2022 7:07 p.m.
eggNOG
metasource: Fairsharing.orgversion: FAIRsharing.org: eggNOG; Evolutionary Genealogy of Genes: Non-supervised Orthologous Groups; DOI: https://doi.org/10.25504/FAIRsharing.j1wj7d; Last edited: Jan. 8, 2019, 1:13 p.m.; Last accessed: Jan 03 2022 7:07 p.m.
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657
metasource: bio.tools
version: extracted_at: 2022-11-04T11:29:55.005995
eggnog
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:29:55.005995
Names
More detailed information about this field from each metasource.
Evolutionary Genealogy of Genes: Non-supervised Orthologous Groups
metasource: Fairsharing.orgversion: FAIRsharing.org: eggNOG; Evolutionary Genealogy of Genes: Non-supervised Orthologous Groups; DOI: https://doi.org/10.25504/FAIRsharing.j1wj7d; Last edited: Jan. 8, 2019, 1:13 p.m.; Last accessed: Jan 03 2022 7:07 p.m.
eggNOG
metasource: Fairsharing.orgversion: FAIRsharing.org: eggNOG; Evolutionary Genealogy of Genes: Non-supervised Orthologous Groups; DOI: https://doi.org/10.25504/FAIRsharing.j1wj7d; Last edited: Jan. 8, 2019, 1:13 p.m.; Last accessed: Jan 03 2022 7:07 p.m.
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657
metasource: bio.tools
version: extracted_at: 2022-11-04T11:29:55.005995
eggnog
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:29:55.005995
eggNOG (evolutionary genealogy of genes: Non-supervised Orthologous Groups) is a database of orthologous groups of genes. The orthologous groups are annotated with functional description lines (derived by identifying a common denominator for the genes based on their various annotations), with functional categories (i.e derived from the original COG/KOG categories).
Description
More detailed information about this field from each metasource.
eggNOG (evolutionary genealogy of genes: Non-supervised Orthologous Groups) is a database of orthologous groups of genes. The orthologous groups are annotated with functional description lines (derived by identifying a common denominator for the genes based on their various annotations), with functional categories (i.e derived from the original COG/KOG categories).
metasource: Fairsharing.orgversion: FAIRsharing.org: eggNOG; Evolutionary Genealogy of Genes: Non-supervised Orthologous Groups; DOI: https://doi.org/10.25504/FAIRsharing.j1wj7d; Last edited: Jan. 8, 2019, 1:13 p.m.; Last accessed: Jan 03 2022 7:07 p.m.
Next-generation sequencing technologies are now generating a vast amount of sequence data. This leads to a dramatic increase in the number of predicted protein sequences, which serve as a starting point for structural, functional and phylogenomic studies. In such studies, high-throughput comparative analyses are often required to transfer information between organisms, for which the concept of orthology is crucial. The original definition by Fitch describes orthologs as genes that diverged through a speciation event, as opposed to paralogs, which diverged after a duplication event (1). eggNOG, namely evolutionary genealogy of genes Non-supervised Orthologous Groups, is a database providing clusters of orthologous groups for a vast majority of genes covered by the whole tree of life. The database contains a hierarchy of orthologous groups to balance phylogenetic coverage and resolution, and provides automatic function annotation.
metasource: Nucleic Acid Research database catalogueversion: extracted_at: 2022-11-04T11:16:25.468657
eggNOG is a database of nested orthologous gene groups (NOGs) inferred using unsupervised clustering applied to >5,000 complete genomes followed by comprehensive characterization and analysis of the resulting gene families. eggNOG provides orthologous group assignments at 379 different taxonomic levels as well as multiple sequence alignments, maximum-likelihood trees and broad functional annotations for each group accessible via a web interface or through bulk download.
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:29:55.005995
Webpage:
http://eggnog.embl.deWebpage
More detailed information about this field from each metasource.
http://eggnog.embl.de
metasource: Fairsharing.orgversion: FAIRsharing.org: eggNOG; Evolutionary Genealogy of Genes: Non-supervised Orthologous Groups; DOI: https://doi.org/10.25504/FAIRsharing.j1wj7d; Last edited: Jan. 8, 2019, 1:13 p.m.; Last accessed: Jan 03 2022 7:07 p.m.
http://eggnog.embl.de/
metasource: Nucleic Acid Research database catalogueversion: extracted_at: 2022-11-04T11:16:25.468657
http://eggnogdb.embl.de/#/app/home
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:29:55.005995
Licence:
Name: NIH Web Policies and NoticesLicence name
More detailed information about this field from each metasource.
NIH Web Policies and Notices
metasource: Fairsharing.orgversion: FAIRsharing.org: eggNOG; Evolutionary Genealogy of Genes: Non-supervised Orthologous Groups; DOI: https://doi.org/10.25504/FAIRsharing.j1wj7d; Last edited: Jan. 8, 2019, 1:13 p.m.; Last accessed: Jan 03 2022 7:07 p.m.
GPL-3.0
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:29:55.005995
Licence URL
More detailed information about this field from each metasource.
https://www.nih.gov/web-policies-notices
metasource: Fairsharing.orgversion: FAIRsharing.org: eggNOG; Evolutionary Genealogy of Genes: Non-supervised Orthologous Groups; DOI: https://doi.org/10.25504/FAIRsharing.j1wj7d; Last edited: Jan. 8, 2019, 1:13 p.m.; Last accessed: Jan 03 2022 7:07 p.m.
Publications:
(7)
Publications
More detailed information about this field from each metasource.
eggNOG 4.5: a hierarchical orthology framework with improved functional annotations for eukaryotic, prokaryotic and viral sequences
PMID: 26582926
metasource: bio.tools
version: extracted_at: 2022-11-04T11:29:55.005995
eggNOG 5.0: a hierarchical, functionally and phylogenetically annotated orthology resource based on 5090 organisms and 2502 viruses
PMID: 30418610
metasource: bio.tools
version: extracted_at: 2022-11-04T11:29:55.005995
eggNOG v3.0: orthologous groups covering 1133 organisms at 41 different taxonomic ranges
PMID: 22096231
metasource: bio.tools
version: extracted_at: 2022-11-04T11:29:55.005995
eggNOG v4.0: nested orthology inference across 3686 organisms
PMID: 24297252
metasource: bio.tools
version: extracted_at: 2022-11-04T11:29:55.005995
eggNOG: automated construction and annotation of orthologous groups of genes
PMID: 17942413
metasource: Fairsharing.org
version: FAIRsharing.org: eggNOG; Evolutionary Genealogy of Genes: Non-supervised Orthologous Groups; DOI: https://doi.org/10.25504/FAIRsharing.j1wj7d; Last edited: Jan. 8, 2019, 1:13 p.m.; Last accessed: Jan 03 2022 7:07 p.m.
metasource: bio.tools
version: extracted_at: 2022-11-04T11:29:55.005995
eggNOG v2.0: extending the evolutionary genealogy of genes with enhanced non-supervised orthologous groups, species and functional annotations
PMID: 19900971
metasource: Fairsharing.org
version: FAIRsharing.org: eggNOG; Evolutionary Genealogy of Genes: Non-supervised Orthologous Groups; DOI: https://doi.org/10.25504/FAIRsharing.j1wj7d; Last edited: Jan. 8, 2019, 1:13 p.m.; Last accessed: Jan 03 2022 7:07 p.m.
metasource: bio.tools
version: extracted_at: 2022-11-04T11:29:55.005995
http://dx.doi.org/10.1093/nar/gkt1253
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657
Publications
More detailed information about this field from each metasource.
eggNOG 4.5: a hierarchical orthology framework with improved functional annotations for eukaryotic, prokaryotic and viral sequences
PMID: 26582926
metasource: bio.tools
version: extracted_at: 2022-11-04T11:29:55.005995
eggNOG 5.0: a hierarchical, functionally and phylogenetically annotated orthology resource based on 5090 organisms and 2502 viruses
PMID: 30418610
metasource: bio.tools
version: extracted_at: 2022-11-04T11:29:55.005995
eggNOG v3.0: orthologous groups covering 1133 organisms at 41 different taxonomic ranges
PMID: 22096231
metasource: bio.tools
version: extracted_at: 2022-11-04T11:29:55.005995
eggNOG v4.0: nested orthology inference across 3686 organisms
PMID: 24297252
metasource: bio.tools
version: extracted_at: 2022-11-04T11:29:55.005995
eggNOG: automated construction and annotation of orthologous groups of genes
PMID: 17942413
metasource: Fairsharing.org
version: FAIRsharing.org: eggNOG; Evolutionary Genealogy of Genes: Non-supervised Orthologous Groups; DOI: https://doi.org/10.25504/FAIRsharing.j1wj7d; Last edited: Jan. 8, 2019, 1:13 p.m.; Last accessed: Jan 03 2022 7:07 p.m.
metasource: bio.tools
version: extracted_at: 2022-11-04T11:29:55.005995
eggNOG v2.0: extending the evolutionary genealogy of genes with enhanced non-supervised orthologous groups, species and functional annotations
PMID: 19900971
metasource: Fairsharing.org
version: FAIRsharing.org: eggNOG; Evolutionary Genealogy of Genes: Non-supervised Orthologous Groups; DOI: https://doi.org/10.25504/FAIRsharing.j1wj7d; Last edited: Jan. 8, 2019, 1:13 p.m.; Last accessed: Jan 03 2022 7:07 p.m.
metasource: bio.tools
version: extracted_at: 2022-11-04T11:29:55.005995
http://dx.doi.org/10.1093/nar/gkt1253
metasource: Nucleic Acid Research database catalogueversion: extracted_at: 2022-11-04T11:16:25.468657
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eggNOG 4.5: a hierarchical orthology framework with improved functional annotations for eukaryotic, prokaryotic and viral sequences
PubMed citations: 811.
811 articles citing: eggNOG 4.5: a hierarchical orthology framework with improved functional annotations for eukaryotic, prokaryotic and viral sequences
A balanced gut microbiota is essential to maintain health in captive sika deer. PMID:35922588
Characterization of Cronobacter sakazakii Strains Originating from Plant-Origin Foods Using Comparative Genomic Analyses and Zebrafish Infectivity Studies. PMID:35889115
Realistic Gene Transfer to Gene Duplication Ratios Identify Different Roots in the Bacterial Phylogeny Using a Tree Reconciliation Method. PMID:35888084
Root nitrate uptake in sugarcane (Saccharum spp.) is modulated by transcriptional and presumably posttranscriptional regulation of the NRT2.1/NRT3.1 transport system. PMID:35879567
On the Compatibility of Fish Meal Replacements in Aquafeeds for Rainbow Trout. A Combined Metabolomic, Proteomic and Histological Study. PMID:35846007
The slow-evolving Acorus tatarinowii genome sheds light on ancestral monocot evolution. PMID:35835857
Caenorhabditis elegans MES-3 is a highly divergent ortholog of the canonical PRC2 component SUZ12. PMID:35800781
The evolutionary origin of host association in the Rickettsiales. PMID:35798888
Biomimetic generation of the strongest known biomaterial found in limpet tooth. PMID:35798724
CT295 Is Chlamydia trachomatis' Phosphoglucomutase and a Type 3 Secretion Substrate. PMID:35795184
PCycDB: a comprehensive and accurate database for fast analysis of phosphorus cycling genes. PMID:35787295
Gut microbiota alternation under the intestinal epithelium-specific knockout of mouse Piga gene. PMID:35752737
Sphingopyxis lutea sp. nov., a novel moderately halotolerant bacterium isolated from pebbles. PMID:35723741
Highly Specialized Carbohydrate Metabolism Capability in Bifidobacterium Strains Associated with Intestinal Barrier Maturation in Early Preterm Infants. PMID:35695455
Metagenomic assembled plasmids of the human microbiome vary across disease cohorts. PMID:35654877
Complete Genome Sequence of a Phage Infecting Sphingomonadaceae. PMID:35652632
The functional evolution of termite gut microbiota. PMID:35624491
Single-molecule long-read sequencing analysis improves genome annotation and sheds new light on the transcripts and splice isoforms of Zoysia japonica. PMID:35614434
Dynamic character displacement among a pair of bacterial phyllosphere commensals in situ. PMID:35595740
The spread of the first introns in proto-eukaryotic paralogs. PMID:35589959
Functional Redundancy in Soil Microbial Community Based on Metagenomics Across the Globe. PMID:35586865
Physiological Effects and Transcriptomic Analysis of sbGnRH on the Liver in Pompano (Trachinotus ovatus). PMID:35586618
Genomic Degeneration and Reduction in the Fish Pathogen Mycobacterium shottsii. PMID:35579461
Metagenomic-Metabolomic Mining of Kinema, a Naturally Fermented Soybean Food of the Eastern Himalayas. PMID:35572705
Adaptation of gut microbiome and host metabolic systems to lignocellulosic degradation in bamboo rats. PMID:35568757
Bioinformatic analyses to uncover genes involved in trehalose metabolism in the polyploid sugarcane. PMID:35525890
Evaluating metagenomic assembly approaches for biome-specific gene catalogues. PMID:35524337
Comparative analysis of genome-based CAZyme cassette in Antarctic Microbacterium sp. PAMC28756 with 31 other Microbacterium species. PMID:35486322
Shotgun metagenomic sequencing revealed the prebiotic potential of a grain-based diet in mice. PMID:35468931
Trophic interactions between predatory protists and pathogen-suppressive bacteria impact plant health. PMID:35461357
Coral holobiont cues prime Endozoicomonas for a symbiotic lifestyle. PMID:35444262
Genomic and resistome analysis of Alcaligenes faecalis strain PGB1 by Nanopore MinION and Illumina Technologies. PMID:35443609
Chryseobacterium tagetis sp. nov., a plant growth promoting bacterium with an antimicrobial activity isolated from the roots of medicinal plant (Tagetes patula). PMID:35440770
In-depth genome analysis of Bacillus sp. BH32, a salt stress-tolerant endophyte obtained from a halophyte in a semiarid region. PMID:35435457
Single cell genome sequencing of laboratory mouse microbiota improves taxonomic and functional resolution of this model microbial community. PMID:35417481
Deciphering Genomes: Genetic Signatures of Plant-Associated Micromonospora. PMID:35401599
Significance of both alkB and P450 alkane-degrading systems in Tsukamurella tyrosinosolvens: proteomic evidence. PMID:35396956
Assembly of a Hybrid Formica aquilonia × F. polyctena Ant Genome From a Haploid Male. PMID:35394540
Porcine gut microbiota in mediating host metabolic adaptation to cold stress. PMID:35383199
High Resistance to Quinclorac in Multiple-Resistant Echinochloa colona Associated with Elevated Stress Tolerance Gene Expression and Enriched Xenobiotic Detoxification Pathway. PMID:35328069
Structure and function of the soil microbiome underlying N2O emissions from global wetlands. PMID:35301304
Shotgun Metagenomics of Deep Forest Soil Layers Show Evidence of Altered Microbial Genetic Potential for Biogeochemical Cycling. PMID:35300488
Genome Analysis of the Broad Host Range Necrotroph Nalanthamala psidii Highlights Genes Associated With Virulence. PMID:35283890
Salmonella Salamae and S. Waycross isolated from Nile perch in Lake Victoria show limited human pathogenic potential. PMID:35273308
Genomic, biochemical, and phylogenetic evaluation of bacteria isolated from deep-sea sediment harboring methane hydrates. PMID:35266047
Genome-wide identification and characterization of Fusarium circinatum-responsive lncRNAs in Pinus radiata. PMID:35264109
A faecal microbiota signature with high specificity for pancreatic cancer. PMID:35260444
RNA-Seq reveals miRNA role in thermogenic regulation in brown adipose tissues of goats. PMID:35255830
Phosphonate production by marine microbes: Exploring new sources and potential function. PMID:35254902
Whole-genome sequencing for the characterization of resistance mechanisms and epidemiology of colistin-resistant Acinetobacter baumannii. PMID:35245298
Siderophores as an iron source for picocyanobacteria in deep chlorophyll maximum layers of the oligotrophic ocean. PMID:35241788
Transcriptome changes in the developing sugarcane culm associated with high yield and early-season high sugar content. PMID:35224663
Investigating the Mechanism of Unilateral Cross Incompatibility in Longan (Dimocarpus longan Lour.) Cultivars (Yiduo × Shixia). PMID:35222456
Genome Characterization and Probiotic Potential of Corynebacterium amycolatum Human Vaginal Isolates. PMID:35208706
Cultivating Lentinula edodes on Substrate Containing Composted Sawdust Affects the Expression of Carbohydrate and Aromatic Amino Acid Metabolism-Related Genes. PMID:35191774
Impact of dietary fructooligosaccharides (FOS) on murine gut microbiota and intestinal IgA secretion. PMID:35186653
Comparative Genome Analyses of Clavibacter michiganensis Type Strain LMG7333T Reveal Distinct Gene Contents in Plasmids From Other Clavibacter Species. PMID:35178040
Comparative transcriptome and weighted correlation network analyses reveal candidate genes involved in chlorogenic acid biosynthesis in sweet potato. PMID:35177832
METABOLIC: high-throughput profiling of microbial genomes for functional traits, metabolism, biogeochemistry, and community-scale functional networks. PMID:35172890
Investigation and characterization of human gut phageome in advanced liver cirrhosis of defined etiologies. PMID:35168645
De Novo Assembly and Annotation of the Vaginal Metatranscriptome Associated with Bacterial Vaginosis. PMID:35163545
Integration of Microbial Transformation Mechanism of Polyphosphate Accumulation and Sulfur Cycle in Subtropical Marine Mangrove Ecosystems with Spartina alterniflora Invasion. PMID:35157108
Characterization of a Novel Hot-Spring Cyanobacterium Leptodesmis sichuanensis sp. Nov. and Genomic Insights of Molecular Adaptations Into Its Habitat. PMID:35154020
Differential gene expression associated with a floral scent polymorphism in the evening primrose Oenothera harringtonii (Onagraceae). PMID:35151274
The microbiome of the buffalo digestive tract. PMID:35145088
Chromosome-Level Genome Assembly of the Rare and Endangered Tropical Plant Speranskia yunnanensis (Euphorbiaceae). PMID:35140736
Changes in Gut Microbiota of Patients with Atopic Dermatitis During Balneotherapy. PMID:35140493
Genome Sequence of Dermacoccus Strain Tok2021, a Soil Actinobacterium Isolated from a Pinus radiata Forest. PMID:35112892
Assembly of 97 Novel Bacterial Genomes in the Microbial Community Affiliated with Polyvinyl Alcohol in Soil of Northern China. PMID:35087906
Enrichment of phosphate-accumulating organisms (PAOs) in a microfluidic model biofilm system by mimicking a typical aerobic granular sludge feast/famine regime. PMID:35032186
Inferring early-life host and microbiome functions by mass spectrometry-based metaproteomics and metabolomics. PMID:35024099
Insight into the symbiotic lifestyle of DPANN archaea revealed by cultivation and genome analyses. PMID:35022241
Evolutionary Ecology of Natural Comammox Nitrospira Populations. PMID:35014874
Complete de novo assembly of Wolbachia endosymbiont of Diaphorina citri Kuwayama (Hemiptera: Liviidae) using long-read genome sequencing. PMID:34996906
Inferring the genetic responses to acute drought stress across an ecological gradient. PMID:34983380
Effects of DISC1 on Alzheimer's disease cell models assessed by iTRAQ proteomics analysis. PMID:34981809
Physiological, Biochemical and Transcriptomic Analysis of the Aerial Parts (Leaf-Blade and Petiole) of Asarum sieboldii Responding to Drought Stress. PMID:34948197
Safety Evaluation of Weissella cibaria JW15 by Phenotypic and Genotypic Property Analysis. PMID:34946052
De Novo Assembly and Species-Specific Marker Development as a Useful Tool for the Identification of Scutellaria L. Species. PMID:34940126
Shotgun sequence-based metataxonomic and predictive functional profiles of Pe poke, a naturally fermented soybean food of Myanmar. PMID:34919575
Worldwide distribution and environmental origin of the Adelaide imipenemase (AIM-1), a potent carbapenemase in Pseudomonas aeruginosa. PMID:34919514
Genomic adaptations of Campylobacter jejuni to long-term human colonization. PMID:34893079
Ciliary photoreceptors in sea urchin larvae indicate pan-deuterostome cell type conservation. PMID:34863182
The whole-genome sequence of the novel yeast species Metschnikowia persimmonesis isolated from medicinal plant Diospyros kaki Thunb. PMID:34849782
Protective role of the Arabidopsis leaf microbiota against a bacterial pathogen. PMID:34819644
Hundreds of Out-of-Frame Remodeled Gene Families in the Escherichia coli Pangenome. PMID:34792602
Salinity Drives Functional and Taxonomic Diversities in Global Water Metagenomes. PMID:34790175
Unraveling gene content variation across eukaryotic giant viruses based on network analyses and host associations. PMID:34754514
Genomic Insights Into the Archaea Inhabiting an Australian Radioactive Legacy Site. PMID:34737728
Sex without crossing over in the yeast Saccharomycodes ludwigii. PMID:34732243
Citrullination Was Introduced into Animals by Horizontal Gene Transfer from Cyanobacteria. PMID:34730808
DNA Viral Diversity, Abundance, and Functional Potential Vary across Grassland Soils with a Range of Historical Moisture Regimes. PMID:34724822
Lactitol Supplementation Modulates Intestinal Microbiome in Liver Cirrhotic Patients. PMID:34722597
Integrating full-length transcriptomics and metabolomics reveals the regulatory mechanisms underlying yellow pigmentation in tree peony (Paeonia suffruticosa Andr.) flowers. PMID:34719694
De novo transcriptome analysis provides insights into the salt tolerance of Podocarpus macrophyllus under salinity stress. PMID:34696735
Stable Soil Microbial Functional Structure Responding to Biodiversity Loss Based on Metagenomic Evidences. PMID:34690962
The Semi-Supervised Strategy of Machine Learning on the Gene Family Diversity to Unravel Resveratrol Synthesis. PMID:34685867
Aspergillus fumigatus versus Genus Aspergillus: Conservation, Adaptive Evolution and Specific Virulence Genes. PMID:34683335
Genome-Wide Identification of Ralstonia solanacearum Genes Required for Survival in Tomato Plants. PMID:34636662
Phytoplankton exudates and lysates support distinct microbial consortia with specialized metabolic and ecophysiological traits. PMID:34620710
Lectin receptor-like kinase LecRK-VIII.2 is a missing link in MAPK signaling-mediated yield control. PMID:34618128
A chromosome-level genome assembly for the eastern fence lizard (Sceloporus undulatus), a reptile model for physiological and evolutionary ecology. PMID:34599334
Genomic analysis of the nomenclatural type strain of the nematode-associated entomopathogenic bacterium Providencia vermicola. PMID:34598677
Genome assembly of the popular Korean soybean cultivar Hwangkeum. PMID:34568925
Improved draft reference genome for the Glassy-winged Sharpshooter (Homalodisca vitripennis), a vector for Pierce's disease. PMID:34568917
Transcriptome repository of North-Western Himalayan endangered medicinal herbs: a paramount approach illuminating molecular perspective of phytoactive molecules and secondary metabolism. PMID:34557965
Diverse Host Immune Responses of Different Geographical Populations of the Coconut Rhinoceros Beetle to Oryctes Rhinoceros Nudivirus (OrNV) Infection. PMID:34523987
Can functional genomic diversity provide novel insights into mechanisms of community assembly? A pilot study from an invaded alpine streambed. PMID:34522362
Chromosomal neighbourhoods allow identification of organ specific changes in gene expression. PMID:34506480
Verrucomicrobiota are specialist consumers of sulfated methyl pentoses during diatom blooms. PMID:34493810
Understanding molt control switches: Transcriptomic and expression analysis of the genes involved in ecdysteroidogenesis and cholesterol uptake pathways in the Y-organ of the blue crab, Callinectes sapidus. PMID:34478479
A Meta-Analysis of Bioelectric Data in Cancer, Embryogenesis, and Regeneration. PMID:34476377
Niche differentiation of belowground microorganisms and their functional signatures in Assam type tea (Camellia sinensis var. assamica). PMID:34462787
Moisture modulates soil reservoirs of active DNA and RNA viruses. PMID:34446837
Cappable-Seq Reveals Specific Patterns of Metabolism and Virulence for Salmonella Typhimurium Intracellular Survival within Acanthamoeba castellanii. PMID:34445780
Using Functional Annotations to Study Pairwise Interactions in Urinary Tract Infection Communities. PMID:34440394
Biomolecule and Bioentity Interaction Databases in Systems Biology: A Comprehensive Review. PMID:34439912
Comparative Transcriptomic Analysis Reveals the Effects of Drought on the Biosynthesis of Methyleugenol in Asarum sieboldii Miq. PMID:34439899
A global map of associations between types of protein posttranslational modifications and human genetic diseases. PMID:34430807
DiTing: A Pipeline to Infer and Compare Biogeochemical Pathways From Metagenomic and Metatranscriptomic Data. PMID:34408730
Protein Integrated Network Analysis to Reveal Potential Drug Targets Against Extended Drug-Resistant Mycobacterium tuberculosis XDR1219. PMID:34382159
Data on the first functionally-annotated de novo transcriptome assembly for North American flying squirrels (genus Glaucomys). PMID:34381854
Gonadal transcriptomes associated with sex phenotypes provide potential male and female candidate genes of sex determination or early differentiation in Crassostrea gigas, a sequential hermaphrodite mollusc. PMID:34372770
Transcriptome analysis of differentially expressed genes in chrysanthemum MET1 RNA interference lines. PMID:34366589
Biological Effect of Streptococcus pyogenes-Released Extracellular Vesicles on Human Monocytic Cells, Induction of Cytotoxicity, and Inflammatory Response. PMID:34350134
De novo sequencing and analysis of the transcriptome of two highbush blueberry (Vaccinium corymbosum L.) cultivars 'Bluecrop' and 'Legacy' at harvest and following post-harvest storage. PMID:34339434
Automated Phylogenetic Analysis Using Best Reciprocal BLAST. PMID:34313983
Deciphering Symbiotic Interactions of "Candidatus Aenigmarchaeota" with Inferred Horizontal Gene Transfers and Co-occurrence Networks. PMID:34313464
Transcriptome Characterization and Identification of Molecular Markers (SNP, SSR, and Indels) in the Medicinal Plant Sarcandra glabra spp. PMID:34307686
Genomic Analysis of Staphylococcus aureus Isolates Associated With Peracute Non-gangrenous or Gangrenous Mastitis and Comparison With Other Mastitis-Associated Staphylococcus aureus Isolates. PMID:34305849
Genome-Wide Identification, Structure Characterization, and Expression Pattern Profiling of the Aquaporin Gene Family in Betula pendula. PMID:34298887
Genome of the world's smallest flowering plant, Wolffia australiana, helps explain its specialized physiology and unique morphology. PMID:34294872
Hymenobacter taeanensis sp. nov., radiation resistant bacterium isolated from coastal sand dune. PMID:34292424
Bacteria associated with wood tissues of Esca-diseased grapevines: functional diversity and synergy with Fomitiporia mediterranea to degrade wood components. PMID:34288352
Analysis of the Taxonomy and Pathogenic Factors of Pectobacterium aroidearum L6 Using Whole-Genome Sequencing and Comparative Genomics. PMID:34276610
Towards omics-based predictions of planktonic functional composition from environmental data. PMID:34272373
High Transcriptional Activity and Diverse Functional Repertoires of Hundreds of Giant Viruses in a Coastal Marine System. PMID:34254826
Global transcriptome analysis of Stenotrophomonas maltophilia in response to growth at human body temperature. PMID:34252021
Full-Length Transcriptome Analysis Reveals Candidate Genes Involved in Terpenoid Biosynthesis in Artemisia argyi. PMID:34239538
Informative Regions In Viral Genomes. PMID:34207030
TRAPID 2.0: a web application for taxonomic and functional analysis of de novo transcriptomes. PMID:34197621
Draft genome sequence and potential identification of a biosurfactant from Brevibacterium casei strain LS14 an isolate from fresh water Loktak Lake. PMID:34194910
Pangenomics reveals alternative environmental lifestyles among chlamydiae. PMID:34188040
Proteomic and Transcriptomic Analyses Provide Novel Insights into the Crucial Roles of Host-Induced Carbohydrate Metabolism Enzymes in Xanthomonas oryzae pv. oryzae Virulence and Rice-Xoo Interaction. PMID:34176023
GRINS: Genetic elements that recode assembly-line polyketide synthases and accelerate their diversification. PMID:34162709
Niche adaptation promoted the evolutionary diversification of tiny ocean predators. PMID:34155140
Flavobacterium difficile sp. nov., isolated from a freshwater waterfall. PMID:34136928
Genome mining Streptomyces sp. KCTC 0041BP as a producer of dihydrochalcomycin. PMID:34136924
An integrated gene catalog and over 10,000 metagenome-assembled genomes from the gastrointestinal microbiome of ruminants. PMID:34118976
Identification of sequence changes in myosin II that adjust muscle contraction velocity. PMID:34111116
Complete genome sequence of Arthrobacter sp. PAMC25564 and its comparative genome analysis for elucidating the role of CAZymes in cold adaptation. PMID:34078272
Dual RNA-Sequencing Analysis of Resistant (Pinus pinea) and Susceptible (Pinus radiata) Hosts during Fusarium circinatum Challenge. PMID:34063405
Genome Scale Analysis Reveals IscR Directly and Indirectly Regulates Virulence Factor Genes in Pathogenic Yersinia. PMID:34060331
Characterization of the public transit air microbiome and resistome reveals geographical specificity. PMID:34039416
De novo transcriptome sequencing and anthocyanin metabolite analysis reveals leaf color of Acer pseudosieboldianum in autumn. PMID:34034673
Enlightening the taxonomy darkness of human gut microbiomes with a cultured biobank. PMID:34020714
Redox homeostasis in Mycobacterium tuberculosis is modulated by a novel actinomycete-specific transcription factor. PMID:34018220
Radical genome remodelling accompanied the emergence of a novel host-restricted bacterial pathogen. PMID:34015034
Genome-wide insights into population structure and host specificity of Campylobacter jejuni. PMID:33990625
Molecular dynamics shows complex interplay and long-range effects of post-translational modifications in yeast protein interactions. PMID:33979327
Viruses infecting a warm water picoeukaryote shed light on spatial co-occurrence dynamics of marine viruses and their hosts. PMID:33972727
Genome Recovery, Functional Profiling, and Taxonomic Classification from Metagenomes. PMID:33961223
Comparative Analysis of Core and Accessory Genes in Coexpression Network. PMID:33961216
A stony coral cell atlas illuminates the molecular and cellular basis of coral symbiosis, calcification, and immunity. PMID:33945788
Integrating taxonomic, functional, and strain-level profiling of diverse microbial communities with bioBakery 3. PMID:33944776
Microbial iron and carbon metabolism as revealed by taxonomy-specific functional diversity in the Southern Ocean. PMID:33941887
Characterizing rumen microbiota and CAZyme profile of Indian dromedary camel (Camelus dromedarius) in response to different roughages. PMID:33931716
Proteomic Charting of Imipenem Adaptive Responses in a Highly Carbapenem Resistant Clinical Enterobacter roggenkampii Isolate. PMID:33924830
Blood Pressure Regulation Evolved from Basic Homeostatic Components. PMID:33923023
Microdiversity of Enterococcus faecalis isolates in cases of infective endocarditis: selection of non-synonymous mutations and large deletions is associated with phenotypic modifications. PMID:33913790
Metagenome of a polluted river reveals a reservoir of metabolic and antibiotic resistance genes. PMID:33902720
Genomic Characterization of Salmonella enterica Isolates From Retail Meat in Beijing, China. PMID:33897640
Quantitative proteome comparison of human hearts with those of model organisms. PMID:33872299
Multi-omics analysis provides insights into lignocellulosic biomass degradation by Laetiporus sulphureus ATCC 52600. PMID:33865436
Nocardioides luti sp. nov., belonging to the family Nocardioidaceae isolated from kaolinite, exhibiting the biosynthesis potential of alkylresorcinol. PMID:33864547
Shotgun metagenomics reveals distinct functional diversity and metabolic capabilities between 12 000-year-old permafrost and active layers on Muot da Barba Peider (Swiss Alps). PMID:33848236
Multiple concurrent and convergent stages of genome reduction in bacterial symbionts across a stink bug family. PMID:33833268
Genomic characterization of four Escherichia coli strains isolated from oral lichen planus biopsies. PMID:33828821
Ten Years of Collaborative Progress in the Quest for Orthologs. PMID:33822172
Database limitations for studying the human gut microbiome. PMID:33816940
Absence of 4-Formylaminooxyvinylglycine Production by Pseudomonas fluorescens WH6 Results in Resource Reallocation from Secondary Metabolite Production to Rhizocompetence. PMID:33807194
Bioinformatic Analysis of Genome-Predicted Bat Cathelicidins. PMID:33806967
Genome-Wide Identification of Genes Involved in Acid Stress Resistance of Salmonella Derby. PMID:33806186
High-throughput fitness screening and transcriptomics identify a role for a type IV secretion system in the pathogenesis of Crohn's disease-associated Escherichia coli. PMID:33795670
Comparative Genomics and Environmental Distribution of Large dsDNA Viruses in the Family Asfarviridae. PMID:33790885
Microbiome meta-analysis and cross-disease comparison enabled by the SIAMCAT machine learning toolbox. PMID:33785070
Analysis of Fungal Genomes Reveals Commonalities of Intron Gain or Loss and Functions in Intron-Poor Species. PMID:33772558
Screening and identification of endometrial proteins as novel potential biomarkers for repeated implantation failure. PMID:33763303
Characterization and Functional Test of Canine Probiotics. PMID:33763044
A novel class of sulfur-containing aminolipids widespread in marine roseobacters. PMID:33750904
Pre-Cambrian roots of novel Antarctic cryptoendolithic bacterial lineages. PMID:33741058
Metagenomic sequencing revealed the potential of banknotes as a repository of microbial genes. PMID:33706718
Mapping Gene-by-Gene Single-Nucleotide Variation in 8,535 Mycobacterium tuberculosis Genomes: a Resource To Support Potential Vaccine and Drug Development. PMID:33692198
Metagenomic Analysis Reveals Microbial Community Structure and Metabolic Potential for Nitrogen Acquisition in the Oligotrophic Surface Water of the Indian Ocean. PMID:33679623
The Distribution of Several Genomic Virulence Determinants Does Not Corroborate the Established Serotyping Classification of Bacillus thuringiensis. PMID:33668147
Anaerobic endosymbiont generates energy for ciliate host by denitrification. PMID:33658719
Evolutionary Dynamics Based on Comparative Genomics of Pathogenic Escherichia coli Lineages Harboring Polyketide Synthase (pks) Island. PMID:33653937
Whole genome strategies and bioremediation insight into dehalogenase-producing bacteria. PMID:33650078
Cysteinyl-specialized proresolving mediators link resolution of infectious inflammation and tissue regeneration via TRAF3 activation. PMID:33649212
Whole genome sequencing of Streptomyces actuosus ISP-5337, Streptomyces sioyaensis B-5408, and Actinospica acidiphila B-2296 reveals secondary metabolomes with antibiotic potential. PMID:33643857
Five key aspects of metaproteomics as a tool to understand functional interactions in host-associated microbiomes. PMID:33630960
Genome sequences of Tropheus moorii and Petrochromis trewavasae, two eco-morphologically divergent cichlid fishes endemic to Lake Tanganyika. PMID:33619328
De novo whole-genome assembly and resequencing resources for the roan (Hippotragus equinus), an iconic African antelope. PMID:33604669
Proteomic Analysis of Listeria monocytogenes FBUNT During Biofilm Formation at 10°C in Response to Lactocin AL705. PMID:33584610
Deciphering a Marine Bone-Degrading Microbiome Reveals a Complex Community Effort. PMID:33563781
Shift and Metabolic Potentials of Microbial Eukaryotic Communities Across the Full Depths of the Mariana Trench. PMID:33537012
Independent component analysis recovers consistent regulatory signals from disparate datasets. PMID:33529205
Human pathways in animal models: possibilities and limitations. PMID:33524155
Isolation, Biochemical and Genomic Characterization of Glyphosate Tolerant Bacteria to Perform Microbe-Assisted Phytoremediation. PMID:33519737
Amynthas corticis genome reveals molecular mechanisms behind global distribution. PMID:33514865
Antimicrobial-specific response from resistance gene carriers studied in a natural, highly diverse microbiome. PMID:33504360
Heat stress destabilizes symbiotic nutrient cycling in corals. PMID:33500354
Gene Duplication and Gain in the Trematode Atriophallophorus winterbourni Contributes to Adaptation to Parasitism. PMID:33484570
Translational landscape and protein biogenesis demands of the early secretory pathway in Komagataella phaffii. PMID:33472617
Monitoring Microbial Populations and Antibiotic Resistance Gene Enrichment Associated with Arctic Waste Stabilization Ponds. PMID:33452030
Distribution of Mixotrophy and Desiccation Survival Mechanisms across Microbial Genomes in an Arid Biological Soil Crust Community. PMID:33436509
Hidden Diversity within Common Protozoan Parasites as Revealed by a Novel Genomotyping Scheme. PMID:33397705
Linkage mapping evidence for a syntenic QTL associated with flowering time in perennial C4 rhizomatous grasses Miscanthus and switchgrass. PMID:33381230
