FAIRsharing.62evqh; Last edited: Feb. 13, 2020, 2:46 p.m.; Last accessed: Jan 03 2022 7:06 p.m.

metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657

metasource: bio.tools
version: extracted_at: 2022-11-04T11:29:57.269498

nextprot
metasource: bio.tools
version: extracted_at: 2022-11-04T11:29:57.269498

Other names: nextprot

neXtProt is a comprehensive human-centric discovery platform, offering its users a seamless integration of and navigation through protein-related data.

Webpage:

https://www.nextprot.org

Licence:

Name: NextProt Data Policies and Disclaimer
URL: https://www.nextprot.org/legal-disclaimer/

Publications: (6)

Publications
More detailed information about this field from each metasource.

The neXtProt knowledgebase on human proteins: 2017 update
PMID: 27899619
metasource: Fairsharing.org
version: FAIRsharing.org: neXtProt; neXtProt; DOI: https://doi.org/10.25504/FAIRsharing.62evqh; Last edited: Feb. 13, 2020, 2:46 p.m.; Last accessed: Jan 03 2022 7:06 p.m.

neXtProt: a knowledge platform for human proteins
PMID: 22139911
metasource: Fairsharing.org
version: FAIRsharing.org: neXtProt; neXtProt; DOI: https://doi.org/10.25504/FAIRsharing.62evqh; Last edited: Feb. 13, 2020, 2:46 p.m.; Last accessed: Jan 03 2022 7:06 p.m.

metasource: bio.tools
version: extracted_at: 2022-11-04T11:29:57.269498

The neXtProt knowledgebase in 2020: data, tools and usability improvements
PMID: 31724716
metasource: Fairsharing.org
version: FAIRsharing.org: neXtProt; neXtProt; DOI: https://doi.org/10.25504/FAIRsharing.62evqh; Last edited: Feb. 13, 2020, 2:46 p.m.; Last accessed: Jan 03 2022 7:06 p.m.

metasource: bio.tools
version: extracted_at: 2022-11-04T11:29:57.269498

The neXtProt knowledgebase on human proteins: current status
PMID: 25593349
metasource: Fairsharing.org
version: FAIRsharing.org: neXtProt; neXtProt; DOI: https://doi.org/10.25504/FAIRsharing.62evqh; Last edited: Feb. 13, 2020, 2:46 p.m.; Last accessed: Jan 03 2022 7:06 p.m.

neXtProt: organizing protein knowledge in the context of human proteome projects
PMID: 23205526
metasource: Fairsharing.org
version: FAIRsharing.org: neXtProt; neXtProt; DOI: https://doi.org/10.25504/FAIRsharing.62evqh; Last edited: Feb. 13, 2020, 2:46 p.m.; Last accessed: Jan 03 2022 7:06 p.m.

http://dx.doi.org/10.1093/nar/gkz995
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657

The neXtProt knowledgebase on human proteins: 2017 update PubMed citations: 70.

