ParameciumDB

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ParameciumDB

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

metasource: bio.tools
version: extracted_at: 2022-11-04T11:31:15.244526

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parameciumdb

metasource: bio.tools
version: extracted_at: 2022-11-04T11:31:15.244526

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Other names: parameciumdb

ParameciumDB is a new model organism database for Paramecium, built using components of the Generic Model Organism Database (http://www.gmod.org) construction set (Chado relational database schema, Turnkey generic web framework and Gbrowse). The database currently includes the genome sequence and annotations from the sequencing project at Genoscope (http://www.genoscope.cns.fr) and genetic data (RNAi, stocks). It is possible to query the database using gene, allele or stock names, annotation or phenotype key words, or by browsing certain tables. The database is designed to optimize integration of sequence and genetic data.

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Publications

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ParameciumDB in 2011: new tools and new data for functional and comparative genomics of the model ciliate Paramecium tetraurelia
PMID: 20952411

metasource: bio.tools
version: extracted_at: 2022-11-04T11:31:15.244526

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• ParameciumDB in 2011: new tools and new data for functional and comparative genomics of the model ciliate Paramecium tetraurelia PubMed citations: 54.

  54 articles citing: ParameciumDB in 2011: new tools and new data for functional and comparative genomics of the model ciliate Paramecium tetraurelia

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  One Cell, Two Gears: Extensive Somatic Genome Plasticity Accompanies High Germline Genome Stability in Paramecium. PMID:34849843

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  Two Piwis with Ago-like functions silence somatic genes at the chromatin level. PMID:34663180

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  The macronuclear genome of the Antarctic psychrophilic marine ciliate Euplotes focardii reveals new insights on molecular cold adaptation. PMID:34548559

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  Integrative Neuroscience of Paramecium, a "Swimming Neuron". PMID:33952615

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  The Compact Macronuclear Genome of the Ciliate Halteria grandinella: A Transcriptome-Like Genome with 23,000 Nanochromosomes. PMID:33500338

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  Cross-Generational Effects and Non-random Developmental Response to Temperature Variation in Paramecium. PMID:33195230

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  Functional diversification of Paramecium Ku80 paralogs safeguards genome integrity during precise programmed DNA elimination. PMID:32298257

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  What's Genetic Variation Got to Do with It? Starvation-Induced Self-Fertilization Enhances Survival in Paramecium. PMID:32163147

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  ParameciumDB 2019: integrating genomic data across the genus for functional and evolutionary biology. PMID:31733062

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  SF-Assemblin genes in Paramecium: phylogeny and phenotypes of RNAi silencing on the ciliary-striated rootlets and surface organization. PMID:31673332

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  Environmentally induced plasticity of programmed DNA elimination boosts somatic variability in Paramecium tetraurelia. PMID:31548355

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  Exogenous RNAi mechanisms contribute to transcriptome adaptation by phased siRNA clusters in Paramecium. PMID:31251800

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  Genome analyses of the new model protist Euplotes vannus focusing on genome rearrangement and resistance to environmental stressors. PMID:30985983

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  Tetrahymena Comparative Genomics Database (TCGD): a community resource for Tetrahymena. PMID:30810209

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  CiliateGEM: an open-project and a tool for predictions of ciliate metabolic variations and experimental condition design. PMID:30497359

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  Antarctic marine ciliates under stress: superoxide dismutases from the psychrophilic Euplotes focardii are cold-active yet heat tolerant enzymes. PMID:30283056

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  Six domesticated PiggyBac transposases together carry out programmed DNA elimination in Paramecium. PMID:30223944

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  Intraflagellar transport 46 (IFT46) is essential for trafficking IFT proteins between cilia and cytoplasm in Paramecium. PMID:29915351

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  Improved methods and resources for paramecium genomics: transcription units, gene annotation and gene expression. PMID:28651633

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  Circular Concatemers of Ultra-Short DNA Segments Produce Regulatory RNAs. PMID:28283070

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  Multimerization properties of PiggyMac, a domesticated piggyBac transposase involved in programmed genome rearrangements. PMID:28104713

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  A meiosis-specific Spt5 homolog involved in non-coding transcription. PMID:28053118

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  Sfr1, a Tetrahymena thermophila Sfi1 Repeat Protein, Modulates the Production of Cortical Row Basal Bodies. PMID:27904881