Epigenetic Modifiers Affect the Bioactive Compounds Secreted by an Endophyte of the Tropical Plant Piper longum. PMID:33374682
Salmonella enterica Serovars Dublin and Enteritidis Comparative Proteomics Reveals Differential Expression of Proteins Involved in Stress Resistance, Virulence, and Anaerobic Metabolism. PMID:33361201
Comparative genomics of Klebsiella michiganensis BD177 and related members of Klebsiella sp. reveal the symbiotic relationship with Bactrocera dorsalis. PMID:33339499
Plant Roots Release Small Extracellular Vesicles with Antifungal Activity. PMID:33333782
Single-Nucleotide RNA Maps for the Two Major Nosocomial Pathogens Enterococcus faecalis and Enterococcus faecium. PMID:33324581
Protein quality control and regulated proteolysis in the genome-reduced organism Mycoplasma pneumoniae. PMID:33320415
A collection of bacterial isolates from the pig intestine reveals functional and taxonomic diversity. PMID:33319778
Rewiring the specificity of extracytoplasmic function sigma factors. PMID:33318184
Geochemical transition zone powering microbial growth in subsurface sediments. PMID:33288718
Bioinformatic analysis and functional predictions of selected regeneration-associated transcripts expressed by zebrafish microglia. PMID:33287696
Exploring the Influence of Signal Molecules on Marine Biofilms Development. PMID:33281767
Transmembrane signaling and cytoplasmic signal conversion by dimeric transmembrane helix 2 and a linker domain of the DcuS sensor kinase. PMID:33277358
Utilization of low-molecular-weight organic compounds by the filterable fraction of a lotic microbiome. PMID:33264383
Functional partitioning of a liquid-like organelle during assembly of axonemal dyneins. PMID:33263282
Elucidating Essential Genes in Plant-Associated Pseudomonas protegens Pf-5 Using Transposon Insertion Sequencing. PMID:33257523
Differential gene expression analysis reveals pathways important in early post-traumatic osteoarthritis in an equine model. PMID:33256611
Dataset of full-length transcriptome assembly and annotation of apocynum venetum using pacbio sequel II. PMID:33251304
Clostridium manihotivorum sp. nov., a novel mesophilic anaerobic bacterium that produces cassava pulp-degrading enzymes. PMID:33240652
Transcriptome analysis of Xanthomonas fragariae in strawberry leaves. PMID:33239704
Functional characterisation of the transcriptome from leaf tissue of the fluoroacetate-producing plant, Dichapetalum cymosum, in response to mechanical wounding. PMID:33239700
Associations of the gut microbiome and clinical factors with acute GVHD in allogeneic HSCT recipients. PMID:33232475
Genome Sequence of Klebsiella pneumoniae YBQ, a Clinical Strain Isolated from the Sputum of a Patient with Severe Pneumonia. PMID:33214313
Widespread endogenization of giant viruses shapes genomes of green algae. PMID:33208937
Comprehensive genome analyses of Sellimonas intestinalis, a potential biomarker of homeostasis gut recovery. PMID:33206037
OrthoDB in 2020: evolutionary and functional annotations of orthologs. PMID:33196836
Metagenomic assessment of the global diversity and distribution of bacteria and fungi. PMID:33185929
Adaptive response to iterative passages of five Lactobacillus species in simulated vaginal fluid. PMID:33172400
Coevolving Plasmids Drive Gene Flow and Genome Plasticity in Host-Associated Intracellular Bacteria. PMID:33157023
Arrayed CRISPRi and quantitative imaging describe the morphotypic landscape of essential mycobacterial genes. PMID:33155979
Chromosome-scale genome assembly for the duckweed Spirodela intermedia, integrating cytogenetic maps, PacBio and Oxford Nanopore libraries. PMID:33154426
Comparative Genomic Analysis of Dactylonectria torresensis Strains from Grapevine, Soil and Weed Highlights Potential Mechanisms in Pathogenicity and Endophytic Lifestyle. PMID:33138048
Comparative Genomics of Pathogenic Clavibacter michiganensis subsp. michiganensis Strains from Chile Reveals Potential Virulence Features for Tomato Plants. PMID:33137950
From sequence to information. PMID:33131436
Hikarchaeia demonstrate an intermediate stage in the methanogen-to-halophile transition. PMID:33127909
Uncovering the genomic potential of the Amazon River microbiome to degrade rainforest organic matter. PMID:33126925
Staphylococcal Protein A (spa) Locus Is a Hot Spot for Recombination and Horizontal Gene Transfer in Staphylococcus pseudintermedius. PMID:33115833
Transcriptome Analysis of Amyloodinium ocellatum Tomonts Revealed Basic Information on the Major Potential Virulence Factors. PMID:33114415
Timing the origin of eukaryotic cellular complexity with ancient duplications. PMID:33106602
Integrated Phenotypic-Genotypic Analysis of Candidate Probiotic Weissella Cibaria Strains Isolated from Dairy Cows in Kuwait. PMID:33085038
Genome-wide analysis of the Firmicutes illuminates the diderm/monoderm transition. PMID:33077930
A high-quality Brassica napus genome reveals expansion of transposable elements, subgenome evolution and disease resistance. PMID:33073445
Deciphering the Role of Trehalose in Tripartite Symbiosis Among Rhizobia, Arbuscular Mycorrhizal Fungi, and Legumes for Enhancing Abiotic Stress Tolerance in Crop Plants. PMID:33042042
Integrated metabolic profiling and transcriptome analysis of pigment accumulation in diverse petal tissues in the lily cultivar 'Vivian'. PMID:32993487
Transcriptome analysis reveals underlying immune response mechanism of fungal (Penicillium oxalicum) disease in Gastrodia elata Bl. f. glauca S. chow (Orchidaceae). PMID:32993485
From Inquilines to Gall Inducers: Genomic Signature of a Life-Style Transition in Synergus Gall Wasps. PMID:32986797
Aerobic microbial communities in the sediments of a marine oxygen minimum zone. PMID:32975580
Phylogenetic and genomic analysis reveals high genomic openness and genetic diversity of Clostridium perfringens. PMID:32975504
Temporal dynamics of bacterial communities during seed development and maturation. PMID:32966572
Complete genome sequence of the biocontrol agent Serratia marcescens strain N4-5 uncovers an assembly artefact. PMID:32965626
Human SIRT1 Multispecificity Is Modulated by Active-Site Vicinity Substitutions during Natural Evolution. PMID:32956445
DGINN, an automated and highly-flexible pipeline for the detection of genetic innovations on protein-coding genes. PMID:32941639
Benchmarking orthology methods using phylogenetic patterns defined at the base of Eukaryotes. PMID:32935832
Chlamydial contribution to anaerobic metabolism during eukaryotic evolution. PMID:32923644
Comparative analyses of saprotrophy in Salisapilia sapeloensis and diverse plant pathogenic oomycetes reveal lifestyle-specific gene expression. PMID:32918444
Genomic analysis of facultatively oligotrophic haloarchaea of the genera Halarchaeum, Halorubrum, and Halolamina, isolated from solar salt. PMID:32918097
Comparative Genomics of Microbacterium Species to Reveal Diversity, Potential for Secondary Metabolites and Heavy Metal Resistance. PMID:32903828
Integrated Metabolic Modeling, Culturing, and Transcriptomics Explain Enhanced Virulence of Vibrio cholerae during Coinfection with Enterotoxigenic Escherichia coli. PMID:32900868
A systematic, label-free method for identifying RNA-associated proteins in vivo provides insights into vertebrate ciliary beating machinery. PMID:32898505
De novo transcriptome sequencing of Rhododendron molle and identification of genes involved in the biosynthesis of secondary metabolites. PMID:32887550
CoreCruncher: Fast and Robust Construction of Core Genomes in Large Prokaryotic Data Sets. PMID:32886787
Transcription Profile and Genomic Variations of Oryctes Rhinoceros Nudivirus in Coconut Rhinoceros Beetles. PMID:32878889
Multi-omics analysis to examine microbiota, host gene expression and metabolites in the intestine of black tiger shrimp (Penaeus monodon) with different growth performance. PMID:32864208
A complete and flexible workflow for metaproteomics data analysis based on MetaProteomeAnalyzer and Prophane. PMID:32859984
Genome Sequence of a Blattabacterium Strain Isolated from the Viviparous Cockroach, Diploptera punctata. PMID:32855240
Improved Reference Genome Uncovers Novel Sex-Linked Regions in the Guppy (Poecilia reticulata). PMID:32853348
Woeseiales transcriptional response to shallow burial in Arctic fjord surface sediment. PMID:32853201
A cross-kingdom conserved ER-phagy receptor maintains endoplasmic reticulum homeostasis during stress. PMID:32851973
Whole-Genome Sequencing and Bioinformatics Analysis of Apiotrichum mycotoxinivorans: Predicting Putative Zearalenone-Degradation Enzymes. PMID:32849454
Gammaproteobacteria mediating utilization of methyl-, sulfur- and petroleum organic compounds in deep ocean hydrothermal plumes. PMID:32820229
Grad-seq shines light on unrecognized RNA and protein complexes in the model bacterium Escherichia coli. PMID:32813020
Lactobacillus Mucosae Strain Promoted by a High-Fiber Diet in Genetic Obese Child Alleviates Lipid Metabolism and Modifies Gut Microbiota in ApoE-/- Mice on a Western Diet. PMID:32806628
Sharing a β-Glucan Meal: Transcriptomic Eavesdropping on a Bacteroides ovatus-Subdoligranulum variabile-Hungatella hathewayi Consortium. PMID:32801182
S-layer associated proteins contribute to the adhesive and immunomodulatory properties of Lactobacillus acidophilus NCFM. PMID:32787778
Gut microbiome of endangered Tor putitora (Ham.) as a reservoir of antibiotic resistance genes and pathogens associated with fish health. PMID:32787773
Data on proteomic profiling of extracellular vesicles of Acholeplasma laidlawii strains with increased resistance to antibiotics of different classes - ciprofloxacin and tetracycline. PMID:32775567
The Expression of NOX From Synthetic Promoters Reveals an Important Role of the Redox Status in Regulating Secondary Metabolism of Saccharopolyspora erythraea. PMID:32766231
Terabase Metagenome Sequencing of Grassland Soil Microbiomes. PMID:32763940
Characterization of Spodoptera litura Gut Bacteria and Their Role in Feeding and Growth of the Host. PMID:32714311
The wheat pathogen Zymoseptoria tritici senses and responds to different wavelengths of light. PMID:32711450
In vitro Edwardsiella piscicida CK108 Transcriptome Profiles with Subinhibitory Concentrations of Phenol and Formalin Reveal New Insights into Bacterial Pathogenesis Mechanisms. PMID:32709101
Integrated transcriptomic and metabolomic analyses of yellow horn (Xanthoceras sorbifolia) in response to cold stress. PMID:32706804
Transcriptomic differences between male and female Trachycarpus fortunei. PMID:32704095
Scalable phylogenetic profiling using MinHash uncovers likely eukaryotic sexual reproduction genes. PMID:32697802
The genetic factors of bilaterian evolution. PMID:32672535
From bag-of-genes to bag-of-genomes: metabolic modelling of communities in the era of metagenome-assembled genomes. PMID:32670511
Chromosome Architecture and Gene Content of the Emergent Pathogen Acinetobacter haemolyticus. PMID:32670207
Selection for Reducing Energy Cost of Protein Production Drives the GC Content and Amino Acid Composition Bias in Gene Transfer Agents. PMID:32665274
Comparative Genomics of Stenotrophomonas maltophilia and Stenotrophomonas rhizophila Revealed Characteristic Features of Both Species. PMID:32664682
Comparative Genomics Uncovers the Genetic Diversity and Characters of Veillonella atypica and Provides Insights Into Its Potential Applications. PMID:32655519
A Genomic Perspective on the Potential of Wild-Type Rumen Bacterium Enterobacter sp. LU1 as an Industrial Platform for Bio-Based Succinate Production. PMID:32650546
TreeSAPP: the Tree-based Sensitive and Accurate Phylogenetic Profiler. PMID:32637989
Deconstructing the Soil Microbiome into Reduced-Complexity Functional Modules. PMID:32636252
Differential Dynamics of the Ruminal Microbiome of Jersey Cows in a Heat Stress Environment. PMID:32630754
Dual RNA-seq of Orientia tsutsugamushi informs on host-pathogen interactions for this neglected intracellular human pathogen. PMID:32620750
Evolutionary History of the Globin Gene Family in Annelids. PMID:32597988
Diverse and unique viruses discovered in the surface water of the East China Sea. PMID:32590932
Alterations of gut microbiota contribute to the progression of unruptured intracranial aneurysms. PMID:32587239
Distinctive Growth and Transcriptional Changes of the Diatom Seminavis robusta in Response to Quorum Sensing Related Compounds. PMID:32582129
Methyl Jasmonate Affects Photosynthesis Efficiency, Expression of HvTIP Genes and Nitrogen Homeostasis in Barley. PMID:32570736
Putative circumsporozoite protein (CSP) of Plasmodium vivax is considerably distinct from the well-known CSP and plays a role in the protein ubiquitination pathway. PMID:32550551
Heterotrophic Thaumarchaea with Small Genomes Are Widespread in the Dark Ocean. PMID:32546674
Transcriptomic Analysis of the Early Strobilar Development of Echinococcus granulosus. PMID:32545493
Cholesterol Metabolism by Uncultured Human Gut Bacteria Influences Host Cholesterol Level. PMID:32544460
Rampant Nuclear Transfer and Substitutions of Plastid Genes in Passiflora. PMID:32539116
Isolation and transcriptomic analysis of Anopheles gambiae oenocytes enables the delineation of hydrocarbon biosynthesis. PMID:32538778
Phylogenetic background and habitat drive the genetic diversification of Escherichia coli. PMID:32530914
Data of de novo assembly and annotation of transcriptome from Aspidistra fenghuangensis (Asparagaceae: Nolinoideae). PMID:32529008
Systematic Humanization of the Yeast Cytoskeleton Discerns Functionally Replaceable from Divergent Human Genes. PMID:32522745
Evaluating Eucalyptus leaf colonization by Brasilonema octagenarum (Cyanobacteria, Scytonemataceae) using in planta experiments and genomics. PMID:32518725
Defining Critical Genes During Spherule Remodeling and Endospore Development in the Fungal Pathogen, Coccidioides posadasii. PMID:32499817
Metagenomic growth rate inferences of strains in situ. PMID:32494636
Pan-Proteomic Analysis and Elucidation of Protein Abundance among the Closely Related Brucella Species, Brucella abortus and Brucella melitensis. PMID:32486122
An evolutionary path to altered cofactor specificity in a metalloenzyme. PMID:32483131
Cultivation-independent and cultivation-dependent metagenomes reveal genetic and enzymatic potential of microbial community involved in the degradation of a complex microbial polymer. PMID:32482164
Global Distribution and Evolution of Mycobacterium bovis Lineages. PMID:32477295
Pan-transcriptomic analysis identified common differentially expressed genes of Acinetobacter baumannii in response to polymyxin treatments. PMID:32469363
Transposon Insertion Site Sequencing of Providencia stuartii: Essential Genes, Fitness Factors for Catheter-Associated Urinary Tract Infection, and the Impact of Polymicrobial Infection on Fitness Requirements. PMID:32461277
Metagenomics reveals impact of geography and acute diarrheal disease on the Central Indian human gut microbiome. PMID:32459982
A novel cyanobacterial geosmin producer, revising GeoA distribution and dispersion patterns in Bacteria. PMID:32457360
QTG-Finder2: A Generalized Machine-Learning Algorithm for Prioritizing QTL Causal Genes in Plants. PMID:32430305
The Architecture of Metabolism Maximizes Biosynthetic Diversity in the Largest Class of Fungi. PMID:32421770
Sorghum Growth Promotion by Paraburkholderia tropica and Herbaspirillum frisingense: Putative Mechanisms Revealed by Genomics and Metagenomics. PMID:32414048
Genome diversification in globally distributed novel marine Proteobacteria is linked to environmental adaptation. PMID:32393808
Genomic variation among closely related Vibrio alginolyticus strains is located on mobile genetic elements. PMID:32393168
Mechanoradicals in tensed tendon collagen as a source of oxidative stress. PMID:32385229
A Modular Metagenomics Pipeline Allowing for the Inclusion of Prior Knowledge Using the Example of Anaerobic Digestion. PMID:32380653
Genome Sequencing and Analysis of the Hypocrellin-Producing Fungus Shiraia bambusicola S4201. PMID:32373091
Phages Actively Challenge Niche Communities in Antarctic Soils. PMID:32371471
Comparative Genomics Uncovers the Genetic Diversity and Synthetic Biology of Secondary Metabolite Production of Trametes. PMID:32363038
Homoeolog expression bias and expression level dominance (ELD) in four tissues of natural allotetraploid Brassica napus. PMID:32349676
Draft genome sequences of Hirudo medicinalis and salivary transcriptome of three closely related medicinal leeches. PMID:32349672
Genomic characterization of Lactobacillus fermentum DSM 20052. PMID:32349666
MetaPhOrs 2.0: integrative, phylogeny-based inference of orthology and paralogy across the tree of life. PMID:32343307
Updated review of research on the gut microbiota and their relation to depression in animals and human beings. PMID:32332994
Aspartate aminotransferase Rv3722c governs aspartate-dependent nitrogen metabolism in Mycobacterium tuberculosis. PMID:32327655
Single-molecule long-read sequencing of the full-length transcriptome of Rhododendron lapponicum L. PMID:32317724
Mechanisms Underlying the Rhizosphere-To-Rhizoplane Enrichment of Cellvibrio Unveiled by Genome-Centric Metagenomics and Metatranscriptomics. PMID:32316533
RNA-Induced Conformational Switching and Clustering of G3BP Drive Stress Granule Assembly by Condensation. PMID:32302572
Complete Genome Sequence of Athalassotoga saccharophila Strain NAS-01, a Deep-Branching Thermophilic Lineage in the Phylum Thermotogae. PMID:32299888
Differential Expression of Immune Genes between Two Closely Related Beetle Species with Different Immunocompetence following Attack by Asecodes parviclava. PMID:32282901
Distinct Life Histories Impact Dikaryotic Genome Evolution in the Rust Fungus Puccinia striiformis Causing Stripe Rust in Wheat. PMID:32271913
Comparative Genomic and Transcriptomic Analyses of Mycobacterium kansasii Subtypes Provide New Insights Into Their Pathogenicity and Taxonomy. PMID:32266172
Patterns of gene evolution following duplications and speciations in vertebrates. PMID:32266119
Unraveling 1,4-Butanediol Metabolism in Pseudomonas putida KT2440. PMID:32256468
Deletion of S-Layer Associated Ig-Like Domain Protein Disrupts the Lactobacillus acidophilus Cell Surface. PMID:32256464
Dynamic genome evolution and complex virocell metabolism of globally-distributed giant viruses. PMID:32249765
Microbiome and ecology of a hot spring-microbialite system on the Trans-Himalayan Plateau. PMID:32246033
Draft Genome Sequence of the Yeast Rhodotorula sp. Strain CCFEE 5036, Isolated from McMurdo Dry Valleys, Antarctica. PMID:32241854
Metagenomic views of microbial dynamics influenced by hydrocarbon seepage in sediments of the Gulf of Mexico. PMID:32238866
A systematic pipeline for classifying bacterial operons reveals the evolutionary landscape of biofilm machineries. PMID:32236097
Functional Divergence of Microtubule-Associated TPX2 Family Members in Arabidopsis thaliana. PMID:32235723
Metaproteomics characterizes human gut microbiome function in colorectal cancer. PMID:32210237
Transcriptomic Insights into Mechanisms of Early Seed Maturation in the Garden Pea (Pisum sativum L.). PMID:32210065
Association of colitis with gut-microbiota dysbiosis in clathrin adapter AP-1B knockout mice. PMID:32208434
Evidence of defined temporal expression patterns that lead a gram-negative cell out of dormancy. PMID:32203501
First Genome of the Brown Alga Undaria pinnatifida: Chromosome-Level Assembly Using PacBio and Hi-C Technologies. PMID:32184805
Cell cycle transcriptomics of Capsaspora provides insights into the evolution of cyclin-CDK machinery. PMID:32176685
Meta-analysis Reveals Potential Influence of Oxidative Stress on the Airway Microbiomes of Cystic Fibrosis Patients. PMID:32171662
Ecosystem-wide metagenomic binning enables prediction of ecological niches from genomes. PMID:32170201
Gill transcriptomes reveal expression changes of genes related with immune and ion transport under salinity stress in silvery pomfret (Pampus argenteus). PMID:32162151
Low mutational load and high mutation rate variation in gut commensal bacteria. PMID:32155146
Complete genome sequence data of a broad-spectrum antipathogen, Bacillus amyloliquefaciens KCTC 18343P, isolated from Makgeolli, Korean traditional rice wine. PMID:32154350
Metagenomic analysis reveals the microbiome and resistome in migratory birds. PMID:32122398
Comparative Insights Into the Complete Genome Sequence of Highly Metal Resistant Cupriavidus metallidurans Strain BS1 Isolated From a Gold-Copper Mine. PMID:32117100
Whole genome sequencing reveals extended natural transformation in Campylobacter impacting diagnostics and the pathogens adaptive potential. PMID:32111893
The Evolution History of Fe-S Cluster A-Type Assembly Protein Reveals Multiple Gene Duplication Events and Essential Protein Motifs. PMID:32108236
A comprehensive non-redundant gene catalog reveals extensive within-community intraspecies diversity in the human vagina. PMID:32103005
Sequencing and Analysis of the Genome of Propionibacterium Freudenreichii T82 Strain: Importance for Industry. PMID:32102319
Multi-Omic Analyses Provide Links between Low-Dose Antibiotic Treatment and Induction of Secondary Metabolism in Burkholderia thailandensis. PMID:32098820
Comparative Genomics and Evolutionary Analysis of RNA-Binding Proteins of Burkholderia cenocepacia J2315 and Other Members of the B. cepacia Complex. PMID:32098200
Assembly-free single-molecule sequencing recovers complete virus genomes from natural microbial communities. PMID:32075851
Prophage-Mediated Disruption of Genetic Competence in Staphylococcus pseudintermedius. PMID:32071159
Similar genomic patterns of clinical infective endocarditis and oral isolates of Streptococcus sanguinis and Streptococcus gordonii. PMID:32066773
Data on the genome analysis of the wood-rotting fungus Steccherinum ochraceum LE-BIN 3174. PMID:32055659
Disentangling the impact of environmental and phylogenetic constraints on prokaryotic within-species diversity. PMID:32047279
Active sulfur cycling in the terrestrial deep subsurface. PMID:32047278
Transcriptomic and Metabolomic Changes Triggered by Fusarium solani in Common Bean (Phaseolus vulgaris L.). PMID:32046085
Genome analysis of a wild rumen bacterium Enterobacter aerogenes LU2 - a novel bio-based succinic acid producer. PMID:32029880
Community diversity and habitat structure shape the repertoire of extracellular proteins in bacteria. PMID:32029728
Valence and patterning of aromatic residues determine the phase behavior of prion-like domains. PMID:32029630
The Genome of Setaria digitata: A Cattle Nematode Closely Related to Human Filarial Parasites. PMID:32022853
Streptomyces sp. VN1, a producer of diverse metabolites including non-natural furan-type anticancer compound. PMID:32019976
Ferric Citrate Regulator FecR Is Translocated across the Bacterial Inner Membrane via a Unique Twin-Arginine Transport-Dependent Mechanism. PMID:32015149
Genome-based analysis for the bioactive potential of Streptomyces yeochonensis CN732, an acidophilic filamentous soil actinobacterium. PMID:32013859
Host-Specific Evolutionary and Transmission Dynamics Shape the Functional Diversification of Staphylococcus epidermidis in Human Skin. PMID:32004459
Tools for Analysis of the Microbiome. PMID:32002757
Discovery of two novel and adjacent QTLs on chromosome B02 controlling resistance against bacterial wilt in peanut variety Zhonghua 6. PMID:31980836
Four high-quality draft genome assemblies of the marine heterotrophic nanoflagellate Cafeteria roenbergensis. PMID:31964893
Culture-enriched metagenomic sequencing enables in-depth profiling of the cystic fibrosis lung microbiota. PMID:31959969
Characterizing the microbiomes of Antarctic sponges: a functional metagenomic approach. PMID:31959785
Genomic Analysis of Wolbachia from Laodelphax striatellus (Delphacidae, Hemiptera) Reveals Insights into Its "Jekyll and Hyde" Mode of Infection Pattern. PMID:31958110
Comparative Genomics of Streptococcus thermophilus Support Important Traits Concerning the Evolution, Biology and Technological Properties of the Species. PMID:31956321
Beneficial Endophytic Bacteria-Serendipita indica Interaction for Crop Enhancement and Resistance to Phytopathogens. PMID:31921065
The transcriptome of Pinus pinaster under Fusarium circinatum challenge. PMID:31914917
Genome- and Community-Level Interaction Insights into Carbon Utilization and Element Cycling Functions of Hydrothermarchaeota in Hydrothermal Sediment. PMID:31911466
Genome sequencing of Mycobacterium pinnipedii strains: genetic characterization and evidence of superinfection in a South American sea lion (Otaria flavescens). PMID:31888476
Tomato RNA-seq Data Mining Reveals the Taxonomic and Functional Diversity of Root-Associated Microbiota. PMID:31878183
Genome Sequencing of Mesonia algae K4-1 Reveals Its Adaptation to the Arctic Ocean. PMID:31866978
Patterns of diverse gene functions in genomic neighborhoods predict gene function and phenotype. PMID:31863070
Small Molecules Produced by Commensal Staphylococcus epidermidis Disrupt Formation of Biofilms by Staphylococcus aureus. PMID:31862721
Comparative Pangenomics of the Mammalian Gut Commensal Bifidobacterium longum. PMID:31861401
Complete genome sequences of Streptomyces spp. isolated from disease-suppressive soils. PMID:31856709
Combined De Novo Transcriptome and Metabolome Analysis of Common Bean Response to Fusarium oxysporum f. sp. phaseoli Infection. PMID:31842411
Membrane Transporters in Citrus clementina Fruit Juice-Derived Nanovesicles. PMID:31835328
The green peach aphid gut contains host plant microRNAs identified by comprehensive annotation of Brassica oleracea small RNA data. PMID:31827121
A Novel Genus of Actinobacterial Tectiviridae. PMID:31817897
Functional identification of lncRNAs in sweet cherry (Prunus avium) pollen tubes via transcriptome analysis using single-molecule long-read sequencing. PMID:31814988
Phylogenomic Analyses of Members of the Widespread Marine Heterotrophic Genus Pseudovibrio Suggest Distinct Evolutionary Trajectories and a Novel Genus, Polycladidibacter gen. nov. PMID:31811036
Casimicrobium huifangae gen. nov., sp. nov., a Ubiquitous "Most-Wanted" Core Bacterial Taxon from Municipal Wastewater Treatment Plants. PMID:31811031
Paenibacillus lutrae sp. nov., A Chitinolytic Species Isolated from A River Otter in Castril Natural Park, Granada, Spain. PMID:31810255
Comparative analysis of corrected tiger genome provides clues to its neuronal evolution. PMID:31804567
Comparative Genomics Reveals Metabolic Specificity of Endozoicomonas Isolated from a Marine Sponge and the Genomic Repertoire for Host-Bacteria Symbioses. PMID:31801294
Complete genome sequence and comparative analysis of Streptomyces seoulensis, a pioneer strain of nickel superoxide dismutase. PMID:31797314
Piscirickettsia salmonis Cryptic Plasmids: Source of Mobile DNA and Virulence Factors. PMID:31795181
Calcium sensing via EF-hand 4 enables thioredoxin activity in the sensor-responder protein calredoxin in the green alga Chlamydomonas reinhardtii. PMID:31776187
Novel redox-active enzymes for ligninolytic applications revealed from multiomics analyses of Peniophora sp. CBMAI 1063, a laccase hyper-producer strain. PMID:31772294
Genome analyses of a placozoan rickettsial endosymbiont show a combination of mutualistic and parasitic traits. PMID:31772223
VCGIDB: A Database and Web Resource for the Genomic Islands from Vibrio Cholerae. PMID:31771223
Wolbachia supplement biotin and riboflavin to enhance reproduction in planthoppers. PMID:31767943
Complete genome sequence of Sphingomonas paucimobilis AIMST S2, a xenobiotic-degrading bacterium. PMID:31767854
Do Organic Substrates Drive Microbial Community Interactions in Arctic Snow? PMID:31749784
Integrated Meta-omics Approaches To Understand the Microbiome of Spontaneous Fermentation of Traditional Chinese Pu-erh Tea. PMID:31744906
Cultivation and functional characterization of 79 planctomycetes uncovers their unique biology. PMID:31740763
Breast milk-derived human milk oligosaccharides promote Bifidobacterium interactions within a single ecosystem. PMID:31740752
Gene Expression Changes and Community Turnover Differentially Shape the Global Ocean Metatranscriptome. PMID:31730850
Integrated transcriptome and miRNA analysis uncovers molecular regulators of aerial stem-to-rhizome transition in the medical herb Gynostemma pentaphyllum. PMID:31730459
Cultivation-Assisted Genome of Candidatus Fukatsuia symbiotica; the Enigmatic "X-Type" Symbiont of Aphids. PMID:31725149
Exploring the Molecular Mechanism underlying the Stable Purple-Red Leaf Phenotype in Lagerstroemia indica cv. Ebony Embers. PMID:31718025
Emergence of the Ug99 lineage of the wheat stem rust pathogen through somatic hybridisation. PMID:31699975
MGnify: the microbiome analysis resource in 2020. PMID:31696235
Fungal Adaptation to the Advanced Stages of Wood Decomposition: Insights from the Steccherinum ochraceum. PMID:31694151
Nanopore sequencing improves the draft genome of the human pathogenic amoeba Naegleria fowleri. PMID:31690847
Differentiation of Long Non-Coding RNA and mRNA Expression Profiles in Male and Female Aedes albopictus. PMID:31681418
Structure and activity of PPX/GppA homologs from Escherichia coli and Helicobacter pylori. PMID:31679177
Metabolic and gut microbiome changes following GLP-1 or dual GLP-1/GLP-2 receptor agonist treatment in diet-induced obese mice. PMID:31666597
Microevolution within ST11 group Clostridioides difficile isolates through mobile genetic elements based on complete genome sequencing. PMID:31666016
Prophages and satellite prophages are widespread in Streptococcus and may play a role in pneumococcal pathogenesis. PMID:31649284
PhyloMagnet: fast and accurate screening of short-read meta-omics data using gene-centric phylogenetics. PMID:31647547
MicroScope: an integrated platform for the annotation and exploration of microbial gene functions through genomic, pangenomic and metabolic comparative analysis. PMID:31647104
A high-quality cucumber genome assembly enhances computational comparative genomics. PMID:31620884
Search for Nutritional Fitness Traits in a Biological Pest Control Agent Harmonia axyridis Using Comparative Transcriptomics. PMID:31620008
Identification of keratinases from Fervidobacterium islandicum AW-1 using dynamic gene expression profiling. PMID:31613061
The Prevotella copri Complex Comprises Four Distinct Clades Underrepresented in Westernized Populations. PMID:31607556
Depth-dependent transcriptomic response of diatoms during spring bloom in the western subarctic Pacific Ocean. PMID:31601926
Combined cultivation and single-cell approaches to the phylogenomics of nucleariid amoebae, close relatives of fungi. PMID:31587649
Complete Genome Sequence of the Biocontrol Agent Bacillus velezensis UFLA258 and Its Comparison with Related Species: Diversity within the Commons. PMID:31580420
Protective Role of Leaf Variegation in Pittosporum tobira under Low Temperature: Insights into the Physio-Biochemical and Molecular Mechanisms. PMID:31574927
Targeted isolation and cultivation of uncultivated bacteria by reverse genomics. PMID:31570900
De novo transcriptome assembly and analysis of the freshwater araphid diatom Fragilaria radians, Lake Baikal. PMID:31562323
Gene Expression of Haloferax volcanii on Intermediate and Abundant Sources of Fixed Nitrogen. PMID:31561502
Differential Gene Expression in Articular Cartilage and Subchondral Bone of Neonatal and Adult Horses. PMID:31557843
Comparative Genomic Analysis of Staphylococcus haemolyticus Reveals Key to Hospital Adaptation and Pathogenicity. PMID:31552006
Active Fungal Communities in Asymptomatic Eucalyptus grandis Stems Differ between a Susceptible and Resistant Clone. PMID:31547186
Sample Preservation and Storage Significantly Impact Taxonomic and Functional Profiles in Metaproteomics Studies of the Human Gut Microbiome. PMID:31546776
Comparative analysis of amplicon and metagenomic sequencing methods reveals key features in the evolution of animal metaorganisms. PMID:31521200
Comparative transcriptomic analysis of a wing-dimorphic stonefly reveals candidate wing loss genes. PMID:31516688
DIFFUSE: predicting isoform functions from sequences and expression profiles via deep learning. PMID:31510699
Metagenomes from Coastal Marine Sediments Give Insights into the Ecological Role and Cellular Features of Loki- and Thorarchaeota. PMID:31506313
Differential Regulation of Anthocyanins in Green and Purple Turnips Revealed by Combined De Novo Transcriptome and Metabolome Analysis. PMID:31500111
Genome Sequence of Metarhizium rileyi, a Microbial Control Agent for Lepidoptera. PMID:31488537
Fast and accurate average genome size and 16S rRNA gene average copy number computation in metagenomic data. PMID:31488068
Dual RNA-Seq Analysis of the Pine-Fusarium circinatum Interaction in Resistant (Pinus tecunumanii) and Susceptible (Pinus patula) Hosts. PMID:31487786
Whole genome sequencing and identification of host-interactive genes in the rice endophytic Leifsonia sp. ku-ls. PMID:31482368
Comparative Genomic Analysis of the 2016 Vibrio cholerae Outbreak in South Korea. PMID:31475130
Eukaryote Genes Are More Likely than Prokaryote Genes to Be Composites. PMID:31466252
Mucilaginibacter limnophilus sp. nov., isolated from a lake. PMID:31463791
Measuring the impact of gene prediction on gene loss estimates in Eukaryotes by quantifying falsely inferred absences. PMID:31461468
Systems Biology and Pangenome of Salmonella O-Antigens. PMID:31455646
Data on proteomic profiling of cells and extracellular vesicles of the melittin-resistant Acholeplasma laidlawii strain. PMID:31440540
Metagenomes and metatranscriptomes shed new light on the microbial-mediated sulfur cycle in a Siberian soda lake. PMID:31438955
Antibiotic resistance and metabolic profiles as functional biomarkers that accurately predict the geographic origin of city metagenomics samples. PMID:31429791
Associated Bacteria Affect Sexual Reproduction by Altering Gene Expression and Metabolic Processes in a Biofilm Inhabiting Diatom. PMID:31428077
Transcriptome Landscape Variation in the Genus Thymus. PMID:31426352
A CEP104-CSPP1 Complex Is Required for Formation of Primary Cilia Competent in Hedgehog Signaling. PMID:31412255
A consensus S. cerevisiae metabolic model Yeast8 and its ecosystem for comprehensively probing cellular metabolism. PMID:31395883
Combining sequencing approaches to fully resolve a carbapenemase-encoding megaplasmid in a Pseudomonas shirazica clinical strain. PMID:31381486
Metabolic Potential of As-yet-uncultured Archaeal Lineages of Candidatus Hydrothermarchaeota Thriving in Deep-sea Metal Sulfide Deposits. PMID:31378759
Multifaceted mechanisms of colistin resistance revealed by genomic analysis of multidrug-resistant Klebsiella pneumoniae isolates from individual patients before and after colistin treatment. PMID:31374222
Biological Soil Crusts from Different Soil Substrates Harbor Distinct Bacterial Groups with the Potential to Produce Exopolysaccharides and Lipopolysaccharides. PMID:31372685
Coherence of Microcystis species revealed through population genomics. PMID:31363173
From Root to Tips: Sporulation Evolution and Specialization in Bacillus subtilis and the Intestinal Pathogen Clostridioides difficile. PMID:31350897
High-throughput time-resolved morphology screening in bacteria reveals phenotypic responses to antibiotics. PMID:31341968
Ambient pH Alters the Protein Content of Outer Membrane Vesicles, Driving Host Development in a Beneficial Symbiosis. PMID:31331976
Cold seawater induces early sexual developmental stages in the BPG axis of European eel males. PMID:31331264
Highly variable mRNA half-life time within marine bacterial taxa and functional genes. PMID:31298776
Strain-level metagenomic assignment and compositional estimation for long reads with MetaMaps. PMID:31296857
A transcriptional and functional analysis of heat hardening in two invasive fruit fly species, Bactrocera dorsalis and Bactrocera correcta. PMID:31293628
The Transcriptome Landscape of Walnut Interspecies Hybrid (Juglans hindsii × Juglans regia) and Regulation of Cambial Activity in Relation to Grafting. PMID:31293615
Genomic Comparison of Lactobacillus helveticus Strains Highlights Probiotic Potential. PMID:31293536
Finding Functional Differences Between Species in a Microbial Community: Case Studies in Wine Fermentation and Kefir Culture. PMID:31293529
Transcriptomic response in symptomless roots of clubroot infected kohlrabi (Brassica oleracea var. gongylodes) mirrors resistant plants. PMID:31262271
Listeria monocytogenes Biofilm Adaptation to Different Temperatures Seen Through Shotgun Proteomics. PMID:31259174
Draft Genome Sequence of the Yeast Kodamaea ohmeri, a Symbiont of the Small Hive Beetle. PMID:31248992
Advances and Applications in the Quest for Orthologs. PMID:31241141
Mining traits for the enrichment and isolation of not-yet-cultured populations. PMID:31238973