70 articles citing: The neXtProt knowledgebase on human proteins: 2017 update

Variomes: a high recall search engine to support the curation of genomic variants. PMID:35274687
The methyltransferase METTL3 negatively regulates nonalcoholic steatohepatitis (NASH) progression. PMID:34893641
Prediction of Peptide Detectability Based on CapsNet and Convolutional Block Attention Module. PMID:34769509
SmProt: A Reliable Repository with Comprehensive Annotation of Small Proteins Identified from Ribosome Profiling. PMID:34536568
Multiomic Analyses of Dopaminergic Neurons Isolated from Human Substantia Nigra in Parkinson's Disease: A Descriptive and Exploratory Study. PMID:34528139
Toward a Coronavirus Knowledge Graph. PMID:34209818
The Y Chromosome: A Complex Locus for Genetic Analyses of Complex Human Traits. PMID:33137877
The Dynamic Proteome of Oligodendrocyte Lineage Differentiation Features Planar Cell Polarity and Macroautophagy Pathways. PMID:33128372
A high-stringency blueprint of the human proteome. PMID:33067450
Quality Matters: Biocuration Experts on the Impact of Duplication and Other Data Quality Issues in Biological Databases. PMID:32652120
Predicting Functions of Uncharacterized Human Proteins: From Canonical to Proteoforms. PMID:32575886
Progress, Challenges, and Surprises in Annotating the Human Genome. PMID:32421357
RESTful API for iPTMnet: a resource for protein post-translational modification network discovery. PMID:32395768
SIB Literature Services: RESTful customizable search engines in biomedical literature, enriched with automatically mapped biomedical concepts. PMID:32379317
Exploring the HeLa Dark Mitochondrial Proteome. PMID:32195257
Exploration of databases and methods supporting drug repurposing: a comprehensive survey. PMID:32055842
Population-specific, recent positive directional selection suggests adaptation of human male reproductive genes to different environmental conditions. PMID:32054438
The landscape of chimeric RNAs in non-diseased tissues and cells. PMID:31965184
Beyond mass spectrometry, the next step in proteomics. PMID:31950079
Finding the Keys to the CAR: Identifying Novel Target Antigens for T Cell Redirection Immunotherapies. PMID:31947597
Natural and pathogenic protein sequence variation affecting prion-like domains within and across human proteomes. PMID:31914925
A Perspective on the Confident Comparison of Glycoprotein Site-Specific Glycosylation in Sample Cohorts. PMID:31833756
Proteomics: a powerful tool to study plant responses to biotic stress. PMID:31832077
The neXtProt knowledgebase in 2020: data, tools and usability improvements. PMID:31724716
The ProteomeXchange consortium in 2020: enabling 'big data' approaches in proteomics. PMID:31686107
ChlamDB: a comparative genomics database of the phylum Chlamydiae and other members of the Planctomycetes-Verrucomicrobiae-Chlamydiae superphylum. PMID:31665454
Blinded Testing of Function Annotation for uPE1 Proteins by I-TASSER/COFACTOR Pipeline Using the 2018-2019 Additions to neXtProt and the CAFA3 Challenge. PMID:31581775
Discovery of high-confidence human protein-coding genes and exons by whole-genome PhyloCSF helps elucidate 118 GWAS loci. PMID:31537640
Progress on Identifying and Characterizing the Human Proteome: 2019 Metrics from the HUPO Human Proteome Project. PMID:31430157
The project MinE databrowser: bringing large-scale whole-genome sequencing in ALS to researchers and the public. PMID:31280677
PRECOG: PREdicting COupling probabilities of G-protein coupled receptors. PMID:31143927
Proteomics Standards Initiative Extended FASTA Format. PMID:31081335
ProteinExplorer: A Repository-Scale Resource for Exploration of Protein Detection in Public Mass Spectrometry Data Sets. PMID:30985146
Integrated Transcriptomic and Proteomic Analysis of Primary Human Umbilical Vein Endothelial Cells. PMID:30983154
Integrated Transcriptomic and Proteomic Analysis of Human Eccrine Sweat Glands Identifies Missing and Novel Proteins. PMID:30979791
