R3089Z last accessed: 2022-11-04

wormbase
metasource: bio.tools
version: extracted_at: 2022-11-04T11:34:46.720726

Other names: facilitating insights into nematode biology, wormbase

WormBase is an international consortium of biologists and computer scientists dedicated to providing the research community with accurate, current, accessible information concerning the genetics, genomics and biology of C. elegans and related nematodes.

Webpage:

http://www.wormbase.org/

Licence:

Name: Copyrights
URL: https://wormbase.org/about/policies#2--10

Publications: (13)

Publications
More detailed information about this field from each metasource.

The BioGRID Interaction Database: 2011 update
PMID: 21071413
metasource: Fairsharing.org
version: FAIRsharing.org: WormBase; WormBase; DOI: https://doi.org/10.25504/FAIRsharing.zx1td8; Last edited: Feb. 23, 2021, 3:54 p.m.; Last accessed: Jan 03 2022 7:09 p.m.

The Gene Ontology in 2010: extensions and refinements
PMID: 19920128
metasource: Fairsharing.org
version: FAIRsharing.org: WormBase; WormBase; DOI: https://doi.org/10.25504/FAIRsharing.zx1td8; Last edited: Feb. 23, 2021, 3:54 p.m.; Last accessed: Jan 03 2022 7:09 p.m.

WormBase: a comprehensive resource for nematode research
PMID: 19910365
metasource: Fairsharing.org
version: FAIRsharing.org: WormBase; WormBase; DOI: https://doi.org/10.25504/FAIRsharing.zx1td8; Last edited: Feb. 23, 2021, 3:54 p.m.; Last accessed: Jan 03 2022 7:09 p.m.

WormBase: a modern Model Organism Information Resource
PMID: 31642470
metasource: Fairsharing.org
version: FAIRsharing.org: WormBase; WormBase; DOI: https://doi.org/10.25504/FAIRsharing.zx1td8; Last edited: Feb. 23, 2021, 3:54 p.m.; Last accessed: Jan 03 2022 7:09 p.m.

The Gene Ontology's Reference Genome Project: a unified framework for functional annotation across species
PMID: 19578431
metasource: Fairsharing.org
version: FAIRsharing.org: WormBase; WormBase; DOI: https://doi.org/10.25504/FAIRsharing.zx1td8; Last edited: Feb. 23, 2021, 3:54 p.m.; Last accessed: Jan 03 2022 7:09 p.m.

WormBase 2017: molting into a new stage
PMID: 29069413
metasource: Fairsharing.org
version: FAIRsharing.org: WormBase; WormBase; DOI: https://doi.org/10.25504/FAIRsharing.zx1td8; Last edited: Feb. 23, 2021, 3:54 p.m.; Last accessed: Jan 03 2022 7:09 p.m.

Semi-automated curation of protein subcellular localization: a text mining-based approach to Gene Ontology (GO) Cellular Component curation
PMID: 19622167
metasource: Fairsharing.org
version: FAIRsharing.org: WormBase; WormBase; DOI: https://doi.org/10.25504/FAIRsharing.zx1td8; Last edited: Feb. 23, 2021, 3:54 p.m.; Last accessed: Jan 03 2022 7:09 p.m.

nGASP--the nematode genome annotation assessment project
PMID: 19099578
metasource: Fairsharing.org
version: FAIRsharing.org: WormBase; WormBase; DOI: https://doi.org/10.25504/FAIRsharing.zx1td8; Last edited: Feb. 23, 2021, 3:54 p.m.; Last accessed: Jan 03 2022 7:09 p.m.

Toward an interactive article: integrating journals and biological databases
PMID: 21595960
metasource: Fairsharing.org
version: FAIRsharing.org: WormBase; WormBase; DOI: https://doi.org/10.25504/FAIRsharing.zx1td8; Last edited: Feb. 23, 2021, 3:54 p.m.; Last accessed: Jan 03 2022 7:09 p.m.

Localizing triplet periodicity in DNA and cDNA sequences
PMID: 21059240
metasource: Fairsharing.org
version: FAIRsharing.org: WormBase; WormBase; DOI: https://doi.org/10.25504/FAIRsharing.zx1td8; Last edited: Feb. 23, 2021, 3:54 p.m.; Last accessed: Jan 03 2022 7:09 p.m.

Representing ontogeny through ontology: a developmental biologist's guide to the gene ontology
PMID: 19921742
metasource: Fairsharing.org
version: FAIRsharing.org: WormBase; WormBase; DOI: https://doi.org/10.25504/FAIRsharing.zx1td8; Last edited: Feb. 23, 2021, 3:54 p.m.; Last accessed: Jan 03 2022 7:09 p.m.

http://dx.doi.org/10.1093/nar/gkx998
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657

http://dx.doi.org/10.1093/nar/gkt1063
metasource: bio.tools
version: extracted_at: 2022-11-04T11:34:46.720726

The BioGRID Interaction Database: 2011 update PubMed citations: 422.