Suppressor mutations in ribosomal proteins and FliY restore Bacillus subtilis swarming motility in the absence of EF-P. PMID:31237868
OMA standalone: orthology inference among public and custom genomes and transcriptomes. PMID:31235654
Single-cell genomics unveiled a cryptic cyanobacterial lineage with a worldwide distribution hidden by a dinoflagellate host. PMID:31235587
De Novo Assembly and Annotation of the Larval Transcriptome of Two Spadefoot Toads Widely Divergent in Developmental Rate. PMID:31217263
De novo European eel transcriptome provides insights into the evolutionary history of duplicated genes in teleost lineages. PMID:31188893
Comparison of de-novo assembly tools for plasmid metagenome analysis. PMID:31187446
Alteration of Proteomes in First-Generation Cultures of Bacillus pumilus Spores Exposed to Outer Space. PMID:31186338
Paenibacillus lutimineralis sp. nov., Isolated From Bentonite. PMID:31177311
Comparative transcriptomic and proteomic analysis of yellow shell and black shell pearl oysters, Pinctada fucata martensii. PMID:31176356
Isolation and characterization of a thermophilic sulfur- and iron-reducing thaumarchaeote from a terrestrial acidic hot spring. PMID:31171857
Alterations to the Lung Microbiome in Idiopathic Pulmonary Fibrosis Patients. PMID:31165050
Comprehensive transcriptome analysis reveals genes potentially involved in isoflavone biosynthesis in Pueraria thomsonii Benth. PMID:31163077
NG-meta-profiler: fast processing of metagenomes using NGLess, a domain-specific language. PMID:31159881
Disordered gut microbiota and alterations in metabolic patterns are associated with atrial fibrillation. PMID:31149718
Back to the Salt Mines: Genome and Transcriptome Comparisons of the Halophilic Fungus Aspergillus salisburgensis and Its Halotolerant Relative Aspergillus sclerotialis. PMID:31137536
An Integrated Systems Approach Unveils New Aspects of Microoxia-Mediated Regulation in Bradyrhizobium diazoefficiens. PMID:31134003
Variable Carbon Source Utilization, Stress Resistance, and Virulence Profiles Among Listeria monocytogenes Strains Responsible for Listeriosis Outbreaks in Switzerland. PMID:31130938
Biological composition and microbial dynamics of sinking particulate organic matter at abyssal depths in the oligotrophic open ocean. PMID:31127042
Investigating function roles of hypothetical proteins encoded by the Mycobacterium tuberculosis H37Rv genome. PMID:31113361
Investigation of candidate genes involved in the rhodoquinone biosynthetic pathway in Rhodospirillum rubrum. PMID:31112563
Effect of Baicalin-Aluminum Complexes on Fecal Microbiome in Piglets. PMID:31091773
Life at Home and on the Roam: Genomic Adaptions Reflect the Dual Lifestyle of an Intracellular, Facultative Symbiont. PMID:31086829
Draft Genome Sequence of an Antarctic Isolate of the Black Yeast Fungus Exophiala mesophila. PMID:31072892
Dysbiosis of the Gut Microbiome in Lung Cancer. PMID:31065547
Tree reconciliation combined with subsampling improves large scale inference of orthologous group hierarchies. PMID:31060495
Revisiting the Role of Transcription Factors in Coordinating the Defense Response Against Citrus Bark Cracking Viroid Infection in Commercial Hop (Humulus Lupulus L.). PMID:31060295
Differences in resource use lead to coexistence of seed-transmitted microbial populations. PMID:31040301
Isolation and Characterization of Live Yeast Cells from Ancient Vessels as a Tool in Bio-Archaeology. PMID:31040238
Genomic and Physiological Traits of the Marine Bacterium Alcaligenes aquatilis QD168 Isolated From Quintero Bay, Central Chile, Reveal a Robust Adaptive Response to Environmental Stressors. PMID:31024465
Genomic Features, Comparative Genomic Analysis, and Antimicrobial Susceptibility Patterns of Chryseobacterium arthrosphaerae Strain ED882-96 Isolated in Taiwan. PMID:31010035
FuncTree2: an interactive radial tree for functional hierarchies and omics data visualization. PMID:31004476
Niche-specific metabolic adaptation in biotrophic and necrotrophic oomycetes is manifested in differential use of nutrients, variation in gene content, and enzyme evolution. PMID:31002734
Resequencing the Genome of Malassezia restricta Strain KCTC 27527. PMID:31000550
Whole Genome Sequencing and Re-sequencing of the Sable Antelope (Hippotragus niger): A Resource for Monitoring Diversity in ex Situ and in Situ Populations. PMID:31000506
Phosphate-limited ocean regions select for bacterial populations enriched in the carbon-phosphorus lyase pathway for phosphonate degradation. PMID:30972938
Meta-analysis of fecal metagenomes reveals global microbial signatures that are specific for colorectal cancer. PMID:30936547
Proteome profiling of Pseudomonas aeruginosa PAO1 identifies novel responders to copper stress. PMID:30935370
EZHIP/CXorf67 mimics K27M mutated oncohistones and functions as an intrinsic inhibitor of PRC2 function in aggressive posterior fossa ependymoma. PMID:30923826
Identification of Functional Gene Modules Associated With STAT-Mediated Antiviral Responses to White Spot Syndrome Virus in Shrimp. PMID:30914969
Plasma-sensitive Escherichia coli mutants reveal plasma resistance mechanisms. PMID:30913981
AYbRAH: a curated ortholog database for yeasts and fungi spanning 600 million years of evolution. PMID:30893420
Identifying High Confidence microRNAs in the Developing Seeds of Jatropha curcas. PMID:30872797
Genomic Analyses of >3,100 Nasopharyngeal Pneumococci Revealed Significant Differences Between Pneumococci Recovered in Four Different Geographical Regions. PMID:30858837
Analysis of Predicted Host-Parasite Interactomes Reveals Commonalities and Specificities Related to Parasitic Lifestyle and Tissues Tropism. PMID:30815000
The draft genome of strain cCpun from biting midges confirms insect Cardinium are not a monophyletic group and reveals a novel gene family expansion in a symbiont. PMID:30809447
An alkaline active feruloyl-CoA synthetase from soil metagenome as a potential key enzyme for lignin valorization strategies. PMID:30802241
White shark genome reveals ancient elasmobranch adaptations associated with wound healing and the maintenance of genome stability. PMID:30782839
Genomic correlates of extraintestinal infection are linked with changes in cell morphology in Campylobacter jejuni. PMID:30777818
Genus-Wide Comparative Genomics Analysis of Neisseria to Identify New Genes Associated with Pathogenicity and Niche Adaptation of Neisseria Pathogens. PMID:30775379
Proteome profiling of secreted and membrane vesicle associated proteins of an invasive and a commensal Staphylococcus haemolyticus isolate. PMID:30766906
Long-Term Transcriptional Activity at Zero Growth of a Cosmopolitan Rare Biosphere Member. PMID:30755506
SqueezeMeta, A Highly Portable, Fully Automatic Metagenomic Analysis Pipeline. PMID:30733714
Complete Genome Sequence of the Wolbachia wAlbB Endosymbiont of Aedes albopictus. PMID:30715337
Bifidobacterium bifidum ATCC 15696 and Bifidobacterium breve 24b Metabolic Interaction Based on 2'-O-Fucosyl-Lactose Studied in Steady-State Cultures in a Freter-Style Chemostat. PMID:30683741
High-affinity transport, cyanide-resistant respiration, and ethanol production under aerobiosis underlying efficient high glycerol consumption by Wickerhamomyces anomalus. PMID:30680472
Ask1 and Akt act synergistically to promote ROS-dependent regeneration in Drosophila. PMID:30677014
Newly Discovered Occurrences and Gene Tree of the Extracellular Globins and Linker Chains from the Giant Hexagonal Bilayer Hemoglobin in Metazoans. PMID:30668717
Extensive Unexplored Human Microbiome Diversity Revealed by Over 150,000 Genomes from Metagenomes Spanning Age, Geography, and Lifestyle. PMID:30661755
Proteogenomics Reveals Novel Reductive Dehalogenases and Methyltransferases Expressed during Anaerobic Dichloromethane Metabolism. PMID:30658979
Genomes of Three Closely Related Caribbean Amazons Provide Insight for Species History and Conservation. PMID:30654561
Comparative metagenomic and metatranscriptomic analyses reveal the breed effect on the rumen microbiome and its associations with feed efficiency in beef cattle. PMID:30642389
Genomic characterisation of the new Dickeya fangzhongdai species regrouping plant pathogens and environmental isolates. PMID:30634913
Challenges in Clinical Metaproteomics Highlighted by the Analysis of Acute Leukemia Patients with Gut Colonization by Multidrug-Resistant Enterobacteriaceae. PMID:30626002
Identification of Cross-Protective Potential Antigens against Pathogenic Brucella spp. through Combining Pan-Genome Analysis with Reverse Vaccinology. PMID:30622973
The use of next generation sequencing for improving food safety: Translation into practice. PMID:30621881
The Network of Cancer Genes (NCG): a comprehensive catalogue of known and candidate cancer genes from cancer sequencing screens. PMID:30606230
Analysis of transcripts and splice isoforms in Medicago sativa L. by single-molecule long-read sequencing. PMID:30600412
The Chinese Medicinal Formulation Guzhi Zengsheng Zhitongwan Modulates Chondrocyte Structure, Dynamics, and Metabolism by Controlling Multiple Functional Proteins. PMID:30596102
Global transcriptome analysis of the aphelid Paraphelidium tribonemae supports the phagotrophic origin of fungi. PMID:30588510
Genome rearrangements and selection in multi-chromosome bacteria Burkholderia spp. PMID:30587126
Genotypic differences between strains of the opportunistic pathogen Corynebacterium bovis isolated from humans, cows, and rodents. PMID:30586440
Microbial metal-sulfide oxidation in inactive hydrothermal vent chimneys suggested by metagenomic and metaproteomic analyses. PMID:30585382
Cross-ID: Analysis and Visualization of Complex XL-MS-Driven Protein Interaction Networks. PMID:30575379
Gut colonization by a novel Clostridium species is associated with the onset of epizootic rabbit enteropathy. PMID:30572930
Metabolic and Proteomic Responses to Salinity in Synthetic Nitrifying Communities of Nitrosomonas spp. and Nitrobacter spp. PMID:30555445
Coupled Carbon, Sulfur, and Nitrogen Cycles Mediated by Microorganisms in the Water Column of a Shallow-Water Hydrothermal Ecosystem. PMID:30555427
Comparative genomic analysis of Parageobacillus thermoglucosidasius strains with distinct hydrogenogenic capacities. PMID:30522433
Draft genomes of Cronobacter sakazakii strains isolated from dried spices bring unique insights into the diversity of plant-associated strains. PMID:30519380
Genomic and transcriptomic insights into the ecology and metabolism of benthic archaeal cosmopolitan, Thermoprofundales (MBG-D archaea). PMID:30514872
iHam and pyHam: visualizing and processing hierarchical orthologous groups. PMID:30508066
Multilevel comparative bioinformatics to investigate evolutionary relationships and specificities in gene annotations: an example for tomato and grapevine. PMID:30497367
The chicken gut metagenome and the modulatory effects of plant-derived benzylisoquinoline alkaloids. PMID:30482240
STRING v11: protein-protein association networks with increased coverage, supporting functional discovery in genome-wide experimental datasets. PMID:30476243
The essential genome of the crenarchaeal model Sulfolobus islandicus. PMID:30464174
MBGD update 2018: microbial genome database based on hierarchical orthology relations covering closely related and distantly related comparisons. PMID:30462302
Reconstructing the functions of endosymbiotic Mollicutes in fungus-growing ants. PMID:30454555
Automated selection of homologs to track the evolutionary history of proteins. PMID:30453878
Genetic Signatures of Dairy Lactobacillus casei Group. PMID:30425707
eggNOG 5.0: a hierarchical, functionally and phylogenetically annotated orthology resource based on 5090 organisms and 2502 viruses. PMID:30418610
Transcriptome-based mining and expression profiling of Pythium responsive transcription factors in Zingiber sp. PMID:30415383
CRM Discovery Beyond Model Insects. PMID:30414115
Bacteriocyte Reprogramming to Cope With Nutritional Stress in a Phloem Sap Feeding Hemipteran, the Pea Aphid Acyrthosiphon pisum. PMID:30410449
The Enterococcus Cassette Chromosome, a Genomic Variation Enabler in Enterococci. PMID:30404935
OrthoDB v10: sampling the diversity of animal, plant, fungal, protist, bacterial and viral genomes for evolutionary and functional annotations of orthologs. PMID:30395283
Microbial activity response to hydrogen injection in thermophilic anaerobic digesters revealed by genome-centric metatranscriptomics. PMID:30368244
De Novo Hepatic Transcriptome Assembly and Systems Level Analysis of Three Species of Dietary Fish, Sardinops sagax, Scomber japonicus, and Pleuronichthys verticalis. PMID:30366465
The mesophilic archaeon Methanosarcina acetivorans counteracts uracil in DNA with multiple enzymes: EndoQ, ExoIII, and UDG. PMID:30361558
High genomic variability in the plant pathogenic bacterium Pectobacterium parmentieri deciphered from de novo assembled complete genomes. PMID:30326842
Comparative Genomics of Degradative Novosphingobium Strains With Special Reference to Microcystin-Degrading Novosphingobium sp. THN1. PMID:30319567
Horizontal gene cluster transfer increased hallucinogenic mushroom diversity. PMID:30283667
Genome Sequence of Peacock Reveals the Peculiar Case of a Glittering Bird. PMID:30283495
Integrated systems analysis reveals conserved gene networks underlying response to spinal cord injury. PMID:30277459
Complete genome sequence of Kocuria rhizophila BT304, isolated from the small intestine of castrated beef cattle. PMID:30275909
The Origin of Mitochondria-Specific Outer Membrane β-Barrels from an Ancestral Bacterial Fragment. PMID:30265295
Viruses.STRING: A Virus-Host Protein-Protein Interaction Database. PMID:30249048
Rapid Divergence of Genome Architectures Following the Origin of an Ectomycorrhizal Symbiosis in the Genus Amanita. PMID:30239843
A metagenomics roadmap to the uncultured genome diversity in hypersaline soda lake sediments. PMID:30231921
Differential expression of olive flounder (Paralichthys olivaceus) transcriptome during viral hemorrhagic septicemia virus (VHSV) infection at warmer and colder temperature. PMID:30229076
Parallel Evolution of Genome Streamlining and Cellular Bioenergetics across the Marine Radiation of a Bacterial Phylum. PMID:30228235
Origin of exon skipping-rich transcriptomes in animals driven by evolution of gene architecture. PMID:30223879
Data on genome annotation and analysis of earthworm Eisenia fetida. PMID:30191166
Effects of Acetylation and Phosphorylation on Subunit Interactions in Three Large Eukaryotic Complexes. PMID:30181345
Establishment of Transgenesis in the Demosponge Suberites domuncula. PMID:30143594
Defence transcriptome assembly and pathogenesis related gene family analysis in Pinus tecunumanii (low elevation). PMID:30139335
Tracing mother-infant transmission of bacteriophages by means of a novel analytical tool for shotgun metagenomic datasets: METAnnotatorX. PMID:30126456
Functional metagenomics reveals abundant polysaccharide-degrading gene clusters and cellobiose utilization pathways within gut microbiota of a wood-feeding higher termite. PMID:30116044
Comparative mitochondrial genomics reveals a possible role of a recent duplication of NADH dehydrogenase subunit 5 in gene regulation. PMID:30085012
JustOrthologs: a fast, accurate and user-friendly ortholog identification algorithm. PMID:30084941
Conducting metagenomic studies in microbiology and clinical research. PMID:30078138
Gonadal transcriptome sequencing of the critically endangered Acipenser dabryanus to discover candidate sex-related genes. PMID:30065900
BARM and BalticMicrobeDB, a reference metagenome and interface to meta-omic data for the Baltic Sea. PMID:30063227
Complex Evolutionary History of Translation Elongation Factor 2 and Diphthamide Biosynthesis in Archaea and Parabasalids. PMID:30060184
The genomic impact of historical hybridization with massive mitochondrial DNA introgression. PMID:30056805
mTOR Complex 1 Implicated in Aphid/Buchnera Host/Symbiont Integration. PMID:30049746
Analysis of codon usage patterns in Hirudinaria manillensis reveals a preference for GC-ending codons caused by dominant selection constraints. PMID:30016953
Deep mutational analysis reveals functional trade-offs in the sequences of EGFR autophosphorylation sites. PMID:30012625
Patterns of Nucleotide Deletion and Insertion Inferred from Bacterial Pseudogenes. PMID:29982456
Disentangling the drivers of functional complexity at the metagenomic level in Shark Bay microbial mat microbiomes. PMID:29980796
Genome Analysis of Vallitalea guaymasensis Strain L81 Isolated from a Deep-Sea Hydrothermal Vent System. PMID:29973550
Draft Genome Resource for the Potato Powdery Scab Pathogen Spongospora subterranea. PMID:29969057
Microbial Community Structure-Function Relationships in Yaquina Bay Estuary Reveal Spatially Distinct Carbon and Nitrogen Cycling Capacities. PMID:29963029
Comparative Genomic and Phenotypic Analysis of the Vaginal Probiotic Lactobacillus rhamnosus GR-1. PMID:29963028
A pan-genome-based machine learning approach for predicting antimicrobial resistance activities of the Escherichia coli strains. PMID:29949970
Comparative Genomics of Lactobacillus acidipiscis ACA-DC 1533 Isolated From Traditional Greek Kopanisti Cheese Against Species Within the Lactobacillus salivarius Clade. PMID:29942291
Site-specific characterization of endogenous SUMOylation across species and organs. PMID:29942033
Optofluidic Single-Cell Genome Amplification of Sub-micron Bacteria in the Ocean Subsurface. PMID:29937754
A CAZyme-Rich Genome of a Taxonomically Novel Rhodophyte-Associated Carrageenolytic Marine Bacterium. PMID:29936557
Expression of putative circadian clock components in the arbuscular mycorrhizal fungus Rhizoglomus irregulare. PMID:29931403
Secondary Plastids of Euglenids and Chlorarachniophytes Function with a Mix of Genes of Red and Green Algal Ancestry. PMID:29924337
Host Range and Genetic Plasticity Explain the Coexistence of Integrative and Extrachromosomal Mobile Genetic Elements. PMID:29905872
Reconstruction of the Bifidobacterial Pan-Secretome Reveals the Network of Extracellular Interactions between Bifidobacteria and the Infant Gut. PMID:29884754
Hundreds of novel composite genes and chimeric genes with bacterial origins contributed to haloarchaeal evolution. PMID:29880023
Data on genome sequencing, analysis and annotation of a pathogenic Bacillus cereus 062011msu. PMID:29876371
De novo assembly and comparative transcriptome analysis of Monilinia fructicola, Monilinia laxa and Monilinia fructigena, the causal agents of brown rot on stone fruits. PMID:29866047
Partnering With a Pest: Genomes of Hemlock Woolly Adelgid Symbionts Reveal Atypical Nutritional Provisioning Patterns in Dual-Obligate Bacteria. PMID:29860412
Comparative expression analysis identifies the respiratory transition-related miRNAs and their target genes in tissues of metamorphosing Chinese giant salamander (Andrias davidianus). PMID:29843595
The draft genome sequence of cork oak. PMID:29786699
Transcriptome and miRNA analyses of the response to Corynespora cassiicola in cucumber. PMID:29773833
Machine learning identifies signatures of host adaptation in the bacterial pathogen Salmonella enterica. PMID:29738521
Microbial Diversity and Toxin Risk in Tropical Freshwater Reservoirs of Cape Verde. PMID:29734762
High quality draft genome sequences of Mycoplasma agassizii strains PS6T and 723 isolated from Gopherus tortoises with upper respiratory tract disease. PMID:29725499
iPath3.0: interactive pathways explorer v3. PMID:29718427
Innovative assembly strategy contributes to understanding the evolution and conservation genetics of the endangered Solenodon paradoxus from the island of Hispaniola. PMID:29718205
Metagenome, metatranscriptome, and metaproteome approaches unraveled compositions and functional relationships of microbial communities residing in biogas plants. PMID:29713790
Single-cell metagenomics: challenges and applications. PMID:29696589
Navigating the disease landscape: knowledge representations for contextualizing molecular signatures. PMID:29684165
High quality draft genome sequence of Mycoplasma testudineum strain BH29T, isolated from the respiratory tract of a desert tortoise. PMID:29682170
Comparison of normalization methods for the analysis of metagenomic gene abundance data. PMID:29678163
The complete replicons of 16 Ensifer meliloti strains offer insights into intra- and inter-replicon gene transfer, transposon-associated loci, and repeat elements. PMID:29671722
Whole Genome Sequence of an Edible and Potential Medicinal Fungus, Cordyceps guangdongensis. PMID:29666196
TISSUES 2.0: an integrative web resource on mammalian tissue expression. PMID:29617745
Higher Rates of Protein Evolution in the Self-Fertilizing Plant Arabidopsis thaliana than in the Out-Crossers Arabidopsis lyrata and Arabidopsis halleri. PMID:29608724
Assembly of the Boechera retrofracta Genome and Evolutionary Analysis of Apomixis-Associated Genes. PMID:29597328
Lignolytic-consortium omics analyses reveal novel genomes and pathways involved in lignin modification and valorization. PMID:29588660
Embryophyte stress signaling evolved in the algal progenitors of land plants. PMID:29581286
Inter-replicon Gene Flow Contributes to Transcriptional Integration in the Sinorhizobium meliloti Multipartite Genome. PMID:29563186
Transcriptome Analysis of Epithelioma Papulosum Cyprini Cells Infected by Reovirus Isolated from Allogynogenetic Silver Crucian Carp. PMID:29562634
Presence of a Haloarchaeal Halorhodopsin-Like Cl- Pump in Marine Bacteria. PMID:29553064
Insights into the Evolution of Host Association through the Isolation and Characterization of a Novel Human Periodontal Pathobiont, Desulfobulbus oralis. PMID:29535201
Formation of chimeric genes with essential functions at the origin of eukaryotes. PMID:29534719
Identifying RNA splicing factors using IFT genes in Chlamydomonas reinhardtii. PMID:29514868
Complete genome sequence of Lactobacillus rhamnosus Pen, a probiotic component of a medicine used in prevention of antibiotic-associated diarrhoea in children. PMID:29483943
Pseudomonas orientalis F9: A Potent Antagonist against Phytopathogens with Phytotoxic Effect in the Apple Flower. PMID:29479340
Peatland Acidobacteria with a dissimilatory sulfur metabolism. PMID:29476143
Proteorhodopsin variability and distribution in the North Pacific Subtropical Gyre. PMID:29476140
Codominant grasses differ in gene expression under experimental climate extremes in native tallgrass prairie. PMID:29473008
Specialized plant biochemistry drives gene clustering in fungi. PMID:29463891
A Near-Complete Haplotype-Phased Genome of the Dikaryotic Wheat Stripe Rust Fungus Puccinia striiformis f. sp. tritici Reveals High Interhaplotype Diversity. PMID:29463659
Long-term treatment with green tea polyphenols modifies the gut microbiome of female sprague-dawley rats. PMID:29454999
Comparative Genomics of Completely Sequenced Lactobacillus helveticus Genomes Provides Insights into Strain-Specific Genes and Resolves Metagenomics Data Down to the Strain Level. PMID:29441050
Proteome Data Improves Protein Function Prediction in the Interactome of Helicobacter pylori. PMID:29414760
Solar-panel and parasol strategies shape the proteorhodopsin distribution pattern in marine Flavobacteriia. PMID:29410487
Updating the genomic taxonomy and epidemiology of Campylobacter hyointestinalis. PMID:29403020
Disseminating Metaproteomic Informatics Capabilities and Knowledge Using the Galaxy-P Framework. PMID:29385081
Use of a Regression Model to Study Host-Genomic Determinants of Phage Susceptibility in MRSA. PMID:29382143
De novo assembly and characterization of the Hucho taimen transcriptome. PMID:29375797
Cyclic AMP Regulates Bacterial Persistence through Repression of the Oxidative Stress Response and SOS-Dependent DNA Repair in Uropathogenic Escherichia coli. PMID:29317513
Assessing the Performances of Protein Function Prediction Algorithms from the Perspectives of Identification Accuracy and False Discovery Rate. PMID:29316706
Probing Genomic Aspects of the Multi-Host Pathogen Clostridium perfringens Reveals Significant Pangenome Diversity, and a Diverse Array of Virulence Factors. PMID:29312194
Identification of a Novel Genomic Island Associated with vanD-Type Vancomycin Resistance in Six Dutch Vancomycin-Resistant Enterococcus faecium Isolates. PMID:29311068
De novo assembling and primary analysis of genome and transcriptome of gray whale Eschrichtius robustus. PMID:29297306
Phenotype inference in an Escherichia coli strain panel. PMID:29280730
Complete genome sequence analysis of Archaeoglobus fulgidus strain 7324 (DSM 8774), a hyperthermophilic archaeal sulfate reducer from a North Sea oil field. PMID:29270248
FANCD2 binding identifies conserved fragile sites at large transcribed genes in avian cells. PMID:29253234
Subspecies in the global human gut microbiome. PMID:29242367
Comparative genome analysis of the vineyard weed endophyte Pseudomonas viridiflava CDRTc14 showing selective herbicidal activity. PMID:29229911
LeishDB: a database of coding gene annotation and non-coding RNAs in Leishmania braziliensis. PMID:29220437
Annotation of nerve cord transcriptome in earthworm Eisenia fetida. PMID:29204349
PlanNET: homology-based predicted interactome for multiple planarian transcriptomes. PMID:29186384
An orphan cbb3-type cytochrome oxidase subunit supports Pseudomonas aeruginosa biofilm growth and virulence. PMID:29160206
Assessing species biomass contributions in microbial communities via metaproteomics. PMID:29146960
An integrative strategy to identify the entire protein coding potential of prokaryotic genomes by proteogenomics. PMID:29141959
ECOdrug: a database connecting drugs and conservation of their targets across species. PMID:29140522
Comparative transcriptome analysis of a lowly virulent strain of Erwinia amylovora in shoots of two apple cultivars - susceptible and resistant to fire blight. PMID:29132313
Identification of New Features from Known Bacterial Protective Vaccine Antigens Enhances Rational Vaccine Design. PMID:29123525
The OMA orthology database in 2018: retrieving evolutionary relationships among all domains of life through richer web and programmatic interfaces. PMID:29106550
Isolation and Characterization of Bacteria That Degrade Phosphonates in Marine Dissolved Organic Matter. PMID:29085339
Determination of the Genome and Primary Transcriptome of Syngas Fermenting Eubacterium limosum ATCC 8486. PMID:29057933
Genome sequencing of 39 Akkermansia muciniphila isolates reveals its population structure, genomic and functional diverisity, and global distribution in mammalian gut microbiotas. PMID:29047329
Preterm Infant-Associated Clostridium tertium, Clostridium cadaveris, and Clostridium paraputrificum Strains: Genomic and Evolutionary Insights. PMID:29044436
20 years of the SMART protein domain annotation resource. PMID:29040681
DeepGO: predicting protein functions from sequence and interactions using a deep ontology-aware classifier. PMID:29028931
Distinct Subfamilies of Odorant Binding Proteins in Locust (Orthoptera, Acrididae): Molecular Evolution, Structural Variation, and Sensilla-Specific Expression. PMID:29018357
Gearing up to handle the mosaic nature of life in the quest for orthologs. PMID:28968857
Microbial genome analysis: the COG approach. PMID:28968633
Phylogenomic, Pan-genomic, Pathogenomic and Evolutionary Genomic Insights into the Agronomically Relevant Enterobacteria Pantoea ananatis and Pantoea stewartii. PMID:28959245
De novo transcriptome of the cosmopolitan dinoflagellate Amphidinium carterae to identify enzymes with biotechnological potential. PMID:28916825
Parallel Evolution of Group B Streptococcus Hypervirulent Clonal Complex 17 Unveils New Pathoadaptive Mutations. PMID:28904998
Seasonal variation in nutrient utilization shapes gut microbiome structure and function in wild giant pandas. PMID:28904137
A practical guide to build de-novo assemblies for single tissues of non-model organisms: the example of a Neotropical frog. PMID:28879061
Prokaryotic and Highly-Repetitive WD40 Proteins: A Systematic Study. PMID:28878378
Genomic and transcriptomic analyses reveal differential regulation of diverse terpenoid and polyketides secondary metabolites in Hericium erinaceus. PMID:28860534
Transposable Element Misregulation Is Linked to the Divergence between Parental piRNA Pathways in Drosophila Hybrids. PMID:28854624
A Key Regulator of the Glycolytic and Gluconeogenic Central Metabolic Pathways in Sinorhizobium meliloti. PMID:28851745
Lactobacillus plantarum LP‑Onlly alters the gut flora and attenuates colitis by inducing microbiome alteration in interleukin‑10 knockout mice. PMID:28849048
Large-Scale Phylogenomics of the Lactobacillus casei Group Highlights Taxonomic Inconsistencies and Reveals Novel Clade-Associated Features. PMID:28845461
Large-scale comparative metagenomics of Blastocystis, a common member of the human gut microbiome. PMID:28837129
Systematic and Quantitative Assessment of Hydrogen Peroxide Reactivity With Cysteines Across Human Proteomes. PMID:28827280
Association of coral algal symbionts with a diverse viral community responsive to heat shock. PMID:28818037
Torix group Rickettsia are widespread in Culicoides biting midges (Diptera: Ceratopogonidae), reach high frequency and carry unique genomic features. PMID:28805302
A clinician's guide to microbiome analysis. PMID:28790452
Modelling the evolution of transcription factor binding preferences in complex eukaryotes. PMID:28790414
Comparative genomic and phylogenomic analyses of the Bifidobacteriaceae family. PMID:28764658
Inferring Methionine Sulfoxidation and serine Phosphorylation crosstalk from Phylogenetic analyses. PMID:28750604
The Protein Interactome of Streptococcus pneumoniae and Bacterial Meta-interactomes Improve Function Predictions. PMID:28744484
Protein-protein binding selectivity and network topology constrain global and local properties of interface binding networks. PMID:28717235
Deep-Sea Hydrothermal Vent Viruses Compensate for Microbial Metabolism in Virus-Host Interactions. PMID:28698277
Genome-resolved metaproteomic characterization of preterm infant gut microbiota development reveals species-specific metabolic shifts and variabilities during early life. PMID:28693612
Response of Microbial Community Function to Fluctuating Geochemical Conditions within a Legacy Radioactive Waste Trench Environment. PMID:28667104
Systematic bacterialization of yeast genes identifies a near-universally swappable pathway. PMID:28661399
Expression, Localization of SUMO-1, and Analyses of Potential SUMOylated Proteins in Bubalus bubalis Spermatozoa. PMID:28659810
Comparative transcriptomic analysis of the evolution and development of flower size in Saltugilia (Polemoniaceae). PMID:28645249
Unexpected genomic features in widespread intracellular bacteria: evidence for motility of marine chlamydiae. PMID:28644443
Bifidobacterium Bacteremia: Clinical Characteristics and a Genomic Approach To Assess Pathogenicity. PMID:28490487
Fast Genome-Wide Functional Annotation through Orthology Assignment by eggNOG-Mapper. PMID:28460117
Co-occurring protein phosphorylation are functionally associated. PMID:28459814
Interplay of buried histidine protonation and protein stability in prion misfolding. PMID:28408762
Characterization of Brucella abortus mutant strain Δ22915, a potential vaccine candidate. PMID:28376905
Systematic identification of phosphorylation-mediated protein interaction switches. PMID:28346509
Dietary emulsifiers directly alter human microbiota composition and gene expression ex vivo potentiating intestinal inflammation. PMID:28325746
Identification of an RNase that preferentially cleaves A/G nucleotides. PMID:28322335
Complete genome sequence of Pseudomonas citronellolis P3B5, a candidate for microbial phyllo-remediation of hydrocarbon-contaminated sites. PMID:28300228
Bacterial protein meta-interactomes predict cross-species interactions and protein function. PMID:28298180
Metabolic anchor reactions for robust biorefining. PMID:28232136
Antibiotic Resistance Determinant-Focused Acinetobacter baumannii Vaccine Designed Using Reverse Vaccinology. PMID:28230771
-Genomic data mining of the marine actinobacteria Streptomyces sp. H-KF8 unveils insights into multi-stress related genes and metabolic pathways involved in antimicrobial synthesis. PMID:28229018
Transcriptome-wide microRNA and target dynamics in the fat body during the gonadotrophic cycle of Aedes aegypti. PMID:28223504
Construction and Analysis of Two Genome-Scale Deletion Libraries for Bacillus subtilis. PMID:28189581
Recruitment of PP1 to the centrosomal scaffold protein CEP192. PMID:28188792
The complete genome sequence of the yogurt isolate Streptococcus thermophilus ACA-DC 2. PMID:28163827
Bioengineering a bacterial pathogen to assemble its own particulate vaccine capable of inducing cellular immunity. PMID:28150705
RAIN: RNA-protein Association and Interaction Networks. PMID:28077569
Fast and accurate phylogeny reconstruction using filtered spaced-word matches. PMID:28073754
Reading the Evolution of Compartmentalization in the Ribosome Assembly Toolbox: The YRG Protein Family. PMID:28072865
Plant genome and transcriptome annotations: from misconceptions to simple solutions. PMID:28062412
proGenomes: a resource for consistent functional and taxonomic annotations of prokaryotic genomes. PMID:28053165
The 24th annual Nucleic Acids Research database issue: a look back and upcoming changes. PMID:28053160
Identification of candidate infection genes from the model entomopathogenic nematode Heterorhabditis bacteriophora. PMID:28049427
Label-Free Quantitative Proteomic Analysis of Harmless and Pathogenic Strains of Infectious Microalgae, Prototheca spp. PMID:28036087
Secreted Proteins Defy the Expression Level-Evolutionary Rate Anticorrelation. PMID:28007979
Architecture of the yeast Elongator complex. PMID:27974378
Spatial distribution of planktonic bacterial and archaeal communities in the upper section of the tidal reach in Yangtze River. PMID:27966673
The STRING database in 2017: quality-controlled protein-protein association networks, made broadly accessible. PMID:27924014
RAID v2.0: an updated resource of RNA-associated interactions across organisms. PMID:27899615
Draft Genome Sequence of Curtobacterium sp. Strain ER1/6, an Endophytic Strain Isolated from Citrus sinensis with Potential To Be Used as a Biocontrol Agent. PMID:27856581
Prokaryotic Virus Orthologous Groups (pVOGs): a resource for comparative genomics and protein family annotation. PMID:27789703
A computational interactome and functional annotation for the human proteome. PMID:27770567
Construction and Analysis of Functional Networks in the Gut Microbiome of Type 2 Diabetes Patients. PMID:27746285
HieranoiDB: a database of orthologs inferred by Hieranoid. PMID:27742821
Probing the diversity of healthy oral microbiome with bioinformatics approaches. PMID:27697111
Functional Metabolomics Describes the Yeast Biosynthetic Regulome. PMID:27693354
Metaproteomics of saliva identifies human protein markers specific for individuals with periodontitis and dental caries compared to orally healthy controls. PMID:27672500
Functional Annotations of Paralogs: A Blessing and a Curse. PMID:27618105
Complete genome sequence of Desulfurivibrio alkaliphilus strain AHT2(T), a haloalkaliphilic sulfidogen from Egyptian hypersaline alkaline lakes. PMID:27617057
The Genetic Analysis of an Acinetobacter johnsonii Clinical Strain Evidenced the Presence of Horizontal Genetic Transfer. PMID:27548264
Culture Independent Genomic Comparisons Reveal Environmental Adaptations for Altiarchaeales. PMID:27547202
The multiple evolutionary origins of the eukaryotic N-glycosylation pathway. PMID:27492357
HoloVir: A Workflow for Investigating the Diversity and Function of Viruses in Invertebrate Holobionts. PMID:27375564
Wolbachia Endosymbionts Modify Drosophila Ovary Protein Levels in a Context-Dependent Manner. PMID:27342560
The sorghum SWEET gene family: stem sucrose accumulation as revealed through transcriptome profiling. PMID:27330561
Capturing One of the Human Gut Microbiome's Most Wanted: Reconstructing the Genome of a Novel Butyrate-Producing, Clostridial Scavenger from Metagenomic Sequence Data. PMID:27303377
Towards Consensus Gene Ages. PMID:27259914
Sticky Genomes: Using NGS Evidence to Test Hybrid Speciation Hypotheses. PMID:27187689
MOCAT2: a metagenomic assembly, annotation and profiling framework. PMID:27153620
Requirements for Carnitine Shuttle-Mediated Translocation of Mitochondrial Acetyl Moieties to the Yeast Cytosol. PMID:27143389
The drug-minded protein interaction database (DrumPID) for efficient target analysis and drug development. PMID:27055828
The gut microbiome of healthy Japanese and its microbial and functional uniqueness. PMID:26951067
ETE 3: Reconstruction, Analysis, and Visualization of Phylogenomic Data. PMID:26921390 -
eggNOG 5.0: a hierarchical, functionally and phylogenetically annotated orthology resource based on 5090 organisms and 2502 viruses
PubMed citations: 634.