A deep proteome and transcriptome abundance atlas of 29 healthy human tissues. PMID:30777892
HuVarBase: A human variant database with comprehensive information at gene and protein levels. PMID:30703169
Accelerating annotation of articles via automated approaches: evaluation of the neXtA5 curation-support tool by neXtProt. PMID:30576492
ECO, the Evidence & Conclusion Ontology: community standard for evidence information. PMID:30407590
Overview of the BioCreative VI text-mining services for Kinome Curation Track. PMID:30329035
Exhaustive non-synonymous variants functionality prediction enables high resolution characterization of the neurofibromin architecture. PMID:30274822
Launching the C-HPP neXt-CP50 Pilot Project for Functional Characterization of Identified Proteins with No Known Function. PMID:30269496
Structure and Protein Interaction-Based Gene Ontology Annotations Reveal Likely Functions of Uncharacterized Proteins on Human Chromosome 17. PMID:30265558
Identifying High-Priority Proteins Across the Human Diseasome Using Semantic Similarity. PMID:30256117
Fast Open Modification Spectral Library Searching through Approximate Nearest Neighbor Indexing. PMID:30184435
Integrated Dissection of Cysteine Oxidative Post-translational Modification Proteome During Cardiac Hypertrophy. PMID:30141336
PRDM Histone Methyltransferase mRNA Levels Increase in Response to Curative Hormone Treatment for Cryptorchidism-Dependent Male Infertility. PMID:30071651
IDPpi: Protein-Protein Interaction Analyses of Human Intrinsically Disordered Proteins. PMID:30002402
Whole exome sequencing identified two novel homozygous missense variants in the same codon of CLCN7 underlying autosomal recessive infantile malignant osteopetrosis in a Pakistani family. PMID:29926385
A Fast and Quantitative Method for Post-translational Modification and Variant Enabled Mapping of Peptides to Genomes. PMID:29889196
Exploring the mechanistic insights of Cas scaffolding protein family member 4 with protein tyrosine kinase 2 in Alzheimer's disease by evaluating protein interactions through molecular docking and dynamic simulations. PMID:29789968
Integrative annotation and knowledge discovery of kinase post-translational modifications and cancer-associated mutations through federated protein ontologies and resources. PMID:29695735
Loss and gain of N-linked glycosylation sequons due to single-nucleotide variation in cancer. PMID:29531238
Kinases and Cancer. PMID:29494549
How many human proteoforms are there? PMID:29443976
Protein biomarkers for subtyping breast cancer and implications for future research. PMID:29271260
Large Scale Identification of Variant Proteins in Glioma Stem Cells. PMID:29254333
Triage by ranking to support the curation of protein interactions. PMID:29220432
iPTMnet: an integrated resource for protein post-translational modification network discovery. PMID:29145615
An update on sORFs.org: a repository of small ORFs identified by ribosome profiling. PMID:29140531
ProteomicsDB. PMID:29106664
SABIO-RK: an updated resource for manually curated biochemical reaction kinetics. PMID:29092055
Advances in the Chromosome-Centric Human Proteome Project: looking to the future. PMID:29039980
Enhanced Missing Proteins Detection in NCI60 Cell Lines Using an Integrative Search Engine Approach. PMID:28960077
Proteomics Identifies Golgi phosphoprotein 3 (GOLPH3) with A Link Between Golgi Structure, Cancer, DNA Damage and Protection from Cell Death. PMID:28954815
Progress on the HUPO Draft Human Proteome: 2017 Metrics of the Human Proteome Project. PMID:28853897
Elucidating Protein-DNA Interactions in Human Alphoid Chromatin via Hybridization Capture and Mass Spectrometry. PMID:28704058
Last rolls of the yoyo: Assessing the human canonical protein count. PMID:28529709
The neXtProt peptide uniqueness checker: a tool for the proteomics community. PMID:28520855
Annotation of functional impact of voltage-gated sodium channel mutations. PMID:28168870
neXtProt: a knowledge platform for human proteins PubMed citations: 63.