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  Two sets of RNAi components are required for heterochromatin formation in trans triggered by truncated transgenes. PMID:27085807

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  <mds_ies_db>: a database of ciliate genome rearrangements. PMID:26586804

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  DNA deletion as a mechanism for developmentally programmed centromere loss. PMID:26503246

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  Cis-acting signals modulate the efficiency of programmed DNA elimination in Paramecium tetraurelia. PMID:26304543

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  Epigenetic regulation of serotype expression antagonizes transcriptome dynamics in Paramecium tetraurelia. PMID:26231545

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  Novel Insights into the Development and Function of Cilia Using the Advantages of the Paramecium Cell and Its Many Cilia. PMID:26230712

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  TFIIS-Dependent Non-coding Transcription Regulates Developmental Genome Rearrangements. PMID:26177014

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  Origin, structure and function of millions of chromosomes present in the macronucleus of unicellular eukaryotic ciliate, Oxytricha trifallax: a model organism for transgenerationally programmed genome rearrangements. PMID:26174664

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  Maintenance and Loss of Duplicated Genes by Dosage Subfunctionalization. PMID:25908670

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  The BioMart community portal: an innovative alternative to large, centralized data repositories. PMID:25897122

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  Pdsg1 and Pdsg2, novel proteins involved in developmental genome remodelling in Paramecium. PMID:25397898

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  Genomic characterization of variable surface antigens reveals a telomere position effect as a prerequisite for RNA interference-mediated silencing in Paramecium tetraurelia. PMID:25389173

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  Local effect of enhancer of zeste-like reveals cooperation of epigenetic and cis-acting determinants for zygotic genome rearrangements. PMID:25254958

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  Ku-mediated coupling of DNA cleavage and repair during programmed genome rearrangements in the ciliate Paramecium tetraurelia. PMID:25166013

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  Differential retention and divergent resolution of duplicate genes following whole-genome duplication. PMID:25085612

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  Genome-wide analysis of genetic and epigenetic control of programmed DNA deletion. PMID:25016527

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  Identification of two nickel ion-induced genes, NCI16 and PcGST1, in Paramecium caudatum. PMID:25001407

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  Insights into three whole-genome duplications gleaned from the Paramecium caudatum genome sequence. PMID:24840360

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  Genome-wide analysis of the phosphoinositide kinome from two ciliates reveals novel evolutionary links for phosphoinositide kinases in eukaryotic cells. PMID:24244373

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  Phytophthora have distinct endogenous small RNA populations that include short interfering and microRNAs. PMID:24204767

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  Computational framework to support integration of biomolecular and clinical data within a translational approach. PMID:23742129

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  Spliced DNA sequences in the Paramecium germline: their properties and evolutionary potential. PMID:23737328

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  The Oxytricha trifallax macronuclear genome: a complex eukaryotic genome with 16,000 tiny chromosomes. PMID:23382650

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  Proteomic analysis of the cilia membrane of Paramecium tetraurelia. PMID:23146917

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  Extraordinary genome stability in the ciliate Paramecium tetraurelia. PMID:23129619

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  The Paramecium germline genome provides a niche for intragenic parasitic DNA: evolutionary dynamics of internal eliminated sequences. PMID:23071448

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  An evolutionary perspective on the kinome of malaria parasites. PMID:22889911

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  Outer dynein arm light chain 1 is essential for controlling the ciliary response to cyclic AMP in Paramecium tetraurelia. PMID:22427431

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  BioMart Central Portal: an open database network for the biological community. PMID:21930507

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  BioMart: a data federation framework for large collaborative projects. PMID:21930506

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  Functional study of genes essential for autogamy and nuclear reorganization in Paramecium. PMID:21257794

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genomics databases (non-vertebrate)

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

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general genomics databases

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

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model organisms

metasource: bio.tools
version: extracted_at: 2022-11-04T11:31:15.244526

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ontology and terminology

metasource: bio.tools
version: extracted_at: 2022-11-04T11:31:15.244526

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sequence analysis

metasource: bio.tools
version: extracted_at: 2022-11-04T11:31:15.244526

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sequence sites, features and motifs

metasource: bio.tools
version: extracted_at: 2022-11-04T11:31:15.244526

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molecular genetics

metasource: bio.tools
version: extracted_at: 2022-11-04T11:31:15.244526

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genomics general genomics model organisms ontology and terminology sequence analysis sequence sites, features and motifs molecular genetics