422 articles citing: The BioGRID Interaction Database: 2011 update

DEMA: a distance-bounded energy-field minimization algorithm to model and layout biomolecular networks with quantitative features. PMID:35758816
Contribution of Model Organisms to Investigating the Far-Reaching Consequences of PRPP Metabolism on Human Health and Well-Being. PMID:35741038
Protein-Protein Interaction (PPI) Network of Zebrafish Oestrogen Receptors: A Bioinformatics Workflow. PMID:35629318
Uncompensated mitochondrial oxidative stress underlies heart failure in an iPSC-derived model of congenital heart disease. PMID:35395180
Integrating protein copy numbers with interaction networks to quantify stoichiometry in clathrin-mediated endocytosis. PMID:35354856
Protein interaction networks provide insight into fetal origins of chronic obstructive pulmonary disease. PMID:35331221
Correlation Imputation for Single-Cell RNA-seq. PMID:35325552
Identifying large-scale interaction atlases using probabilistic graphs and external knowledge. PMID:35321220
Protein Function Prediction Based on PPI Networks: Network Reconstruction vs Edge Enrichment. PMID:34970299
The Hippo Signaling Pathway in Cancer: A Cell Cycle Perspective. PMID:34944834
Convolutional neural network for human cancer types prediction by integrating protein interaction networks and omics data. PMID:34667236
LncTx: A network-based method to repurpose drugs acting on the survival-related lncRNAs in lung cancer. PMID:34377365
Correlation Imputation in Single cell RNA-seq using Auxiliary Information and Ensemble Learning. PMID:34278382
Environmental robustness of the global yeast genetic interaction network. PMID:33958448
The contributions from the progenitor genomes of the mesopolyploid Brassiceae are evolutionarily distinct but functionally compatible. PMID:33863805
Genome analyses of 174 strains of Mycobacterium tuberculosis provide insight into the evolution of drug resistance and reveal potential drug targets. PMID:33750515
Chemical-Genetic Interactions of Bacopa monnieri Constituents in Cells Deficient for the DNA Repair Endonuclease RAD1 Appear Linked to Vacuolar Disruption. PMID:33668176
A large accessory protein interactome is rewired across environments. PMID:32924934
Network-principled deep generative models for designing drug combinations as graph sets. PMID:32657357
Predicting Self-Interacting Proteins Using a Recurrent Neural Network and Protein Evolutionary Information. PMID:32550764
Systematic analysis of ovarian cancer platinum-resistance mechanisms via text mining. PMID:32160916
The Need for SMN-Independent Treatments of Spinal Muscular Atrophy (SMA) to Complement SMN-Enhancing Drugs. PMID:32117013
Systematic genetics and single-cell imaging reveal widespread morphological pleiotropy and cell-to-cell variability. PMID:32064787
Genome-wide inference of the Camponotus floridanus protein-protein interaction network using homologous mapping and interacting domain profile pairs. PMID:32047225
A comparative study of topology-based pathway enrichment analysis methods. PMID:31684881
Speeding up the drug discovery process: structural similarity searches using molecular surfaces. PMID:31440460
Membrane protein-regulated networks across human cancers. PMID:31311925
Gnal haploinsufficiency causes genomic instability and increased sensitivity to haloperidol. PMID:31034808
A Comprehensive Drosophila melanogaster Transcription Factor Interactome. PMID:30995488
Analysis of Predicted Host-Parasite Interactomes Reveals Commonalities and Specificities Related to Parasitic Lifestyle and Tissues Tropism. PMID:30815000
Molecular subtyping of cancer and nomination of kinase candidates for inhibition with phosphoproteomics: Reanalysis of CPTAC ovarian cancer. PMID:30594550
A Network Pharmacology Approach to Uncover the Molecular Mechanisms of Herbal Formula Ban-Xia-Xie-Xin-Tang. PMID:30410554
Context-enriched interactome powered by proteomics helps the identification of novel regulators of macrophage activation. PMID:30303482
Evidence that RNA Viruses Drove Adaptive Introgression between Neanderthals and Modern Humans. PMID:30290142
MiRNA-BD: an evidence-based bioinformatics model and software tool for microRNA biomarker discovery. PMID:30081733
Automatic extraction of protein-protein interactions using grammatical relationship graph. PMID:30066644
Proximal Pathway Enrichment Analysis for Targeting Comorbid Diseases via Network Endopharmacology. PMID:29932108
A systems immunology approach identifies the collective impact of 5 miRs in Th2 inflammation. PMID:29875322
Systematic Evaluation of Molecular Networks for Discovery of Disease Genes. PMID:29605183
Preferential retention of genes from one parental genome after polyploidy illustrates the nature and scope of the genomic conflicts induced by hybridization. PMID:29590103
Key genes and regulatory networks involved in the initiation, progression and invasion of colorectal cancer. PMID:29568567
A homologous mapping method for three-dimensional reconstruction of protein networks reveals disease-associated mutations. PMID:29560828
Prediction of Disordered Regions and Their Roles in the Anti-Pathogenic and Immunomodulatory Functions of Butyrophilins. PMID:29401697
Co-complex protein membership evaluation using Maximum Entropy on GO ontology and InterPro annotation. PMID:29390084
Support vector machine classifier for prediction of the metastasis of colorectal cancer. PMID:29328363
Protein-protein interaction analysis to identify biomarker networks for endometriosis. PMID:29201163
SPRINT: ultrafast protein-protein interaction prediction of the entire human interactome. PMID:29141584
CRISPR/Cas9-Based Engineering of the Epigenome. PMID:28985525
High rate of adaptation of mammalian proteins that interact with Plasmodium and related parasites. PMID:28957326
Genome wide host gene expression analysis in mice experimentally infected with Pasteurella multocida. PMID:28704394
Application of a systems approach to study developmental gene regulation. PMID:28510076
iTRAQ-based quantitative proteomic analysis of Yamanaka factors reprogrammed breast cancer cells. PMID:28423718
RNA Seq analysis for transcriptome profiling in response to classical swine fever vaccination in indigenous and crossbred pigs. PMID:28361233
Gene Expression, Protein Function and Pathways of Arabidopsis thaliana Responding to Silver Nanoparticles in Comparison to Silver Ions, Cold, Salt, Drought, and Heat. PMID:28347022
Downstream targets of GWAS-detected genes for breast, lung, and prostate and colon cancer converge to G1/S transition pathway. PMID:28334950
IODNE: An integrated optimization method for identifying the deregulated subnetwork for precision medicine in cancer. PMID:28266149
Systematic analysis of molecular mechanisms for HCC metastasis via text mining approach. PMID:28108733
Properties of human disease genes and the role of genes linked to Mendelian disorders in complex disease aetiology. PMID:28053046
CanProVar 2.0: An Updated Database of Human Cancer Proteome Variation. PMID:27977206
Personalized anticancer therapy selection using molecular landscape topology and thermodynamics. PMID:27793055
Protein folding, binding, and droplet formation in cell-like conditions. PMID:27771543
A computational interactome and functional annotation for the human proteome. PMID:27770567
A global genetic interaction network maps a wiring diagram of cellular function. PMID:27708008
Systems Medicine as an Emerging Tool for Cardiovascular Genetics. PMID:27626034
Entropy-based divergent and convergent modular pattern reveals additive and synergistic anticerebral ischemia mechanisms. PMID:27480252
Identification of key target genes and pathways in laryngeal carcinoma. PMID:27446427
Mining Functional Modules in Heterogeneous Biological Networks Using Multiplex PageRank Approach. PMID:27446133
Relational Network for Knowledge Discovery through Heterogeneous Biomedical and Clinical Features. PMID:27427091
Network analysis and juvenile idiopathic arthritis (JIA): a new horizon for the understanding of disease pathogenesis and therapeutic target identification. PMID:27411317
Quantitative Determination of Flexible Pharmacological Mechanisms Based On Topological Variation in Mice Anti-Ischemic Modular Networks. PMID:27383195
BcCluster: A Bladder Cancer Database at the Molecular Level. PMID:27376128
Endophenotype Network Models: Common Core of Complex Diseases. PMID:27278246
Systematic analysis of the molecular mechanism underlying atherosclerosis using a text mining approach. PMID:27251057
Viruses are a dominant driver of protein adaptation in mammals. PMID:27187613
A Network of Splice Isoforms for the Mouse. PMID:27079421
Dissecting dysfunctional crosstalk pathways regulated by miRNAs during glioma progression. PMID:27013589
Regulatory consequences of neuronal ELAV-like protein binding to coding and non-coding RNAs in human brain. PMID:26894958
Network-based in silico drug efficacy screening. PMID:26831545
Identification of miRNA-mRNA regulatory modules by exploring collective group relationships. PMID:26817421
CSGene: a literature-based database for cell senescence genes and its application to identify critical cell aging pathways and associated diseases. PMID:26775705
BioGRID: A Resource for Studying Biological Interactions in Yeast. PMID:26729913