63 articles citing: neXtProt: a knowledge platform for human proteins

Engineered SH2 Domains for Targeted Phosphoproteomics. PMID:35613471
Mass Spectrometry-Based Proteomics Reveal Alcohol Dehydrogenase 1B as a Blood Biomarker Candidate to Monitor Acetaminophen-Induced Liver Injury. PMID:34681731
HBFP: a new repository for human body fluid proteome. PMID:34642750
Proteomic Tools for the Analysis of Cytoskeleton Proteins. PMID:34542864
Biomolecule and Bioentity Interaction Databases in Systems Biology: A Comprehensive Review. PMID:34439912
Reflections on the HUPO Human Proteome Project, the Flagship Project of the Human Proteome Organization, at 10 Years. PMID:33640492
An empirical meta-analysis of the life sciences linked open data on the web. PMID:33479214
A high-stringency blueprint of the human proteome. PMID:33067450
Verification of a Blood-Based Targeted Proteomics Signature for Malignant Pleural Mesothelioma. PMID:32732250
Post-translational Modification Crosstalk and Hotspots in Sirtuin Interactors Implicated in Cardiovascular Diseases. PMID:32425973
Natural and pathogenic protein sequence variation affecting prion-like domains within and across human proteomes. PMID:31914925
Enabling Web-scale data integration in biomedicine through Linked Open Data. PMID:31531395
Predictive proteomic signatures for response of pancreatic cancer patients receiving chemotherapy. PMID:31346328
Laying the foundation for genomically-based risk assessment in chronic myeloid leukemia. PMID:31209280
FusionPro, a Versatile Proteogenomic Tool for Identification of Novel Fusion Transcripts and Their Potential Translation Products in Cancer Cells. PMID:31208993
OsteoporosAtlas: a human osteoporosis-related gene database. PMID:31086734
AllerGAtlas 1.0: a human allergy-related genes database. PMID:29688358
In-Depth Proteomic Characterization of Classical and Non-Classical Monocyte Subsets. PMID:29401756
Confronting the catalytic dark matter encoded by sequenced genomes. PMID:29059321
Upregulation of long non-coding RNA MALAT-1 confers poor prognosis and influences cell proliferation and apoptosis in acute monocytic leukemia. PMID:28713913
A community proposal to integrate proteomics activities in ELIXIR. PMID:28713550
Platelet proteome reveals novel pathways of platelet activation and platelet-mediated immunoregulation in dengue. PMID:28542641
On patterns and re-use in bioinformatics databases. PMID:28525546
Identifying the missing proteins in human proteome by biological language model. PMID:28155671
Accelerating the search for the missing proteins in the human proteome. PMID:28117396
The neXtProt knowledgebase on human proteins: 2017 update. PMID:27899619
The Human Skeletal Muscle Proteome Project: a reappraisal of the current literature. PMID:27897395
Flexible Data Analysis Pipeline for High-Confidence Proteogenomics. PMID:27786492
neXtA5: accelerating annotation of articles via automated approaches in neXtProt. PMID:27374119
The Size of the Human Proteome: The Width and Depth. PMID:27298622
Improving GENCODE reference gene annotation using a high-stringency proteogenomics workflow. PMID:27250503
Enteroviral proteases: structure, host interactions and pathogenicity. PMID:27145174
Exploring the potential of public proteomics data. PMID:26449181
Mining Missing Membrane Proteins by High-pH Reverse-Phase StageTip Fractionation and Multiple Reaction Monitoring Mass Spectrometry. PMID:26202522
Structural Bioinformatics Inspection of neXtProt PE5 Proteins in the Human Proteome. PMID:26193931
The Confidence Information Ontology: a step towards a standard for asserting confidence in annotations. PMID:25957950
Key challenges for the creation and maintenance of specialist protein resources. PMID:25820941
The neXtProt knowledgebase on human proteins: current status. PMID:25593349
Recombinant renewable polyclonal antibodies. PMID:25530082
Proteomics for systems toxicology. PMID:25379146
MALAT1 long non-coding RNA is overexpressed in multiple myeloma and may serve as a marker to predict disease progression. PMID:25369863
Onco-proteogenomics: cancer proteomics joins forces with genomics. PMID:25357240
Cross-talking noncoding RNAs contribute to cell-specific neurodegeneration in SCA7. PMID:25306109
Profiling the mitochondrial proteome of Leber's Hereditary Optic Neuropathy (LHON) in Thailand: down-regulation of bioenergetics and mitochondrial protein quality control pathways in fibroblasts with the 11778G>A mutation. PMID:25215595
Using PeptideAtlas, SRMAtlas, and PASSEL: Comprehensive Resources for Discovery and Targeted Proteomics. PMID:24939129
Network analyses reveal pervasive functional regulation between proteases in the human protease web. PMID:24865846
Integrating omics technologies to study pulmonary physiology and pathology at the systems level. PMID:24802001
The role of quantitative mass spectrometry in the discovery of pancreatic cancer biomarkers for translational science. PMID:24708694
C2orf62 and TTC17 are involved in actin organization and ciliogenesis in zebrafish and human. PMID:24475127
Lysine deacetylase (KDAC) regulatory pathways: an alternative approach to selective modulation. PMID:24449617
The WAVE regulatory complex links diverse receptors to the actin cytoskeleton. PMID:24439376
Protein domains of unknown function are essential in bacteria. PMID:24381303
Analysis of the human tissue-specific expression by genome-wide integration of transcriptomics and antibody-based proteomics. PMID:24309898
Can inferred provenance and its visualisation be used to detect erroneous annotation? A case study using UniProtKB. PMID:24143170
The Enzyme Portal: a case study in applying user-centred design methods in bioinformatics. PMID:23514033
Isobar(PTM): a software tool for the quantitative analysis of post-translationally modified proteins. PMID:23470796
Evidence classification of high-throughput protocols and confidence integration in RegulonDB. PMID:23327937
Identification of HYPK-interacting proteins reveals involvement of HYPK in regulating cell growth, cell cycle, unfolded protein response and cell death. PMID:23272104
A chromosome-centric human proteome project (C-HPP) to characterize the sets of proteins encoded in chromosome 17. PMID:23259914
The PRoteomics IDEntifications (PRIDE) database and associated tools: status in 2013. PMID:23203882
The TissueNet database of human tissue protein-protein interactions. PMID:23193266
Minireview: progress and challenges in proteomics data management, sharing, and integration. PMID:22902541
The 2012 Nucleic Acids Research Database Issue and the online Molecular Biology Database Collection. PMID:22144685
The neXtProt knowledgebase in 2020: data, tools and usability improvements PubMed citations: 57.

57 articles citing: The neXtProt knowledgebase in 2020: data, tools and usability improvements