634 articles citing: eggNOG 5.0: a hierarchical, functionally and phylogenetically annotated orthology resource based on 5090 organisms and 2502 viruses
De Novo Transcriptome Assembly and Analysis of the Flat Oyster Pathogenic Protozoa Bonamia Ostreae. PMID:35909967
Co-evolutionary adaptations of Acinetobacter baumannii and a clinical carbapenemase-encoding plasmid during carbapenem exposure. PMID:35899254
Complete Genomes of Theileria orientalis Chitose and Buffeli Genotypes Reveal within Species Translocations and Differences in ABC Transporter Content. PMID:35890045
Genomic Characteristics and Comparative Genomics Analysis of Parafenestella ontariensis sp. nov. PMID:35887487
Identification of a Putative CodY Regulon in the Gram-Negative Phylum Synergistetes. PMID:35887256
Emerging Computational Approaches for Antimicrobial Peptide Discovery. PMID:35884190
The First Genome Survey and De Novo Assembly of the Short Mackerel (Rastrelliger brachysoma) and Indian Mackerel (Rastrelliger kanagurta). PMID:35883316
A Cocktail of Three Virulent Phages Controls Multidrug-Resistant Salmonella Enteritidis Infection in Poultry. PMID:35875532
SANA: cross-species prediction of Gene Ontology GO annotations via topological network alignment. PMID:35859153
Activity-based protein profiling identifies alternating activation of enzymes involved in the bifidobacterium shunt pathway or mucin degradation in the gut microbiome response to soluble dietary fiber. PMID:35858888
Analysis of phylogenetic markers for classification of a hydrogen peroxide producing Streptococcus oralis isolated from saliva by a newly devised differential medium. PMID:35835959
IS6110 Copy Number in Multi-Host Mycobacterium bovis Strains Circulating in Bovine Tuberculosis Endemic French Regions. PMID:35814675
Peribacillus castrilensis sp. nov.: A Plant-Growth-Promoting and Biocontrol Species Isolated From a River Otter in Castril, Granada, Southern Spain. PMID:35812926
The evolutionary origin of host association in the Rickettsiales. PMID:35798888
Pan-transcriptome assembly combined with multiple association analysis provides new insights into the regulatory network of specialized metabolites in the tea plant Camellia sinensis. PMID:35795389
Conserved and lineage-specific hypothetical proteins may have played a central role in the rise and diversification of major archaeal groups. PMID:35790962
An expanded reference map of the human gut microbiome reveals hundreds of previously unknown species. PMID:35790781
Metaproteomics reveals enzymatic strategies deployed by anaerobic microbiomes to maintain lignocellulose deconstruction at high solids. PMID:35790765
A consensus view of the proteome of the last universal common ancestor. PMID:35784055
Genomic Insight Into Lacticaseibacillus paracasei SP5, Reveals Genes and Gene Clusters of Probiotic Interest and Biotechnological Potential. PMID:35783439
First Report of Chromosome-Level Genome Assembly for Flathead Grey Mullet, Mugil cephalus (Linnaeus, 1758). PMID:35783261
A chromosome-level genome assembly of Neotoxoptera formosana (Takahashi, 1921) (Hemiptera: Aphididae). PMID:35775933
Reference nodule transcriptomes for Melilotus officinalis and Medicago sativa cv. Algonquin. PMID:35774624
Genome-wide analysis of Brucella melitensis genes required throughout intranasal infection in mice. PMID:35771771
Strain Variation in Clostridioides difficile Cytotoxicity Associated with Genomic Variation at Both Pathogenic and Nonpathogenic Loci. PMID:35766503
Introduction to the principles and methods underlying the recovery of metagenome-assembled genomes from metagenomic data. PMID:35765182
A chromosome-level genome assembly and intestinal transcriptome of Trypoxylus dichotomus (Coleoptera: Scarabaeidae) to understand its lignocellulose digestion ability. PMID:35764601
A genome and gene catalog of glacier microbiomes. PMID:35760913
Phage-host coevolution in natural populations. PMID:35760840
Novel thermophilic polyhydroxyalkanoates producing strain Aneurinibacillus thermoaerophilus CCM 8960. PMID:35759037
Chromosome-level genome assembly of the aquatic plant Nymphoides indica reveals transposable element bursts and NBS-LRR gene family expansion shedding light on its invasiveness. PMID:35751614
Assembly and Comparison of Ca. Neoehrlichia mikurensis Genomes. PMID:35744652
A Comprehensive Study of the WRKY Transcription Factor Family in Strawberry. PMID:35736736
Biosynthetic potential of the global ocean microbiome. PMID:35732736
Old genes in new places: A taxon-rich analysis of interdomain lateral gene transfer events. PMID:35731825
N6-methyladenosine modification of the Aedes aegypti transcriptome and its alteration upon dengue virus infection in Aag2 cell line. PMID:35725909
Comparative genomic analysis reveals contraction of gene families with putative roles in pathogenesis in the fungal boxwood pathogens Calonectria henricotiae and C. pseudonaviculata. PMID:35725368
Comparative Genomics Provides Insights Into Genetic Diversity of Clostridium tyrobutyricum and Potential Implications for Late Blowing Defects in Cheese. PMID:35722315
A de novo genome assembly of cultivated Prunus persica cv. 'Sovetskiy'. PMID:35714114
Genome-Wide Identification and Expression Pattern Analysis of KNOX Gene Family in Orchidaceae. PMID:35712569
Identification of miRNAs of Strongyloides stercoralis L1 and iL3 larvae isolated from human stool. PMID:35705621
Differential regulation of degradation and immune pathways underlies adaptation of the ectosymbiotic nematode Laxus oneistus to oxic-anoxic interfaces. PMID:35697683
Draft Genome Sequences of Five Cystobasidium ongulense Strains Isolated from Areas near Syowa Station, East Antarctica. PMID:35695498
A transcriptomic atlas underlying developmental plasticity of seasonal forms of Bicyclus anynana butterflies. PMID:35679434
Taxonomy, comparative genomics and evolutionary insights of Penicillium ucsense: a novel species in series Oxalica. PMID:35678932
RNA Biomarker Trends across Type I and Type II Aerobic Methanotrophs in Response to Methane Oxidation Rates and Transcriptome Response to Short-Term Methane and Oxygen Limitation in Methylomicrobium album BG8. PMID:35678574
Disturbance-based management of ecosystem services and disservices in partial nitritation-anammox biofilms. PMID:35676296
Short- and long-read metagenomics expand individualized structural variations in gut microbiomes. PMID:35676264
Comparative genomics reveals low levels of inter- and intraspecies diversity in the causal agents of dwarf and common bunt of wheat and hint at conspecificity of Tilletia caries and T. laevis. PMID:35672841
Exosome Mimetics-Loaded Hydrogel Accelerates Wound Repair by Transferring Functional Mitochondrial Proteins. PMID:35669057
Antibiotic-resistant organisms establish reservoirs in new hospital built environments and are related to patient blood infection isolates. PMID:35664456
Genomic Analyses Identify Manganese Homeostasis as a Driver of Group B Streptococcal Vaginal Colonization. PMID:35658538
Genomic insights into the recent chromosome reduction of autopolyploid sugarcane Saccharum spontaneum. PMID:35654976
UG/Abi: a highly diverse family of prokaryotic reverse transcriptases associated with defense functions. PMID:35648479
Chromosome-Scale, Haplotype-Resolved Genome Assembly of Suaeda Glauca. PMID:35646071
FUNAGE-Pro: comprehensive web server for gene set enrichment analysis of prokaryotes. PMID:35641095
GeCoViz: genomic context visualisation of prokaryotic genes from a functional and evolutionary perspective. PMID:35639770
Myriapod genomes reveal ancestral horizontal gene transfer and hormonal gene loss in millipedes. PMID:35637228
Genomic and Physiological Characterization of Metabacillus flavus sp. nov., a Novel Carotenoid-Producing Bacilli Isolated from Korean Marine Mud. PMID:35630423
Genome-Wide Identification and Transcriptional Expression Profiles of PP2C in the Barley (Hordeum vulgare L.) Pan-Genome. PMID:35627219
Comprehensive evolutionary analysis and nomenclature of plant G3BPs. PMID:35618429
Lake microbiome and trophy fluctuations of the ancient hemp rettery. PMID:35614182
Novel Bioinformatics Strategies Driving Dynamic Metaproteomic Studies. PMID:35612752
Comprehensive Analysis Reveals the Genetic and Pathogenic Diversity of Ralstonia solanacearum Species Complex and Benefits Its Taxonomic Classification. PMID:35602040
A chromosome-level genome assembly of the pollinating fig wasp Valisia javana. PMID:35595238
Combined GWAS and Transcriptome Analyses Provide New Insights Into the Response Mechanisms of Sunflower Against Drought Stress. PMID:35592557
Fuel source shift or cost reduction: Context-dependent adaptation strategies in closely related Neodon fuscus and Lasiopodomys brandtii against hypoxia. PMID:35585802
Environmentally induced DNA methylation is inherited across generations in an aquatic keystone species. PMID:35573201
Whole genome sequencing of cyanobacterium Nostoc sp. CCCryo 231-06 using microfluidic single cell technology. PMID:35573199
Natural selenium stress influences the changes of antibiotic resistome in seleniferous forest soils. PMID:35570296
Analysis of Comparative Transcriptome and Positively Selected Genes Reveal Adaptive Evolution in Leaf-Less and Root-Less Whisk Ferns. PMID:35567199
Identification of Key Factors for Anoxic Survival of B. cenocepacia H111. PMID:35562951
The Isolation and Characterization of Rare Mycobiome Associated With Spacecraft Assembly Cleanrooms. PMID:35558115
Metagenomic Insights Into Competition Between Denitrification and Dissimilatory Nitrate Reduction to Ammonia Within One-Stage and Two-Stage Partial-Nitritation Anammox Bioreactor Configurations. PMID:35547121
Opportunities and challenges of using metagenomic data to bring uncultured microbes into cultivation. PMID:35546409
PhyloCloud: an online platform for making sense of phylogenomic data. PMID:35544233
The flying spider-monkey tree fern genome provides insights into fern evolution and arborescence. PMID:35534720
Fungal communities represent the majority of root-specific transcripts in the transcriptomes of Agave plants grown in semiarid regions. PMID:35529479
Sugars dominate the seagrass rhizosphere. PMID:35501482
Patterns and ecological drivers of viral communities in acid mine drainage sediments across Southern China. PMID:35501347
Marine Sponge Endosymbionts: Structural and Functional Specificity of the Microbiome within Euryspongia arenaria Cells. PMID:35499324
Genomic and Phenotypic Characterization of Clostridium botulinum Isolates from an Infant Botulism Case Suggests Adaptation Signatures to the Gut. PMID:35499308
Faster Growth Enhances Low Carbon Fuel and Chemical Production Through Gas Fermentation. PMID:35497340
Identification of BgP, a Cutinase-Like Polyesterase From a Deep-Sea Sponge-Derived Actinobacterium. PMID:35495686
ImitateDB: A database for domain and motif mimicry incorporating host and pathogen protein interactions. PMID:35487995
Systems biology approach to functionally assess the Clostridioides difficile pangenome reveals genetic diversity with discriminatory power. PMID:35476524
Comparative Genomics of Synechococcus elongatus Explains the Phenotypic Diversity of the Strains. PMID:35475644
Whole-Genome Shotgun Metagenomic Sequencing Reveals Distinct Gut Microbiome Signatures of Obese Cats. PMID:35467389
Human gut metatranscriptome changes induced by a fermented milk product are associated with improved tolerance to a flatulogenic diet. PMID:35465165
Bioprospecting of Ribosomally Synthesized and Post-translationally Modified Peptides Through Genome Characterization of a Novel Probiotic Lactiplantibacillus plantarum UTNGt21A Strain: A Promising Natural Antimicrobials Factory. PMID:35464932
Draft genome sequence of 'Candidatus Phytoplasma australasia', strain SS02 associated with sesame phyllody disease. PMID:35462955
Characterisation of Bacteriophage vB_SmaM_Ps15 Infective to Stenotrophomonas maltophilia Clinical Ocular Isolates. PMID:35458438
Multidimensional Gene Regulatory Landscape of Motor Organ Pulvinus in the Model Legume Medicago truncatula. PMID:35457256
Safety Assessment of Lactiplantibacillus plantarum TWK10 Based on Whole-Genome Sequencing, Phenotypic, and Oral Toxicity Analysis. PMID:35456834
Molecular and Genomic Characterization of the Pseudomonas syringae Phylogroup 4: An Emerging Pathogen of Arabidopsis thaliana and Nicotiana benthamiana. PMID:35456758
Genomic and metabolic adaptations of biofilms to ecological windows of opportunity in glacier-fed streams. PMID:35444202
Hydrogenophaga crocea sp. nov. associated with cyanobacterial mat isolated from farmland mud. PMID:35435503
Data on RNA-seq analysis of the oviducts of five closely related species genus Littorina (Mollusca, Caenogastropoda): L. saxatilis, L. arcana, L. compressa, L. obtusata, L. fabalis. PMID:35434228
Pan-Genome Analysis of Laribacter hongkongensis: Virulence Gene Profiles, Carbohydrate-Active Enzyme Prediction, and Antimicrobial Resistance Characterization. PMID:35432229
Comprehensive Analysis of the Nocardia cyriacigeorgica Complex Reveals Five Species-Level Clades with Different Evolutionary and Pathogenicity Characteristics. PMID:35430877
The first de novo genome assembly and sex marker identification of Pluang Chomphu fish (Tor tambra) from Southern Thailand. PMID:35422970
Degradation of long-chain n-alkanes by a novel thermal-tolerant Rhodococcus strain. PMID:35419660
Unraveling the Genotypic and Phenotypic Diversity of the Psychrophilic Clostridium estertheticum Complex, a Meat Spoilage Agent. PMID:35418954
The PeptideAtlas of a widely cultivated fish Labeo rohita: A resource for the Aquaculture Community. PMID:35418183
The Ovarian Transcriptome at the Early Stage of Testis Removal-Induced Male-To-Female Sex Change in the Protandrous Black Porgy Acanthopagrus schlegelii. PMID:35401660
Genome-Wide Identification and Expression Analysis of the R2R3-MYB Transcription Factor Family Revealed Their Potential Roles in the Flowering Process in Longan (Dimocarpus longan). PMID:35401601
Deep whole-genome resequencing sheds light on the distribution and effect of amphioxus SNPs. PMID:35395709
Enterobacteriaceae and Bacteroidaceae provide resistance to travel-associated intestinal colonization by multi-drug resistant Escherichia coli. PMID:35388735
Extensive epigenetic modification with large-scale chromosomal and plasmid recombination characterise the Legionella longbeachae serogroup 1 genome. PMID:35388097
Weaning Time Affects the Archaeal Community Structure and Functional Potential in Pigs. PMID:35387077
A Large-Scale Genome-Based Survey of Acidophilic Bacteria Suggests That Genome Streamlining Is an Adaption for Life at Low pH. PMID:35387071
Responses of the Soil Bacterial Community, Resistome, and Mobilome to a Decade of Annual Exposure to Macrolide Antibiotics. PMID:35384705
Cerebral Intraparenchymal Hemorrhage Changes Patients' Gut Bacteria Composition and Function. PMID:35372117
Genome Assembly and Genome Annotation of Leishmania martiniquensis Isolated from a Leishmaniasis Patient in Thailand. PMID:35371566
The phyllosphere microbiome shifts toward combating melanose pathogen. PMID:35366955
Time-course transcriptome and WGCNA analysis revealed the drought response mechanism of two sunflower inbred lines. PMID:35363798
Machine Learning and Deep Learning Applications in Metagenomic Taxonomy and Functional Annotation. PMID:35359727
Tracing back variations in archaeal ESCRT-based cell division to protein domain architectures. PMID:35358274
Unifying the known and unknown microbial coding sequence space. PMID:35356891
Genetic Diversity and Pathogenic Features in Klebsiella pneumoniae Isolates from Patients with Pyogenic Liver Abscess and Pneumonia. PMID:35352958
Microbial communities of Auka hydrothermal sediments shed light on vent biogeography and the evolutionary history of thermophily. PMID:35352015
Multikingdom interactions govern the microbiome in subterranean cultural heritage sites. PMID:35344401
Genomic Surveillance of Vancomycin-Resistant Enterococcus faecium Reveals Spread of a Linear Plasmid Conferring a Nutrient Utilization Advantage. PMID:35343787
Genomic and Functional Variation of the Chlorophyll d-Producing Cyanobacterium Acaryochloris marina. PMID:35336144
Genomic and Experimental Analysis of the Insecticidal Factors Secreted by the Entomopathogenic Fungus Beauveria pseudobassiana RGM 2184. PMID:35330256
An Extremely Streamlined Macronuclear Genome in the Free-Living Protozoan Fabrea salina. PMID:35325184
Landscape of mobile genetic elements and their antibiotic resistance cargo in prokaryotic genomes. PMID:35323968
Microbiomes in the Challenger Deep slope and bottom-axis sediments. PMID:35314706
Hyperosmolality in CHO cell culture: effects on the proteome. PMID:35312825
Computational Tools for the Analysis of Uncultivated Phage Genomes. PMID:35311574
Comparative Genomics of Cyclic di-GMP Metabolism and Chemosensory Pathways in Shewanella algae Strains: Novel Bacterial Sensory Domains and Functional Insights into Lifestyle Regulation. PMID:35311563
A Comprehensive Overview of the Genes and Functions Required for Lettuce Infection by the Hemibiotrophic Phytopathogen Xanthomonas hortorum pv. vitians. PMID:35311560
The Rcs System Contributes to the Motility Defects of the Twin-Arginine Translocation System Mutant of Extraintestinal Pathogenic Escherichia coli. PMID:35311558
Resistance-Guided Mining of Bacterial Genotoxins Defines a Family of DNA Glycosylases. PMID:35311535
Transcriptomic Analysis of the Dual Response of Rhodococcus aetherivorans BCP1 to Inorganic Arsenic Oxyanions. PMID:35311511
Proteomic Responses of Dark-Adapted Euglena gracilis and Bleached Mutant Against Light Stimuli. PMID:35309998
Genome-Wide Transcriptional Response of Mycobacterium smegmatis MC2155 to G-Quadruplex Ligands BRACO-19 and TMPyP4. PMID:35308348
Chromosomal-Level Genome Assembly of the Springtail Tomocerus qinae (Collembola: Tomoceridae). PMID:35298623
Methods for the targeted sequencing and analysis of integrons and their gene cassettes from complex microbial communities. PMID:35298369
An artificial host system enables the obligate parasite Cuscuta campestris to grow and reproduce in vitro. PMID:35294033
A peroxisomal heterodimeric enzyme is involved in benzaldehyde synthesis in plants. PMID:35292635
The genomic basis of the Streptococcus thermophilus health-promoting properties. PMID:35291951
Nitrogen Metabolism in Pseudomonas putida: Functional Analysis Using Random Barcode Transposon Sequencing. PMID:35285712
Bulinus truncatus transcriptome - a resource to enable molecular studies of snail and schistosome biology. PMID:35284899
The genome of an apodid holothuroid (Chiridota heheva) provides insights into its adaptation to a deep-sea reducing environment. PMID:35273345
Conserved exchange of paralog proteins during neuronal differentiation. PMID:35273078
Deciphering the Potential Coding of Human Cytomegalovirus: New Predicted Transmembrane Proteome. PMID:35269907
Outer Membrane Vesicles of Acinetobacter baumannii DS002 Are Selectively Enriched with TonB-Dependent Transporters and Play a Key Role in Iron Acquisition. PMID:35266817
Infection strategy and biogeography distinguish cosmopolitan groups of marine jumbo bacteriophages. PMID:35260829
Contrasting a reference cranberry genome to a crop wild relative provides insights into adaptation, domestication, and breeding. PMID:35255111
The genome of the rice variety LTH provides insight into its universal susceptibility mechanism to worldwide rice blast fungal strains. PMID:35242291
Considerations for constructing a protein sequence database for metaproteomics. PMID:35242286
Cysteine dependence of Lactobacillus iners is a potential therapeutic target for vaginal microbiota modulation. PMID:35241796
Correlative proteomics identify the key roles of stress tolerance strategies in Acinetobacter baumannii in response to polymyxin and human macrophages. PMID:35231068
Stimulated Organic Carbon Cycling and Microbial Community Shift Driven by a Simulated Cold-Seep Eruption. PMID:35229641
Insights into the species evolution of Calanus copepods in the northern seas revealed by de novo transcriptome sequencing. PMID:35228861
Transcriptome changes in the developing sugarcane culm associated with high yield and early-season high sugar content. PMID:35224663
Scaling laws in enzyme function reveal a new kind of biochemical universality. PMID:35217602
Genome Analysis of Celeribacter sp. PS-C1 Isolated from Sekinchan Beach in Selangor, Malaysia, Reveals Its β-Glucosidase and Licheninase Activities. PMID:35208867
RNA Sequencing Reveals Widespread Transcription of Natural Antisense RNAs in Entamoeba Species. PMID:35208849
In Silico Characterisation of Putative Prophages in Lactobacillaceae Used in Probiotics for Vaginal Health. PMID:35208669
IMA Genome - F16 : Draft genome assemblies of Fusarium marasasianum, Huntiella abstrusa, two Immersiporthe knoxdaviesiana isolates, Macrophomina pseudophaseolina, Macrophomina phaseolina, Naganishia randhawae, and Pseudocercospora cruenta. PMID:35197126
Comparative Genomic Analysis Reveals Preserved Features in Organohalide-Respiring Sulfurospirillum Strains. PMID:35196120
Unveiling the genomic potential of Pseudomonas type strains for discovering new natural products. PMID:35195510
Kin selection for cooperation in natural bacterial populations. PMID:35193981
Using AnnoTree to Get More Assignments, Faster, in DIAMOND+MEGAN Microbiome Analysis. PMID:35191776
Nuclear genome of Bulinus truncatus, an intermediate host of the carcinogenic human blood fluke Schistosoma haematobium. PMID:35190553
Heat-Killed Lacticaseibacillus paracasei GMNL-653 Exerts Antiosteoporotic Effects by Restoring the Gut Microbiota Dysbiosis in Ovariectomized Mice. PMID:35187034
Population genomic signatures of the oriental fruit moth related to the Pleistocene climates. PMID:35177826
Genome-Annotated Bacterial Collection of the Barley Rhizosphere Microbiota. PMID:35175125
METABOLIC: high-throughput profiling of microbial genomes for functional traits, metabolism, biogeochemistry, and community-scale functional networks. PMID:35172890
Paraphocaeicola brunensis gen. nov., sp. nov., Carrying Two Variants of nimB Resistance Gene from Bacteroides fragilis, and Caecibacteroides pullorum gen. nov., sp. nov., Two Novel Genera Isolated from Chicken Caeca. PMID:35170999
Chromosome-level genome of Schistosoma haematobium underpins genome-wide explorations of molecular variation. PMID:35167626
Genome of the ramshorn snail Biomphalaria straminea-an obligate intermediate host of schistosomiasis. PMID:35166339
Role of Fasciola hepatica Small RNAs in the Interaction With the Mammalian Host. PMID:35155272
Chromosome-Level Genome Assembly of Anthidium xuezhongi Niu & Zhu, 2020 (Hymenoptera: Apoidea: Megachilidae: Anthidiini). PMID:35150256
Extracellular electron transfer increases fermentation in lactic acid bacteria via a hybrid metabolism. PMID:35147079
Molecular Characterization of Candida auris Isolates at a Major Tertiary Care Center in Lebanon. PMID:35145489
Alternative splicing in seasonal plasticity and the potential for adaptation to environmental change. PMID:35136048
Genome-wide evolutionary response of European oaks during the Anthropocene. PMID:35127134
The crewed journey to Mars and its implications for the human microbiome. PMID:35125119
Description of Pseudoclavibacter triregionum sp. nov. from human blood and Pseudoclavibacter albus comb. nov., and revised classification of the genus Pseudoclavibacter: proposal of Caespitibacter gen. nov., with Caespitibacter soli comb. nov. and Caespitibacter caeni comb. nov. PMID:35107701
Genomic Features and Pervasive Negative Selection in Rhodanobacter Strains Isolated from Nitrate and Heavy Metal Contaminated Aquifer. PMID:35107332
Gradients in gene essentiality reshape antibacterial research. PMID:35104846
A Chromosome-Level Genome Assembly of the Parasitic Wasp Chelonus formosanus Sonan 1932 (Hymenoptera: Braconidae). PMID:35104339
Genomic insight into the scale specialization of the biological control agent Novius pumilus (Weise, 1892). PMID:35100986
Probiotic Properties of Bifidobacterium longum KABP042 and Pediococcus pentosaceus KABP041 Show Potential to Counteract Functional Gastrointestinal Disorders in an Observational Pilot Trial in Infants. PMID:35095783
Novel Viral Communities Potentially Assisting in Carbon, Nitrogen, and Sulfur Metabolism in the Upper Slope Sediments of Mariana Trench. PMID:35089086
Turicibacter bilis sp. nov., a novel bacterium isolated from the chicken eggshell and swine ileum. PMID:35084297
Sequence Divergence and Functional Specializations of the Ancient Spliceosomal SF3b: Implications in Flexibility and Adaptations of the Multi-Protein Complex. PMID:35082828
Comparative assessment of genes driving cancer and somatic evolution in non-cancer tissues: an update of the Network of Cancer Genes (NCG) resource. PMID:35078504
A simple guide to de novo transcriptome assembly and annotation. PMID:35076693
CANT-HYD: A Curated Database of Phylogeny-Derived Hidden Markov Models for Annotation of Marker Genes Involved in Hydrocarbon Degradation. PMID:35069469
Differential microRNA expression, microRNA arm switching, and microRNA:long noncoding RNA interaction in response to salinity stress in soybean. PMID:35057741
The Landscape of Autophagy-Related (ATG) Genes and Functional Characterization of TaVAMP727 to Autophagy in Wheat. PMID:35055085
Improved High-Quality Genome Assembly and Annotation of Pineapple (Ananas comosus) Cultivar MD2 Revealed Extensive Haplotype Diversity and Diversified FRS/FRF Gene Family. PMID:35052394
Genome-resolved evidence for functionally redundant communities and novel nitrogen fixers in the deyin-1 hydrothermal field, Mid-Atlantic Ridge. PMID:35045876
Genomic and Phenotypic Evolution of Tigecycline-Resistant Acinetobacter baumannii in Critically Ill Patients. PMID:35044218
Resolving the structure of phage-bacteria interactions in the context of natural diversity. PMID:35042853
Unique mobile elements and scalable gene flow at the prokaryote-eukaryote boundary revealed by circularized Asgard archaea genomes. PMID:35027677
Integrated analysis of long non-coding RNAs and mRNAs reveals the regulatory network of maize seedling root responding to salt stress. PMID:35026983
Description of Aureibaculum luteum sp. nov. and Aureibaculum flavum sp. nov. isolated from Antarctic intertidal sediments. PMID:35022928
A Novel Phage Indirectly Regulates Diatom Growth by Infecting a Diatom-Associated Biofilm-Forming Bacterium. PMID:35020448
Genomic Characterization of Potential Plant Growth-Promoting Features of Sphingomonas Strains Isolated from the International Space Station. PMID:35019675
Towards a metagenomics machine learning interpretable model for understanding the transition from adenoma to colorectal cancer. PMID:35013454
Analysis of the Genome of the Heavy Metal Resistant and Hydrocarbon-Degrading Rhizospheric Pseudomonas qingdaonensis ZCR6 Strain and Assessment of Its Plant-Growth-Promoting Traits. PMID:35008639
Metabolic Processes Are Differentially Regulated During Wild-Type and Attenuated Dengue Virus Infection in Aedes aegypti. PMID:35008057
Transcriptional response of Wolbachia-transinfected Aedes aegypti mosquito cells to dengue virus at early stages of infection. PMID:35006065
Combined assembly of long and short sequencing reads improve the efficiency of exploring the soil metagenome. PMID:34996356
Changpingibacter yushuensis gen. nov., sp. nov., isolated from fluvial sediment in Qinghai Tibet Plateau of China. PMID:34994958
Saline lakes on the Qinghai-Tibet Plateau harbor unique viral assemblages mediating microbial environmental adaption. PMID:34988389
Soils and sediments host Thermoplasmata archaea encoding novel copper membrane monooxygenases (CuMMOs). PMID:34987183
Diversity and Function of Wolf Spider Gut Microbiota Revealed by Shotgun Metagenomics. PMID:34975785
The Mouse Gastrointestinal Bacteria Catalogue enables translation between the mouse and human gut microbiotas via functional mapping. PMID:34971560
Comparative Genomic Analysis of Labrenzia aggregata (Alphaproteobacteria) Strains Isolated From the Mariana Trench: Insights Into the Metabolic Potentials and Biogeochemical Functions. PMID:34970235
A catalogue of 1,167 genomes from the human gut archaeome. PMID:34969981
Exploration of Autophagy Families in Legumes and Dissection of the ATG18 Family with a Special Focus on Phaseolus vulgaris. PMID:34961093
Complete genome sequencing and comparative genomic analysis of Lactobacillus acidophilus C5 as a potential canine probiotics. PMID:34957454
Genome Analysis of Lagocephalus sceleratus: Unraveling the Genomic Landscape of a Successful Invader. PMID:34956332
Not All That Glitters Is Gold: The Paradox of CO-dependent Hydrogenogenesis in Parageobacillus thermoglucosidasius. PMID:34956151
First Comparative Analysis of Clostridium septicum Genomes Provides Insights Into the Taxonomy, Species Genetic Diversity, and Virulence Related to Gas Gangrene. PMID:34956133
The Genome of the "Sea Vomit" Didemnum vexillum. PMID:34947908
DNA Methylation Patterns Differ between Free-Living Rhizobium leguminosarum RCAM1026 and Bacteroids Formed in Symbiosis with Pea (Pisum sativum L.). PMID:34946059
Comparative Phenotypic, Proteomic, and Phosphoproteomic Analysis Reveals Different Roles of Serine/Threonine Phosphatase and Kinase in the Growth, Cell Division, and Pathogenicity of Streptococcus suis. PMID:34946045
Loss of YhcB results in dysregulation of coordinated peptidoglycan, LPS and phospholipid synthesis during Escherichia coli cell growth. PMID:34941903
Pneumococcal capsule blocks protection by immunization with conserved surface proteins. PMID:34930916
Genome-wide analysis of fitness-factors in uropathogenic Escherichia coli during growth in laboratory media and during urinary tract infections. PMID:34928200
De novo transcriptome assembly and annotation of parthenogenetic lizard Darevskia unisexualis and its parental ancestors Darevskia valentini and Darevskia raddei nairensis. PMID:34917712
Towards the biogeography of prokaryotic genes. PMID:34912116
Critical Assessment of MetaProteome Investigation (CAMPI): a multi-laboratory comparison of established workflows. PMID:34911965
Complete Genome Sequence of the Type Strain Tepidimonas taiwanensis LMG 22826T, a Thermophilic Alkaline Protease and Polyhydroxyalkanoate Producer. PMID:34908127
Genome analysis provides insight into hyper-virulence of Streptococcus suis LSM178, a human strain with a novel sequence type 1005. PMID:34907269
A review of computational tools for generating metagenome-assembled genomes from metagenomic sequencing data. PMID:34900140
Evolution of a histone variant involved in compartmental regulation of NAD metabolism. PMID:34887560
Comparative Transcriptome Analysis Revealed the Key Genes Regulating Ascorbic Acid Synthesis in Actinidia. PMID:34884699
Different Regulatory Modes of Synechocystis sp. PCC 6803 in Response to Photosynthesis Inhibitory Conditions. PMID:34874777
Diverse ecophysiological adaptations of subsurface Thaumarchaeota in floodplain sediments revealed through genome-resolved metagenomics. PMID:34873295
Phylogenetic Relatedness and Genome Structure of Yersinia ruckeri Revealed by Whole Genome Sequencing and a Comparative Analysis. PMID:34867924
Comparative Genomic and Pan-Genomic Characterization of Staphylococcus epidermidis From Different Sources Unveils the Molecular Basis and Potential Biomarkers of Pathogenic Strains. PMID:34867904
Evolutionary Divergence of the Novel Staphylococcal Species Staphylococcus argenteus. PMID:34867903
Regulation of iron homeostasis by peroxide-sensitive CatR, a Fur-family regulator in Streptomyces coelicolor. PMID:34865197
Hybrid de novo Genome Assembly of Erwinia sp. E602 and Bioinformatic Analysis Characterized a New Plasmid-Borne lac Operon Under Positive Selection. PMID:34858382
Cross-species analysis of viral nucleic acid interacting proteins identifies TAOKs as innate immune regulators. PMID:34853303
Draft genome assemblies for tree pathogens Phytophthora pseudosyringae and Phytophthora boehmeriae. PMID:34849788
To catch a hijacker: abundance, evolution and genetic diversity of P4-like bacteriophage satellites. PMID:34839713
Genetic Characterization of Salmonella Infantis with Multiple Drug Resistance Profiles Isolated from a Poultry-Farm in Chile. PMID:34835497
An Isoform of the Eukaryotic Translation Elongation Factor 1A (eEF1a) Acts as a Pro-Viral Factor Required for Tomato Spotted Wilt Virus Disease in Nicotiana benthamiana. PMID:34834996
Genomic and Phylogenetic Analysis of Lactiplantibacillus plantarum L125, and Evaluation of Its Anti-Proliferative and Cytotoxic Activity in Cancer Cells. PMID:34829947
Transcriptomic Profile of the Cockle Cerastoderma edule Exposed to Seasonal Diarrhetic Shellfish Toxin Contamination. PMID:34822568
Complete Genome Sequence of Two Deep-Sea Streptomyces Isolates from Madeira Archipelago and Evaluation of Their Biosynthetic Potential. PMID:34822492
De novo assembly and functional annotation of blood transcriptome of loggerhead turtle, and in silico characterization of peroxiredoxins and thioredoxins. PMID:34820176
Comparative Genomic Analyses and CRISPR-Cas Characterization of Cutibacterium acnes Provide Insights Into Genetic Diversity and Typing Applications. PMID:34803983
Protein innovation through template switching in the Saccharomyces cerevisiae lineage. PMID:34799587
Metagenome-assembled genomes and gene catalog from the chicken gut microbiome aid in deciphering antibiotic resistomes. PMID:34795385
Draft genome sequences of strains CBS6241 and CBS6242 of the basidiomycetous yeast Filobasidium floriforme. PMID:34791213
Vaccine Design by Reverse Vaccinology and Machine Learning. PMID:34784028
Anaerobic peroxisomes in Entamoeba histolytica metabolize myo-inositol. PMID:34780573
Transcriptomic Responses of Rhizobium phaseoli to Root Exudates Reflect Its Capacity to Colonize Maize and Common Bean in an Intercropping System. PMID:34777287
Genomic Epidemiology and Antimicrobial Susceptibility Profile of Enterotoxigenic Escherichia coli From Outpatients With Diarrhea in Shenzhen, China, 2015-2020. PMID:34777281
Whole-Genome Sequencing, Phylogenetic and Genomic Analysis of Lactiplantibacillus pentosus L33, a Potential Probiotic Strain Isolated From Fermented Sausages. PMID:34764945
PangenomeNet: a pan-genome-based network reveals functional modules on antimicrobial resistome for Escherichia coli strains. PMID:34758735
Resolving the Microalgal Gene Landscape at the Strain Level: a Novel Hybrid Transcriptome of Emiliania huxleyi CCMP3266. PMID:34757817
A Practical Guide to Small Protein Discovery and Characterization Using Mass Spectrometry. PMID:34748388
Flavobacterium flabelliforme sp. nov. and Flavobacterium geliluteum sp. nov., Two Multidrug-Resistant Psychrotrophic Species Isolated From Antarctica. PMID:34745033
Transcriptome profiling reveals the developmental regulation of NaCl-treated Forcipomyia taiwana eggs. PMID:34732124
Metagenomic insights into the microbial communities of inert and oligotrophic outdoor pier surfaces of a coastal city. PMID:34724986
High-quality reference genome and annotation aids understanding of berry development for evergreen blueberry (Vaccinium darrowii). PMID:34719668
PhylomeDB V5: an expanding repository for genome-wide catalogues of annotated gene phylogenies. PMID:34718760
Draft Genome Sequence of Cellulomonas sp. PS-H5, Isolated from Sekinchan Beach in Selangor, Malaysia. PMID:34709049
A phylogenomic framework for charting the diversity and evolution of giant viruses. PMID:34705818
Rhesus macaques self-curing from a schistosome infection can display complete immunity to challenge. PMID:34702841
Plastic-Degrading Potential across the Global Microbiome Correlates with Recent Pollution Trends. PMID:34700384
The Response of Airborne Mycobiome to Dust Storms in the Eastern Mediterranean. PMID:34682226
Exoproteome Analysis of Antagonistic Interactions between the Probiotic Bacteria Limosilactobacillus reuteri LR1 and Lacticaseibacillus rhamnosus F and Multidrug Resistant Strain of Klebsiella pneumonia. PMID:34681658
FA-nf: A Functional Annotation Pipeline for Proteins from Non-Model Organisms Implemented in Nextflow. PMID:34681040
Co-Occurrence of blaOXA-23 in the Chromosome and Plasmid: Increased Fitness in Carbapenem-Resistant Acinetobacter baumannii. PMID:34680777
The Human NUP58 Nucleoporin Can Form Amyloids In Vitro and In Vivo. PMID:34680573
Depside and Depsidone Synthesis in Lichenized Fungi Comes into Focus through a Genome-Wide Comparison of the Olivetoric Acid and Physodic Acid Chemotypes of Pseudevernia furfuracea. PMID:34680078
Chromosome-Level Genome Assembly of Nephotettix cincticeps (Uhler, 1896) (Hemiptera: Cicadellidae: Deltocephalinae). PMID:34677607
Yeast metabolic innovations emerged via expanded metabolic network and gene positive selection. PMID:34676984
Comparative Genomics of Mycobacterium avium Complex Reveals Signatures of Environment-Specific Adaptation and Community Acquisition. PMID:34665012
Transcriptomic and Metabolomic Analyses Reveals That Exogenous Methyl Jasmonate Regulates Galanthamine Biosynthesis in Lycoris longituba Seedlings. PMID:34659286
Cross-Sectional Study on the Gut Microbiome of Parkinson's Disease Patients in Central China. PMID:34650532
Comparative genome characterization of Leptospira interrogans from mild and severe leptospirosis patients. PMID:34638178
Transcriptomic Profiling Reveals Shared Signalling Networks Between Flower Development and Herbivory-Induced Responses in Tomato. PMID:34630470
Comparative transcriptomic analysis of races 1, 2, 5 and 6 of Fusarium oxysporum f.sp. pisi in a susceptible pea host identifies differential pathogenicity profiles. PMID:34627148
Comparative analysis of integrative and conjugative mobile genetic elements in the genus Mesorhizobium. PMID:34605762
eggNOG-mapper v2: Functional Annotation, Orthology Assignments, and Domain Prediction at the Metagenomic Scale. PMID:34597405
Dynamically expressed genes provide candidate viability biomarkers in a model coccidian. PMID:34597342
Elucidating gene expression adaptation of phylogenetically divergent coral holobionts under heat stress. PMID:34593802
Metagenomic analysis of ancient dental calculus reveals unexplored diversity of oral archaeal Methanobrevibacter. PMID:34593021
Chromosome-Level Genome Assembly and Annotation of the Fiber Flax (Linum usitatissimum) Genome. PMID:34589116
Candidatus Kaistella beijingensis sp. nov., Isolated from a Municipal Wastewater Treatment Plant, Is Involved in Sludge Foaming. PMID:34586909
The Archean origin of oxygenic photosynthesis and extant cyanobacterial lineages. PMID:34583585
Single-colony sequencing reveals microbe-by-microbiome phylosymbiosis between the cyanobacterium Microcystis and its associated bacteria. PMID:34579777
Genome Analysis of Streptomyces nojiriensis JCM 3382 and Distribution of Gene Clusters for Three Antibiotics and an Azasugar across the Genus Streptomyces. PMID:34576698
Hybrid Deep Learning Based on a Heterogeneous Network Profile for Functional Annotations of Plasmodium falciparum Genes. PMID:34576183
Genome Sequence Analysis of the Fungal Pathogen Fusarium graminearum Using Oxford Nanopore Technology. PMID:34575738
Identification of Key Transcription Factors Related to Bacterial Spot Resistance in Pepper through Regulatory Network Analyses. PMID:34573336
Comparative Genomic Analysis of the DUF34 Protein Family Suggests Role as a Metal Ion Chaperone or Insertase. PMID:34572495
Comprehensive Characterization of Multitissue Expression Landscape, Co-Expression Networks and Positive Selection in Pikeperch. PMID:34571938
Insights into Alexandrium minutum Nutrient Acquisition, Metabolism and Saxitoxin Biosynthesis through Comprehensive Transcriptome Survey. PMID:34571703
Comparative Genome Analysis and Spore Heat Resistance Assay Reveal a New Component to Population Structure and Genome Epidemiology Within Clostridium perfringens Enterotoxin-Carrying Isolates. PMID:34566921
Adaptation of Fig Wasps (Agaodinae) to Their Host Revealed by Large-Scale Transcriptomic Data. PMID:34564255
PANNZER-A practical tool for protein function prediction. PMID:34562305
Cohnella cholangitidis sp. nov., a novel species of the genus Cohnella isolated from a clinical specimen in Korea. PMID:34562146
Transcriptome repository of North-Western Himalayan endangered medicinal herbs: a paramount approach illuminating molecular perspective of phytoactive molecules and secondary metabolism. PMID:34557965
The influence of the gut microbiome on BCG-induced trained immunity. PMID:34551799
Comparative genome analysis of Clostridium beijerinckii strains isolated from pit mud of Chinese strong flavor baijiu ecosystem. PMID:34542586
KinOrtho: a method for mapping human kinase orthologs across the tree of life and illuminating understudied kinases. PMID:34537014
Structural characterization of NrnC identifies unifying features of dinucleotidases. PMID:34533457
Disease-induced changes in plant microbiome assembly and functional adaptation. PMID:34526096