Scope and limitations of yeast as a model organism for studying human tissue-specific pathways. PMID:26714768
Transcriptome analysis in calorie-restricted rats implicates epigenetic and post-translational mechanisms in neuroprotection and aging. PMID:26694192
CancerNet: a database for decoding multilevel molecular interactions across diverse cancer types. PMID:26690544
Properly defining the targets of a transcription factor significantly improves the computational identification of cooperative transcription factor pairs in yeast. PMID:26679776
YAGM: a web tool for mining associated genes in yeast based on diverse biological associations. PMID:26678566
PCTFPeval: a web tool for benchmarking newly developed algorithms for predicting cooperative transcription factor pairs in yeast. PMID:26677932
A network pharmacology approach reveals new candidate caloric restriction mimetics in C. elegans. PMID:26676933
Application of Gene Expression Trajectories Initiated from ErbB Receptor Activation Highlights the Dynamics of Divergent Promoter Usage. PMID:26658111
NDEx, the Network Data Exchange. PMID:26594663
Interpreting functional effects of coding variants: challenges in proteome-scale prediction, annotation and assessment. PMID:26494363
Integrative analysis of human protein, function and disease networks. PMID:26399914
Systematic Analysis of the Molecular Mechanism Underlying Decidualization Using a Text Mining Approach. PMID:26222155
Genes Caught In Flagranti: Integrating Renal Transcriptional Profiles With Genotypes and Phenotypes. PMID:26215861
The BioPlex Network: A Systematic Exploration of the Human Interactome. PMID:26186194
Transcriptomic-Wide Discovery of Direct and Indirect HuR RNA Targets in Activated CD4+ T Cells. PMID:26162078
A reproducible approach to high-throughput biological data acquisition and integration. PMID:26157642
Biology-Driven Gene-Gene Interaction Analysis of Age-Related Cataract in the eMERGE Network. PMID:25982363
FNTM: a server for predicting functional networks of tissues in mouse. PMID:25940632
Follicle Online: an integrated database of follicle assembly, development and ovulation. PMID:25931457
Lineage-specific sequence evolution and exon edge conservation partially explain the relationship between evolutionary rate and expression level in A. thaliana. PMID:25930165
Predicted protein-protein interactions in the moss Physcomitrella patens: a new bioinformatic resource. PMID:25885037
Inhibition of cathepsin proteases attenuates migration and sensitizes aggressive N-Myc amplified human neuroblastoma cells to doxorubicin. PMID:25883214
A DIseAse MOdule Detection (DIAMOnD) algorithm derived from a systematic analysis of connectivity patterns of disease proteins in the human interactome. PMID:25853560
Recent positive selection has acted on genes encoding proteins with more interactions within the whole human interactome. PMID:25840415
Genomic analysis of host - Peste des petits ruminants vaccine viral transcriptome uncovers transcription factors modulating immune regulatory pathways. PMID:25827022
The pentameric nucleoplasmin fold is present in Drosophila FKBP39 and a large number of chromatin-related proteins. PMID:25813344
MDM2 turnover and expression of ATRX determine the choice between quiescence and senescence in response to CDK4 inhibition. PMID:25803170
Module organization and variance in protein-protein interaction networks. PMID:25797237
Network-based proteomic approaches reveal the neurodegenerative, neuroprotective and pain-related mechanisms involved after retrograde axonal damage. PMID:25784190
LC-MS/MS-based serum proteomics for identification of candidate biomarkers for hepatocellular carcinoma. PMID:25778709
The identification of specific methylation patterns across different cancers. PMID:25774687
Expression profile of mitrogen-activated protein kinase (MAPK) signaling genes in the skeletal muscle & liver of rat with type 2 diabetes: role in disease pathology. PMID:25758573
Efficient prediction of progesterone receptor interactome using a support vector machine model. PMID:25741764
Network tuned multiple rank aggregation and applications to gene ranking. PMID:25708095
An integrative approach for a network based meta-analysis of viral RNAi screens. PMID:25691914
Reconstructing genome-wide protein-protein interaction networks using multiple strategies with homologous mapping. PMID:25602759
The molecular genetic architecture of attention deficit hyperactivity disorder. PMID:25600112
Protein interactome of muscle invasive bladder cancer. PMID:25569276
Integrated systems analysis reveals a molecular network underlying autism spectrum disorders. PMID:25549968
Network-based association of hypoxia-responsive genes with cardiovascular diseases. PMID:25530704
Complex-based analysis of dysregulated cellular processes in cancer. PMID:25521701
A comprehensive performance evaluation on the prediction results of existing cooperative transcription factors identification algorithms. PMID:25521604
A proteomic analysis reveals that Snail regulates the expression of the nuclear orphan receptor Nuclear Receptor Subfamily 2 Group F Member 6 (Nr2f6) and interleukin 17 (IL-17) to inhibit adipocyte differentiation. PMID:25505127
Pathway crosstalk analysis of microarray gene expression profile in human hepatocellular carcinoma. PMID:25480734
Systems Medicine: from molecular features and models to the clinic in COPD. PMID:25471042
In silico prediction of synthetic lethality by meta-analysis of genetic interactions, functions, and pathways in yeast and human cancer. PMID:25452682
Tissue-aware data integration approach for the inference of pathway interactions in metazoan organisms. PMID:25431329
Systematic identification of cell size regulators in budding yeast. PMID:25411401
Spotlite: web application and augmented algorithms for predicting co-complexed proteins from affinity purification--mass spectrometry data. PMID:25300367
Identification of essential proteins based on ranking edge-weights in protein-protein interaction networks. PMID:25268881
Characterizing protein interactions employing a genome-wide siRNA cellular phenotyping screen. PMID:25255318
Drug-Like Protein-Protein Interaction Modulators: Challenges and Opportunities for Drug Discovery and Chemical Biology. PMID:25254076
Integration strategy is a key step in network-based analysis and dramatically affects network topological properties and inferring outcomes. PMID:25243127
Finding trans-regulatory genes and protein complexes modulating meiotic recombination hotspots of human, mouse and yeast. PMID:25208583
Unbiased functional clustering of gene variants with a phenotypic-linkage network. PMID:25166029
Bioinformatics analysis of biomarkers and transcriptional factor motifs in Down syndrome. PMID:25118625
Modeling dynamic functional relationship networks and application to ex vivo human erythroid differentiation. PMID:25115705
An integrative omics strategy to assess the germ cell secretome and to decipher sertoli-germ cell crosstalk in the Mammalian testis. PMID:25111155
Prediction and functional analysis of the sweet orange protein-protein interaction network. PMID:25091279
A dedicated database system for handling multi-level data in systems biology. PMID:25053973
Large Scale Chemical Cross-linking Mass Spectrometry Perspectives. PMID:25045217
Construction and analysis of microRNA-transcription factor regulation network in Arabidopsis. PMID:25014374
The domain landscape of virus-host interactomes. PMID:24991570
Building a hierarchical organization of protein complexes out of protein association data. PMID:24978199
Correlating information contents of gene ontology terms to infer semantic similarity of gene products. PMID:24963342
Scale-space measures for graph topology link protein network architecture to function. PMID:24931989
Improving functional annotation for industrial microbes: a case study with Pichia pastoris. PMID:24929579
Comparative analysis of human tissue interactomes reveals factors leading to tissue-specific manifestation of hereditary diseases. PMID:24921629
Essential functional modules for pathogenic and defensive mechanisms in Candida albicans infections. PMID:24757665
Stringent homology-based prediction of H. sapiens-M. tuberculosis H37Rv protein-protein interactions. PMID:24708540
Tissue-specific expression and regulatory networks of pig microRNAome. PMID:24699212
A second-generation protein-protein interaction network of Helicobacter pylori. PMID:24627523
Modelling the yeast interactome. PMID:24589662
Protein-protein interactions prediction based on iterative clique extension with gene ontology filtering. PMID:24578640
M-Finder: Uncovering functionally associated proteins from interactome data integrated with GO annotations. PMID:24565382
Stringent DDI-based prediction of H. sapiens-M. tuberculosis H37Rv protein-protein interactions. PMID:24564941
Identifying conserved protein complexes between species by constructing interolog networks. PMID:24564762
RRHGE: a novel approach to classify the estrogen receptor based breast cancer subtypes. PMID:24563630
Navigating the multilayered organization of eukaryotic signaling: a new trend in data integration. PMID:24550716
A Network Approach to Wound Healing. PMID:24527361
Discovery and characterization of two Nimrod superfamily members in Anopheles gambiae. PMID:24428830