Global Profiling of Genes Expressed in the Silk Glands of Philippine-Reared Mulberry Silkworms (Bombyx mori). PMID:35893024
Platelet proteome reveals features of cell death, antiviral response and viral replication in covid-19. PMID:35842415
Revealing the human mucinome. PMID:35725833
Case Report: Balanced Reciprocal Translocation t (17; 22) (p11.2; q11.2) and 10q23.31 Microduplication in an Infertile Male Patient Suffering From Teratozoospermia. PMID:35719406
Method for Independent Estimation of the False Localization Rate for Phosphoproteomics. PMID:35640880
Multiaspect Examinations of Possible Alternative Mappings of Identified Variant Peptides: A Case Study on the HEK293 Cell Line. PMID:35601313
Transcriptome profiling and proteomic validation reveals targets of the androgen receptor signaling in the BT-474 breast cancer cell line. PMID:35568821
A Community-Driven, Openly Accessible Molecular Pathway Integrating Knowledge on Malignant Pleural Mesothelioma. PMID:35558518
Human endogenous retrovirus K in the respiratory tract is associated with COVID-19 physiopathology. PMID:35459226
Proteomics and Metabolomics Profiling of Platelets and Plasma Mediators of Thrombo-Inflammation in Gestational Hypertension and Preeclampsia. PMID:35455936
Simple, efficient and thorough shotgun proteomic analysis with PatternLab V. PMID:35411045
Providing Adverse Outcome Pathways from the AOP-Wiki in a Semantic Web Format to Increase Usability and Accessibility of the Content. PMID:35388368
Evolution of Protein Functional Annotation: Text Mining Study. PMID:35330478
Interferon-β Activity Is Affected by S100B Protein. PMID:35216109
Enzymatic activity of glycosyltransferase GLT8D1 promotes human glioblastoma cell migration. PMID:35198895
FET fusion oncoproteins interact with BRD4 and SWI/SNF chromatin remodelling complex subtypes in sarcoma. PMID:35182012
Recent Developments in Clinical Plasma Proteomics-Applied to Cardiovascular Research. PMID:35052841
Inferring early-life host and microbiome functions by mass spectrometry-based metaproteomics and metabolomics. PMID:35024099
Current status of PTMs structural databases: applications, limitations and prospects. PMID:35020020
Case Report: Combination of Olaparib With Chemotherapy in a Patient With ATM-Deficient Colorectal Cancer. PMID:35004311
MYCL promotes iPSC-like colony formation via MYC Box 0 and 2 domains. PMID:34930932
Subcellular Transcriptomics and Proteomics: A Comparative Methods Review. PMID:34922010
ProteoDisco: A flexible R approach to generate customized protein databases for extended search space of novel and variant proteins in proteogenomic studies. PMID:34864882
Novel genetic variants associated with mortality after unrelated donor allogeneic hematopoietic cell transplantation. PMID:34746714
Progress Identifying and Analyzing the Human Proteome: 2021 Metrics from the HUPO Human Proteome Project. PMID:34670092
Functionathon: a manual data mining workflow to generate functional hypotheses for uncharacterized human proteins and its application by undergraduate students. PMID:34318869
Proteomics reveals disturbances in the immune response and energy metabolism of monocytes from patients with septic shock. PMID:34312428
DIA-Based Proteome Profiling of Nasopharyngeal Swabs from COVID-19 Patients. PMID:34292740
Alterations in Gene Expression of Renin-Angiotensin System Components and Related Proteins in Colorectal Cancer. PMID:34285715
Identification of bone morphogenetic protein 4 in the saliva after the placement of fixed orthodontic appliance. PMID:34250561
Genome of the Single Human Chromosome 18 as a "Gold Standard" for Its Transcriptome. PMID:34194472
Whole-exome sequencing reveals a novel homozygous mutation in the COQ8B gene associated with nephrotic syndrome. PMID:34172776
IDSM ChemWebRDF: SPARQLing small-molecule datasets. PMID:33980298
Long-read cDNA sequencing identifies functional pseudogenes in the human transcriptome. PMID:33971925
Proteostasis in the Male and Female Germline: A New Outlook on the Maintenance of Reproductive Health. PMID:33937261
Expanding the Genotypic Spectrum of Congenital Sensory and Autonomic Neuropathies Using Whole-Exome Sequencing. PMID:33884296
A novel predicted ADP-ribosyltransferase-like family conserved in eukaryotic evolution. PMID:33854844
Expasy, the Swiss Bioinformatics Resource Portal, as designed by its users. PMID:33849055
Resourcing, annotating, and analysing synthetic peptides of SARS-CoV-2 for immunopeptidomics and other immunological studies. PMID:33811468
Interpreting Sequence Variation in PDAC-Predisposing Genes Using a Multi-Tier Annotation Approach Performed at the Gene, Patient, and Cohort Level. PMID:33747920
Melanoma-associated glycosyltransferase GCNT2 as an emerging biomarker and therapeutic target. PMID:33660254
ADDRESS: A Database of Disease-associated Human Variants Incorporating Protein Structure and Folding Stabilities. PMID:33539887
Integrative functional genomic analysis of intron retention in human and mouse brain with Alzheimer's disease. PMID:33480174
Amniotic Fluid Stem Cell-Derived Extracellular Vesicles Counteract Steroid-Induced Osteoporosis In Vitro. PMID:33375177
WikiPathways: connecting communities. PMID:33211851
OpenProt 2021: deeper functional annotation of the coding potential of eukaryotic genomes. PMID:33179748
Understanding the causes of errors in eukaryotic protein-coding gene prediction: a case study of primate proteomes. PMID:33172385
Enhanced Validation of Antibodies Enables the Discovery of Missing Proteins. PMID:33170010
Ensembl 2021. PMID:33137190
A high-stringency blueprint of the human proteome. PMID:33067450
Development of a Parallel Reaction Monitoring Mass Spectrometry Assay for the Detection of SARS-CoV-2 Spike Glycoprotein and Nucleoprotein. PMID:32966064
Research on the Human Proteome Reaches a Major Milestone: >90% of Predicted Human Proteins Now Credibly Detected, According to the HUPO Human Proteome Project. PMID:32931287
Human carbonic anhydrases and post-translational modifications: a hidden world possibly affecting protein properties and functions. PMID:32648529
Mass Spectrometry-Based Characterization of the Virion Proteome, Phosphoproteome, and Associated Kinase Activity of Human Cytomegalovirus. PMID:32486127
PlaToLoCo: the first web meta-server for visualization and annotation of low complexity regions in proteins. PMID:32421769
Extending Comet for Global Amino Acid Variant and Post-Translational Modification Analysis Using the PSI Extended FASTA Format. PMID:32106352
MichelaNglo: sculpting protein views on web pages without coding. PMID:32061125
The neXtProt knowledgebase on human proteins: current status PubMed citations: 50.