Proteogenomic Analysis Provides Novel Insight into Genome Annotation and Nitrogen Metabolism in Nostoc sp. PCC 7120. PMID:34523988
The time course of molecular acclimation to seawater in a euryhaline fish. PMID:34518569
Prokaryotic viruses impact functional microorganisms in nutrient removal and carbon cycle in wastewater treatment plants. PMID:34518545
Evolution of Acinetobacter baumannii in Clinical Bacteremia Patients. PMID:34511946
Chromosome-level genome assembly of Gynostemma pentaphyllum provides insights into gypenoside biosynthesis. PMID:34499150
Bacteria and Archaea Synergistically Convert Glycine Betaine to Biogenic Methane in the Formosa Cold Seep of the South China Sea. PMID:34491083
Comparative Analysis of Genomic and Transcriptome Sequences Reveals Divergent Patterns of Codon Bias in Wheat and Its Ancestor Species. PMID:34490050
Characterization of Campylobacter spp. Strains Isolated From Wild Birds in Turkey. PMID:34489902
Pseudomonas palmensis sp. nov., a Novel Bacterium Isolated From Nicotiana glauca Microbiome: Draft Genome Analysis and Biological Potential for Agriculture. PMID:34489881
Comparative genomic analysis reveals metabolic flexibility of Woesearchaeota. PMID:34489402
Physiology of the Nitrite-Oxidizing Bacterium Candidatus Nitrotoga sp. CP45 Enriched From a Colorado River. PMID:34484146
Gulosibacter hominis sp. nov.: a novel human microbiome bacterium that may cause opportunistic infections. PMID:34480670
Duo: A Signature Based Method to Batch-Analyze Functional Similarities of Proteins. PMID:34475860
Genome erosion and evidence for an intracellular niche - exploring the biology of mycoplasmas in Atlantic salmon. PMID:34471330
A Probabilistic Model for Indel Evolution: Differentiating Insertions from Deletions. PMID:34469521
Metagenome-assembled genome of a Chitinophaga sp. and its potential in plant biomass degradation, as well of affiliated Pandoraea and Labrys species. PMID:34448059
Human reference gut microbiome catalog including newly assembled genomes from under-represented Asian metagenomes. PMID:34446072
Metatranscriptomic Analysis of Bacterial Communities on Laundered Textiles: A Pilot Case Study. PMID:34442670
Sequencing and de Novo Assembly of Abaca (Musa textilis Née) var. Abuab Genome. PMID:34440376
Whole genome sequencing reveals the genomic diversity, taxonomic classification, and evolutionary relationships of the genus Nocardia. PMID:34437546
Genetic response to nitrogen starvation in the aggressive Eucalyptus foliar pathogen Teratosphaeria destructans. PMID:34432124
Rapid Genomic Evolution Drives the Diversification of Male Reproductive Genes in Dung Beetles. PMID:34426833
Streptomyces tardus sp. nov.: A Slow-Growing Actinobacterium Producing Candicidin, Isolated From Sediments of the Trondheim Fjord. PMID:34421874
Evolution of mechanisms controlling epithelial morphogenesis across animals: new insights from dissociation-reaggregation experiments in the sponge Oscarella lobularis. PMID:34418961
Comparative genome analysis of Salmonella enterica serovar Gallinarum biovars Pullorum and Gallinarum decodes strain specific genes. PMID:34411120
Adaptive Laboratory Evolution as a Means To Generate Lactococcus lactis Strains with Improved Thermotolerance and Ability To Autolyze. PMID:34406823
Genome Evolution in Bacteria Isolated from Million-Year-Old Subseafloor Sediment. PMID:34399613
Plant developmental stage drives the differentiation in ecological role of the maize microbiome. PMID:34389047
Aspergillus sp. A31 and Curvularia geniculata P1 mitigate mercury toxicity to Oryza sativa L. PMID:34387704
Bog ecosystems as a playground for plant-microbe coevolution: bryophytes and vascular plants harbour functionally adapted bacteria. PMID:34380552
Classification of a Violacein-Producing Psychrophilic Group of Isolates Associated with Freshwater in Antarctica and Description of Rugamonas violacea sp. nov. PMID:34378950
Expanding Asgard members in the domain of Archaea sheds new light on the origin of eukaryotes. PMID:34378142
PHROG: families of prokaryotic virus proteins clustered using remote homology. PMID:34377978
De novo transcriptome characterization of Iris atropurpurea (the Royal Iris) and phylogenetic analysis of MADS-box and R2R3-MYB gene families. PMID:34376711
OMICs, Epigenetics, and Genome Editing Techniques for Food and Nutritional Security. PMID:34371624
Clostridium cellulovorans Proteomic Responses to Butanol Stress. PMID:34367082
Comparative Genomics of Clinical Isolates of the Emerging Tick-Borne Pathogen Neoehrlichia mikurensis. PMID:34361922
The Histidine Biosynthetic Genes in the Superphylum Bacteroidota-Rhodothermota-Balneolota-Chlorobiota: Insights into the Evolution of Gene Structure and Organization. PMID:34361875
Interstrain Variability of Human Vaginal Lactobacillus crispatus for Metabolism of Biogenic Amines and Antimicrobial Activity against Urogenital Pathogens. PMID:34361691
Genome-wide analysis of HECT E3 ubiquitin ligase gene family in Solanum lycopersicum. PMID:34354159
Antimicrobial susceptibilities and comparative whole genome analysis of two isolates of the probiotic bacterium Lactiplantibacillus plantarum, strain ATCC 202195. PMID:34354117
The Dynamic Transition of Persistence toward the Viable but Nonculturable State during Stationary Phase Is Driven by Protein Aggregation. PMID:34340538
Screening and Isolation of a Novel Polyene-Producing Streptomyces Strain Inhibiting Phytopathogenic Fungi in the Soil Environment. PMID:34322478
Molecular Characteristics of IS1216 Carrying Multidrug Resistance Gene Cluster in Serotype III/Sequence Type 19 Group B Streptococcus. PMID:34319128
Functionathon: a manual data mining workflow to generate functional hypotheses for uncharacterized human proteins and its application by undergraduate students. PMID:34318869
The balance of crystalline and amorphous regions in the fibroin structure underpins the tensile strength of bagworm silk. PMID:34311769
Current production by non-methanotrophic bacteria enriched from an anaerobic methane-oxidizing microbial community. PMID:34308332
Root Endophytes and Ginkgo biloba Are Likely to Share and Compensate Secondary Metabolic Processes, and Potentially Exchange Genetic Information by LTR-RTs. PMID:34305992
Tudor staphylococcal nuclease is a docking platform for stress granule components and is essential for SnRK1 activation in Arabidopsis. PMID:34287990
Pan-Genome Portrait of Bacillus mycoides Provides Insights into the Species Ecology and Evolution. PMID:34287030
Transcriptome and proteome of the corm, leaf and flower of Hypoxis hemerocallidea (African potato). PMID:34283859
The Interspecific Fungal Hybrid Verticillium longisporum Displays Subgenome-Specific Gene Expression. PMID:34281400
Global biogeography of chemosynthetic symbionts reveals both localized and globally distributed symbiont groups. PMID:34272286
High Potential for Secondary Metabolite Production of Paracoccus marcusii CP157, Isolated From the Crustacean Cancer pagurus. PMID:34262548
Proteome, Bioinformatic, and Functional Analyses Reveal a Distinct and Conserved Metabolic Pathway for Bile Salt Degradation in the Sphingomonadaceae. PMID:34260303
Metagenomics: a path to understanding the gut microbiome. PMID:34259891
Genome mapping coupled with CRISPR gene editing reveals a P450 gene confers avermectin resistance in the beet armyworm. PMID:34252082
T cell composition and polygenic multiple sclerosis risk: A population-based study in children. PMID:34251726
Wheat Rhizosphere Metagenome Reveals Newfound Potential Soil Zn-Mobilizing Bacteria Contributing to Cultivars' Variation in Grain Zn Concentration. PMID:34248914
Diploidy within a Haploid Genus of Entomopathogenic Fungi. PMID:34247231
Sulfobacillus harzensis sp. nov., an acidophilic bacterium inhabiting mine tailings from a polymetallic mine. PMID:34236956
Comparative genomic analysis of Escherichia coli isolates from cases of bovine clinical mastitis identifies nine specific pathotype marker genes. PMID:34227932
Genomic Analysis of Delftia tsuruhatensis Strain TR1180 Isolated From A Patient From China With In4-Like Integron-Associated Antimicrobial Resistance. PMID:34222039
Zetaproteobacteria Pan-Genome Reveals Candidate Gene Cluster for Twisted Stalk Biosynthesis and Export. PMID:34220764
Printing Microbial Dark Matter: Using Single Cell Dispensing and Genomics to Investigate the Patescibacteria/Candidate Phyla Radiation. PMID:34220732
Early response of methanogenic archaea to H2 as evaluated by metagenomics and metatranscriptomics. PMID:34217274
Comprehensive pan-genome analysis of Lactiplantibacillus plantarum complete genomes. PMID:34216519
Genome sequences and in silico effector mining of Corynespora cassiicola CC_29 and Corynespora olivacea CBS 114450. PMID:34213598
Genomic Aromatic Compound Degradation Potential of Novel Paraburkholderia Species: Paraburkholderia domus sp. nov., Paraburkholderia haematera sp. nov. and Paraburkholderia nemoris sp. nov. PMID:34209778
Phylogeny and Evolutionary History of Respiratory Complex I Proteins in Melainabacteria. PMID:34207155
Assessment of the Degradation Potential and Genomic Insights towards Phenanthrene by Dietzia psychralcaliphila JI1D. PMID:34205451
Exploring Codon Adjustment Strategies towards Escherichia coli-Based Production of Viral Proteins Encoded by HTH1, a Novel Prophage of the Marine Bacterium Hypnocyclicus thermotrophus. PMID:34201869
Complete Genome Sequence and Function Gene Identify of Prometryne-Degrading Strain Pseudomonas sp. DY-1. PMID:34200754
Mutations in bdcA and valS Correlate with Quinolone Resistance in Wastewater Escherichia coli. PMID:34199768
Draft Genome Sequences of Two Cadophora Strains Isolated from Water and a Nonalcoholic Beverage Ingredient. PMID:34197206
Pseudocrossidium replicatum (Taylor) R.H. Zander is a fully desiccation-tolerant moss that expresses an inducible molecular mechanism in response to severe abiotic stress. PMID:34189708
Prediction of Human-Plasmodium vivax Protein Associations From Heterogeneous Network Structures Based on Machine-Learning Approach. PMID:34188457
Comparative genomics of the Pseudomonas corrugata subgroup reveals high species diversity and allows the description of Pseudomonas ogarae sp. nov. PMID:34184980
Mosaic Ends Tagmentation (METa) Assembly for Highly Efficient Construction of Functional Metagenomic Libraries. PMID:34184912
Enhanced mutualistic symbiosis between soil phages and bacteria with elevated chromium-induced environmental stress. PMID:34183048
FINER: enhancing the prediction of tissue-specific functions of isoforms by refining isoform interaction networks. PMID:34169280
Next-Generation Sequencing for Whole-Genome Characterization of Weissella cibaria UTNGt21O Strain Originated From Wild Solanum quitoense Lam. Fruits: An Atlas of Metabolites With Biotechnological Significance. PMID:34163450
Microbiomes attached to fresh perennial ryegrass are temporally resilient and adapt to changing ecological niches. PMID:34154659
Extensive Variation in Drought-Induced Gene Expression Changes Between Loblolly Pine Genotypes. PMID:34140968
Novel clades of soil biphenyl degraders revealed by integrating isotope probing, multi-omics, and single-cell analyses. PMID:34117322
The Genome Assembly and Annotation of the Apollo Butterfly Parnassius apollo, a Flagship Species for Conservation Biology. PMID:34115121
Dispersal strategies shape persistence and evolution of human gut bacteria. PMID:34111423
Integrated Multi-omics Investigations Reveal the Key Role of Synergistic Microbial Networks in Removing Plasticizer Di-(2-Ethylhexyl) Phthalate from Estuarine Sediments. PMID:34100638
Viral Metagenome-Based Precision Surveillance of Pig Population at Large Scale Reveals Viromic Signatures of Sample Types and Influence of Farming Management on Pig Virome. PMID:34100634
Insight into phenotypic and genotypic differences between vaginal Lactobacillus crispatus BC5 and Lactobacillus gasseri BC12 to unravel nutritional and stress factors influencing their metabolic activity. PMID:34096840
Generation of unequal nuclear genotype proportions in Rhizophagus irregularis progeny causes allelic imbalance in gene transcription. PMID:34085297
Genome-Inferred Correspondence between Phylogeny and Metabolic Traits in the Wild Drosophila Gut Microbiome. PMID:34081101
Mantis: flexible and consensus-driven genome annotation. PMID:34076241
De Novo Transcriptome Meta-Assembly of the Mixotrophic Freshwater Microalga Euglena gracilis. PMID:34072576
Comparative Genomics Analysis of Keratin-Degrading Chryseobacterium Species Reveals Their Keratinolytic Potential for Secondary Metabolite Production. PMID:34066089
Development and Validation of Enzyme-Linked Immunosorbent Assay for Group B Streptococcal Polysaccharide Vaccine. PMID:34064299
An Integrative Bioinformatic Analysis for Keratinase Detection in Marine-Derived Streptomyces. PMID:34063876
Genome-Wide Analyses of the Temperature-Responsive Genetic Loci of the Pectinolytic Plant Pathogenic Pectobacterium atrosepticum. PMID:34063632
Unraveling a Lignocellulose-Decomposing Bacterial Consortium from Soil Associated with Dry Sugarcane Straw by Genomic-Centered Metagenomics. PMID:34063014
VB12Path for Accurate Metagenomic Profiling of Microbially Driven Cobalamin Synthesis Pathways. PMID:34060913
Genome-Scale Metabolic Model of Caldicellulosiruptor bescii Reveals Optimal Metabolic Engineering Strategies for Bio-based Chemical Production. PMID:34060912
The effects of combined environmental factors on the intestinal flora of mice based on ground simulation experiments. PMID:34059794
Distinct microbial community along the chronic oil pollution continuum of the Persian Gulf converge with oil spill accidents. PMID:34059729
The holobiont transcriptome of teneral tsetse fly species of varying vector competence. PMID:34058984
Diversity and prevalence of ANTAR RNAs across actinobacteria. PMID:34051745
Whole-Genome Analysis of Mycobacterium avium subsp. paratuberculosis IS900 Insertions Reveals Strain Type-Specific Modalities. PMID:34040595
Characterization of the public transit air microbiome and resistome reveals geographical specificity. PMID:34039416
Tutorial: guidelines for annotating single-cell transcriptomic maps using automated and manual methods. PMID:34031612
The Rhododendron Plant Genome Database (RPGD): a comprehensive online omics database for Rhododendron. PMID:34022814
Two high-quality de novo genomes from single ethanol-preserved specimens of tiny metazoans (Collembola). PMID:34018554
Redox homeostasis in Mycobacterium tuberculosis is modulated by a novel actinomycete-specific transcription factor. PMID:34018220
A Chromosome-Level Genome Assembly of Ephestia elutella (Hübner, 1796) (Lepidoptera: Pyralidae). PMID:34014321
Vaxign2: the second generation of the first Web-based vaccine design program using reverse vaccinology and machine learning. PMID:34009334
Bioactive small molecules produced by the human gut microbiome modulate Vibrio cholerae sessile and planktonic lifestyles. PMID:34006192
High quality genome sequence of Treponema phagedenis KS1 isolated from bovine digital dermatitis. PMID:33987574
Phenotypic changes in group B streptococci grown in the presence of the polyols, erythritol, sorbitol and mannitol. PMID:33985431
Species and population specific gene expression in blood transcriptomes of marine turtles. PMID:33985425
Insights on the Evolutionary Genomics of the Blautia Genus: Potential New Species and Genetic Content Among Lineages. PMID:33981291
Freshwater Chlorobia Exhibit Metabolic Specialization among Cosmopolitan and Endemic Populations. PMID:33975970
Competition for DNA binding between paralogous transcription factors determines their genomic occupancy and regulatory functions. PMID:33975875
Diversity and distribution of viruses inhabiting the deepest ocean on Earth. PMID:33972725
Complete genome sequence of Photobacterium ganghwense C2.2: A new polyhydroxyalkanoate production candidate. PMID:33970538
Accurate Annotation of Microbial Metagenomic Genes and Identification of Core Sets. PMID:33961221
Updates to HCOP: the HGNC comparison of orthology predictions tool. PMID:33959747
Mapping single-cell atlases throughout Metazoa unravels cell type evolution. PMID:33944782
Genetic basis of high aroma and stress tolerance in the oolong tea cultivar genome. PMID:33931633
Comparative genomics of the coconut crab and other decapod crustaceans: exploring the molecular basis of terrestrial adaptation. PMID:33931033
Cocultivation of an ultrasmall environmental parasitic bacterium with lytic ability against bacteria associated with wastewater foams. PMID:33927381
Unraveling the Metabolic Potential of Asgardarchaeota in a Sediment from the Mediterranean Hydrocarbon-Contaminated Water Basin Mar Piccolo (Taranto, Italy). PMID:33923677
An Introduction to Next Generation Sequencing Bioinformatic Analysis in Gut Microbiome Studies. PMID:33918473
Genome Characterization of Lactiplantibacillus plantarum Strain UTNGt2 Originated from Theobroma grandiflorum (White Cacao) of Ecuadorian Amazon: Antimicrobial Peptides from Safety to Potential Applications. PMID:33916842
Chromosome-scale assembly and analysis of biomass crop Miscanthus lutarioriparius genome. PMID:33911077
Genomic Insight of Alicyclobacillus mali FL18 Isolated From an Arsenic-Rich Hot Spring. PMID:33897644
ZapG (YhcB/DUF1043), a novel cell division protein in gamma-proteobacteria linking the Z-ring to septal peptidoglycan synthesis. PMID:33895137
Transcriptomic and Metabolomic Responses to Carbon and Nitrogen Sources in Methylomicrobium album BG8. PMID:33893121
Spatially resolved cell polarity proteomics of a human epiblast model. PMID:33893097
Ongoing repair of migration-coupled DNA damage allows planarian adult stem cells to reach wound sites. PMID:33890575
Biological structure and function emerge from scaling unsupervised learning to 250 million protein sequences. PMID:33876751
Short-range quorum sensing controls horizontal gene transfer at micron scale in bacterial communities. PMID:33875666
Ancestral sequence reconstruction - An underused approach to understand the evolution of gene function in plants? PMID:33868595
Symbiont Genomic Features and Localization in the Bean Beetle Callosobruchus maculatus. PMID:33863703
Grassland fairy rings of Leucocalocybe mongolica represent the center of a rich soil microbial community. PMID:33847922
Aspirin Modulation of the Colorectal Cancer-Associated Microbe Fusobacterium nucleatum. PMID:33824205
Ten Years of Collaborative Progress in the Quest for Orthologs. PMID:33822172
Database limitations for studying the human gut microbiome. PMID:33816940
Effects of Simulated Microgravity on the Proteome and Secretome of the Polyextremotolerant Black Fungus Knufia chersonesos. PMID:33815472
Argonaute-CLIP delineates versatile, functional RNAi networks in Aedes aegypti, a major vector of human viruses. PMID:33794184
OMAmer: tree-driven and alignment-free protein assignment to subfamilies outperforms closest sequence approaches. PMID:33787851
Environmental Plasticity of the RNA Content of Staphylococcus aureus Extracellular Vesicles. PMID:33776967
Transcribed germline-limited coding sequences in Oxytricha trifallax. PMID:33772542
Subzero, saline incubations of Colwellia psychrerythraea reveal strategies and biomarkers for sustained life in extreme icy environments. PMID:33760340
Revealing taxon-specific heavy metal-resistance mechanisms in denitrifying phosphorus removal sludge using genome-centric metaproteomics. PMID:33752740
The chromosome-level genome of dragon fruit reveals whole-genome duplication and chromosomal co-localization of betacyanin biosynthetic genes. PMID:33750805
Hybrid assembly of an agricultural slurry virome reveals a diverse and stable community with the potential to alter the metabolism and virulence of veterinary pathogens. PMID:33743832
A chromosome-level genome of the spider Trichonephila antipodiana reveals the genetic basis of its polyphagy and evidence of an ancient whole-genome duplication event. PMID:33739402
Genome-wide methylome analysis of two strains belonging to the hypervirulent Neisseria meningitidis serogroup W ST-11 clonal complex. PMID:33737546
A high-quality, chromosome-level genome assembly of the Black Soldier Fly (Hermetia illucens L.). PMID:33734373
gapseq: informed prediction of bacterial metabolic pathways and reconstruction of accurate metabolic models. PMID:33691770
The very early evolution of protein translocation across membranes. PMID:33684113
A Mucoralean White Collar-1 Photoreceptor Controls Virulence by Regulating an Intricate Gene Network during Host Interactions. PMID:33672193
The Transcriptional Regulatory Network of Corynebacterium pseudotuberculosis. PMID:33671149
Analysis of Human Gut Microbiome: Taxonomy and Metabolic Functions in Thai Adults. PMID:33668840
Novel combination of CRISPR-based gene drives eliminates resistance and localises spread. PMID:33664305
Proteogenomic Insights into the Physiology of Marine, Sulfate-Reducing, Filamentous Desulfonema limicola and Desulfonema magnum. PMID:33611323
Massive expansion of human gut bacteriophage diversity. PMID:33606979
Complete Characterization of Incorrect Orthology Assignments in Best Match Graphs. PMID:33606106
Comparative genomics reveals broad genetic diversity, extensive recombination and nascent ecological adaptation in Micrococcus luteus. PMID:33602135
Genome sequence of Monilinia vaccinii-corymbosi sheds light on mummy berry disease infection of blueberry and mating type. PMID:33598705
Expanded catalog of microbial genes and metagenome-assembled genomes from the pig gut microbiome. PMID:33597514
Comparative Fungal Community Analyses Using Metatranscriptomics and Internal Transcribed Spacer Amplicon Sequencing from Norway Spruce. PMID:33594001
Bacteria have numerous distinctive groups of phage-plasmids with conserved phage and variable plasmid gene repertoires. PMID:33590101
A chromosome-level assembly of the black tiger shrimp (Penaeus monodon) genome facilitates the identification of growth-associated genes. PMID:33586292
Diagnostic Sequences That Distinguish M. avium Subspecies Strains. PMID:33585607
The Isolate Caproiciproducens sp. 7D4C2 Produces n-Caproate at Mildly Acidic Conditions From Hexoses: Genome and rBOX Comparison With Related Strains and Chain-Elongating Bacteria. PMID:33584563
Host and body site-specific adaptation of Lactobacillus crispatus genomes. PMID:33575551
Causes and Consequences of Bacteriophage Diversification via Genetic Exchanges across Lifestyles and Bacterial Taxa. PMID:33570565
A High-Quality Reference Genome for a Parasitic Bivalve with Doubly Uniparental Inheritance (Bivalvia: Unionida). PMID:33570560
Pangenome analysis reveals genetic isolation in Campylobacter hyointestinalis subspecies adapted to different mammalian hosts. PMID:33564053
Metagenomics workflow for hybrid assembly, differential coverage binning, metatranscriptomics and pathway analysis (MUFFIN). PMID:33561126
Transcriptomic and Proteomic Analyses of Nepenthes ampullaria and Nepenthes rafflesiana Reveal Parental Molecular Expression in the Pitchers of Their Hybrid, Nepenthes × hookeriana. PMID:33552113
A Highly Contiguous Genome Assembly of a Polyphagous Predatory Mite Stratiolaelaps scimitus (Womersley) (Acari: Laelapidae). PMID:33528489
Human pathways in animal models: possibilities and limitations. PMID:33524155
Genome-wide comparison of four MRSA clinical isolates from Germany and Hungary. PMID:33520430
Whole-Genome Comparisons of Ergot Fungi Reveals the Divergence and Evolution of Species within the Genus Claviceps Are the Result of Varying Mechanisms Driving Genome Evolution and Host Range Expansion. PMID:33512490
Barley Anther and Meiocyte Transcriptome Dynamics in Meiotic Prophase I. PMID:33510760
Higher genome variability within metabolism genes associates with recurrent Clostridium difficile infection. PMID:33509087
Proteomic evaluation of kimchi, a traditional Korean fermented vegetable, and comparison of kimchi manufactured in China and Korea. PMID:33505084
Barley Anther and Meiocyte Transcriptome Dynamics in Meiotic Prophase I. PMID:33510760
Higher genome variability within metabolism genes associates with recurrent Clostridium difficile infection. PMID:33509087
Proteomic evaluation of kimchi, a traditional Korean fermented vegetable, and comparison of kimchi manufactured in China and Korea. PMID:33505084
A Draft Genome Assembly of Culex pipiens pallens (Diptera: Culicidae) Using PacBio Sequencing. PMID:33501937
ViralRecall-A Flexible Command-Line Tool for the Detection of Giant Virus Signatures in 'Omic Data. PMID:33498458
Peeling the Layers Away: The Genomic Characterization of Bacillus pumilus 64-1, an Isolate With Antimicrobial Activity From the Marine Sponge Plakina cyanorosea (Porifera, Homoscleromorpha). PMID:33488540
Cellinker: a platform of ligand-receptor interactions for intercellular communication analysis. PMID:33471060
DeepLPI: a multimodal deep learning method for predicting the interactions between lncRNAs and protein isoforms. PMID:33461501
Early infection-induced natural antibody response. PMID:33452341
Genome-wide identification, characterization and transcriptional profiling of NHX-type (Na+/H+) antiporters under salinity stress in soybean. PMID:33442515
Genome-wide macroevolutionary signatures of key innovations in butterflies colonizing new host plants. PMID:33441560
Bacterial dormancy: A subpopulation of viable but non-culturable cells demonstrates better fitness for revival. PMID:33439894
Transcriptome characterization and generation of marker resource for Himalayan vulnerable species, Ulmus wallichiana. PMID:33439411
Nonadditive Transcriptomic Signatures of Genotype-by-Genotype Interactions during the Initiation of Plant-Rhizobium Symbiosis. PMID:33436514
First Complete Genome of the Thermophilic Polyhydroxyalkanoates-Producing Bacterium Schlegelella thermodepolymerans DSM 15344. PMID:33432323
Berberine alters gut microbial function through modulation of bile acids. PMID:33430766
Escherichia ruysiae sp. nov., a novel Gram-stain-negative bacterium, isolated from a faecal sample of an international traveller. PMID:33406029
Coastal Bacterial Community Response to Glacier Melting in the Western Antarctic Peninsula. PMID:33401391
Isolation, draft genome sequencing and identification of Enterobacter roggenkampii CCI9. PMID:33391549
Genome-wide identification of novel genes involved in Corynebacteriales cell envelope biogenesis using Corynebacterium glutamicum as a model. PMID:33383576
Metage2Metabo, microbiota-scale metabolic complementarity for the identification of key species. PMID:33372654
Proteomic Analysis of the Venom of Jellyfishes Rhopilema esculentum and Sanderia malayensis. PMID:33371176
DeepNOG: Fast and accurate protein orthologous group assignment. PMID:33367584
The Integrator complex at the crossroad of coding and noncoding RNA. PMID:33340967
Differential Adaptation of Propionibacterium freudenreichii CIRM-BIA129 to Cow's Milk Versus Soymilk Environments Modulates Its Stress Tolerance and Proteome. PMID:33335514
Metagenomic Association Analysis of Gut Symbiont Limosilactobacillus reuteri Without Host-Specific Genome Isolation. PMID:33329454
Vertical stratification patterns of methanotrophs and their genetic controllers in water columns of oxygen-stratified boreal lakes. PMID:33316049
Environmental conditions modulate the protein content and immunomodulatory activity of extracellular vesicles produced by the probiotic Propionibacterium freudenreichii. PMID:33310709
Lower Density and Shorter Duration of Nasopharyngeal Carriage by Pneumococcal Serotype 1 (ST217) May Explain Its Increased Invasiveness over Other Serotypes. PMID:33293378
Functional Characterization of the γ-Aminobutyric Acid Transporter from Mycobacterium smegmatis MC2 155 Reveals Sodium-Driven GABA Transport. PMID:33288625
Enhanced Symbiotic Characteristics in Bacterial Genomes with the Disruption of rRNA Operon. PMID:33287185
Elucidating Essential Genes in Plant-Associated Pseudomonas protegens Pf-5 Using Transposon Insertion Sequencing. PMID:33257523
MOB: Pivotal Conserved Proteins in Cytokinesis, Cell Architecture and Tissue Homeostasis. PMID:33255245
Taxonomic Novelty and Distinctive Genomic Features of Hot Spring Cyanobacteria. PMID:33250920
Genome- and Proteome-Wide Analysis of Lysine Acetylation in Vibrio vulnificus Vv180806 Reveals Its Regulatory Roles in Virulence and Antibiotic Resistance. PMID:33250879
CAPRIB: a user-friendly tool to study amino acid changes and selection for the exploration of intra-genus evolution. PMID:33243176
Deep metagenomics examines the oral microbiome during dental caries, revealing novel taxa and co-occurrences with host molecules. PMID:33239396
Marine Dadabacteria exhibit genome streamlining and phototrophy-driven niche partitioning. PMID:33230264
Genome Mining and Evaluation of the Biocontrol Potential of Pseudomonas fluorescens BRZ63, a New Endophyte of Oilseed Rape (Brassica napus L.) against Fungal Pathogens. PMID:33228091
Moniliella spathulata, an oil-degrading yeast, which promotes growth of barley in oil-polluted soil. PMID:33219393
Widespread endogenization of giant viruses shapes genomes of green algae. PMID:33208937
Reclassification of the biocontrol agents Bacillus subtilis BY-2 and Tu-100 as Bacillus velezensis and insights into the genomic and specialized metabolite diversity of the species. PMID:33205747
Campylobacter jejuni 11168H Exposed to Penicillin Forms Persister Cells and Cells With Altered Redox Protein Activity. PMID:33194805
A haplotype-phased genome of wheat stripe rust pathogen Puccinia striiformis f. sp. tritici, race PST-130 from the Western USA. PMID:33175843
Evidence of homologous recombination as a driver of diversity in Brachyspira pilosicoli. PMID:33174833
Identification of Zinc-Dependent Mechanisms Used by Group B Streptococcus To Overcome Calprotectin-Mediated Stress. PMID:33173000
Understanding the causes of errors in eukaryotic protein-coding gene prediction: a case study of primate proteomes. PMID:33172385
COG database update: focus on microbial diversity, model organisms, and widespread pathogens. PMID:33167031
Bacterial-fungal interactions revealed by genome-wide analysis of bacterial mutant fitness. PMID:33139882
Construction of a complete set of Neisseria meningitidis mutants and its use for the phenotypic profiling of this human pathogen. PMID:33139723
Genome-scale metabolic reconstruction of the non-model yeast Issatchenkia orientalis SD108 and its application to organic acids production. PMID:33134082
Cyanorak v2.1: a scalable information system dedicated to the visualization and expert curation of marine and brackish picocyanobacteria genomes. PMID:33125079
Genetic, transcriptional, and regulatory landscape of monolignol biosynthesis pathway in Miscanthus × giganteus. PMID:33117433
Differential Effects of Varying Concentrations of Phosphorus, Iron, and Nitrogen in N2-Fixing Cyanobacteria. PMID:33101223
DEG 15, an update of the Database of Essential Genes that includes built-in analysis tools. PMID:33095861
mMGE: a database for human metagenomic extrachromosomal mobile genetic elements. PMID:33074335
No Assembly Required: Using BTyper3 to Assess the Congruency of a Proposed Taxonomic Framework for the Bacillus cereus Group With Historical Typing Methods. PMID:33072050
Life-history strategies of soil microbial communities in an arid ecosystem. PMID:33051582
Population Genomic Analysis of Mycoplasma bovis Elucidates Geographical Variations and Genes associated with Host-Types. PMID:33050495
Atribacteria Reproducing over Millions of Years in the Atlantic Abyssal Subseafloor. PMID:33024037
ProminTools: shedding light on proteins of unknown function in biomineralization with user friendly tools illustrated using mollusc shell matrix protein sequences. PMID:32974096
Proteomic Studies to Understand the Mechanisms of Peach Tissue Degradation by Monilinia laxa. PMID:32973845
Abiotic and past climatic conditions drive protein abundance variation among natural populations of the caddisfly Crunoecia irrorata. PMID:32968134
Genome-Centric Metagenomic Insights into the Impact of Alkaline/Acid and Thermal Sludge Pretreatment on the Microbiome in Digestion Sludge. PMID:32948522
Nanaerobic growth enables direct visualization of dynamic cellular processes in human gut symbionts. PMID:32938803
A distinct lineage of Caudovirales that encodes a deeply branching multi-subunit RNA polymerase. PMID:32908149
Molecular action of pyriproxyfen: Role of the Methoprene-tolerant protein in the pyriproxyfen-induced sterilization of adult female mosquitoes. PMID:32866146
RIGD: A Database for Intronless Genes in the Rosaceae. PMID:32849839
Transcriptome of the Southern Muriqui Brachyteles arachnoides (Primates:Platyrrhini), a Critically Endangered New World Monkey: Evidence of Adaptive Evolution. PMID:32849820
Symbiosis islands of Loteae-nodulating Mesorhizobium comprise three radiating lineages with concordant nod gene complements and nodulation host-range groupings. PMID:32845829
Comprehensive genome data analysis establishes a triple whammy of carbapenemases, ICEs and multiple clinically relevant bacteria. PMID:32841111
Transcriptome dataset for RNA-seq analysis of axolotl embryonic oropharyngeal endoderm explants. PMID:32802925
Amoeba Genome Reveals Dominant Host Contribution to Plastid Endosymbiosis. PMID:32790833
Exploring the Extracellular Macromolecular Composition of Crude Extracts of Penicillium rubens Strain 212 for Elucidation Its Mode of Action as a Biocontrol Agent. PMID:32785198
Effects of Different Hosts on Bacterial Communities of Parasitic Wasp Nasonia vitripennis. PMID:32774328
ICEs Are the Main Reservoirs of the Ciprofloxacin-Modifying crpP Gene in Pseudomonas aeruginosa. PMID:32759827
Bactopia: a Flexible Pipeline for Complete Analysis of Bacterial Genomes. PMID:32753501
Extracellular Vesicles Produced by the Probiotic Propionibacterium freudenreichii CIRM-BIA 129 Mitigate Inflammation by Modulating the NF-κB Pathway. PMID:32733422
Mining sequences with similarity to XTH genes in the Solanum tuberosum L. transcriptome: introductory step for identifying homologous XTH genes. PMID:32727267
High diversity and variability of pipolins among a wide range of pathogenic Escherichia coli strains. PMID:32719405
A unified catalog of 204,938 reference genomes from the human gut microbiome. PMID:32690973
From bag-of-genes to bag-of-genomes: metabolic modelling of communities in the era of metagenome-assembled genomes. PMID:32670511
A non-canonical RNAi pathway controls virulence and genome stability in Mucorales. PMID:32658892
Proteomic analysis of Rickettsia akari proposes a 44 kDa-OMP as a potential biomarker for Rickettsialpox diagnosis. PMID:32640994
An expanded cell wall damage signaling network is comprised of the transcription factors Rlm1 and Sko1 in Candida albicans. PMID:32639995
Time-resolved multi-omics analysis reveals the role of nutrient stress-induced resource reallocation for TAG accumulation in oleaginous fungus Mortierella alpina. PMID:32625246
A guide to human microbiome research: study design, sample collection, and bioinformatics analysis. PMID:32604176
The First Draft Genome Assembly of Snow Sheep (Ovis nivicola). PMID:32592471
A New High-Quality Draft Genome Assembly of the Chinese Cordyceps Ophiocordyceps sinensis. PMID:32579174
ATLAS: a Snakemake workflow for assembly, annotation, and genomic binning of metagenome sequence data. PMID:32571209
Cholesterol Metabolism by Uncultured Human Gut Bacteria Influences Host Cholesterol Level. PMID:32544460
GTDB: an integrated resource for glycosyltransferase sequences and annotations. PMID:32542364
Fatty acid bioconversion in harpacticoid copepods in a changing environment: a transcriptomic approach. PMID:32536309
Enhanced Triacylglycerol Metabolism Contributes to Efficient Oil Utilization and High-Level Production of Salinomycin in Streptomyces albus ZD11. PMID:32532869
Vast Differences in Strain-Level Diversity in the Gut Microbiota of Two Closely Related Honey Bee Species. PMID:32531278
Characterization of Burkholderia cepacia Complex Core Genome and the Underlying Recombination and Positive Selection. PMID:32528528
Depth-related variability in viral communities in highly stratified sulfidic mine tailings. PMID:32517753
Defining Critical Genes During Spherule Remodeling and Endospore Development in the Fungal Pathogen, Coccidioides posadasii. PMID:32499817
The nuclear and mitochondrial genomes of Frieseomelitta varia - a highly eusocial stingless bee (Meliponini) with a permanently sterile worker caste. PMID:32493270
dbPSP 2.0, an updated database of protein phosphorylation sites in prokaryotes. PMID:32472030
Genome-Wide Characterization and Comparative Analysis of MYB Transcription Factors in Ganoderma Species. PMID:32471942
In Silico Identification of Type III PKS Chalcone and Stilbene Synthase Homologs in Marine Photosynthetic Organisms. PMID:32456002
Genome Comparison Identifies Different Bacillus Species in a Bast Fibre-Retting Bacterial Consortium and Provides Insights into Pectin Degrading Genes. PMID:32424209
Import of Aspartate and Malate by DcuABC Drives H2/Fumarate Respiration to Promote Initial Salmonella Gut-Lumen Colonization in Mice. PMID:32416061
In silico Prediction of Virus-Host Interactions for Marine Bacteroidetes With the Use of Metagenome-Assembled Genomes. PMID:32411107
Genomic variation among closely related Vibrio alginolyticus strains is located on mobile genetic elements. PMID:32393168
A systematic machine learning and data type comparison yields metagenomic predictors of infant age, sex, breastfeeding, antibiotic usage, country of origin, and delivery type. PMID:32392251
Complete Genome Sequence of an Efficient Rhizobium leguminosarum bv. viciae Strain, A1. PMID:32381612
The Quest for Orthologs benchmark service and consensus calls in 2020. PMID:32374845
Selection following Gene Duplication Shapes Recent Genome Evolution in the Pea Aphid Acyrthosiphon pisum. PMID:32359152
Honey-bee-associated prokaryotic viral communities reveal wide viral diversity and a profound metabolic coding potential. PMID:32341166
Development of new genetic resources for faba bean (Vicia faba L.) breeding through the discovery of gene-based SNP markers and the construction of a high-density consensus map. PMID:32321933
Identification of surface proteins in a clinical Staphylococcus haemolyticus isolate by bacterial surface shaving. PMID:32264835
One-carbon metabolism, folate, zinc and translation. PMID:32153134
Rhizosphere protists are key determinants of plant health. PMID:32127034
Differential Accumulation of Innate- and Adaptive-Immune-Response-Derived Transcripts during Antagonism between Papaya Ringspot Virus and Papaya Mosaic Virus. PMID:32092910
Comparative Analysis of Lactobacillus gasseri and Lactobacillus crispatus Isolated From Human Urogenital and Gastrointestinal Tracts. PMID:32038579
High quality 3C de novo assembly and annotation of a multidrug resistant ST-111 Pseudomonas aeruginosa genome: Benchmark of hybrid and non-hybrid assemblers. PMID:31996747
Gene gain and loss across the metazoan tree of life. PMID:31988444
An Integrated Model of Minor Intron Emergence and Conservation. PMID:31798628
Draft Genome Sequences of Longimonas halophila KCTC 42399 and Longibacter salinarum KCTC 52045. PMID:31727717
MaGenDB: a functional genomics hub for Malvaceae plants. PMID:31665439
The spinal cord-gut-immune axis as a master regulator of health and neurological function after spinal cord injury. PMID:31654639
proGenomes2: an improved database for accurate and consistent habitat, taxonomic and functional annotations of prokaryotic genomes. PMID:31647096
Global Transcriptional Response of Three Highly Acid-Tolerant Field Strains of Listeria monocytogenes to HCl Stress. PMID:31623206
Comparative proteomics of stenotopic caddisfly Crunoecia irrorata identifies acclimation strategies to warming. PMID:31478292
In Silico Analysis of Gardnerella Genomospecies Detected in the Setting of Bacterial Vaginosis. PMID:31462445
Improved Reference Genome Sequence of Coccidioides immitis Strain WA_211, Isolated in Washington State. PMID:31416856
Horizontally transmitted symbiont populations in deep-sea mussels are genetically isolated. PMID:31395952
Continuous Culture Adaptation of Methylobacterium extorquens AM1 and TK 0001 to Very High Methanol Concentrations. PMID:31281294
The 'in vivo lifestyle' of bile acid 7α-dehydroxylating bacteria: comparative genomics, metatranscriptomic, and bile acid metabolomics analysis of a defined microbial community in gnotobiotic mice. PMID:31177942
NG-meta-profiler: fast processing of metagenomes using NGLess, a domain-specific language. PMID:31159881
Proteomic and Metabolomic Characteristics of Extremophilic Fungi Under Simulated Mars Conditions. PMID:31156574
INGA 2.0: improving protein function prediction for the dark proteome. PMID:31073595
Clostridium scindens ATCC 35704: Integration of Nutritional Requirements, the Complete Genome Sequence, and Global Transcriptional Responses to Bile Acids. PMID:30737348 -
eggNOG v3.0: orthologous groups covering 1133 organisms at 41 different taxonomic ranges
PubMed citations: 269.