Dynamics of regulatory networks in gastrin-treated adenocarcinoma cells. PMID:24416123
Computational Prediction of Protein-Protein Interaction Networks: Algo-rithms and Resources. PMID:24396273
Identifying functional transcription factor binding sites in yeast by considering their positional preference in the promoters. PMID:24386279
Low frequency variants, collapsed based on biological knowledge, uncover complexity of population stratification in 1000 genomes project data. PMID:24385916
Reverse engineering molecular hypergraphs. PMID:24384702
An association-adjusted consensus deleterious scheme to classify homozygous Mis-sense mutations for personal genome interpretation. PMID:24365473
Identification of unstable network modules reveals disease modules associated with the progression of Alzheimer's disease. PMID:24348898
Causal inference of gene regulation with subnetwork assembly from genetical genomics data. PMID:24322297
SysBioCube: A Data Warehouse and Integrative Data Analysis Platform Facilitating Systems Biology Studies of Disorders of Military Relevance. PMID:24303294
Expression of integrin alpha 10 is transcriptionally activated by pRb in mouse osteoblasts and is downregulated in multiple solid tumors. PMID:24287699
Integrating structure to protein-protein interaction networks that drive metastasis to brain and lung in breast cancer. PMID:24278371
Protein function prediction by collective classification with explicit and implicit edges in protein-protein interaction networks. PMID:24267980
P³DB 3.0: From plant phosphorylation sites to protein networks. PMID:24243849
Integrating protein-protein interaction networks with phenotypes reveals signs of interactions. PMID:24240319
Genotype to phenotype via network analysis. PMID:24238873
Integrating in silico resources to map a signaling network. PMID:24233784
Discovering disease-disease associations by fusing systems-level molecular data. PMID:24232732
Bayesian network prior: network analysis of biological data using external knowledge. PMID:24215027
Synthetic genetic targeting of genome instability in cancer. PMID:24202319
High-resolution network biology: connecting sequence with function. PMID:24197012
Conserved versatile master regulators in signalling pathways in response to stress in plants. PMID:24147216
Systematic identification of transcriptional regulatory modules from protein-protein interaction networks. PMID:24137002
NP-MuScL: unsupervised global prediction of interaction networks from multiple data sources. PMID:24134391
Simple topological features reflect dynamics and modularity in protein interaction networks. PMID:24130468
Protein kinase PKN1 represses Wnt/β-catenin signaling in human melanoma cells. PMID:24114839
Exploring mechanisms of human disease through structurally resolved protein interactome networks. PMID:24096645
Identification of small exonic CNV from whole-exome sequence data and application to autism spectrum disorder. PMID:24094742
Integration of new genes into cellular networks, and their structural maturation. PMID:24056411
Detecting non-uniform clusters in large-scale interaction graphs. PMID:24050498
PainNetworks: a web-based resource for the visualisation of pain-related genes in the context of their network associations. PMID:24036287
IQdb: an intelligence quotient score-associated gene resource for human intelligence. PMID:24030781
Predicting whole genome protein interaction networks from primary sequence data in model and non-model organisms using ENTS. PMID:24015873
ExoCarta as a resource for exosomal research. PMID:24009883
Inferring the effective TOR-dependent network: a computational study in yeast. PMID:24005029
Research prioritization through prediction of future impact on biomedical science: a position paper on inference-analytics. PMID:24001106
Computational analysis of virus-host interactomes. PMID:23996253
Network clusters analysis based on protein-protein interaction network constructed in phosgene-induced acute lung injury. PMID:23963411
Ultrasensitivity in phosphorylation-dephosphorylation cycles with little substrate. PMID:23950701
Human growth is associated with distinct patterns of gene expression in evolutionarily conserved networks. PMID:23941278
Association study of 167 candidate genes for schizophrenia selected by a multi-domain evidence-based prioritization algorithm and neurodevelopmental hypothesis. PMID:23922650
Cloud-based uniform ChIP-Seq processing tools for modENCODE and ENCODE. PMID:23875683
SMETANA: accurate and scalable algorithm for probabilistic alignment of large-scale biological networks. PMID:23874484
Genome evolution predicts genetic interactions in protein complexes and reveals cancer drug targets. PMID:23851603
Widespread evidence of cooperative DNA binding by transcription factors in Drosophila development. PMID:23847101
DBATE: database of alternative transcripts expression. PMID:23842462
PhosphoChain: a novel algorithm to predict kinase and phosphatase networks from high-throughput expression data. PMID:23832245
Mapping the functional yeast ABC transporter interactome. PMID:23831759
Link clustering reveals structural characteristics and biological contexts in signed molecular networks. PMID:23826198
BioBin: a bioinformatics tool for automating the binning of rare variants using publicly available biological knowledge. PMID:23819467
A nutrigenomic framework to identify time-resolving responses of hepatic genes in diet-induced obese mice. PMID:23813319
Integrating sequence, expression and interaction data to determine condition-specific miRNA regulation. PMID:23813013
A context-sensitive framework for the analysis of human signalling pathways in molecular interaction networks. PMID:23812986
Arbor: comparative analysis workflows for the tree of life. PMID:23811960
Mining breast cancer genes with a network based noise-tolerant approach. PMID:23799982
Integrative approaches for predicting protein function and prioritizing genes for complex phenotypes using protein interaction networks. PMID:23788799
ResponseNet2.0: Revealing signaling and regulatory pathways connecting your proteins and genes--now with human data. PMID:23761447
Optimization criteria and biological process enrichment in homologous multiprotein modules. PMID:23757502
Construction of protein phosphorylation networks by data mining, text mining and ontology integration: analysis of the spindle checkpoint. PMID:23749465
The development of a universal in silico predictor of protein-protein interactions. PMID:23741499
Comparison of modules of wild type and mutant Huntingtin and TP53 protein interaction networks: implications in biological processes and functions. PMID:23741403
Passing messages between biological networks to refine predicted interactions. PMID:23741402
Integrated analysis of recurrent properties of cancer genes to identify novel drivers. PMID:23718799
NRF2-ome: an integrated web resource to discover protein interaction and regulatory networks of NRF2. PMID:23710289
Genome-wide methylated DNA immunoprecipitation analysis of patients with polycystic ovary syndrome. PMID:23705014
Evolutionary pressure on the topology of protein interface interaction networks. PMID:23701316
A genome-wide resource of cell cycle and cell shape genes of fission yeast. PMID:23697806
A "candidate-interactome" aggregate analysis of genome-wide association data in multiple sclerosis. PMID:23696811
Human monogenic disease genes have frequently functionally redundant paralogs. PMID:23696728
Interface-resolved network of protein-protein interactions. PMID:23696724
Cross-species protein interactome mapping reveals species-specific wiring of stress response pathways. PMID:23695164
Adjusting for High-dimensional Covariates in Sparse Precision Matrix Estimation by ℓ1-Penalization. PMID:23687392
The PhosphoGRID Saccharomyces cerevisiae protein phosphorylation site database: version 2.0 update. PMID:23674503
All or nothing: protein complexes flip essentiality between distantly related eukaryotes. PMID:23661563
Protein complex detection via weighted ensemble clustering based on Bayesian nonnegative matrix factorization. PMID:23658709
Genotype to phenotype mapping and the fitness landscape of the E. coli lac promoter. PMID:23650500
Top-down network analysis to drive bottom-up modeling of physiological processes. PMID:23641868
PCorral--interactive mining of protein interactions from MEDLINE. PMID:23640984
Use of the protein ontology for multi-faceted analysis of biological processes: a case study of the spindle checkpoint. PMID:23637705
Chapter 15: disease gene prioritization. PMID:23633938
Genome-wide association study of sleep in Drosophila melanogaster. PMID:23617951
Large-scale event extraction from literature with multi-level gene normalization. PMID:23613707
INstruct: a database of high-quality 3D structurally resolved protein interactome networks. PMID:23599502
Interplay between chromatin state, regulator binding, and regulatory motifs in six human cell types. PMID:23595227
Evolutionary capacitance and control of protein stability in protein-protein interaction networks. PMID:23592969
Physical and genetic-interaction density reveals functional organization and informs significance cutoffs in genome-wide screens. PMID:23589890