50 articles citing: The neXtProt knowledgebase on human proteins: current status

Comprehensive and systematic characterization of multi-functionalized cisplatin nano-conjugate: from the chemistry and proteomic biocompatibility to the animal model. PMID:35858906
Deciphering Biomarkers for Leptomeningeal Metastasis in Malignant Hemopathies (Lymphoma/Leukemia) Patients by Comprehensive Multipronged Proteomics Characterization of Cerebrospinal Fluid. PMID:35053611
Deepening into Intracellular Signaling Landscape through Integrative Spatial Proteomics and Transcriptomics in a Lymphoma Model. PMID:34944421
VISPR-online: a web-based interactive tool to visualize CRISPR screening experiments. PMID:34167459
IDSM ChemWebRDF: SPARQLing small-molecule datasets. PMID:33980298
Pan-cancer analysis of transcripts encoding novel open-reading frames (nORFs) and their potential biological functions. PMID:33495453
Integrative functional genomic analysis of intron retention in human and mouse brain with Alzheimer's disease. PMID:33480174
Is It Possible to Find Needles in a Haystack? Meta-Analysis of 1000+ MS/MS Files Provided by the Russian Proteomic Consortium for Mining Missing Proteins. PMID:32456206
Comprehensive Identification and Characterization of Human Secretome Based on Integrative Proteomic and Transcriptomic Data. PMID:31824949
Human Proteome Project Mass Spectrometry Data Interpretation Guidelines 3.0. PMID:31599596
Novel functional proteins coded by the human genome discovered in metastases of melanoma patients. PMID:31599373
Using deep learning to identify translational research in genomic medicine beyond bench to bedside. PMID:30753477
Overview of the BioCreative VI text-mining services for Kinome Curation Track. PMID:30329035
Analysis of impact metrics for the Protein Data Bank. PMID:30325351
The jPOST environment: an integrated proteomics data repository and database. PMID:30295851
Chromosome 17 Missing Proteins: Recent Progress and Future Directions as Part of the neXt-MP50 Challenge. PMID:30280577
Flexible and Fast Mapping of Peptides to a Proteome with ProteoMapper. PMID:30230343
Assembling the Community-Scale Discoverable Human Proteome. PMID:30172843
Complex overlapping concepts: An effective auditing methodology for families of similarly structured BioPortal ontologies. PMID:29852316
The Cellosaurus, a Cell-Line Knowledge Resource. PMID:29805321
The Challenge of Human Spermatozoa Proteome: A Systematic Review. PMID:29062791
AAgMarker 1.0: a resource of serological autoantigen biomarkers for clinical diagnosis and prognosis of various human diseases. PMID:28977551
Proteomics Standards Initiative: Fifteen Years of Progress and Future Work. PMID:28849660
"Omics"-Informed Drug and Biomarker Discovery: Opportunities, Challenges and Future Perspectives. PMID:28248238
A Golden Age for Working with Public Proteomics Data. PMID:28118949
The 24th annual Nucleic Acids Research database issue: a look back and upcoming changes. PMID:28053160
AAgAtlas 1.0: a human autoantigen database. PMID:27924021
The neXtProt knowledgebase on human proteins: 2017 update. PMID:27899619
GenomeCRISPR - a database for high-throughput CRISPR/Cas9 screens. PMID:27789686
Silencing of Profilin-1 suppresses cell adhesion and tumor growth via predicted alterations in integrin and Ca2+ signaling in T24M-based bladder cancer models. PMID:27683119
Detection of Missing Proteins Using the PRIDE Database as a Source of Mass Spectrometry Evidence. PMID:27581094
Tiered Human Integrated Sequence Search Databases for Shotgun Proteomics. PMID:27577934
Human Proteome Project Mass Spectrometry Data Interpretation Guidelines 2.1. PMID:27490519
Protein function in precision medicine: deep understanding with machine learning. PMID:27423136
neXtA5: accelerating annotation of articles via automated approaches in neXtProt. PMID:27374119
PepPSy: a web server to prioritize gene products in experimental and biocuration workflows. PMID:27173522
Integrative analysis of extracellular and intracellular bladder cancer cell line proteome with transcriptome: improving coverage and validity of -omics findings. PMID:27167498
Utilization of HPASubC for the Identification of Sinusoid-Specific Proteins in the Liver. PMID:27005832
Identification of epistatic interactions through genome-wide association studies in sporadic medullary and juvenile papillary thyroid carcinomas. PMID:26690675
An Analysis of the Sensitivity of Proteogenomic Mapping of Somatic Mutations and Novel Splicing Events in Cancer. PMID:26631509
The SIB Swiss Institute of Bioinformatics' resources: focus on curated databases. PMID:26615188
2016 update of the PRIDE database and its related tools. PMID:26527722
The potential clinical impact of the release of two drafts of the human proteome. PMID:26496066
The IUPHAR/BPS Guide to PHARMACOLOGY in 2016: towards curated quantitative interactions between 1300 protein targets and 6000 ligands. PMID:26464438
Peptidase specificity from the substrate cleavage collection in the MEROPS database and a tool to measure cleavage site conservation. PMID:26455268
Devising a Consensus Framework for Validation of Novel Human Coding Loci. PMID:26367542
MI-PVT: A Tool for Visualizing the Chromosome-Centric Human Proteome. PMID:26204236
Mining Missing Membrane Proteins by High-pH Reverse-Phase StageTip Fractionation and Multiple Reaction Monitoring Mass Spectrometry. PMID:26202522
Metrics for the Human Proteome Project 2015: Progress on the Human Proteome and Guidelines for High-Confidence Protein Identification. PMID:26155816
The path of no return--Truncated protein N-termini and current ignorance of their genesis. PMID:26010509
neXtProt: organizing protein knowledge in the context of human proteome projects PubMed citations: 42.