269 articles citing: eggNOG v3.0: orthologous groups covering 1133 organisms at 41 different taxonomic ranges
Application of young maize plant residues alters the microbiome composition and its functioning in a soil under conservation agriculture: a metagenomics study. PMID:35788780
A role for the mitotic proteins Bub3 and BuGZ in transcriptional regulation of catalase-3 expression. PMID:35666721
Biotechnological Combination for Co-contaminated Soil Remediation: Focus on Tripartite "Meta-Enzymatic" Activity. PMID:35599908
The Isolation and Characterization of Rare Mycobiome Associated With Spacecraft Assembly Cleanrooms. PMID:35558115
Genomic Analysis Based on Chromosome-Level Genome Assembly Reveals an Expansion of Terpene Biosynthesis of Azadirachta indica. PMID:35528946
Relation between two evolutionary clocks reveal new insights in bacterial evolution. PMID:35355876
Transcriptional regulation of metal metabolism- and nutrient absorption-related genes in Eucalyptus grandis by arbuscular mycorrhizal fungi at different zinc concentrations. PMID:35193499
De Novo Transcriptome of Mammillaria bombycina (Cactaceae) under In Vitro Conditions and Identification of Glyoxalase Genes. PMID:35161380
Gut microbiome alterations in colitis rats after moxibustion at bilateral Tianshu acupoints. PMID:35151255
Single-cell genomics for resolution of conserved bacterial genes and mobile genetic elements of the human intestinal microbiota using flow cytometry. PMID:35130125
Transcriptome Analysis of Arbuscular Mycorrhizal Casuarina glauca in Damage Mitigation of Roots on NaCl Stress. PMID:35056464
Early transcriptomic response of the mycoparasite Sphaerodes mycoparasitica to the mycotoxigenic Fusarium graminearum 3-ADON, the cause of Fusarium head blight. PMID:34993050
Functional Genomics and Comparative Lineage-Specific Region Analyses Reveal Novel Insights into Race Divergence in Verticillium dahliae. PMID:34937170
Understanding the Role of Prevotella Genus in the Digestion of Lignocellulose and Other Substrates in Vietnamese Native Goats' Rumen by Metagenomic Deep Sequencing. PMID:34827987
Deep (Meta)genomics and (Meta)transcriptome Analyses of Fungal and Bacteria Consortia From Aircraft Tanks and Kerosene Identify Key Genes in Fuel and Tank Corrosion. PMID:34675897
Performance of Multiple Metagenomics Pipelines in Understanding Microbial Diversity of a Low-Biomass Spacecraft Assembly Facility. PMID:34650522
Whole Genome Sequence of Alternaria alternata, the Causal Agent of Black Spot of Kiwifruit. PMID:34616379
A high-quality chromosome-level genome of wild Rosa rugosa. PMID:34499118
Data on the first functionally-annotated de novo transcriptome assembly for North American flying squirrels (genus Glaucomys). PMID:34381854
Revealing the full biosphere structure and versatile metabolic functions in the deepest ocean sediment of the Challenger Deep. PMID:34256809
Trajectories of Homoeolog-Specific Expression in Allotetraploid Tragopogon castellanus Populations of Independent Origins. PMID:34249049
Databases for Protein-Protein Interactions. PMID:34236665
Covariance of Phytoplankton, Bacteria, and Zooplankton Communities Within Microcystis Blooms in San Francisco Estuary. PMID:34163439
The Human Gut Phageome: Origins and Roles in the Human Gut Microbiome. PMID:34150671
HoSeIn: A Workflow for Integrating Various Homology Search Results from Metagenomic and Metatranscriptomic Sequence Datasets. PMID:33659350
Limited effects of long-term daily cranberry consumption on the gut microbiome in a placebo-controlled study of women with recurrent urinary tract infections. PMID:33596852
Protuberances are organized distinct regions of long-term callus: histological and transcriptomic analyses in kiwifruit. PMID:33544186
A structurally unique Fusobacterium nucleatum tannase provides detoxicant activity against gallotannins and pathogen resistance. PMID:33336898
A Multi-Omics Protocol for Swine Feces to Elucidate Longitudinal Dynamics in Microbiome Structure and Function. PMID:33260576
Assessing the Risk of Transfer of Microorganisms at the International Space Station Due to Cargo Delivery by Commercial Resupply Vehicles. PMID:33240227
Drivers and sites of diversity in the DNA adenine methylomes of 93 Mycobacterium tuberculosis complex clinical isolates. PMID:33107429
Comparative transcriptome analysis of flower bud transition and functional characterization of EjAGL17 involved in regulating floral initiation in loquat. PMID:33031442
Gene expression during bacterivorous growth of a widespread marine heterotrophic flagellate. PMID:32920602
A tree frog (Boana pugnax) dataset of skin transcriptome for the identification of biomolecules with potential antimicrobial activities. PMID:32875010
Comparative genomic analysis of Vibrios yields insights into genes associated with virulence towards C. gigas larvae. PMID:32867668
Data on the de novo transcriptome assembly for the migratory bird, the Common quail (Coturnix coturnix). PMID:32775561
Microbiome and Metagenome Analyses of a Closed Habitat during Human Occupation. PMID:32723791
An Integrative Analysis of Transcriptome, Proteome and Hormones Reveals Key Differentially Expressed Genes and Metabolic Pathways Involved in Flower Development in Loquat. PMID:32698310
Shared up-regulation and contrasting down-regulation of gene expression distinguish desiccation-tolerant from intolerant green algae. PMID:32636259
Transcriptome Profiling of Pacu (Piaractus mesopotamicus) Challenged With Pathogenic Aeromonas hydrophila: Inference on Immune Gene Response. PMID:32582300
Shifting evolutionary sands: transcriptome characterization of the Aptostichus atomarius species complex. PMID:32539685
Transcriptome Analysis of Maternal Gene Transcripts in Unfertilized Eggs of Misgurnus anguillicaudatus and Identification of Immune-Related Maternal Genes. PMID:32485896
A high-quality reference genome of wild Cannabis sativa. PMID:32377363
Logicome Profiler: Exhaustive detection of statistically significant logic relationships from comparative omics data. PMID:32357172
Transcriptomic profiling and discovery of key genes involved in adventitious root formation from green cuttings of highbush blueberry (Vaccinium corymbosum L.). PMID:32334538
Temporal transcriptome change of Oncomelania hupensis revealed by Schistosoma japonicum invasion. PMID:32328235
De novo transcriptome assembly and data for the blue-winged teal (Spatula discors). PMID:32258268
Detecting horizontal gene transfer: a probabilistic approach. PMID:32138652
MicroRNA and mRNA interactions coordinate the immune response in non-lethal heat stressed Litopenaeus vannamei against AHPND-causing Vibrio parahaemolyticus. PMID:31964916
Network-Based Prediction of Novel CRISPR-Associated Genes in Metagenomes. PMID:31937679
Local Adaptation of Bacterial Symbionts within a Geographic Mosaic of Antibiotic Coevolution. PMID:31676475
Synergistic action of the transcription factors Krüppel homolog 1 and Hairy in juvenile hormone/Methoprene-tolerant-mediated gene-repression in the mosquito Aedes aegypti. PMID:31661489
Potential Interactions between Clade SUP05 Sulfur-Oxidizing Bacteria and Phages in Hydrothermal Vent Sponges. PMID:31492669
From the Amazon: A comprehensive liver transcriptome dataset of the teleost fish tambaqui, Colossoma macropomum. PMID:31372415
Comparative transcriptomic analysis of dermal wound healing reveals de novo skeletal muscle regeneration in Acomys cahirinus. PMID:31141508
Leaf Transcriptome Assembly of Protium copal (Burseraceae) and Annotation of Terpene Biosynthetic Genes. PMID:31121954
An annual cycle of gene regulation in the red-legged salamander mental gland: from hypertrophy to expression of rapidly evolving pheromones. PMID:31029098
Whole-Genome Annotation with BRAKER. PMID:31020555
Diversities and potential biogeochemical impacts of mangrove soil viruses. PMID:30975205
Complete Genome Sequence of Shewanella sp. Strain TH2012, Isolated from Shrimp in a Cultivation Pond Exhibiting Early Mortality Syndrome. PMID:30923247
A novel transcriptome-derived SNPs array for tench (Tinca tinca L.). PMID:30889192
Production Phase Affects the Bioaerosol MicrobialComposition and Functional Potential in SwineConfinement Buildings. PMID:30871116
The neuroactive potential of the human gut microbiota in quality of life and depression. PMID:30718848
Genomic and Transcriptomic Changes that Mediate Increased Platinum Resistance in Cupriavidus metallidurans. PMID:30669395
Comprehensive assembly and analysis of the transcriptome of maritime pine developing embryos. PMID:30594130
Identifying Differential Gene Expression in Wing Polymorphism of Adult Males of the Largest Water Strider: De novo Transcriptome Assembly for Gigantometra gigas (Hemiptera: Gerridae). PMID:30535417
k-mer Similarity, Networks of Microbial Genomes, and Taxonomic Rank. PMID:30505941
Genome sequence of the opportunistic human pathogen Magnusiomyces capitatus. PMID:30456648
Succession and persistence of microbial communities and antimicrobial resistance genes associated with International Space Station environmental surfaces. PMID:30424821
A phylogenomic study quantifies competing mechanisms for pseudogenization in prokaryotes-The Mycobacterium leprae case. PMID:30383852
Reconstruction of real and simulated phylogenies based on quartet plurality inference. PMID:30367577
Species groups distributed across elevational gradients reveal convergent and continuous genetic adaptation to high elevations. PMID:30348757
Phylogenomics Reveal the Dynamic Evolution of Fungal Nitric Oxide Reductases and Their Relationship to Secondary Metabolism. PMID:30165640
Establishment of a Macaca fascicularis gut microbiome gene catalog and comparison with the human, pig, and mouse gut microbiomes. PMID:30137359
Specific expression pattern of IMP metabolism related-genes in chicken muscle between cage and free range conditions. PMID:30133460
Juvenile hormone-regulated alternative splicing of the taiman gene primes the ecdysteroid response in adult mosquitoes. PMID:30061397
Identification of a putative polyketide synthase gene involved in usnic acid biosynthesis in the lichen Nephromopsis pallescens. PMID:30020937
The evolutionary signal in metagenome phyletic profiles predicts many gene functions. PMID:29991352
Viruses of the Nahant Collection, characterization of 251 marine Vibrionaceae viruses. PMID:29969110
Accurate prediction of orthologs in the presence of divergence after duplication. PMID:29950018
A resource for sustainable management: De novo assembly and annotation of the liver transcriptome of the Atlantic chub mackerel, Scomber colias. PMID:29896516
The Presence or Absence of Intestinal Microbiota Affects Lipid Deposition and Related Genes Expression in Zebrafish (Danio rerio). PMID:29896183
Comparative Metatranscriptomics of Wheat Rhizosphere Microbiomes in Disease Suppressive and Non-suppressive Soils for Rhizoctonia solani AG8. PMID:29780371
Flexible metagenome analysis using the MGX framework. PMID:29690922
MEGAN-LR: new algorithms allow accurate binning and easy interactive exploration of metagenomic long reads and contigs. PMID:29678199
Comparison of normalization methods for the analysis of metagenomic gene abundance data. PMID:29678163
Metabolomics and Transcriptomics Identify Multiple Downstream Targets of Paraburkholderia phymatum σ54 During Symbiosis with Phaseolus vulgaris. PMID:29614780
Two Phytoplasmas Elicit Different Responses in the Insect Vector Euscelidius variegatus Kirschbaum. PMID:29531134
Zygosaccharomyces bailii Is a Potential Producer of Various Flavor Compounds in Chinese Maotai-Flavor Liquor Fermentation. PMID:29312273
Deciphering the unexplored Leptospira diversity from soils uncovers genomic evolution to virulence. PMID:29310748
Enterotypes in the landscape of gut microbial community composition. PMID:29255284
Transcriptome Analysis of Paraburkholderia phymatum under Nitrogen Starvation and during Symbiosis with Phaseolus Vulgaris. PMID:29244728
The genomic study of an environmental isolate of Scedosporium apiospermum shows its metabolic potential to degrade hydrocarbons. PMID:29225727
Mountain hare transcriptome and diagnostic markers as resources to monitor hybridization with European hares. PMID:29206218
Improving amphibian genomic resources: a multitissue reference transcriptome of an iconic invader. PMID:29186423
The first draft reference genome of the American mink (Neovison vison). PMID:29109430
RNA-Seq de novo assembly and differential transcriptome analysis of the nematode Ascaridia galli in relation to in vivo exposure to flubendazole. PMID:29099835
The Production of Curli Amyloid Fibers Is Deeply Integrated into the Biology of Escherichia coli. PMID:29088115
Comparative genomics reveals cotton-specific virulence factors in flexible genomic regions in Verticillium dahliae and evidence of horizontal gene transfer from Fusarium. PMID:29084346
Hybrid Sequencing of Full-Length cDNA Transcripts of Stems and Leaves in Dendrobium officinale. PMID:28981454
Association Between Gut Microbiota and Bone Health: Potential Mechanisms and Prospective. PMID:28973392
Towards standards for human fecal sample processing in metagenomic studies. PMID:28967887
Metatranscriptomics Reveals the Functions and Enzyme Profiles of the Microbial Community in Chinese Nong-Flavor Liquor Starter. PMID:28955318
A practical guide to build de-novo assemblies for single tissues of non-model organisms: the example of a Neotropical frog. PMID:28879061
Phylo_dCor: distance correlation as a novel metric for phylogenetic profiling. PMID:28870256
Multi-tissue RNA-seq and transcriptome characterisation of the spiny dogfish shark (Squalus acanthias) provides a molecular tool for biological research and reveals new genes involved in osmoregulation. PMID:28832628
A Different Microbiome Gene Repertoire in the Airways of Cystic Fibrosis Patients with Severe Lung Disease. PMID:28758937
Annotation of gene sequence and protein structure of brinjal EDS1. PMID:28584443
Sex-specific differences in transcriptome profiles of brain and muscle tissue of the tropical gar. PMID:28388875
Integrated proteomic analysis of Brachypodium distachyon roots and leaves reveals a synergistic network in the response to drought stress and recovery. PMID:28387352
Olfactory effects of a hypervariable multicomponent pheromone in the red-legged salamander, Plethodon shermani. PMID:28358844
Discovery of genes coding for carbohydrate-active enzyme by metagenomic analysis of lignocellulosic biomasses. PMID:28198423
TipMT: Identification of PCR-based taxon-specific markers. PMID:28187714
Draft Genome Sequence of Staphylococcus hominis BHG17 Isolated from Wild Bar-Headed Goose (Anser indicus) Feces. PMID:28153901
De novo transcriptome assemblies of four accessions of the metal hyperaccumulator plant Noccaea caerulescens. PMID:28140388
Fast and simple protein-alignment-guided assembly of orthologous gene families from microbiome sequencing reads. PMID:28122610
Nematophagous fungus Arthrobotrys oligospora mimics olfactory cues of sex and food to lure its nematode prey. PMID:28098555
Divergent functional isoforms drive niche specialisation for nutrient acquisition and use in rumen microbiome. PMID:28085156
Metagenomic profiling of gut microbial communities in both wild and artificially reared Bar-headed goose (Anser indicus). PMID:27998035
A Graph-Centric Approach for Metagenome-Guided Peptide and Protein Identification in Metaproteomics. PMID:27918579
The landscape of microbial phenotypic traits and associated genes. PMID:27915291
Characterization of the Verticillium dahliae Exoproteome Involves in Pathogenicity from Cotton-Containing Medium. PMID:27840627
Metagenomic and metaproteomic analyses of a corn stover-adapted microbial consortium EMSD5 reveal its taxonomic and enzymatic basis for degrading lignocellulose. PMID:27833656
Unique Features of Ethnic Mongolian Gut Microbiome revealed by metagenomic analysis. PMID:27708392
Draft Genome Sequence of Bacillus litoralis C44, Isolated from Chinese Scholar Tree (Sophora japonica) Forest Soil. PMID:27688317
The tubulin repertoire of C. elegans sensory neurons and its context-dependent role in process outgrowth. PMID:27654945
A Natural Light/Dark Cycle Regulation of Carbon-Nitrogen Metabolism and Gene Expression in Rice Shoots. PMID:27625675
The De Novo Transcriptome and Its Functional Annotation in the Seed Beetle Callosobruchus maculatus. PMID:27442123
Functional Comparison of Bacteria from the Human Gut and Closely Related Non-Gut Bacteria Reveals the Importance of Conjugation and a Paucity of Motility and Chemotaxis Functions in the Gut Environment. PMID:27416027
Here We Are, But Where Do We Go? A Systematic Review of Crustacean Transcriptomic Studies from 2014-2015. PMID:27400974
Salinity-induced changes in gene expression from anterior and posterior gills of Callinectes sapidus (Crustacea: Portunidae) with implications for crustacean ecological genomics. PMID:27337176
MEGAN Community Edition - Interactive Exploration and Analysis of Large-Scale Microbiome Sequencing Data. PMID:27327495
Genetic factors contributing to human primary ciliary dyskinesia and male infertility. PMID:27270341
Transcriptome sequences spanning key developmental states as a resource for the study of the cestode Schistocephalus solidus, a threespine stickleback parasite. PMID:27259971
Genome-wide analysis of gene expression reveals gene regulatory networks that regulate chasmogamous and cleistogamous flowering in Pseudostellaria heterophylla (Caryophyllaceae). PMID:27206349
Adaptive evolution of complex innovations through stepwise metabolic niche expansion. PMID:27197754
Draft Genome Sequence of Bacillus megaterium BHG1.1, a Strain Isolated from Bar-Headed Goose (Anser indicus) Feces on the Qinghai-Tibet Plateau. PMID:27174262
Comparative transcriptomics across the prokaryotic tree of life. PMID:27154273
Analysis of the complete genome sequence of the archaeon Pyrococcus chitonophagus DSM 10152 (formerly Thermococcus chitonophagus). PMID:27016195
New features of desiccation tolerance in the lichen photobiont Trebouxia gelatinosa are revealed by a transcriptomic approach. PMID:26992400
Comparative transcriptomics and proteomics of three different aphid species identifies core and diverse effector sets. PMID:26935069
Genome-guided Investigation of Antibiotic Substances produced by Allosalinactinospora lopnorensis CA15-2(T) from Lop Nor region, China. PMID:26864220
Integration of multi-omics data of a genome-reduced bacterium: Prevalence of post-transcriptional regulation and its correlation with protein abundances. PMID:26773059
Hairy and Groucho mediate the action of juvenile hormone receptor Methoprene-tolerant in gene repression. PMID:26744312
Evolutionary loss of peroxisomes--not limited to parasites. PMID:26700421
A New N-Acyl Homoserine Lactone Synthase in an Uncultured Symbiont of the Red Sea Sponge Theonella swinhoei. PMID:26655754
Disentangling type 2 diabetes and metformin treatment signatures in the human gut microbiota. PMID:26633628
Improved orthologous databases to ease protozoan targets inference. PMID:26416523
Microbial diversity and activity in the Nematostella vectensis holobiont: insights from 16S rRNA gene sequencing, isolate genomes, and a pilot-scale survey of gene expression. PMID:26388838
The function and dynamics of the apical scaffolding protein E3KARP are regulated by cell-cycle phosphorylation. PMID:26310448
Regulation of Gene Expression Patterns in Mosquito Reproduction. PMID:26274815
Draft De Novo Transcriptome of the Rat Kangaroo Potorous tridactylus as a Tool for Cell Biology. PMID:26252667
Comparative Transcriptome Analysis Reveals Sex-Biased Gene Expression in Juvenile Chinese Mitten Crab Eriocheir sinensis. PMID:26193085
Dual Transcriptomic Profiling of Host and Microbiota during Health and Disease in Pediatric Asthma. PMID:26125632
Lengths of Orthologous Prokaryotic Proteins Are Affected by Evolutionary Factors. PMID:26114113
A de novo Assembly of the Common Frog (Rana temporaria) Transcriptome and Comparison of Transcription Following Exposure to Ranavirus and Batrachochytrium dendrobatidis. PMID:26111016
The FAD-dependent glycerol-3-phosphate dehydrogenase of Giardia duodenalis: an unconventional enzyme that interacts with the g14-3-3 and it is a target of the antitumoral compound NBDHEX. PMID:26082764
High-throughput sequencing of small RNAs and anatomical characteristics associated with leaf development in celery. PMID:26057455
Lifestyle evolution in cyanobacterial symbionts of sponges. PMID:26037118
Whole-Genome Sequence Analysis and Genome-Wide Virulence Gene Identification of Riemerella anatipestifer Strain Yb2. PMID:26002892
Transcriptome profiling of trichome-less reveals genes associated with multicellular trichome development in Cucumis sativus. PMID:25952908
Sequencing and beyond: integrating molecular 'omics' for microbial community profiling. PMID:25915636
Inter-individual differences in the gene content of human gut bacterial species. PMID:25896518
Temporal and technical variability of human gut metagenomes. PMID:25888008
Prokaryotic assemblages and metagenomes in pelagic zones of the South China Sea. PMID:25879764
Construction of an ortholog database using the semantic web technology for integrative analysis of genomic data. PMID:25875762
Average genome size estimation improves comparative metagenomics and sheds light on the functional ecology of the human microbiome. PMID:25853934
Comprehensive data resources and analytical tools for pathological association of aminoacyl tRNA synthetases with cancer. PMID:25824651
Protein complexes in bacteria. PMID:25723151
De novo assembly, transcriptome characterization, lignin accumulation, and anatomic characteristics: novel insights into lignin biosynthesis during celery leaf development. PMID:25651889
Identifying gene clusters by discovering common intervals in indeterminate strings. PMID:25571793
A Novel Mutation in the ROGDI Gene in a Patient with Kohlschütter-Tönz Syndrome. PMID:25565929
Ancient and modern environmental DNA. PMID:25487334
Transcriptome changes in Eriocheir sinensis megalopae after desalination provide insights into osmoregulation and stress adaption in larvae. PMID:25470496
An integrated approach for genome annotation of the eukaryotic thermophile Chaetomium thermophilum. PMID:25398899
A phylogeny-based benchmarking test for orthology inference reveals the limitations of function-based validation. PMID:25369365
Fine-tuned characterization of Staphylococcus aureus Newbould 305, a strain associated with mild and chronic mastitis in bovines. PMID:25316113
RNA sequencing and de novo assembly of the digestive gland transcriptome in Mytilus galloprovincialis fed with toxinogenic and non-toxic strains of Alexandrium minutum. PMID:25314922
Optimizing high performance computing workflow for protein functional annotation. PMID:25313296
Complete genome sequence of producer of the glycopeptide antibiotic Aculeximycin Kutzneria albida DSM 43870T, a representative of minor genus of Pseudonocardiaceae. PMID:25301375
Genomic insights into processes driving the infection of Alexandrium tamarense by the Parasitoid Amoebophrya sp. PMID:25239978
Comparative analysis of functional metagenomic annotation and the mappability of short reads. PMID:25148512
Defining the estimated core genome of bacterial populations using a Bayesian decision model. PMID:25144616
Phylogenetic analysis and evolutionary origins of DNA polymerase X-family members. PMID:25112931
Depth-stratified functional and taxonomic niche specialization in the 'core' and 'flexible' Pacific Ocean Virome. PMID:25093636
Alterations of the human gut microbiome in liver cirrhosis. PMID:25079328
Gene discovery through transcriptome sequencing for the invasive mussel Limnoperna fortunei. PMID:25047650
Identification and assembly of genomes and genetic elements in complex metagenomic samples without using reference genomes. PMID:24997787
An integrated catalog of reference genes in the human gut microbiome. PMID:24997786
Expansion of biological pathways based on evolutionary inference. PMID:24995987
Molecular evolution of NASP and conserved histone H3/H4 transport pathway. PMID:24951090
Choice of bacterial DNA extraction method from fecal material influences community structure as evaluated by metagenomic analysis. PMID:24949196
Coiled-coil proteins facilitated the functional expansion of the centrosome. PMID:24901223
Improvement of domain-level ortholog clustering by optimizing domain-specific sum-of-pairs score. PMID:24885064
XSAnno: a framework for building ortholog models in cross-species transcriptome comparisons. PMID:24884593
Handling temperature bursts reaching 464°C: different microbial strategies in the sisters peak hydrothermal chimney. PMID:24837379
Phylogenomic reconstruction of archaeal fatty acid metabolism. PMID:24818264
RAID: a comprehensive resource for human RNA-associated (RNA-RNA/RNA-protein) interaction. PMID:24803509
Gut microbiomes of Indian children of varying nutritional status. PMID:24763225
Genome sequence of Ensifer adhaerens OV14 provides insights into its ability as a novel vector for the genetic transformation of plant genomes. PMID:24708309
Comparative analysis of Salmonella genomes identifies a metabolic network for escalating growth in the inflamed gut. PMID:24643865
NCG 4.0: the network of cancer genes in the era of massive mutational screenings of cancer genomes. PMID:24608173
RNA-seq analysis of transcriptome and glucosinolate metabolism in seeds and sprouts of broccoli (Brassica oleracea var. italic). PMID:24586398
Quantitative genome-wide genetic interaction screens reveal global epistatic relationships of protein complexes in Escherichia coli. PMID:24586182
Minimal, encapsulated proteomic-sample processing applied to copy-number estimation in eukaryotic cells. PMID:24487582
The receptor for advanced glycation end-products (RAGE) is only present in mammals, and belongs to a family of cell adhesion molecules (CAMs). PMID:24475194
Training set selection for the prediction of essential genes. PMID:24466248
BuGZ is required for Bub3 stability, Bub1 kinetochore function, and chromosome alignment. PMID:24462187
Comparison of different assembly and annotation tools on analysis of simulated viral metagenomic communities in the gut. PMID:24438450
Construction of a public CHO cell line transcript database using versatile bioinformatics analysis pipelines. PMID:24427317
A new computational strategy for predicting essential genes. PMID:24359534
Comprehensive analysis of the Corynebacterium glutamicum transcriptome using an improved RNAseq technique. PMID:24341750
CLYBL is a polymorphic human enzyme with malate synthase and β-methylmalate synthase activity. PMID:24334609
NECTAR: a database of codon-centric missense variant annotations. PMID:24297257
eggNOG v4.0: nested orthology inference across 3686 organisms. PMID:24297252
MetaRef: a pan-genomic database for comparative and community microbial genomics. PMID:24203705
Metabolic reprogramming by viruses in the sunlit and dark ocean. PMID:24200126
GoMapMan: integration, consolidation and visualization of plant gene annotations within the MapMan ontology. PMID:24194592
Signature protein of the PVC superphylum. PMID:24185849
SIMAP--the database of all-against-all protein sequence similarities and annotations with new interfaces and increased coverage. PMID:24165881
Metagenomic species profiling using universal phylogenetic marker genes. PMID:24141494
Analytical tools and databases for metagenomics in the next-generation sequencing era. PMID:24124405
Response of Burkholderia cenocepacia H111 to micro-oxia. PMID:24023794
Primate genome architecture influences structural variation mechanisms and functional consequences. PMID:24014587
kClust: fast and sensitive clustering of large protein sequence databases. PMID:23945046
Hypothetical proteins present during recovery phase of radiation resistant bacterium Deinococcus radiodurans are under purifying selection. PMID:23934623
Functional profiling of the gut microbiome in disease-associated inflammation. PMID:23906180
Directed shotgun proteomics guided by saturated RNA-seq identifies a complete expressed prokaryotic proteome. PMID:23878158
Minimal genome encoding proteins with constrained amino acid repertoire. PMID:23873957
JBioWH: an open-source Java framework for bioinformatics data integration. PMID:23846595
Microbial and viral metagenomes of a subtropical freshwater reservoir subject to climatic disturbances. PMID:23842651
EGN: a wizard for construction of gene and genome similarity networks. PMID:23841456
Complementing the Eukaryotic Protein Interactome. PMID:23825550
Metagenome reveals potential microbial degradation of hydrocarbon coupled with sulfate reduction in an oil-immersed chimney from Guaymas Basin. PMID:23785357
CoPAP: Coevolution of presence-absence patterns. PMID:23748951
Human monogenic disease genes have frequently functionally redundant paralogs. PMID:23696728
The PhyloFacts FAT-CAT web server: ortholog identification and function prediction using fast approximate tree classification. PMID:23685612
Computational meta'omics for microbial community studies. PMID:23670539
Networks of bZIP protein-protein interactions diversified over a billion years of evolution. PMID:23661758
Phylogeographic origin of Helicobacter pylori determines host-adaptive responses upon coculture with gastric epithelial cells. PMID:23630959
Explaining microbial phenotypes on a genomic scale: GWAS for microbes. PMID:23625995
Comparison of 26 sphingomonad genomes reveals diverse environmental adaptations and biodegradative capabilities. PMID:23563954
Universal distribution of component frequencies in biological and technological systems. PMID:23530195
Bacterial growth at -15 °C; molecular insights from the permafrost bacterium Planococcus halocryophilus Or1. PMID:23389107
Inferring hierarchical orthologous groups from orthologous gene pairs. PMID:23342000
Phosphorylation variation during the cell cycle scales with structural propensities of proteins. PMID:23326221
Gene family assignment-free comparative genomics. PMID:23281826
Updated clusters of orthologous genes for Archaea: a complex ancestor of the Archaea and the byways of horizontal gene transfer. PMID:23241446
Proteomic investigations of lysine acetylation identify diverse substrates of mitochondrial deacetylase sirt3. PMID:23236377
Orthologous gene clusters and taxon signature genes for viruses of prokaryotes. PMID:23222723
OrtholugeDB: a bacterial and archaeal orthology resource for improved comparative genomic analysis. PMID:23203876
STRING v9.1: protein-protein interaction networks, with increased coverage and integration. PMID:23203871
KEGG OC: a large-scale automatic construction of taxonomy-based ortholog clusters. PMID:23193276
Biostimulation induces syntrophic interactions that impact C, S and N cycling in a sediment microbial community. PMID:23190730
The AHL- and BDSF-dependent quorum sensing systems control specific and overlapping sets of genes in Burkholderia cenocepacia H111. PMID:23185499
OrthoDB: a hierarchical catalog of animal, fungal and bacterial orthologs. PMID:23180791
GraphAlignment: Bayesian pairwise alignment of biological networks. PMID:23171476
MBGD update 2013: the microbial genome database for exploring the diversity of microbial world. PMID:23118485
Sifting through genomes with iterative-sequence clustering produces a large, phylogenetically diverse protein-family resource. PMID:23061897
Evolutionary force in confamiliar marine vertebrates of different temperature realms: adaptive trends in zoarcid fish transcriptomes. PMID:23051706
Whole-exome capture and sequencing identifies HEATR2 mutation as a cause of primary ciliary dyskinesia. PMID:23040496
Complete genome sequence of Saccharothrix espanaensis DSM 44229(T) and comparison to the other completely sequenced Pseudonocardiaceae. PMID:22958348
Composition-based classification of short metagenomic sequences elucidates the landscapes of taxonomic and functional enrichment of microorganisms. PMID:22941634
Transcriptomic analysis of acclimation to temperature and light stress in Saccharina latissima (Phaeophyceae). PMID:22937172
Conservation of caspase substrates across metazoans suggests hierarchical importance of signaling pathways over specific targets and cleavage site motifs in apoptosis. PMID:22918439
Meta-analysis of general bacterial subclades in whole-genome phylogenies using tree topology profiling. PMID:22915837
Functional assignment of metagenomic data: challenges and applications. PMID:22772835
BIPS: BIANA Interolog Prediction Server. A tool for protein-protein interaction inference. PMID:22689642
A programmable droplet-based microfluidic device applied to multiparameter analysis of single microbes and microbial communities. PMID:22547789 -
eggNOG v4.0: nested orthology inference across 3686 organisms
PubMed citations: 260.