Endometrial receptivity: a revisit to functional genomics studies on human endometrium and creation of HGEx-ERdb. PMID:23555582
Comparison of hepatocellular carcinoma (HCC), cholangiocarcinoma (CC), and combined HCC-CC (CHC) with each other based on microarray dataset. PMID:23532688
Network pharmacology strategies toward multi-target anticancer therapies: from computational models to experimental design principles. PMID:23530504
Functional knowledge transfer for high-accuracy prediction of under-studied biological processes. PMID:23516347
Functional site plasticity in domain superfamilies. PMID:23499848
Preferential duplication of intermodular hub genes: an evolutionary signature in eukaryotes genome networks. PMID:23468868
Predicting the binding patterns of hub proteins: a study using yeast protein interaction networks. PMID:23431393
Using BioBin to explore rare variant population stratification. PMID:23424138
Next-generation analysis of cataracts: determining knowledge driven gene-gene interactions using Biofilter, and gene-environment interactions using the PhenX Toolkit. PMID:23424120
Epigenetic epistatic interactions constrain the evolution of gene expression. PMID:23423319
Quantitative analysis of chaperone network throughput in budding yeast. PMID:23420633
A genomic toolkit to investigate kinesin and myosin motor function in cells. PMID:23417121
Linking proteomic and transcriptional data through the interactome and epigenome reveals a map of oncogene-induced signaling. PMID:23408876
Benchmarking human protein complexes to investigate drug-related systems and evaluate predicted protein complexes. PMID:23405067
Interactome3D: adding structural details to protein networks. PMID:23399932
A survey of protein interaction data and multigenic inherited disorders. PMID:23398688
The 3rd DBCLS BioHackathon: improving life science data integration with Semantic Web technologies. PMID:23398680
The YeastGenome app: the Saccharomyces Genome Database at your fingertips. PMID:23396302
Structure and dynamics of molecular networks: a novel paradigm of drug discovery: a comprehensive review. PMID:23384594
Identification of ovarian cancer associated genes using an integrated approach in a Boolean framework. PMID:23383610
Turning gold into 'junk': transposable elements utilize central proteins of cellular networks. PMID:23341038
Predicting PDZ domain mediated protein interactions from structure. PMID:23336252
SignaLink 2 - a signaling pathway resource with multi-layered regulatory networks. PMID:23331499
Identification of new protein interactions between dengue fever virus and its hosts, human and mosquito. PMID:23326450
Systems biology approach reveals genome to phenome correlation in type 2 diabetes. PMID:23308243
Evidence for the robustness of protein complexes to inter-species hybridization. PMID:23300466
Adding protein context to the human protein-protein interaction network to reveal meaningful interactions. PMID:23300433
Distinct transcriptional regulatory modules underlie STAT3's cell type-independent and cell type-specific functions. PMID:23295670
Supervised maximum-likelihood weighting of composite protein networks for complex prediction. PMID:23281936
Helminth secretome database (HSD): a collection of helminth excretory/secretory proteins predicted from expressed sequence tags (ESTs). PMID:23281827
GWIDD: a comprehensive resource for genome-wide structural modeling of protein-protein interactions. PMID:23245398
A gene ontology inferred from molecular networks. PMID:23242164
A novel link prediction algorithm for reconstructing protein-protein interaction networks by topological similarity. PMID:23235927
Building an efficient curation workflow for the Arabidopsis literature corpus. PMID:23221298
Mitotic exit and separation of mother and daughter cells. PMID:23212898
An evolutionarily conserved innate immunity protein interaction network. PMID:23209288
Identification of pharmacological targets in amyotrophic lateral sclerosis through genomic analysis of deregulated genes and pathways. PMID:23204922
The BioGRID interaction database: 2013 update. PMID:23203989
STRING v9.1: protein-protein interaction networks, with increased coverage and integration. PMID:23203871
The Disease and Gene Annotations (DGA): an annotation resource for human disease. PMID:23197658
SpermatogenesisOnline 1.0: a resource for spermatogenesis based on manual literature curation and genome-wide data mining. PMID:23193286
The TissueNet database of human tissue protein-protein interactions. PMID:23193266
Systems biology of pathogen-host interaction: networks of protein-protein interaction within pathogens and pathogen-human interactions in the post-genomic era. PMID:23193100
Evolutionary rate and duplicability in the Arabidopsis thaliana protein-protein interaction network. PMID:23160177
Proteomics-based methods for discovery, quantification, and validation of protein-protein interactions. PMID:23157382
Discovery of cell compartment specific protein-protein interactions using affinity purification combined with tandem mass spectrometry. PMID:23157168
Effects of protein interaction data integration, representation and reliability on the use of network properties for drug target prediction. PMID:23146171
The ConsensusPathDB interaction database: 2013 update. PMID:23143270
A travel guide to Cytoscape plugins. PMID:23132118
Spliceosome database: a tool for tracking components of the spliceosome. PMID:23118483
SpliceAid-F: a database of human splicing factors and their RNA-binding sites. PMID:23118479
Identifying novel protein complexes in cancer cells using epitope-tagging of endogenous human genes and affinity-purification mass spectrometry. PMID:23106643
Popular computational methods to assess multiprotein complexes derived from label-free affinity purification and mass spectrometry (AP-MS) experiments. PMID:23071097
Dr. PIAS 2.0: an update of a database of predicted druggable protein-protein interactions. PMID:23060433
Aminopropyltransferases involved in polyamine biosynthesis localize preferentially in the nucleus of plant cells. PMID:23056524
Identification of significant pathways in gastric cancer based on protein-protein interaction networks and cluster analysis. PMID:23055812
PRD: A protein-RNA interaction database. PMID:23055619
Cluster-based assessment of protein-protein interaction confidence. PMID:23050565
Evaluating caveolin interactions: do proteins interact with the caveolin scaffolding domain through a widespread aromatic residue-rich motif? PMID:23028656
Tissue-specific functional networks for prioritizing phenotype and disease genes. PMID:23028291
Protein stickiness, rather than number of functional protein-protein interactions, predicts expression noise and plasticity in yeast. PMID:23017156
Fungal Hsp90: a biological transistor that tunes cellular outputs to thermal inputs. PMID:22976491
RhesusBase: a knowledgebase for the monkey research community. PMID:22965133
Identifying functional modules in interaction networks through overlapping Markov clustering. PMID:22962469
Architecture of the human regulatory network derived from ENCODE data. PMID:22955619
Feature Identification of Compensatory Gene Pairs without Sequence Homology in Yeast. PMID:22952430
Using ProHits to store, annotate, and analyze affinity purification-mass spectrometry (AP-MS) data. PMID:22948730
Analyzing protein-protein interactions from affinity purification-mass spectrometry data with SAINT. PMID:22948729
A network-based approach for predicting missing pathway interactions. PMID:22916002
A network synthesis model for generating protein interaction network families. PMID:22912671
A SPARSE CONDITIONAL GAUSSIAN GRAPHICAL MODEL FOR ANALYSIS OF GENETICAL GENOMICS DATA. PMID:22905077
Minireview: progress and challenges in proteomics data management, sharing, and integration. PMID:22902541
Identifying biologically interpretable transcription factor knockout targets by jointly analyzing the transcription factor knockout microarray and the ChIP-chip data. PMID:22898448
Screening of candidate genes for primary open angle glaucoma. PMID:22876139
HINT: High-quality protein interactomes and their applications in understanding human disease. PMID:22846459
Computational framework for analysis of prey-prey associations in interaction proteomics identifies novel human protein-protein interactions and networks. PMID:22845868
Discovering the hidden sub-network component in a ranked list of genes or proteins derived from genomic experiments. PMID:22844098
atBioNet--an integrated network analysis tool for genomics and biomarker discovery. PMID:22817640
INDI: a computational framework for inferring drug interactions and their associated recommendations. PMID:22806140
Endosomal crosstalk: meeting points for signaling pathways. PMID:22796207
The core regulation module of stress-responsive regulatory networks in yeast. PMID:22784859
Combinatorial drug therapy for cancer in the post-genomic era. PMID:22781697
Integrating genome and functional genomics data to reveal perturbed signaling pathways in ovarian cancers. PMID:22779056
Posterior association networks and functional modules inferred from rich phenotypes of gene perturbations. PMID:22761558
Accuracy improvement in protein complex prediction from protein interaction networks by refining cluster overlaps. PMID:22759580