42 articles citing: neXtProt: organizing protein knowledge in the context of human proteome projects

The Biological Significance of Targeting Acetylation-Mediated Gene Regulation for Designing New Mechanistic Tools and Potential Therapeutics. PMID:33803759
A high-stringency blueprint of the human proteome. PMID:33067450
Simple Targeted Assays for Metabolic Pathways and Signaling: A Powerful Tool for Targeted Proteomics. PMID:32865986
Is It Possible to Find Needles in a Haystack? Meta-Analysis of 1000+ MS/MS Files Provided by the Russian Proteomic Consortium for Mining Missing Proteins. PMID:32456206
FibroAtlas: A Database for the Exploration of Fibrotic Diseases and Their Genes. PMID:32082621
A Perspective on the Confident Comparison of Glycoprotein Site-Specific Glycosylation in Sample Cohorts. PMID:31833756
Assisting document triage for human kinome curation via machine learning. PMID:30239677
Towards a functional definition of the mitochondrial human proteome. PMID:29900096
The Gene-Centric Content Management System and Its Application for Cognitive Proteomics. PMID:29473895
The Human Eye Proteome Project: Updates on an Emerging Proteome. PMID:29356342
The Challenge of Human Spermatozoa Proteome: A Systematic Review. PMID:29062791
Advances in the Chromosome-Centric Human Proteome Project: looking to the future. PMID:29039980
Protein Bioinformatics Databases and Resources. PMID:28150231
Accelerating the search for the missing proteins in the human proteome. PMID:28117396
The neXtProt knowledgebase on human proteins: 2017 update. PMID:27899619
Urine Proteome Biomarkers in Kidney Diseases. I. Limits, Perspectives, and First Focus on Normal Urine. PMID:26997865
The impact of structural genomics: the first quindecennial. PMID:26935210
Common errors in mass spectrometry-based analysis of post-translational modifications. PMID:26667783
TAILS N-terminomic and proteomic datasets of healthy human dental pulp. PMID:26587561
Data for comparative proteomics analysis of the antitumor effect of CIGB-552 peptide in HT-29 colon adenocarcinoma cells. PMID:26306321
Metrics for the Human Proteome Project 2015: Progress on the Human Proteome and Guidelines for High-Confidence Protein Identification. PMID:26155816
State of the Human Proteome in 2014/2015 As Viewed through PeptideAtlas: Enhancing Accuracy and Coverage through the AtlasProphet. PMID:26139527
Shared resources, shared costs--leveraging biocuration resources. PMID:25776020
Version 4.0 of PaxDb: Protein abundance data, integrated across model organisms, tissues, and cell-lines. PMID:25656970
Merging and scoring molecular interactions utilising existing community standards: tools, use-cases and a case study. PMID:25652942
The neXtProt knowledgebase on human proteins: current status. PMID:25593349
PhosphoSitePlus, 2014: mutations, PTMs and recalibrations. PMID:25514926
STRING v10: protein-protein interaction networks, integrated over the tree of life. PMID:25352553
Human germline and pan-cancer variomes and their distinct functional profiles. PMID:25232094
Making proteomics data accessible and reusable: current state of proteomics databases and repositories. PMID:25158685
A draft map of the human proteome. PMID:24870542
Integrating omics technologies to study pulmonary physiology and pathology at the systems level. PMID:24802001
Fifteen years SIB Swiss Institute of Bioinformatics: life science databases, tools and support. PMID:24792157
What's that gene (or protein)? Online resources for exploring functions of genes, transcripts, and proteins. PMID:24723265
Integrated Bio-Search: challenges and trends for the integration, search and comprehensive processing of biological information. PMID:24564249
Metrics for the Human Proteome Project 2013-2014 and strategies for finding missing proteins. PMID:24364385
MOPED enables discoveries through consistently processed proteomics data. PMID:24350770
Changes in mitochondrial carriers exhibit stress-specific signatures in INS-1Eβ-cells exposed to glucose versus fatty acids. PMID:24349266
State of the human proteome in 2013 as viewed through PeptideAtlas: comparing the kidney, urine, and plasma proteomes for the biology- and disease-driven Human Proteome Project. PMID:24261998
The MIntAct project--IntAct as a common curation platform for 11 molecular interaction databases. PMID:24234451
Transcriptome analysis of the dihydrotestosterone-exposed fetal rat gubernaculum identifies common androgen and insulin-like 3 targets. PMID:24174575
The strategy, organization, and progress of the HUPO Human Proteome Project. PMID:24145142