260 articles citing: eggNOG v4.0: nested orthology inference across 3686 organisms
Isolation, Identification, and Investigation of Pathogenic Bacteria From Common Carp (Cyprinus carpio) Naturally Infected With Plesiomonas shigelloides. PMID:35844551
Characterization and Functional Studies of a Novel Depolymerase Against K19-Type Klebsiella pneumoniae. PMID:35814656
Potential Use of Microbial Community Genomes in Various Dimensions of Agriculture Productivity and Its Management: A Review. PMID:35655999
Metagenomics Reveals the Diversity and Taxonomy of Carbohydrate-Active Enzymes and Antibiotic Resistance Genes in Suancai Bacterial Communities. PMID:35627157
Effects of Short-Chain Fatty Acid Modulation on Potentially Diarrhea-Causing Pathogens in Yaks Through Metagenomic Sequencing. PMID:35402298
Antimicrobial resistance patterns and genetic elements associated with the antibiotic resistance of Helicobacter pylori strains from Shanghai. PMID:35354484
Identification and Characterization of Bacillus tequilensis GYUN-300: An Antagonistic Bacterium Against Red Pepper Anthracnose Caused by Colletotrichum acutatum in Korea. PMID:35308370
Dynamic Gene Expression and Alternative Splicing Events Demonstrate Co-Regulation of Testicular Differentiation and Maturation by the Brain and Gonad in Common Carp. PMID:35222265
Differential Transcriptome Analysis Reveals Genes Related to Low- and High-Temperature Stress in the Fall Armyworm, Spodoptera frugiperda. PMID:35173626
Comparative Genomic Analysis of Pathogenic Factors of Pectobacterium Species Isolated in South Korea Using Whole-Genome Sequencing. PMID:35144358
Genome insights into the pharmaceutical and plant growth promoting features of the novel species Nocardia alni sp. nov. PMID:35062865
Comparative Genomic Analysis of Streptococcus pneumoniae Strains: Penicillin Non-susceptible Multi-drug-Resistant Serotype 19A Isolates. PMID:34982234
In Vitro Study of Biocontrol Potential of Rhizospheric Pseudomonas aeruginosa against Pathogenic Fungi of Saffron (Crocus sativus L.). PMID:34832579
ConVarT: a search engine for matching human genetic variants with variants from non-human species. PMID:34718716
Pan-Genome Analysis of Effectors in Korean Strains of the Soybean Pathogen Xanthomonas citri pv. glycines. PMID:34683386
Comparative RNA-Seq Analyses of Solenopsis japonica (Hymenoptera: Formicidae) Reveal Gene in Response to Cold Stress. PMID:34681004
Characterization of the First Cultured Psychrotolerant Representative of Legionella from Antarctica Reveals Its Unique Genome Structure. PMID:34668737
Metagenomic Analysis Identifies Sex-Related Cecal Microbial Gene Functions and Bacterial Taxa in the Quail. PMID:34660751
Genome-Wide Characterization of Glutathione Peroxidase (GPX) Gene Family in Rapeseed (Brassica napus L.) Revealed Their Role in Multiple Abiotic Stress Response and Hormone Signaling. PMID:34573113
Characterization of Martelella soudanensis sp. nov., Isolated from a Mine Sediment. PMID:34442814
Genome-Wide Analysis and Expression Profile of Superoxide Dismutase (SOD) Gene Family in Rapeseed (Brassica napus L.) under Different Hormones and Abiotic Stress Conditions. PMID:34439430
Comparison of gene expression in the red imported fire ant (Solenopsis invicta) under different temperature conditions. PMID:34389756
Identification of Microbiota Biomarkers With Orthologous Gene Annotation for Type 2 Diabetes. PMID:34305880
Diversity and function of culturable actinobacteria in the root-associated of Salvia miltiorrhiza Bunge. PMID:34285837
Informative Regions In Viral Genomes. PMID:34207030
Antimicrobial Resistance Determinants in Genomes and Plasmids from Acinetobacter baumannii Clinical Isolates. PMID:34206348
High-Fat-Diet-Induced Oxidative Stress Linked to the Increased Colonization of Lactobacillus sakei in an Obese Population. PMID:34190593
Gut microbiome and its meta-omics perspectives: profound implications for cardiovascular diseases. PMID:34170211
Midgut transcriptome assessment of the cockroach-hunting wasp Ampulex compressa (Apoidea: Ampulicidae). PMID:34166422
Dispersal strategies shape persistence and evolution of human gut bacteria. PMID:34111423
Metatranscriptomic Analysis Reveals an Imbalance of Hepatopancreatic Flora of Chinese Mitten Crab Eriocheir sinensis with Hepatopancreatic Necrosis Disease. PMID:34071147
Characterization of a new bifunctional endo-1,4-β-xylanase/esterase found in the rumen metagenome. PMID:34001974
A native conjugative plasmid confers potential selective advantages to plant growth-promoting Bacillus velezensis strain GH1-13. PMID:33990691
Ketogenic diet-mediated steroid metabolism reprogramming improves the immune microenvironment and myelin growth in spinal cord injury rats according to gene and co-expression network analyses. PMID:33962394
Integrating taxonomic, functional, and strain-level profiling of diverse microbial communities with bioBakery 3. PMID:33944776
Comparative genomics and physiological investigation supported safety, cold adaptation, efficient hydrolytic and plant growth-promoting potential of psychrotrophic Glutamicibacter arilaitensis LJH19, isolated from night-soil compost. PMID:33910515
Genomic population structure of Helicobacter pylori Shanghai isolates and identification of genomic features uniquely linked with pathogenicity. PMID:33904371
The Composition and Primary Metabolic Potential of Microbial Communities Inhabiting the Surface Water in the Equatorial Eastern Indian Ocean. PMID:33810062
Longitudinal study of the scalp microbiome suggests coconut oil to enrich healthy scalp commensals. PMID:33790324
Microbial Ecological Mechanism for Long-Term Production of High Concentrations of n-Caproate via Lactate-Driven Chain Elongation. PMID:33741616
Reannotation of the cultivated strawberry genome and establishment of a strawberry genome database. PMID:33642572
Chromosome-scale assembly of the genome of Salix dunnii reveals a male-heterogametic sex determination system on chromosome 7. PMID:33609314
Comparative genome analyses of Lactobacillus crispatus isolated from different ecological niches reveal an environmental adaptation of this species to the human vaginal environment. PMID:33579685
The Mastigamoeba balamuthi Genome and the Nature of the Free-Living Ancestor of Entamoeba. PMID:33528570
Long-Term Waterlogging as Factor Contributing to Hypoxia Stress Tolerance Enhancement in Cucumber: Comparative Transcriptome Analysis of Waterlogging Sensitive and Tolerant Accessions. PMID:33525400
Amoxicillin-Clavulanic Acid Resistance in the Genus Bifidobacterium. PMID:33483308
Effects of Co-culture on Improved Productivity and Bioresource for Microalgal Biomass Using the Floc-Forming Bacteria Melaminivora Jejuensis. PMID:33392165
Functional Seasonality of Free-Living and Particle-Associated Prokaryotic Communities in the Coastal Adriatic Sea. PMID:33304331
Analysis of the vaginal microbiome of giant pandas using metagenomics sequencing. PMID:33205903
Effects of Selenium- and Zinc-Enriched Lactobacillus plantarum SeZi on Antioxidant Capacities and Gut Microbiome in an ICR Mouse Model. PMID:33096847
Implementation of homology based and non-homology based computational methods for the identification and annotation of orphan enzymes: using Mycobacterium tuberculosis H37Rv as a case study. PMID:33076816
A new genome allows the identification of genes associated with natural variation in aluminium tolerance in Brachiaria grasses. PMID:33064149
Comparative Analysis of Soil Microbiome Profiles in the Companion Planting of White Clover and Orchard Grass Using 16S rRNA Gene Sequencing Data. PMID:33042174
Complete Genome Sequence of Spirosoma sp. Strain KCTC 42546, Isolated from a Reservoir in South Korea. PMID:32943563
Cell Plasticity and Genomic Structure of a Novel Filterable Rhizobiales Bacterium that Belongs to a Widely Distributed Lineage. PMID:32906802
Clinical BRCA1/2 Reversion Analysis Identifies Hotspot Mutations and Predicted Neoantigens Associated with Therapy Resistance. PMID:32699032
Characterization of the Phenanthrene-Degrading Sphingobium yanoikuyae SJTF8 in Heavy Metal Co-Existing Liquid Medium and Analysis of Its Metabolic Pathway. PMID:32586023
Draft genome sequence data of Paenibacillus Polymyxa strain TH2H2, isolated from a tomato flower in Korea. PMID:32577455
Parallel reductive genome evolution in Desulfovibrio ectosymbionts independently acquired by Trichonympha protists in the termite gut. PMID:32483307
Macromolecular crowding links ribosomal protein gene dosage to growth rate in Vibrio cholerae. PMID:32349767
The preceding root system drives the composition and function of the rhizosphere microbiome. PMID:32252812
WeiBI (web-based platform): Enriching integrated interaction network with increased coverage and functional proteins from genome-wide experimental OMICS data. PMID:32221380
The transcriptome of the newt Cynops orientalis provides new insights into evolution and function of sexual gene networks in sarcopterygians. PMID:32214214
De novo Transcriptome Reveals Gene Changes in the Development of the Endosperm Chalazal Haustorium in Taxillus chinensis (DC.) Danser. PMID:32149138
Twitching and Swimming Motility Play a Role in Ralstonia solanacearum Pathogenicity. PMID:32132161
Integrated metabolomic and transcriptomic analyses identify critical genes in eicosapentaenoic acid biosynthesis and metabolism in the sea urchin Strongylocentrotus intermedius. PMID:32015446
De Novo Transcriptome Identifies Olfactory Genes in Diachasmimorpha longicaudata (Ashmead). PMID:32013248
The Wild Mouse (Micromys minutus): Reservoir of a Novel Campylobacter jejuni Strain. PMID:31993041
Effects of spaceflight on the composition and function of the human gut microbiota. PMID:31924114
Comparative transcriptome reveals the potential modulation mechanisms of estradiol affecting ovarian development of female Portunus trituberculatus. PMID:31856263
A BONCAT-iTRAQ method enables temporally resolved quantitative profiling of newly synthesised proteins in Leishmania mexicana parasites during starvation. PMID:31856154
Transcriptome sequencing of a keystone aquatic herbivore yields insights on the temperature-dependent metabolism of essential lipids. PMID:31752680
OrthoFinder: phylogenetic orthology inference for comparative genomics. PMID:31727128
Transcriptomic analysis of α-synuclein knockdown after T3 spinal cord injury in rats. PMID:31726970
The distinction of CPR bacteria from other bacteria based on protein family content. PMID:31519891
Transcriptome analysis to characterize the genes related to gonad growth and fatty acid metabolism in the sea urchin Strongylocentrotus intermedius. PMID:31485990
Transcriptomic analysis of Pacific white shrimp (Litopenaeus vannamei, Boone 1931) in response to acute hepatopancreatic necrosis disease caused by Vibrio parahaemolyticus. PMID:31408485
Patient-specific cancer genes contribute to recurrently perturbed pathways and establish therapeutic vulnerabilities in esophageal adenocarcinoma. PMID:31308377
Highly variable mRNA half-life time within marine bacterial taxa and functional genes. PMID:31298776
Genome-wide functional association networks: background, data & state-of-the-art resources. PMID:31281921
Genomic and Metagenomic Insights Into the Microbial Community in the Regenerating Intestine of the Sea Cucumber Apostichopus japonicus. PMID:31214136
Involvement of Salicylic Acid in Anthracnose Infection in Tea Plants Revealed by Transcriptome Profiling. PMID:31108845
Transcriptome analysis of activated sludge microbiomes reveals an unexpected role of minority nitrifiers in carbon metabolism. PMID:31098412
Ice-Age Climate Adaptations Trap the Alpine Marmot in a State of Low Genetic Diversity. PMID:31080084
Carbohydrate metabolism genes dominant in a subtropical marine mangrove ecosystem revealed by metagenomics analysis. PMID:31073898
Large-Scale Genomics Reveals the Genetic Characteristics of Seven Species and Importance of Phylogenetic Distance for Estimating Pan-Genome Size. PMID:31068915
Tree reconciliation combined with subsampling improves large scale inference of orthologous group hierarchies. PMID:31060495
Taxonomic and Functional Characterization of the Microbial Community During Spontaneous in vitro Fermentation of Riesling Must. PMID:31024486
Draft Genome Sequence of Broad-Spectrum Antibiotic-Producing Marine Verrucosispora sp. Strain FIM060022. PMID:30975797
Transcriptional profiling of Auricularia cornea in selenium accumulation. PMID:30948778
Man-made microbial resistances in built environments. PMID:30814504
Unveiling Genomic Diversity among Members of the Species Bifidobacterium pseudolongum, a Widely Distributed Gut Commensal of the Animal Kingdom. PMID:30737347
Dissecting the Evolutionary Development of the Species Bifidobacterium animalis through Comparative Genomics Analyses. PMID:30709821
The unique composition of Indian gut microbiome, gene catalogue, and associated fecal metabolome deciphered using multi-omics approaches. PMID:30698687
Metaepigenomic analysis reveals the unexplored diversity of DNA methylation in an environmental prokaryotic community. PMID:30635580
Abnormal Gut Microbiota Metabolism Specific for Liver Cirrhosis. PMID:30619141
Laboratory strains of Bacillus anthracis exhibit pervasive alteration in expression of proteins related to sporulation under laboratory conditions relative to genetically related wild strains. PMID:30557394
Complete Genome Sequence of the Endophytic Bacterium Bacillus cereus PgBE311, Isolated from Panax ginseng. PMID:30533836
Complete Genome Sequence of the Endophytic Bacterium Chryseobacterium indologenes PgBE177, Isolated from Panax quinquefolius. PMID:30533712
The antibiotic action of methylarsenite is an emergent property of microbial communities. PMID:30520200
Multi-tissue transcriptomes of caecilian amphibians highlight incomplete knowledge of vertebrate gene families. PMID:30351380
Comprehensive transcriptome analysis reveals genes in response to water deficit in the leaves of Saccharum narenga (Nees ex Steud.) hack. PMID:30342477
Comparison of Healthy and Dandruff Scalp Microbiome Reveals the Role of Commensals in Scalp Health. PMID:30338244
Identification and genome analysis of Deinococcus actinosclerus SJTR1, a novel 17β-estradiol degradation bacterium. PMID:30306002
Progress of analytical tools and techniques for human gut microbiome research. PMID:30267313
Efficient inference of homologs in large eukaryotic pan-proteomes. PMID:30257640
Comparative Metagenomic Analysis of Rhizosphere Microbial Community Composition and Functional Potentials under Rehmannia glutinosa Consecutive Monoculture. PMID:30110928
Homology Inference Based on a Reconciliation Approach for the Comparative Genomics of Protozoa. PMID:30034216
The evolutionary signal in metagenome phyletic profiles predicts many gene functions. PMID:29991352
Landscape of the genome and host cell response of Mycobacterium shigaense reveals pathogenic features. PMID:29934568
Using WormBase: A Genome Biology Resource for Caenorhabditis elegans and Related Nematodes. PMID:29761466
Biochemical Properties of α-Amylase from Midgut of Alphitobius diaperinus (Panzer) (Coleoptera: Tenebrionidae) Larvae. PMID:29484545
PANDA: Protein function prediction using domain architecture and affinity propagation. PMID:29472600
Induced Salt Tolerance of Perennial Ryegrass by a Novel Bacterium Strain from the Rhizosphere of a Desert Shrub Haloxylon ammodendron. PMID:29401742
Screening and Genomic Characterization of Filamentous Hemagglutinin-Deficient Bordetella pertussis. PMID:29358336
Genomic insights into the Acidobacteria reveal strategies for their success in terrestrial environments. PMID:29327410
Complete Genome Sequence of Mesorhizobium sophorae ICMP 19535T, a Highly Specific, Nitrogen-Fixing Symbiont of New Zealand Endemic Sophora spp. PMID:29074646
Draft Genome Sequence of a Rare Pigmented Mycobacterium avium subsp. paratuberculosis Type C Strain. PMID:29025941
The chromosomal organization of horizontal gene transfer in bacteria. PMID:29018197
Microbial genome analysis: the COG approach. PMID:28968633
Metagenomic assessment of the interplay between the environment and the genetic diversification of Acinetobacter. PMID:28967182
Cloning and expression analysis of tps, and cryopreservation research of trehalose from Antarctic strain Pseudozyma sp. PMID:28955640
Recurrent horizontal transfer of arsenite methyltransferase genes facilitated adaptation of life to arsenic. PMID:28798375
A clinician's guide to microbiome analysis. PMID:28790452
De novo assembly and annotation of the retinal transcriptome for the Nile grass rat (Arvicanthis ansorgei). PMID:28759564
NtrC-dependent control of exopolysaccharide synthesis and motility in Burkholderia cenocepacia H111. PMID:28662146
Adaptations to High Salt in a Halophilic Protist: Differential Expression and Gene Acquisitions through Duplications and Gene Transfers. PMID:28611746
Transcriptologs: A Transcriptome-Based Approach to Predict Orthology Relationships. PMID:28469416
Comparative Analysis of Ralstonia solanacearum Methylomes. PMID:28450872
Draft Genome Sequence of Streptomyces sp. Strain IB2014011-1, Isolated from Trichoptera sp. Larvae of Lake Baikal. PMID:28450500
Using structural knowledge in the protein data bank to inform the search for potential host-microbe protein interactions in sequence space: application to Mycobacterium tuberculosis. PMID:28376709
Comparative study the expression of calcium cycling genes in Bombay duck (Harpadon nehereus) and beltfish (Trichiurus lepturus) with different swimming activities. PMID:28373957
Tracking the evolution of 3D gene organization demonstrates its connection to phenotypic divergence. PMID:28369658
Genomic characterization of Nontuberculous Mycobacteria. PMID:28345639
Development of Gene-Based SSR Markers in Winged Bean (Psophocarpus tetragonolobus (L.) DC.) for Diversity Assessment. PMID:28282950
New natural products identified by combined genomics-metabolomics profiling of marine Streptomyces sp. MP131-18. PMID:28186197
The History of Bordetella pertussis Genome Evolution Includes Structural Rearrangement. PMID:28167525
Protein Bioinformatics Databases and Resources. PMID:28150231
Comparative Analysis of Mitochondrial N-Termini from Mouse, Human, and Yeast. PMID:28122942
MetaSort untangles metagenome assembly by reducing microbial community complexity. PMID:28112173
Metagenomic Analysis of Hot Springs in Central India Reveals Hydrocarbon Degrading Thermophiles and Pathways Essential for Survival in Extreme Environments. PMID:28105025
Transcriptome Sequencing of Gynostemma pentaphyllum to Identify Genes and Enzymes Involved in Triterpenoid Biosynthesis. PMID:28097124
A fibrolytic potential in the human ileum mucosal microbiota revealed by functional metagenomic. PMID:28091525
Age influences the olfactory profiles of the migratory oriental armyworm mythimna separate at the molecular level. PMID:28056777
In silico screening for candidate chassis strains of free fatty acid-producing cyanobacteria. PMID:28056772
Transcriptome Analysis of Taxillusi chinensis (DC.) Danser Seeds in Response to Water Loss. PMID:28046012
Genome Sequence of Pseudomonas citronellolis SJTE-3, an Estrogen- and Polycyclic Aromatic Hydrocarbon-Degrading Bacterium. PMID:27932659
A scored human protein-protein interaction network to catalyze genomic interpretation. PMID:27892958
Systems-level metabolism of the altered Schaedler flora, a complete gut microbiota. PMID:27824342
Proteomic Stable Isotope Probing Reveals Taxonomically Distinct Patterns in Amino Acid Assimilation by Coastal Marine Bacterioplankton. PMID:27822523
An Inducible Operon Is Involved in Inulin Utilization in Lactobacillus plantarum Strains, as Revealed by Comparative Proteogenomics and Metabolic Profiling. PMID:27815279
WORMHOLE: Novel Least Diverged Ortholog Prediction through Machine Learning. PMID:27812085
Genomic Analysis of Vulcanisaeta thermophila Type Strain CBA1501T Isolated from Solfataric Soil. PMID:27807432
Genome of 'Ca. Desulfovibrio trichonymphae', an H2-oxidizing bacterium in a tripartite symbiotic system within a protist cell in the termite gut. PMID:27801909
Comparative Proteomics of Leaves from Phytase-Transgenic Maize and Its Non-transgenic Isogenic Variety. PMID:27582747
Soil and leaf litter metaproteomics-a brief guideline from sampling to understanding. PMID:27549116
Gene content dissimilarity for subclassification of highly similar microbial strains. PMID:27530250
RNA-seq-based evaluation of bicolor tepal pigmentation in Asiatic hybrid lilies (Lilium spp.). PMID:27516339
A tissue-specific protein purification approach in Caenorhabditis elegans identifies novel interaction partners of DLG-1/Discs large. PMID:27506200
Distinct gene expression profile of Xanthomonas retroflexus engaged in synergistic multispecies biofilm formation. PMID:27505346
The Verrucomicrobia LexA-Binding Motif: Insights into the Evolutionary Dynamics of the SOS Response. PMID:27489856
Whole-Metagenome-Sequencing-Based Community Profiles of Vitis vinifera L. cv. Corvina Berries Withered in Two Post-harvest Conditions. PMID:27445999
Osmoadaptative Strategy and Its Molecular Signature in Obligately Halophilic Heterotrophic Protists. PMID:27412608
A Bayesian inference method for the analysis of transcriptional regulatory networks in metagenomic data. PMID:27398089
Reannotation of Yersinia pestis Strain 91001 Based on Omics Data. PMID:27382076
HoloVir: A Workflow for Investigating the Diversity and Function of Viruses in Invertebrate Holobionts. PMID:27375564
Computational Identification of the Paralogs and Orthologs of Human Cytochrome P450 Superfamily and the Implication in Drug Discovery. PMID:27367670
A novel skew analysis reveals substitution asymmetries linked to genetic code GC-biases and PolIII a-subunit isoforms. PMID:27345720
Genome Structural Diversity among 31 Bordetella pertussis Isolates from Two Recent U.S. Whooping Cough Statewide Epidemics. PMID:27303739
The Conserved Tetratricopeptide Repeat-Containing C-Terminal Domain of Pseudomonas aeruginosa FimV Is Required for Its Cyclic AMP-Dependent and -Independent Functions. PMID:27297880
Abasy Atlas: a comprehensive inventory of systems, global network properties and systems-level elements across bacteria. PMID:27242034
Identification of myogenic regulatory genes in the muscle transcriptome of beltfish (Trichiurus lepturus): A major commercial marine fish species with robust swimming ability. PMID:27222805
A single gene of a commensal microbe affects host susceptibility to enteric infection. PMID:27173141
Gut microbiota composition and Clostridium difficile infection in hospitalized elderly individuals: a metagenomic study. PMID:27166072
Survival trade-offs in plant roots during colonization by closely related beneficial and pathogenic fungi. PMID:27150427
Analytic framework for peptidomics applied to large-scale neuropeptide identification. PMID:27142507
Phylogenetic Profiling for Probing the Modular Architecture of the Human Genome. PMID:27135799
Genome sequencing and analysis of the first complete genome of Lactobacillus kunkeei strain MP2, an Apis mellifera gut isolate. PMID:27114887
Heterogeneous molecular processes among the causes of how sequence similarity scores can fail to recapitulate phylogeny. PMID:27103098
Tongue Coating and the Salivary Microbial Communities Vary in Children with Halitosis. PMID:27080513
Improving the catalytic activity of isopentenyl phosphate kinase through protein coevolution analysis. PMID:27052337
Standardized benchmarking in the quest for orthologs. PMID:27043882
Evaluation of genetic diversity among strains of the human gut commensal Bifidobacterium adolescentis. PMID:27035119
Transcriptome analyses of insect cells to facilitate baculovirus-insect expression. PMID:27017378
RNA-seq analysis for plant carnivory gene discovery in Nepenthes × ventrata. PMID:26981352
RNA-seq analysis for secondary metabolite pathway gene discovery in Polygonum minus. PMID:26981350
PhyloPro2.0: a database for the dynamic exploration of phylogenetically conserved proteins and their domain architectures across the Eukarya. PMID:26980519
De novo analysis of transcriptome reveals genes associated with leaf abscission in sugarcane (Saccharum officinarum L.). PMID:26946183
The Lungfish Transcriptome: A Glimpse into Molecular Evolution Events at the Transition from Water to Land. PMID:26908371
Late acquisition of mitochondria by a host with chimaeric prokaryotic ancestry. PMID:26840490
Global biogeography of Prochlorococcus genome diversity in the surface ocean. PMID:26836261
pATsi: Paralogs and Singleton Genes from Arabidopsis thaliana. PMID:26792975
Genomic and metagenomic analysis of microbes in a soil environment affected by the 2011 Great East Japan Earthquake tsunami. PMID:26764021
MycoBASE: expanding the functional annotation coverage of mycobacterial genomes. PMID:26704706
Genomic Patterns of Positive Selection at the Origin of Rust Fungi. PMID:26632820
orthoFind Facilitates the Discovery of Homologous and Orthologous Proteins. PMID:26624019
The SIB Swiss Institute of Bioinformatics' resources: focus on curated databases. PMID:26615188
Investigation of Yersinia pestis Laboratory Adaptation through a Combined Genomics and Proteomics Approach. PMID:26599979
Identification of Putative Nuclear Receptors and Steroidogenic Enzymes in Murray-Darling Rainbowfish (Melanotaenia fluviatilis) Using RNA-Seq and De Novo Transcriptome Assembly. PMID:26599404
EffectiveDB--updates and novel features for a better annotation of bacterial secreted proteins and Type III, IV, VI secretion systems. PMID:26590402
eggNOG 4.5: a hierarchical orthology framework with improved functional annotations for eukaryotic, prokaryotic and viral sequences. PMID:26582926
Optimizing and benchmarking de novo transcriptome sequencing: from library preparation to assembly evaluation. PMID:26581708
Experimental detection of short regulatory motifs in eukaryotic proteins: tips for good practice as well as for bad. PMID:26581338
Yeast Interspecies Comparative Proteomics Reveals Divergence in Expression Profiles and Provides Insights into Proteome Resource Allocation and Evolutionary Roles of Gene Duplication. PMID:26560065
The Transporter Classification Database (TCDB): recent advances. PMID:26546518
Information Commons for Rice (IC4R). PMID:26519466
NCG 5.0: updates of a manually curated repository of cancer genes and associated properties from cancer mutational screenings. PMID:26516186
Bifidobacteria exhibit social behavior through carbohydrate resource sharing in the gut. PMID:26506949
Phosphoproteomic screening identifies Rab GTPases as novel downstream targets of PINK1. PMID:26471730
Comprehensive analysis of the endoplasmic reticulum stress response in the soybean genome: conserved and plant-specific features. PMID:26466891
LRRC31 is induced by IL-13 and regulates kallikrein expression and barrier function in the esophageal epithelium. PMID:26462420
Prediction of microbial phenotypes based on comparative genomics. PMID:26451672
Following the Footsteps of Chlamydial Gene Regulation. PMID:26424812
Improved orthologous databases to ease protozoan targets inference. PMID:26416523
Identification of Newly Synthesized Proteins by Echinococcus granulosus Protoscoleces upon Induction of Strobilation. PMID:26393918
Transcriptomic variation of hepatopancreas reveals the energy metabolism and biological processes associated with molting in Chinese mitten crab, Eriocheir sinensis. PMID:26369734
Metagenomic Analysis of Chicken Gut Microbiota for Improving Metabolism and Health of Chickens - A Review. PMID:26323514
Functional Basis of Microorganism Classification. PMID:26317871
Endosymbiotic origin and differential loss of eukaryotic genes. PMID:26287458
LCGserver: A Webserver for Exploring Evolutionary Trajectory of Gene Orders in a Large Number of Genomes. PMID:26258441
OrthoFinder: solving fundamental biases in whole genome comparisons dramatically improves orthogroup inference accuracy. PMID:26243257
Exploring Vertical Transmission of Bifidobacteria from Mother to Child. PMID:26231653
PlantOrDB: a genome-wide ortholog database for land plants and green algae. PMID:26112452
Uncovering major genomic features of essential genes in Bacteria and a methanogenic Archaea. PMID:26084810
Using the taxon-specific genes for the taxonomic classification of bacterial genomes. PMID:25990029
Metagenomics: tools and insights for analyzing next-generation sequencing data derived from biodiversity studies. PMID:25983555
Domain similarity based orthology detection. PMID:25968113
OrthoVenn: a web server for genome wide comparison and annotation of orthologous clusters across multiple species. PMID:25964301
ProtPhylo: identification of protein-phenotype and protein-protein functional associations via phylogenetic profiling. PMID:25956654
Complex archaea that bridge the gap between prokaryotes and eukaryotes. PMID:25945739
Genomic factors related to tissue tropism in Chlamydia pneumoniae infection. PMID:25887605
Enrichment of Triticum aestivum gene annotations using ortholog cliques and gene ontologies in other plants. PMID:25887590
Average genome size estimation improves comparative metagenomics and sheds light on the functional ecology of the human microbiome. PMID:25853934
σ54-Dependent Response to Nitrogen Limitation and Virulence in Burkholderia cenocepacia Strain H111. PMID:25841012
Evolution of an epigenetic gene ensemble within the genus Anopheles. PMID:25724208
An event-driven approach for studying gene block evolution in bacteria. PMID:25717195
Version 4.0 of PaxDb: Protein abundance data, integrated across model organisms, tissues, and cell-lines. PMID:25656970
Comparison of sister species identifies factors underpinning plastid compatibility in green sea slugs. PMID:25652835
Systematic characterization and prediction of post-translational modification cross-talk. PMID:25605461
Orthology and paralogy constraints: satisfiability and consistency. PMID:25572629
Integrative workflows for metagenomic analysis. PMID:25478562
Determining microbial products and identifying molecular targets in the human microbiome. PMID:25440055
Expanded microbial genome coverage and improved protein family annotation in the COG database. PMID:25428365
OrthoDB v8: update of the hierarchical catalog of orthologs and the underlying free software. PMID:25428351
The OMA orthology database in 2015: function predictions, better plant support, synteny view and other improvements. PMID:25399418
MBGD update 2015: microbial genome database for flexible ortholog analysis utilizing a diverse set of genomic data. PMID:25398900
Cyclebase 3.0: a multi-organism database on cell-cycle regulation and phenotypes. PMID:25378319
TFClass: a classification of human transcription factors and their rodent orthologs. PMID:25361979
Genenames.org: the HGNC resources in 2015. PMID:25361968
PTMcode v2: a resource for functional associations of post-translational modifications within and between proteins. PMID:25361965
STRING v10: protein-protein interaction networks, integrated over the tree of life. PMID:25352553
PLAZA 3.0: an access point for plant comparative genomics. PMID:25324309
Speeding up all-against-all protein comparisons while maintaining sensitivity by considering subsequence-level homology. PMID:25320677
SMART: recent updates, new developments and status in 2015. PMID:25300481
Draft Genome Sequence of the Yeast Pseudozyma antarctica Type Strain JCM10317, a Producer of the Glycolipid Biosurfactants, Mannosylerythritol Lipids. PMID:25291760
MaxBin: an automated binning method to recover individual genomes from metagenomes using an expectation-maximization algorithm. PMID:25136443
Fast and sensitive alignment of microbial whole genome sequencing reads to large sequence datasets on a desktop PC: application to metagenomic datasets and pathogen identification. PMID:25077800
Big data and other challenges in the quest for orthologs. PMID:25064571
Quickly finding orthologs as reciprocal best hits with BLAT, LAST, and UBLAST: how much do we miss? PMID:25013894
An introduction to the analysis of shotgun metagenomic data. PMID:24982662 -
eggNOG: automated construction and annotation of orthologous groups of genes
PubMed citations: 207.