Genes2FANs: connecting genes through functional association networks. PMID:22748121
MC EMiNEM maps the interaction landscape of the Mediator. PMID:22737066
Detecting mutually exclusive interactions in protein-protein interaction maps. PMID:22715412
Beyond hairballs: The use of quantitative mass spectrometry data to understand protein-protein interactions. PMID:22710165
DEFOG: discrete enrichment of functionally organized genes. PMID:22706384
Dynamic network of transcription and pathway crosstalk to reveal molecular mechanism of MGd-treated human lung cancer cells. PMID:22693540
MoNetFamily: a web server to infer homologous modules and module-module interaction networks in vertebrates. PMID:22689643
BIPS: BIANA Interolog Prediction Server. A tool for protein-protein interaction inference. PMID:22689642
IMP: a multi-species functional genomics portal for integration, visualization and prediction of protein functions and networks. PMID:22684505
Hierarchical modularity and the evolution of genetic interactomes across species. PMID:22681890
MAGNET: MicroArray Gene expression and Network Evaluation Toolkit. PMID:22669910
A topology-based metric for measuring term similarity in the gene ontology. PMID:22666244
An interaction map of endoplasmic reticulum chaperones and foldases. PMID:22665516
Integrated analysis of transcriptome and lipid profiling reveals the co-influences of inositol-choline and Snf1 in controlling lipid biosynthesis in yeast. PMID:22622761
MGEx-Udb: a mammalian uterus database for expression-based cataloguing of genes across conditions, including endometriosis and cervical cancer. PMID:22606288
Prediction and comparison of Salmonella-human and Salmonella-Arabidopsis interactomes. PMID:22589098
Mycobacterium tuberculosis and Clostridium difficille interactomes: demonstration of rapid development of computational system for bacterial interactome prediction. PMID:22587966
The human proteome - a scientific opportunity for transforming diagnostics, therapeutics, and healthcare. PMID:22583803
M-Track: detecting short-lived protein-protein interactions in vivo. PMID:22581371
Exploring the yeast acetylome using functional genomics. PMID:22579291
Functional and topological characterization of transcriptional cooperativity in yeast. PMID:22574744
Linking proteins to signaling pathways for experiment design and evaluation. PMID:22558382
System approaches reveal the molecular networks involved in neural stem cell differentiation. PMID:22492180
Swimming upstream: identifying proteomic signals that drive transcriptional changes using the interactome and multiple "-omics" datasets. PMID:22482945
Integrated inference and analysis of regulatory networks from multi-level measurements. PMID:22482944
Network-based functional enrichment. PMID:22479706
The protein expression landscape of the Arabidopsis root. PMID:22447775
A systematic analysis of cell cycle regulators in yeast reveals that most factors act independently of cell size to control initiation of division. PMID:22438835
How to link ontologies and protein-protein interactions to literature: text-mining approaches and the BioCreative experience. PMID:22438567
An Interspecies Regulatory Network Inferred from Simultaneous RNA-seq of Candida albicans Invading Innate Immune Cells. PMID:22416242
Protein misinteraction avoidance causes highly expressed proteins to evolve slowly. PMID:22416125
Purification of the COP9 signalosome complex and binding partners from human T cells. PMID:22414063
Reducing false-positive prediction of minimotifs with a genetic interaction filter. PMID:22403687
AtPAN: an integrated system for reconstructing transcriptional regulatory networks in Arabidopsis thaliana. PMID:22397531
The role of structural disorder in the rewiring of protein interactions through evolution. PMID:22389433
Transparent mediation-based access to multiple yeast data sources using an ontology driven interface. PMID:22372975
Detection of interacting transcription factors in human tissues using predicted DNA binding affinity. PMID:22369666
Transcriptional activity and nuclear localization of Cabut, the Drosophila ortholog of vertebrate TGF-β-inducible early-response gene (TIEG) proteins. PMID:22359651
Short Co-occurring Polypeptide Regions Can Predict Global Protein Interaction Maps. PMID:22355752
HIPPIE: Integrating protein interaction networks with experiment based quality scores. PMID:22348130
Infection Strategies of Bacterial and Viral Pathogens through Pathogen-Human Protein-Protein Interactions. PMID:22347880
Rewiring of PDZ domain-ligand interaction network contributed to eukaryotic evolution. PMID:22346764
ANAP: an integrated knowledge base for Arabidopsis protein interaction network analysis. PMID:22345505
The identification of short linear motif-mediated interfaces within the human interactome. PMID:22328783
Functional dissection of lysine deacetylases reveals that HDAC1 and p300 regulate AMPK. PMID:22318606
Evolution and function of CAG/polyglutamine repeats in protein-protein interaction networks. PMID:22287626
Putting the pieces together: integrative modeling platform software for structure determination of macromolecular assemblies. PMID:22272186
Differential network biology. PMID:22252388
The genetic control of growth rate: a systems biology study in yeast. PMID:22244311
IMID: integrated molecular interaction database. PMID:22238258
Systems pharmacology: network analysis to identify multiscale mechanisms of drug action. PMID:22235860
Prediction and characterization of protein-protein interaction networks in swine. PMID:22230699
Tramtrack is genetically upstream of genes controlling tracheal tube size in Drosophila. PMID:22216153
Evolution of biological interaction networks: from models to real data. PMID:22204388
Molecular links between cellular senescence, longevity and age-related diseases - a systems biology perspective. PMID:22184282
RefNetBuilder: a platform for construction of integrated reference gene regulatory networks from expressed sequence tags. PMID:22166047
The dichotomy in degree correlation of biological networks. PMID:22164269
The Protein-Protein Interaction tasks of BioCreative III: classification/ranking of articles and linking bio-ontology concepts to full text. PMID:22151929
Benchmarking of the 2010 BioCreative Challenge III text-mining competition by the BioGRID and MINT interaction databases. PMID:22151178
The Arabidopsis Information Resource (TAIR): improved gene annotation and new tools. PMID:22140109
AutismKB: an evidence-based knowledgebase of autism genetics. PMID:22139918
iRefR: an R package to manipulate the iRefIndex consolidated protein interaction database. PMID:22115179
modMine: flexible access to modENCODE data. PMID:22080565
AnimalTFDB: a comprehensive animal transcription factor database. PMID:22080564
Network of Cancer Genes (NCG 3.0): integration and analysis of genetic and network properties of cancer genes. PMID:22080562
Systematic exploration of synergistic drug pairs. PMID:22068327
WormBase 2012: more genomes, more data, new website. PMID:22067452
PINA v2.0: mining interactome modules. PMID:22067443
InterEvol database: exploring the structure and evolution of protein complex interfaces. PMID:22053089
PomBase: a comprehensive online resource for fission yeast. PMID:22039153
Heat shock partially dissociates the overlapping modules of the yeast protein-protein interaction network: a systems level model of adaptation. PMID:22022244
PhenoM: a database of morphological phenotypes caused by mutation of essential genes in Saccharomyces cerevisiae. PMID:22009677
Systems-biology approaches to discover anti-viral effectors of the human innate immune response. PMID:21994773
Gadd45 proteins: relevance to aging, longevity and age-related pathologies. PMID:21986581
Structural analysis of hubs in human NR-RTK network. PMID:21974810
Global identification of modular cullin-RING ligase substrates. PMID:21963094
Using the Saccharomyces Genome Database (SGD) for analysis of genomic information. PMID:21901739
ppiTrim: constructing non-redundant and up-to-date interactomes. PMID:21873645
Conserved and differential gene interactions in dynamical biological systems. PMID:21840874
Prediction of body fluids where proteins are secreted into based on protein interaction network. PMID:21829572
Dynamics of the putative RNA helicase Spb4 during ribosome assembly in Saccharomyces cerevisiae. PMID:21825077
Reactome pathway analysis to enrich biological discovery in proteomics data sets. PMID:21751369
g:Profiler--a web server for functional interpretation of gene lists (2011 update). PMID:21646343
A network of SCOP hidden Markov models and its analysis. PMID:21635719
SLiMSearch 2.0: biological context for short linear motifs in proteins. PMID:21622654
CASCADE_SCAN: mining signal transduction network from high-throughput data based on steepest descent method. PMID:21575263
Actin-binding protein ABP140 is a methyltransferase for 3-methylcytidine at position 32 of tRNAs in Saccharomyces cerevisiae. PMID:21518805
Sig2BioPAX: Java tool for converting flat files to BioPAX Level 3 format. PMID:21418653
Worm Phenotype Ontology: integrating phenotype data within and beyond the C. elegans community. PMID:21261995
Protein databases on the internet. PMID:18265344
The Gene Ontology in 2010: extensions and refinements PubMed citations: 252.