http://dx.doi.org/10.1093/nar/gkz995

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curated information
metasource: Fairsharing.org
version: FAIRsharing.org: neXtProt; neXtProt; DOI: https://doi.org/10.25504/FAIRsharing.62evqh; Last edited: Feb. 13, 2020, 2:46 p.m.; Last accessed: Jan 03 2022 7:06 p.m.

genetic polymorphism
metasource: Fairsharing.org
version: FAIRsharing.org: neXtProt; neXtProt; DOI: https://doi.org/10.25504/FAIRsharing.62evqh; Last edited: Feb. 13, 2020, 2:46 p.m.; Last accessed: Jan 03 2022 7:06 p.m.

protein expression
metasource: Fairsharing.org
version: FAIRsharing.org: neXtProt; neXtProt; DOI: https://doi.org/10.25504/FAIRsharing.62evqh; Last edited: Feb. 13, 2020, 2:46 p.m.; Last accessed: Jan 03 2022 7:06 p.m.

sequence annotation
metasource: Fairsharing.org
version: FAIRsharing.org: neXtProt; neXtProt; DOI: https://doi.org/10.25504/FAIRsharing.62evqh; Last edited: Feb. 13, 2020, 2:46 p.m.; Last accessed: Jan 03 2022 7:06 p.m.

sequence variant
metasource: Fairsharing.org
version: FAIRsharing.org: neXtProt; neXtProt; DOI: https://doi.org/10.25504/FAIRsharing.62evqh; Last edited: Feb. 13, 2020, 2:46 p.m.; Last accessed: Jan 03 2022 7:06 p.m.

tissue
metasource: Fairsharing.org
version: FAIRsharing.org: neXtProt; neXtProt; DOI: https://doi.org/10.25504/FAIRsharing.62evqh; Last edited: Feb. 13, 2020, 2:46 p.m.; Last accessed: Jan 03 2022 7:06 p.m.

human and other vertebrate genomes
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657

human orfs
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657

model organisms
metasource: bio.tools
version: extracted_at: 2022-11-04T11:29:57.269498

proteomics
metasource: bio.tools
version: extracted_at: 2022-11-04T11:29:57.269498

proteins
metasource: bio.tools
version: extracted_at: 2022-11-04T11:29:57.269498

protein modifications
metasource: bio.tools
version: extracted_at: 2022-11-04T11:29:57.269498

protein variants
metasource: bio.tools
version: extracted_at: 2022-11-04T11:29:57.269498

rare diseases
metasource: bio.tools
version: extracted_at: 2022-11-04T11:29:57.269498

polymorphism protein expression sequence annotation sequence variant tissue human and other vertebrate genomes human orfs model organisms proteomics proteins protein modifications protein variants rare diseases

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Human Protein Atlas

Human Protein Reference Database

Human Proteinpedia

Human Gene and Protein Database

ExoLocator

Hoppsigen

PReMod

LIFEdb

Locus Reference Genomic sequences

ORFDB

NetAffx

GeneCards: human genes, protein and diseases

trome, trEST and trGEN

SAHG

The Human OligoGenome Resource: A Database for Customized Targeted Resequencing Covering the Human Genome

UCSC Genome Browser database

Human protein-protein interaction network database search

TissueNet v.2

Human Reference Protein Interactome Mapping Project

MoonProt