207 articles citing: eggNOG: automated construction and annotation of orthologous groups of genes
Genome sequence and comparative analysis of fungal antagonistic strain Bacillus velezensis LJBV19. PMID:35913660
Complete gammaproteobacterial endosymbiont genome assembly from a seep tubeworm Lamellibrachia satsuma. PMID:35913594
An Age Effect of Rumen Microbiome in Dairy Buffaloes Revealed by Metagenomics. PMID:35893549
Structural and functional characteristics of soil microbial community in a Pinus massoniana forest at different elevations. PMID:35860041
Genomics analysis and degradation characteristics of lignin by Streptomyces thermocarboxydus strain DF3-3. PMID:35831866
Gradual Enhancement of the Assemblage Stability of the Reed Rhizosphere Microbiome with Recovery Time. PMID:35630381
Metagenomic insights into surface water microbial communities of a South Asian mangrove ecosystem. PMID:35573175
The Genome of Bacillus velezensis SC60 Provides Evidence for Its Plant Probiotic Effects. PMID:35456817
De novo assembly of a fruit transcriptome set identifies AmMYB10 as a key regulator of anthocyanin biosynthesis in Aronia melanocarpa. PMID:35337270
Shinella oryzae sp. nov., a novel zearalenone-resistant bacterium isolated from rice paddy soil. PMID:35312873
Shotgun Metagenomics of Deep Forest Soil Layers Show Evidence of Altered Microbial Genetic Potential for Biogeochemical Cycling. PMID:35300488
Distinctive pattern and mechanism of precipitation changes affecting soil microbial assemblages in the Eurasian steppe. PMID:35243251
SMRT sequencing of full-length transcriptome and gene expression analysis in two chemical types of Pogostemon cablin (Blanco) Benth. PMID:35223208
Chromosome-scale assembly and population diversity analyses provide insights into the evolution of Sapindus mukorossi. PMID:35178562
Genome of the ramshorn snail Biomphalaria straminea-an obligate intermediate host of schistosomiasis. PMID:35166339
The crewed journey to Mars and its implications for the human microbiome. PMID:35125119
Isolation, Classification, and Growth-Promoting Effects of Pantoea sp. YSD J2 from the Aboveground Leaves of Cyperus Esculentus L. var. sativus. PMID:35059843
Genetic and Comparative Genome Analysis of Exiguobacterium aurantiacum SW-20, a Petroleum-Degrading Bacteria with Salt Tolerance and Heavy Metal-Tolerance Isolated from Produced Water of Changqing Oilfield, China. PMID:35056515
Critical Assessment of MetaProteome Investigation (CAMPI): a multi-laboratory comparison of established workflows. PMID:34911965
Centromere-Specific Retrotransposons and Very-Long-Chain Fatty Acid Biosynthesis in the Genome of Yellowhorn (Xanthoceras sorbifolium, Sapindaceae), an Oil-Producing Tree With Significant Drought Resistance. PMID:34880890
Genetic Determinants in Salmonella enterica Serotype Typhimurium Required for Overcoming In Vitro Stressors in the Mimicking Host Environment. PMID:34878334
Multiple acyl-CoA dehydrogenase deficiency kills Mycobacterium tuberculosis in vitro and during infection. PMID:34782606
Genomic insights into biocontrol potential of Bacillus stercoris LJBS06. PMID:34692367
Extracellular Vesicle Proteomes Shed Light on the Evolutionary, Interactive, and Functional Divergence of Their Biogenesis Mechanisms. PMID:34660591
The Biocontrol and Plant Growth-Promoting Properties of Streptomyces alfalfae XN-04 Revealed by Functional and Genomic Analysis. PMID:34630371
Genome-Resolved Meta-Analysis of the Microbiome in Oil Reservoirs Worldwide. PMID:34576708
Towards Building a Quantitative Proteomics Toolbox in Precision Medicine: A Mini-Review. PMID:34512391
Metagenomic Analysis of Antibiotic Resistance Genes in Untreated Wastewater From Three Different Hospitals. PMID:34504480
Genome-Based Characterization of Plant-Associated Rhodococcus qingshengii RL1 Reveals Stress Tolerance and Plant-Microbe Interaction Traits. PMID:34489897
Pseudomonas nanhaiensis sp. nov., a lipase-producing bacterium isolated from deep-sea sediment of the South China Sea. PMID:34392431
P2T2: Protein Panoramic annoTation Tool for the interpretation of protein coding genetic variants. PMID:34377961
Efficacy of Plant Growth-Promoting Bacteria Bacillus cereus YN917 for Biocontrol of Rice Blast. PMID:34354684
Antimicrobial Resistance Determinants in Genomes and Plasmids from Acinetobacter baumannii Clinical Isolates. PMID:34206348
Transcriptomic responses to drought stress among natural populations provide insights into local adaptation of weeping forsythia. PMID:34130656
Generation of unequal nuclear genotype proportions in Rhizophagus irregularis progeny causes allelic imbalance in gene transcription. PMID:34085297
High biodiversity in a benzene-degrading nitrate-reducing culture is sustained by a few primary consumers. PMID:33953314
Quantitative proteome comparison of human hearts with those of model organisms. PMID:33872299
Lineage-Specific Rewiring of Core Pathways Predating Innovation of Legume Nodules Shapes Symbiotic Efficiency. PMID:33850043
De novo assembly, annotation and gene expression profiles of gonads of Cytorace-3, a hybrid lineage of Drosophila nasuta nasuta and D. n. albomicans. PMID:33840172
Applications of Machine Learning in Human Microbiome Studies: A Review on Feature Selection, Biomarker Identification, Disease Prediction and Treatment. PMID:33737920
Primary Metabolism co-Opted for Defensive Chemical Production in the Carabid Beetle, Harpalus pensylvanicus. PMID:33689113
An Introduction to Whole-Metagenome Shotgun Sequencing Studies. PMID:33606255
gNOMO: a multi-omics pipeline for integrated host and microbiome analysis of non-model organisms. PMID:33575609
Metagenomic analysis revealed a wide distribution of antibiotic resistance genes and biosynthesis of antibiotics in the gut of giant pandas. PMID:33413128
Metagenomics survey unravels diversity of biogas microbiomes with potential to enhance productivity in Kenya. PMID:33395690
Phosphate Dosing in Drinking Water Distribution Systems Promotes Changes in Biofilm Structure and Functional Genetic Diversity. PMID:33391216
Global Proteomic Profiling of Piscirickettsia salmonis and Salmon Macrophage-Like Cells during Intracellular Infection. PMID:33255149
The expanding world of plant J-domain proteins. PMID:33223602
Transcriptional response of Bacillus megaterium FDU301 to PEG200-mediated arid stress. PMID:33198631
Diversity, function and assembly of mangrove root-associated microbial communities at a continuous fine-scale. PMID:33184266
CitrusKB: a comprehensive knowledge base for transcriptome and interactome of Citrus spp. infected by Xanthomonas citri subsp. citri at different infection stages. PMID:33181825
Isolation and sequence-based characterization of a koala symbiont: Lonepinella koalarum. PMID:33150080
Implementation of homology based and non-homology based computational methods for the identification and annotation of orphan enzymes: using Mycobacterium tuberculosis H37Rv as a case study. PMID:33076816
RBUD: A New Functional Potential Analysis Approach for Whole Microbial Genome Shotgun Sequencing. PMID:33050530
Seascape genomics as a new tool to empower coral reef conservation strategies: An example on north-western Pacific Acropora digitifera. PMID:32908595
The Transcriptomic Landscape of Cupriavidus metallidurans CH34 Acutely Exposed to Copper. PMID:32899882
An Overview of Duplicated Gene Detection Methods: Why the Duplication Mechanism Has to Be Accounted for in Their Choice. PMID:32899740
The Acidic Stress Response of the Intracellular Pathogen Brucella melitensis: New Insights from a Comparative, Genome-Wide Transcriptome Analysis. PMID:32872264
Reconstruction of time-consistent species trees. PMID:32843891
Composition and Metabolic Functions of the Microbiome in Fermented Grain during Light-Flavor Baijiu Fermentation. PMID:32842618
Gene expression profile analysis on different stages of hypertrophic scarring in a rabbit ear model. PMID:32742383
Mapping the Efficacy and Mode of Action of Ethylzingerone [4-(3-Ethoxy-4-Hydroxyphenyl) Butan-2-One] as an Active Agent against Burkholderia Bacteria. PMID:32737133
Spatial and morphological reorganization of endosymbiosis during metamorphosis accommodates adult metabolic requirements in a weevil. PMID:32723830
Plasmid-Encoded blaNDM-5 Gene That Confers High-Level Carbapenem Resistance in Salmonella Typhimurium of Pork Origin. PMID:32547117
Effects of an external magnetic field on microbial functional genes and metabolism of activated sludge based on metagenomic sequencing. PMID:32483239
The lasting after-effects of an ancient polyploidy on the genomes of teleosts. PMID:32298330
Phylogenomic Insights into Diversity and Evolution of Nonpathogenic Xanthomonas Strains Associated with Citrus. PMID:32295869
Development of a workflow for identification of nuclear genotyping markers for Cyclospora cayetanensis. PMID:32275020
Description of Virulent Factors and Horizontal Gene Transfers of Keratitis-Associated Amoeba Acanthamoeba Triangularis by Genome Analysis. PMID:32188120
Phylogenomics of Rhodocyclales and its distribution in wastewater treatment systems. PMID:32127605
Longitudinal survey of microbiome associated with particulate matter in a megacity. PMID:32127018
Extensive Genomic Rearrangements along with Distinct Mobilome and TALome are Associated with Extreme Pathotypes of a Rice Pathogen. PMID:32031614
Total RNA sequencing reveals multilevel microbial community changes and functional responses to wood ash application in agricultural and forest soil. PMID:32009159
Best match graphs and reconciliation of gene trees with species trees. PMID:32002659
Comparative Genomics Analysis of Lactobacillus mucosae from Different Niches. PMID:31947593
Altered gut microbiome composition in patients with Vogt-Koyanagi-Harada disease. PMID:31928124
Combining transcriptomics and metabolomics to reveal the underlying molecular mechanism of ergosterol biosynthesis during the fruiting process of Flammulina velutipes. PMID:31856715
Conjoint Analysis of SMRT- and Illumina-Based RNA-Sequencing Data of Fenneropenaeus chinensis Provides Insight Into Sex-Biased Expression Genes Involved in Sexual Dimorphism. PMID:31803244
PhySpeTree: an automated pipeline for reconstructing phylogenetic species trees. PMID:31791235
Analysis of high-throughput sequencing for cecal microbiota diversity and function in hens under different rearing systems. PMID:31750036
Oral Microbiome Alterations Associated with Early Childhood Caries Highlight the Importance of Carbohydrate Metabolic Activities. PMID:31690590
Domainoid: domain-oriented orthology inference. PMID:31660857
Whole-Genome Sequence of Enterobacter sp. Strain MF024, Isolated from Soil in Shanghai, China. PMID:31515338
Complete genome sequence of Nitratireductor sp. strain OM-1: A lipid-producing bacterium with potential use in wastewater treatment. PMID:31467863
Comparative metagenomic sequencing analysis of cecum microbiotal diversity and function in broilers and layers. PMID:31406638
Complete genome sequence data of Flavobacterium anhuiense strain GSE09, a volatile-producing biocontrol bacterium isolated from cucumber (Cucumis sativus) root. PMID:31388522
Whole genome sequencing revealed microbiome in lung adenocarcinomas presented as ground-glass nodules. PMID:31367537
Metabolic traits specific for lipid-overproducing strain of Mucor circinelloides WJ11 identified by genome-scale modeling approach. PMID:31316868
De novo genome assembly of the endangered Acer yangbiense, a plant species with extremely small populations endemic to Yunnan Province, China. PMID:31307060
The human gallbladder microbiome is related to the physiological state and the biliary metabolic profile. PMID:31272480
Metagenomic analysis of bile salt biotransformation in the human gut microbiome. PMID:31234773
Chemosensory Gene Families in the Oligophagous Pear Pest Cacopsylla chinensis (Hemiptera: Psyllidae). PMID:31212973
Comparing time series transcriptome data between plants using a network module finding algorithm. PMID:31164912
Tree reconciliation combined with subsampling improves large scale inference of orthologous group hierarchies. PMID:31060495
Application of a Dual Internally Quenched Fluorogenic Substrate in Screening for D-Arginine Specific Proteases. PMID:31001242
Sunbeam: an extensible pipeline for analyzing metagenomic sequencing experiments. PMID:30902113
Oral administration of antibiotics increased the potential mobility of bacterial resistance genes in the gut of the fish Piaractus mesopotamicus. PMID:30773139
Genomic insights from Monoglobus pectinilyticus: a pectin-degrading specialist bacterium in the human colon. PMID:30728469
Marine biofilms constitute a bank of hidden microbial diversity and functional potential. PMID:30705275
eggNOG 5.0: a hierarchical, functionally and phylogenetically annotated orthology resource based on 5090 organisms and 2502 viruses. PMID:30418610
Comparative Genomics of Degradative Novosphingobium Strains With Special Reference to Microcystin-Degrading Novosphingobium sp. THN1. PMID:30319567
Comparison of intestinal microbes in female and male Chinese concave-eared frogs (Odorrana tormota) and effect of nematode infection on gut bacterial communities. PMID:30311422
A metagenomic study of the gut microbiome in Behcet's disease. PMID:30077182
Toward Reducing Phylostratigraphic Errors and Biases. PMID:30060201
A plant diterpene counteracts juvenile hormone-mediated gene regulation during Drosophila melanogaster larval development. PMID:30011330
Functional Microbial Features Driving Community Assembly During Seed Germination and Emergence. PMID:30008730
Identification of Antifungal Targets Based on Computer Modeling. PMID:29973534
Complete Genome Sequence of Multiple-Antibiotic-Resistant Streptococcus parauberis Strain SPOF3K, Isolated from Diseased Olive Flounder (Paralichthys olivaceus). PMID:29700142
Inorganic Polyphosphate Is Essential for Salmonella Typhimurium Virulence and Survival in Dictyostelium discoideum. PMID:29441327
Linking pangenomes and metagenomes: the Prochlorococcus metapangenome. PMID:29423345
Synima: a Synteny imaging tool for annotated genome assemblies. PMID:29162056
Two Cycloartenol Synthases for Phytosterol Biosynthesis in Polygala tenuifolia Willd. PMID:29140303
MMseqs2 enables sensitive protein sequence searching for the analysis of massive data sets. PMID:29035372
Transcriptome sequencing and annotation of the halophytic microalga Dunaliella salina. PMID:28990374
Microbial genome analysis: the COG approach. PMID:28968633
RNA Sequencing and Co-expressed Long Non-coding RNA in Modern and Wild Wheats. PMID:28878329
Orthonome - a new pipeline for predicting high quality orthologue gene sets applicable to complete and draft genomes. PMID:28859620
Genome Sequencing Reveals the Potential of Achromobacter sp. HZ01 for Bioremediation. PMID:28848520
Capturing protein communities by structural proteomics in a thermophilic eukaryote. PMID:28743795
Molecular and genomic features of Mycobacterium bovis strain 1595 isolated from Korean cattle. PMID:28385004
FcRav2, a gene with a ROGDI domain involved in Fusarium head blight and crown rot on durum wheat caused by Fusarium culmorum. PMID:28322011
Ordered orthology as a tool in prokaryotic evolutionary inference. PMID:28090377
Fused Regression for Multi-source Gene Regulatory Network Inference. PMID:27923054
Diversity of Gut Microbiota Metabolic Pathways in 10 Pairs of Chinese Infant Twins. PMID:27583441
Metagenomic Reconstruction of Key Anaerobic Digestion Pathways in Municipal Sludge and Industrial Wastewater Biogas-Producing Systems. PMID:27252693
Standardized benchmarking in the quest for orthologs. PMID:27043882
Inferring Orthologs: Open Questions and Perspectives. PMID:26966373
Ortholog-Finder: A Tool for Constructing an Ortholog Data Set. PMID:26782935
MycoBASE: expanding the functional annotation coverage of mycobacterial genomes. PMID:26704706
Whole-Genome Sequence of Mycobacterium bovis W-1171, Isolated from the Laryngopharyngeal Lymph Node of a Wild Boar in South Korea. PMID:26659693
eggNOG 4.5: a hierarchical orthology framework with improved functional annotations for eukaryotic, prokaryotic and viral sequences. PMID:26582926
Yeast Interspecies Comparative Proteomics Reveals Divergence in Expression Profiles and Provides Insights into Proteome Resource Allocation and Evolutionary Roles of Gene Duplication. PMID:26560065
Systematic discovery of linear binding motifs targeting an ancient protein interaction surface on MAP kinases. PMID:26538579
A catalog of the mouse gut metagenome. PMID:26414350
OrthoFinder: solving fundamental biases in whole genome comparisons dramatically improves orthogroup inference accuracy. PMID:26243257
Production of poly(3-hydroxybutyrate) by Halomonas boliviensis in an air-lift reactor. PMID:26236692
Lengths of Orthologous Prokaryotic Proteins Are Affected by Evolutionary Factors. PMID:26114113
The genomes of closely related Pantoea ananatis maize seed endophytes having different effects on the host plant differ in secretion system genes and mobile genetic elements. PMID:26029184
Inter-individual differences in the gene content of human gut bacterial species. PMID:25896518
Construction of an ortholog database using the semantic web technology for integrative analysis of genomic data. PMID:25875762
Comparison of sister species identifies factors underpinning plastid compatibility in green sea slugs. PMID:25652835
De novo assembly, transcriptome characterization, lignin accumulation, and anatomic characteristics: novel insights into lignin biosynthesis during celery leaf development. PMID:25651889
An integrated approach for genome annotation of the eukaryotic thermophile Chaetomium thermophilum. PMID:25398899
Optimizing high performance computing workflow for protein functional annotation. PMID:25313296
Orthology detection combining clustering and synteny for very large datasets. PMID:25137074
morFeus: a web-based program to detect remotely conserved orthologs using symmetrical best hits and orthology network scoring. PMID:25096057
Fast and sensitive alignment of microbial whole genome sequencing reads to large sequence datasets on a desktop PC: application to metagenomic datasets and pathogen identification. PMID:25077800
Coiled-coil proteins facilitated the functional expansion of the centrosome. PMID:24901223
Improvement of domain-level ortholog clustering by optimizing domain-specific sum-of-pairs score. PMID:24885064
Genome sequence of Ensifer adhaerens OV14 provides insights into its ability as a novel vector for the genetic transformation of plant genomes. PMID:24708309
Abnormal fecal microbiota community and functions in patients with hepatitis B liver cirrhosis as revealed by a metagenomic approach. PMID:24369878
eggNOG v4.0: nested orthology inference across 3686 organisms. PMID:24297252
Comprehensive discovery and characterization of small RNAs in Corynebacterium glutamicum ATCC 13032. PMID:24138339
A new method for extracting skin microbes allows metagenomic analysis of whole-deep skin. PMID:24073227
Richness of human gut microbiome correlates with metabolic markers. PMID:23985870
Accurate and universal delineation of prokaryotic species. PMID:23892899
The evolutionary dynamics of protein-protein interaction networks inferred from the reconstruction of ancient networks. PMID:23526967
Updated clusters of orthologous genes for Archaea: a complex ancestor of the Archaea and the byways of horizontal gene transfer. PMID:23241446
OrtholugeDB: a bacterial and archaeal orthology resource for improved comparative genomic analysis. PMID:23203876
The ac53, ac78, ac101, and ac103 genes are newly discovered core genes in the family Baculoviridae. PMID:22933288
Millimeter-scale patterns of phylogenetic and trait diversity in a salt marsh microbial mat. PMID:22908010
QuartetS-DB: a large-scale orthology database for prokaryotes and eukaryotes inferred by evolutionary evidence. PMID:22726705
Evolutionary patterns of carbohydrate transport and metabolism in Halomonas boliviensis as derived from its genome sequence: influences on polyester production. PMID:22510370
Genome-wide comparative analysis of phylogenetic trees: the prokaryotic forest of life. PMID:22399455
The human small intestinal microbiota is driven by rapid uptake and conversion of simple carbohydrates. PMID:22258098
Dissecting plant genomes with the PLAZA comparative genomics platform. PMID:22198273
Large scale in silico identification of MYB family genes from wheat expressed sequence tags. PMID:22187170
Calculating orthologs in bacteria and Archaea: a divide and conquer approach. PMID:22174796
Identifying single copy orthologs in Metazoa. PMID:22144877
eggNOG v3.0: orthologous groups covering 1133 organisms at 41 different taxonomic ranges. PMID:22096231
Plasmid metagenome reveals high levels of antibiotic resistance genes and mobile genetic elements in activated sludge. PMID:22016806
Orthology prediction methods: a quality assessment using curated protein families. PMID:21853451
Ortholog identification in the presence of domain architecture rearrangement. PMID:21712343
Computational methods for Gene Orthology inference. PMID:21690100
RAPSearch: a fast protein similarity search tool for short reads. PMID:21575167
Processes of fungal proteome evolution and gain of function: gene duplication and domain rearrangement. PMID:21572172
Proteinortho: detection of (co-)orthologs in large-scale analysis. PMID:21526987
Modification of gene duplicability during the evolution of protein interaction network. PMID:21490719
The tree and net components of prokaryote evolution. PMID:20889655
Relative contributions of intrinsic structural-functional constraints and translation rate to the evolution of protein-coding genes. PMID:20624725
PROFESS: a PROtein function, evolution, structure and sequence database. PMID:20624718
Orthology confers intron position conservation. PMID:20598118
A low-polynomial algorithm for assembling clusters of orthologous groups from intergenomic symmetric best matches. PMID:20439257
Transcriptional response of Rhodococcus aetherivorans I24 to polychlorinated biphenyl-contaminated sediments. PMID:20369357
Getting started in gene orthology and functional analysis. PMID:20361041
A human gut microbial gene catalogue established by metagenomic sequencing. PMID:20203603
GeMMA: functional subfamily classification within superfamilies of predicted protein structural domains. PMID:19923231
MBGD update 2010: toward a comprehensive resource for exploring microbial genome diversity. PMID:19906735
Network of Cancer Genes: a web resource to analyze duplicability, orthology and network properties of cancer genes. PMID:19906700
Gene3D: merging structure and function for a Thousand genomes. PMID:19906693
eggNOG v2.0: extending the evolutionary genealogy of genes with enhanced non-supervised orthologous groups, species and functional annotations. PMID:19900971
Combined genomic and proteomic approaches identify gene clusters involved in anaerobic 2-methylnaphthalene degradation in the sulfate-reducing enrichment culture N47. PMID:19854898
Joining forces in the quest for orthologs. PMID:19785718
The phylogenetic forest and the quest for the elusive tree of life. PMID:19687142
Search for a 'Tree of Life' in the thicket of the phylogenetic forest. PMID:19594957
Functional equivalency inferred from "authoritative sources" in networks of homologous proteins. PMID:19521530
EDGAR: a software framework for the comparative analysis of prokaryotic genomes. PMID:19457249
Berkeley PHOG: PhyloFacts orthology group prediction web server. PMID:19435885
Sequence-based prediction of type III secreted proteins. PMID:19390696
Phylogenetic and functional assessment of orthologs inference projects and methods. PMID:19148271
Algorithm of OMA for large-scale orthology inference. PMID:19055798
Genomics of bacteria and archaea: the emerging dynamic view of the prokaryotic world. PMID:18948295
STRING 8--a global view on proteins and their functional interactions in 630 organisms. PMID:18940858
Complete genome sequence of the extremely acidophilic methanotroph isolate V4, Methylacidiphilum infernorum, a representative of the bacterial phylum Verrucomicrobia. PMID:18593465
Exploring the structure and function paradigm. PMID:18554899
Clusters of orthologous genes for 41 archaeal genomes and implications for evolutionary genomics of archaea. PMID:18042280
The Molecular Biology Database Collection: 2008 update. PMID:18025043 -
eggNOG v2.0: extending the evolutionary genealogy of genes with enhanced non-supervised orthologous groups, species and functional annotations
PubMed citations: 119.
119 articles citing: eggNOG v2.0: extending the evolutionary genealogy of genes with enhanced non-supervised orthologous groups, species and functional annotations
Integrating cultivation and metagenomics for a multi-kingdom view of skin microbiome diversity and functions. PMID:34952941
Phosphoproteome analysis reveals the involvement of protein dephosphorylation in ethylene-induced corolla senescence in petunia. PMID:34732145
Genome sequence and transcriptome profiles of pathogenic fungus Paecilomyces penicillatus reveal its interactions with edible fungus Morchella importuna. PMID:34025947
Vegetative cells may perform nitrogen fixation function under nitrogen deprivation in Anabaena sp. strain PCC 7120 based on genome-wide differential expression analysis. PMID:33662009
Metagenomics survey unravels diversity of biogas microbiomes with potential to enhance productivity in Kenya. PMID:33395690
Molecular Mechanism of Tumor Cell Immune Escape Mediated by CD24/Siglec-10. PMID:32765491
Trait-based analysis of the human skin microbiome. PMID:31277701
Temporal Analysis of the Microbial Community from the Crystallizer Ponds in Cabo Rojo, Puerto Rico, Using Metagenomics. PMID:31159288
Chalcone synthase is ubiquitinated and degraded via interactions with a RING-H2 protein in petals of Paeonia 'He Xie'. PMID:31106836
Evolution of the Drosophila melanogaster Chromatin Landscape and Its Associated Proteins. PMID:30689829
Efficient inference of homologs in large eukaryotic pan-proteomes. PMID:30257640
The Growth and Protein Expression of Inflammatory Bowel Disease-Associated Campylobacter concisus Is Affected by the Derivatives of the Food Additive Fumaric Acid. PMID:29867807
Surveying alignment-free features for Ortholog detection in related yeast proteomes by using supervised big data classifiers. PMID:29724166
Searching for signatures across microbial communities: Metagenomic analysis of soil samples from mangrove and other ecosystems. PMID:28821820
Workflow and web application for annotating NCBI BioProject transcriptome data. PMID:28605765
Transcriptome Sequencing of Gynostemma pentaphyllum to Identify Genes and Enzymes Involved in Triterpenoid Biosynthesis. PMID:28097124
Proteomes and Ubiquitylomes Analysis Reveals the Involvement of Ubiquitination in Protein Degradation in Petunias. PMID:27810942
Characterization of Microbial Mat Microbiomes in the Modern Thrombolite Ecosystem of Lake Clifton, Western Australia Using Shotgun Metagenomics. PMID:27458453
A High-resolution Typing Assay for Uropathogenic Escherichia coli Based on Fimbrial Diversity. PMID:27199951
The Pangenome of the Anticarsia gemmatalis Multiple Nucleopolyhedrovirus (AgMNPV). PMID:26615220
An Effective Big Data Supervised Imbalanced Classification Approach for Ortholog Detection in Related Yeast Species. PMID:26605337
Prediction of microbial phenotypes based on comparative genomics. PMID:26451672
The Diversity and Co-occurrence Patterns of N₂-Fixing Communities in a CO₂-Enriched Grassland Ecosystem. PMID:26280746
Predicting and exploring network components involved in pathogenesis in the malaria parasite via novel subnetwork alignments. PMID:26100579
Discovery of new protein families and functions: new challenges in functional metagenomics for biotechnologies and microbial ecology. PMID:26097471
ProtPhylo: identification of protein-phenotype and protein-protein functional associations via phylogenetic profiling. PMID:25956654
Insights from the metagenome of an acid salt lake: the role of biology in an extreme depositional environment. PMID:25923206
Impacts of the Three Gorges Dam on microbial structure and potential function. PMID:25721383
Whole-genome sequencing of the snub-nosed monkey provides insights into folivory and evolutionary history. PMID:25362486
Deep Illumina-based shotgun sequencing reveals dietary effects on the structure and function of the fecal microbiome of growing kittens. PMID:25010839
Core microbial functional activities in ocean environments revealed by global metagenomic profiling analyses. PMID:24921648
Think globally and solve locally: secondary memory-based network learning for automated multi-species function prediction. PMID:24843788
Genomic analysis of Chthonomonas calidirosea, the first sequenced isolate of the phylum Armatimonadetes. PMID:24477196
Microbial stratification in low pH oxic and suboxic macroscopic growths along an acid mine drainage. PMID:24430486
Phylogenetic relationship and virulence inference of Streptococcus Anginosus Group: curated annotation and whole-genome comparative analysis support distinct species designation. PMID:24341328
eggNOG v4.0: nested orthology inference across 3686 organisms. PMID:24297252
A novel subnetwork alignment approach predicts new components of the cell cycle regulatory apparatus in Plasmodium falciparum. PMID:24267797
A negative genetic interaction map in isogenic cancer cell lines reveals cancer cell vulnerabilities. PMID:24104479
WormBase: Annotating many nematode genomes. PMID:24058818
Metagenomic insights into metabolic capacities of the gut microbiota in a fungus-cultivating termite (Odontotermes yunnanensis). PMID:23874908
Neutral genomic microevolution of a recently emerged pathogen, Salmonella enterica serovar Agona. PMID:23637636
CRISPR-Cas systems target a diverse collection of invasive mobile genetic elements in human microbiomes. PMID:23628424
The evolutionary dynamics of protein-protein interaction networks inferred from the reconstruction of ancient networks. PMID:23526967
Protein function prediction by massive integration of evolutionary analyses and multiple data sources. PMID:23514099
The Eimeria transcript DB: an integrated resource for annotated transcripts of protozoan parasites of the genus Eimeria. PMID:23411718
Distinct protein classes in human red cell proteome revealed by similarity of phylogenetic profiles. PMID:23349899
Consistent mutational paths predict eukaryotic thermostability. PMID:23305080
Chapter 12: Human microbiome analysis. PMID:23300406
Module-based subnetwork alignments reveal novel transcriptional regulators in malaria parasite Plasmodium falciparum. PMID:23282319
Genomic variation landscape of the human gut microbiome. PMID:23222524
Integrated metagenomics/metaproteomics reveals human host-microbiota signatures of Crohn's disease. PMID:23209564
PTMcode: a database of known and predicted functional associations between post-translational modifications in proteins. PMID:23193284
Evolutionary rate and duplicability in the Arabidopsis thaliana protein-protein interaction network. PMID:23160177
Evolutionary force in confamiliar marine vertebrates of different temperature realms: adaptive trends in zoarcid fish transcriptomes. PMID:23051706
A comparative analysis of the intestinal metagenomes present in guinea pigs (Cavia porcellus) and humans (Homo sapiens). PMID:23020652
Metagenomic analysis reveals a functional signature for biomass degradation by cecal microbiota in the leaf-eating flying squirrel (Petaurista alborufus lena). PMID:22963241
Uncovering the co-evolutionary network among prokaryotic genes. PMID:22962457
Complete genome sequence of the naphthalene-degrading Pseudomonas putida strain ND6. PMID:22933774
Meta-analysis of general bacterial subclades in whole-genome phylogenies using tree topology profiling. PMID:22915837
Proteome-wide analysis of lysine acetylation suggests its broad regulatory scope in Saccharomyces cerevisiae. PMID:22865919
Multiple independent analyses reveal only transcription factors as an enriched functional class associated with microRNAs. PMID:22824421
Deciphering a global network of functionally associated post-translational modifications. PMID:22806145
Tissue-enriched expression profiles in Aedes aegypti identify hemocyte-specific transcriptome responses to infection. PMID:22796331
Gene duplications contribute to the overrepresentation of interactions between proteins of a similar age. PMID:22732003
QuartetS-DB: a large-scale orthology database for prokaryotes and eukaryotes inferred by evolutionary evidence. PMID:22726705
The M5nr: a novel non-redundant database containing protein sequences and annotations from multiple sources and associated tools. PMID:22720753
A framework for human microbiome research. PMID:22699610
Oral spirochetes implicated in dental diseases are widespread in normal human subjects and carry extremely diverse integron gene cassettes. PMID:22635997
Metagenomics - a guide from sampling to data analysis. PMID:22587947
Predicted Relative Metabolomic Turnover (PRMT): determining metabolic turnover from a coastal marine metagenomic dataset. PMID:22587810
Complete genome sequence of Paenibacillus mucilaginosus 3016, a bacterium functional as microbial fertilizer. PMID:22535950
PaxDb, a database of protein abundance averages across all three domains of life. PMID:22535208
Annotation of the M. tuberculosis hypothetical orfeome: adding functional information to more than half of the uncharacterized proteins. PMID:22485162
Revealing mammalian evolutionary relationships by comparative analysis of gene clusters. PMID:22454131
Evolution of the voltage sensor domain of the voltage-sensitive phosphoinositide phosphatase VSP/TPTE suggests a role as a proton channel in eutherian mammals. PMID:22396523
Assessment of metagenomic assembly using simulated next generation sequencing data. PMID:22384016
Cross-talk between phosphorylation and lysine acetylation in a genome-reduced bacterium. PMID:22373819
Protease-associated cellular networks in malaria parasite Plasmodium falciparum. PMID:22369208
Preimplantation development regulatory pathway construction through a text-mining approach. PMID:22369103
Reconstruction of oomycete genome evolution identifies differences in evolutionary trajectories leading to present-day large gene families. PMID:22230142
A vector space model approach to identify genetically related diseases. PMID:22227640
Evolution of biological interaction networks: from models to real data. PMID:22204388
Experimental and analytical tools for studying the human microbiome. PMID:22179717
MOPED: Model Organism Protein Expression Database. PMID:22139914
eggNOG v3.0: orthologous groups covering 1133 organisms at 41 different taxonomic ranges. PMID:22096231
Network of Cancer Genes (NCG 3.0): integration and analysis of genetic and network properties of cancer genes. PMID:22080562
OGEE: an online gene essentiality database. PMID:22075992
WormBase 2012: more genomes, more data, new website. PMID:22067452
Resources and costs for microbial sequence analysis evaluated using virtual machines and cloud computing. PMID:22028928
Voltage-gated proton channel in a dinoflagellate. PMID:22006335
Sequence-structure relationships in yeast mRNAs. PMID:21954438
A detailed history of intron-rich eukaryotic ancestors inferred from a global survey of 100 complete genomes. PMID:21935348
IONS: Identification of Orthologs by Neighborhood and Similarity-an Automated Method to Identify Orthologs in Chromosomal Regions of Common Evolutionary Ancestry and its Application to Hemiascomycetous Yeasts. PMID:21918595
Computational approaches to selecting and optimising targets for structural biology. PMID:21906678
A proteome-wide, quantitative survey of in vivo ubiquitylation sites reveals widespread regulatory roles. PMID:21890473
Orthology prediction methods: a quality assessment using curated protein families. PMID:21853451
Conceptual framework and pilot study to benchmark phylogenomic databases based on reference gene trees. PMID:21737420
Telling the whole story in a 10,000-genome world. PMID:21714939
Computational methods for Gene Orthology inference. PMID:21690100
Going deeper: metagenome of a hadopelagic microbial community. PMID:21629664
Inferring functional modules of protein families with probabilistic topic models. PMID:21554720
iPath2.0: interactive pathway explorer. PMID:21546551
Enterotypes of the human gut microbiome. PMID:21508958
Bacterial protein structures reveal phylum dependent divergence. PMID:21315656
Comparative and joint analysis of two metagenomic datasets from a biogas fermenter obtained by 454-pyrosequencing. PMID:21297863
Searching the protein structure database for ligand-binding site similarities using CPASS v.2. PMID:21269480
OrthoInspector: comprehensive orthology analysis and visual exploration. PMID:21219603
MetaPhOrs: orthology and paralogy predictions from multiple phylogenetic evidence using a consistency-based confidence score. PMID:21149260
Perturbation of the yeast N-acetyltransferase NatB induces elevation of protein phosphorylation levels. PMID:21126336
OMA 2011: orthology inference among 1000 complete genomes. PMID:21113020
DIMA 3.0: Domain Interaction Map. PMID:21097782
PhylomeDB v3.0: an expanding repository of genome-wide collections of trees, alignments and phylogeny-based orthology and paralogy predictions. PMID:21075798
Effective--a database of predicted secreted bacterial proteins. PMID:21071416
Genes optimized by evolution for accurate and fast translation encode in Archaea and Bacteria a broad and characteristic spectrum of protein functions. PMID:21050470
The STRING database in 2011: functional interaction networks of proteins, globally integrated and scored. PMID:21045058
OrthoDB: the hierarchical catalog of eukaryotic orthologs in 2011. PMID:20972218
A blueprint of ectoine metabolism from the genome of the industrial producer Halomonas elongata DSM 2581 T. PMID:20849449
PROFESS: a PROtein function, evolution, structure and sequence database. PMID:20624718
Cyclebase.org: version 2.0, an updated comprehensive, multi-species repository of cell cycle experiments and derived analysis results. PMID:19934261 - http://dx.doi.org/10.1093/nar/gkt1253
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annotation
metasource: Fairsharing.org
version: FAIRsharing.org: eggNOG; Evolutionary Genealogy of Genes: Non-supervised Orthologous Groups; DOI: https://doi.org/10.25504/FAIRsharing.j1wj7d; Last edited: Jan. 8, 2019, 1:13 p.m.; Last accessed: Jan 03 2022 7:07 p.m.
gene
metasource: Fairsharing.org
version: FAIRsharing.org: eggNOG; Evolutionary Genealogy of Genes: Non-supervised Orthologous Groups; DOI: https://doi.org/10.25504/FAIRsharing.j1wj7d; Last edited: Jan. 8, 2019, 1:13 p.m.; Last accessed: Jan 03 2022 7:07 p.m.
multiple sequence alignment
metasource: Fairsharing.org
version: FAIRsharing.org: eggNOG; Evolutionary Genealogy of Genes: Non-supervised Orthologous Groups; DOI: https://doi.org/10.25504/FAIRsharing.j1wj7d; Last edited: Jan. 8, 2019, 1:13 p.m.; Last accessed: Jan 03 2022 7:07 p.m.
orthologous
metasource: Fairsharing.org
version: FAIRsharing.org: eggNOG; Evolutionary Genealogy of Genes: Non-supervised Orthologous Groups; DOI: https://doi.org/10.25504/FAIRsharing.j1wj7d; Last edited: Jan. 8, 2019, 1:13 p.m.; Last accessed: Jan 03 2022 7:07 p.m.
protein sequence databases
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657
protein domain databases; protein classification
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657
metagenomics
metasource: bio.tools
version: extracted_at: 2022-11-04T11:29:55.005995
genomics
metasource: bio.tools
version: extracted_at: 2022-11-04T11:29:55.005995
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annotation
metasource: Fairsharing.orgversion: FAIRsharing.org: eggNOG; Evolutionary Genealogy of Genes: Non-supervised Orthologous Groups; DOI: https://doi.org/10.25504/FAIRsharing.j1wj7d; Last edited: Jan. 8, 2019, 1:13 p.m.; Last accessed: Jan 03 2022 7:07 p.m.
gene
metasource: Fairsharing.orgversion: FAIRsharing.org: eggNOG; Evolutionary Genealogy of Genes: Non-supervised Orthologous Groups; DOI: https://doi.org/10.25504/FAIRsharing.j1wj7d; Last edited: Jan. 8, 2019, 1:13 p.m.; Last accessed: Jan 03 2022 7:07 p.m.
multiple sequence alignment
metasource: Fairsharing.orgversion: FAIRsharing.org: eggNOG; Evolutionary Genealogy of Genes: Non-supervised Orthologous Groups; DOI: https://doi.org/10.25504/FAIRsharing.j1wj7d; Last edited: Jan. 8, 2019, 1:13 p.m.; Last accessed: Jan 03 2022 7:07 p.m.
orthologous
metasource: Fairsharing.orgversion: FAIRsharing.org: eggNOG; Evolutionary Genealogy of Genes: Non-supervised Orthologous Groups; DOI: https://doi.org/10.25504/FAIRsharing.j1wj7d; Last edited: Jan. 8, 2019, 1:13 p.m.; Last accessed: Jan 03 2022 7:07 p.m.
protein sequence databases
metasource: Nucleic Acid Research database catalogueversion: extracted_at: 2022-11-04T11:16:25.468657
protein domain databases; protein classification
metasource: Nucleic Acid Research database catalogueversion: extracted_at: 2022-11-04T11:16:25.468657
metagenomics
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:29:55.005995
genomics
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:29:55.005995
gene multiple sequence alignment orthology protein sequence protein domains and classification metagenomics genomics
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