252 articles citing: The Gene Ontology in 2010: extensions and refinements

Comprehensive Identification of Human Cell Type Chromatin Activity-Specific and Cell Type Expression-Specific MicroRNAs. PMID:35806329
Eigenvectors from Eigenvalues Sparse Principal Component Analysis (EESPCA). PMID:35693984
Comprehensive genome wide identification and expression analysis of MTP gene family in tomato (Solanum lycopersicum) under multiple heavy metal stress. PMID:34866994
An Emiliania huxleyi pan-transcriptome reveals basal strain specificity in gene expression patterns. PMID:34675226
Genome-Wide Identification and Expression Analysis of Metal Tolerance Protein Gene Family in Medicago truncatula Under a Broad Range of Heavy Metal Stress. PMID:34603378
Identification of disease treatment mechanisms through the multiscale interactome. PMID:33741907
Predicting functions of maize proteins using graph convolutional network. PMID:33323113
Exploring Drug Treatment Patterns Based on the Action of Drug and Multilayer Network Model. PMID:32708644
Automated generation of gene summaries at the Alliance of Genome Resources. PMID:32559296
Arsenic Disulfide Promoted Hypomethylation by Increasing DNA Methyltransferases Expression in Myelodysplastic Syndrome. PMID:32431489
Traditional Chinese Medicine Containing Arsenic Treated MDS Patients Effectively through Regulating Aberrant Hypomethylation. PMID:32215045
A region-based gene association study combined with a leave-one-out sensitivity analysis identifies SMG1 as a pancreatic cancer susceptibility gene. PMID:31469826
Augmenting subnetwork inference with information extracted from the scientific literature. PMID:31246951
RNA sequencing uncovers the key long non-coding RNAs and potential molecular mechanism contributing to XAV939-mediated inhibition of non-small cell lung cancer. PMID:31186710
Analytical Validation of Clinical Whole-Genome and Transcriptome Sequencing of Patient-Derived Tumors for Reporting Targetable Variants in Cancer. PMID:30138725
Candidate gene and mechanism investigations in congenital obstructive nephropathy based on bioinformatics analysis. PMID:30015886
Exploring the functional impact of alternative splicing on human protein isoforms using available annotation sources. PMID:29931155
WEGO 2.0: a web tool for analyzing and plotting GO annotations, 2018 update. PMID:29788377
Effects of Zhizi Chuanxiong Capsule () on the Abnormal Methylation in Rabbits with Atherosclerosis. PMID:29752693
Computation and application of tissue-specific gene set weights. PMID:29659714
Effect of Qinghuang Powder () Combined with Bupi Yishen Decoction () in Treating Patients with Refractory Cytopenia with Multilineage Dysplasia through Regulating DNA Methylation. PMID:29500545
Convergent downstream candidate mechanisms of independent intergenic polymorphisms between co-classified diseases implicate epistasis among noncoding elements. PMID:29218911
A post-gene silencing bioinformatics protocol for plant-defence gene validation and underlying process identification: case study of the Arabidopsis thaliana NPR1. PMID:29169324
A genome-by-environment interaction classifier for precision medicine: personal transcriptome response to rhinovirus identifies children prone to asthma exacerbations. PMID:29016970
Extending XNAT Platform with an Incremental Semantic Framework. PMID:28912709
Perturbed human sub-networks by Fusobacterium nucleatum candidate virulence proteins. PMID:28793925
Comparing sequencing assays and human-machine analyses in actionable genomics for glioblastoma. PMID:28740869
Quality assurance of chemical ingredient classification for the National Drug File - Reference Terminology. PMID:28723580
E3 Ubiquitin ligase ZNRF4 negatively regulates NOD2 signalling and induces tolerance to MDP. PMID:28656966
Bacterial Virus Ontology; Coordinating across Databases. PMID:28545254
Gene set selection via LASSO penalized regression (SLPR). PMID:28472344
The physical characteristics of human proteins in different biological functions. PMID:28459865
Identifying key genes associated with Hirschsprung's disease based on bioinformatics analysis of RNA-sequencing data. PMID:28120235
Unsupervised gene set testing based on random matrix theory. PMID:27809777
Molecular mechanisms underlying COPD-muscle dysfunction unveiled through a systems medicine approach. PMID:27794560
Systematically characterizing dysfunctional long intergenic non-coding RNAs in multiple brain regions of major psychosis. PMID:27661005
Modeling biochemical pathways in the gene ontology. PMID:27589964
Integrative genomics analyses unveil downstream biological effectors of disease-specific polymorphisms buried in intergenic regions. PMID:27482468
Entropy-based divergent and convergent modular pattern reveals additive and synergistic anticerebral ischemia mechanisms. PMID:27480252
Exploring lateral genetic transfer among microbial genomes using TF-IDF. PMID:27452976
Statin Intensity or Achieved LDL? Practice-based Evidence for the Evaluation of New Cholesterol Treatment Guidelines. PMID:27227451
GCGene: a gene resource for gastric cancer with literature evidence. PMID:27127885
GeneAnalytics: An Integrative Gene Set Analysis Tool for Next Generation Sequencing, RNAseq and Microarray Data. PMID:26983021
Long-noncoding RNAs in basal cell carcinoma. PMID:26861560
Multi-tissue transcriptomics for construction of a comprehensive gene resource for the terrestrial snail Theba pisana. PMID:26852673
CSGene: a literature-based database for cell senescence genes and its application to identify critical cell aging pathways and associated diseases. PMID:26775705
CancerNet: a database for decoding multilevel molecular interactions across diverse cancer types. PMID:26690544
An evidence-based knowledgebase of metastasis suppressors to identify key pathways relevant to cancer metastasis. PMID:26486520
An Independent Filter for Gene Set Testing Based on Spectral Enrichment. PMID:26451820
Connectivity Homology Enables Inter-Species Network Models of Synthetic Lethality. PMID:26451775
ExoCarta: A Web-Based Compendium of Exosomal Cargo. PMID:26434508
My Corporis Fabrica Embryo: An ontology-based 3D spatio-temporal modeling of human embryo development. PMID:26413258
Host genetic variation impacts microbiome composition across human body sites. PMID:26374288
Mouse anatomy ontologies: enhancements and tools for exploring and integrating biomedical data. PMID:26208972
Pathway and network analysis of cancer genomes. PMID:26125594
dbEMT: an epithelial-mesenchymal transition associated gene resource. PMID:26099468
Pedican: an online gene resource for pediatric cancers with literature evidence. PMID:26073932
Dynamic changes of RNA-sequencing expression for precision medicine: N-of-1-pathways Mahalanobis distance within pathways of single subjects predicts breast cancer survival. PMID:26072495
Gene set analysis: A step-by-step guide. PMID:26059482
Towards a PBMC "virogram assay" for precision medicine: Concordance between ex vivo and in vivo viral infection transcriptomes. PMID:25797143
The Internet as a new tool in the rehabilitation process of patients--education in focus. PMID:25711359
Identification of Yellow Pigmentation Genes in Brassica rapa ssp. pekinensis Using Br300 Microarray. PMID:25629030
New mode of energy metabolism in the seventh order of methanogens as revealed by comparative genome analysis of “Candidatus methanoplasma termitum”. PMID:25501486
Information content-based Gene Ontology functional similarity measures: which one to use for a given biological data type? PMID:25474538
CMPD: cancer mutant proteome database. PMID:25398898
CATH: comprehensive structural and functional annotations for genome sequences. PMID:25348408
'N-of-1-pathways' unveils personal deregulated mechanisms from a single pair of RNA-Seq samples: towards precision medicine. PMID:25301808
Vitamin D prevents cognitive decline and enhances hippocampal synaptic function in aging rats. PMID:25267625
An integrated ontology resource to explore and study host-virus relationships. PMID:25233094
A semi-automated methodology for finding lipid-related GO terms. PMID:25209026
Systems-based analyses of brain regions functionally impacted in Parkinson's disease reveals underlying causal mechanisms. PMID:25170892
Concordance of deregulated mechanisms unveiled in underpowered experiments: PTBP1 knockdown case study. PMID:25079003
Building a hierarchical organization of protein complexes out of protein association data. PMID:24978199
The gene expression database for mouse development (GXD): putting developmental expression information at your fingertips. PMID:24958384
Structuring osteosarcoma knowledge: an osteosarcoma-gene association database based on literature mining and manual annotation. PMID:24865352
The DNA methylome and transcriptome of different brain regions in schizophrenia and bipolar disorder. PMID:24776767
Phenotype ontologies and cross-species analysis for translational research. PMID:24699242
High-throughput transcriptome sequencing and preliminary functional analysis in four Neotropical tree species. PMID:24673733
HybridGO-Loc: mining hybrid features on gene ontology for predicting subcellular localization of multi-location proteins. PMID:24647341
Annotation enrichment analysis: an alternative method for evaluating the functional properties of gene sets. PMID:24569707
Improving transcriptome construction in non-model organisms: integrating manual and automated gene definition in Emiliania huxleyi. PMID:24559402
DFLAT: functional annotation for human development. PMID:24507166
A Bayesian Hierarchical Model for Relating Multiple SNPs within Multiple Genes to Disease Risk. PMID:24490143
Insights into the maize pan-genome and pan-transcriptome. PMID:24488960
Comparative transcriptional profiling analysis of olive ripe-fruit pericarp and abscission zone tissues shows expression differences and distinct patterns of transcriptional regulation. PMID:24320622
Novel insights into embryonic stem cell self-renewal revealed through comparative human and mouse systems biology networks. PMID:24307629
HuPSON: the human physiology simulation ontology. PMID:24267822
The Reactome pathway knowledgebase. PMID:24243840
Annotating cancer variants and anti-cancer therapeutics in reactome. PMID:24213504
The mouse Gene Expression Database (GXD): 2014 update. PMID:24163257
The Gene Ontology (GO) Cellular Component Ontology: integration with SAO (Subcellular Anatomy Ontology) and other recent developments. PMID:24093723
Information content-based gene ontology semantic similarity approaches: toward a unified framework theory. PMID:24078912
DaGO-Fun: tool for Gene Ontology-based functional analysis using term information content measures. PMID:24067102
The mouse pathology ontology, MPATH; structure and applications. PMID:24033988
IQdb: an intelligence quotient score-associated gene resource for human intelligence. PMID:24030781
EMAP/EMAPA ontology of mouse developmental anatomy: 2013 update. PMID:23972281
Predicting and analyzing interactions between Mycobacterium tuberculosis and its human host. PMID:23844013
A guide to best practices for Gene Ontology (GO) manual annotation. PMID:23842463
Mining breast cancer genes with a network based noise-tolerant approach. PMID:23799982
Pathway databases: making chemical and biological sense of the genomic data flood. PMID:23706629
Similar properties of chondrocytes from osteoarthritis joints and mesenchymal stem cells from healthy donors for tissue engineering of articular cartilage. PMID:23671648
Preliminary evaluation of the CellFinder literature curation pipeline for gene expression in kidney cells and anatomical parts. PMID:23599415
Computational analyses of transcriptomic data reveal the dynamic organization of the Escherichia coli chromosome under different conditions. PMID:23599001
Shotgun proteomic analysis on the diapause and non-diapause eggs of domesticated silkworm Bombyx mori. PMID:23580252
Endometrial receptivity: a revisit to functional genomics studies on human endometrium and creation of HGEx-ERdb. PMID:23555582
Suppression subtractive hybridization (SSH) combined with bioinformatics method: an integrated functional annotation approach for analysis of differentially expressed immune-genes in insects. PMID:23519487
In-depth performance evaluation of PFP and ESG sequence-based function prediction methods in CAFA 2011 experiment. PMID:23514353
Using nanoinformatics methods for automatically identifying relevant nanotoxicology entities from the literature. PMID:23509721
Transcriptomic events involved in melon mature-fruit abscission comprise the sequential induction of cell-wall degrading genes coupled to a stimulation of endo and exocytosis. PMID:23484021
Cell-type-specific predictive network yields novel insights into mouse embryonic stem cell self-renewal and cell fate. PMID:23468881
The repertoires of ubiquitinating and deubiquitinating enzymes in eukaryotic genomes. PMID:23393154
DNA damage and transcriptional changes in the gills of mytilus galloprovincialis exposed to nanomolar doses of combined metal salts (Cd, Cu, Hg). PMID:23355883
Phyletic profiling with cliques of orthologs is enhanced by signatures of paralogy relationships. PMID:23308060
Chapter 5: Network biology approach to complex diseases. PMID:23300411
Building an efficient curation workflow for the Arabidopsis literature corpus. PMID:23221298
BioCreative-2012 virtual issue. PMID:23221175
Karyotype and DNA-Methylation Responses in Myelodysplastic Syndromes following Treatment with Traditional Chinese Formula Containing Arsenic. PMID:23118798
Bio-crude transcriptomics: gene discovery and metabolic network reconstruction for the biosynthesis of the terpenome of the hydrocarbon oil-producing green alga, Botryococcus braunii race B (Showa). PMID:23110428
Cross-Ontology multi-level association rule mining in the Gene Ontology. PMID:23071802
MetNet Online: a novel integrated resource for plant systems biology. PMID:23066841
Metagenomic analysis: the challenge of the data bonanza. PMID:22962339
Analysis of functional pathways altered after mild traumatic brain injury. PMID:22913729
Schizophrenia shows a unique metabolomics signature in plasma. PMID:22892715
Assessment of community-submitted ontology annotations from a novel database-journal partnership. PMID:22859749
Ontologies as integrative tools for plant science. PMID:22847540
Function prediction and analysis of mycobacterium tuberculosis hypothetical proteins. PMID:22837694
Cell type specificity of signaling: view from membrane receptors distribution and their downstream transduction networks. PMID:22802048
Protein interactions with piALU RNA indicates putative participation of retroRNA in the cell cycle, DNA repair and chromatin assembly. PMID:22754750
Quality of computationally inferred gene ontology annotations. PMID:22693439
A topology-based metric for measuring term similarity in the gene ontology. PMID:22666244
Cis-acting polymorphisms affect complex traits through modifications of microRNA regulation pathways. PMID:22606281
BRCT domains: A little more than kin, and less than kind. PMID:22584059
GPSy: a cross-species gene prioritization system for conserved biological processes--application in male gamete development. PMID:22570409
Generation and analysis of a mouse intestinal metatranscriptome through Illumina based RNA-sequencing. PMID:22558305
Logical Gene Ontology Annotations (GOAL): exploring gene ontology annotations with OWL. PMID:22541594
Semantic integration of physiology phenotypes with an application to the Cellular Phenotype Ontology. PMID:22539675
Nprl3 is required for normal development of the cardiovascular system. PMID:22538705
Candidate pathway based analysis for cleft lip with or without cleft palate. PMID:22499695
Multiple apical plasma membrane constituents are associated with susceptibility to meconium ileus in individuals with cystic fibrosis. PMID:22466613
Ontology searching and browsing at the Rat Genome Database. PMID:22434847
CvManGO, a method for leveraging computational predictions to improve literature-based Gene Ontology annotations. PMID:22434836
The mouse-human anatomy ontology mapping project. PMID:22434834
Functional roles for redox genes in ethanol sensitivity in Drosophila. PMID:22430022
An update on the strategies in multicomponent activity monitoring within the phytopharmaceutical field. PMID:22417247
QServer: a biclustering server for prediction and assessment of co-expressed gene clusters. PMID:22403692
On the Use of Gene Ontology Annotations to Assess Functional Similarity among Orthologs and Paralogs: A Short Report. PMID:22359495
CytoSaddleSum: a functional enrichment analysis plugin for Cytoscape based on sum-of-weights scores. PMID:22345616
Implications of functional similarity for gene regulatory interactions. PMID:22298814
vHOG, a multispecies vertebrate ontology of homologous organs groups. PMID:22285560
Detecting local ligand-binding site similarity in nonhomologous proteins by surface patch comparison. PMID:22275074
Transcriptome-based differentiation of closely-related Miscanthus lines. PMID:22253803
Solving the Problem: Genome Annotation Standards before the Data Deluge. PMID:22180819
The impact of focused Gene Ontology curation of specific mammalian systems. PMID:22174742
Using the gene ontology to scan multilevel gene sets for associations in genome wide association studies. PMID:22161999
Minimotif Miner 3.0: database expansion and significantly improved reduction of false-positive predictions from consensus sequences. PMID:22146221
Idiopathic and heritable PAH perturb common molecular pathways, correlated with increased MSX1 expression. PMID:22140629
The Arabidopsis Information Resource (TAIR): improved gene annotation and new tools. PMID:22140109
CharProtDB: a database of experimentally characterized protein annotations. PMID:22140108
ScerTF: a comprehensive database of benchmarked position weight matrices for Saccharomyces species. PMID:22140105
MetaBase--the wiki-database of biological databases. PMID:22139927
Nematode.net update 2011: addition of data sets and tools featuring next-generation sequencing data. PMID:22139919
neXtProt: a knowledge platform for human proteins. PMID:22139911
The UniProt-GO Annotation database in 2011. PMID:22123736
UniPathway: a resource for the exploration and annotation of metabolic pathways. PMID:22102589
The Gene Ontology: enhancements for 2011. PMID:22102568
dbDEPC 2.0: updated database of differentially expressed proteins in human cancers. PMID:22096234
Repercussion of Mitochondria Deformity Induced by Anti-Hsp90 Drug 17AAG in Human Tumor Cells. PMID:22087060
Disease Ontology: a backbone for disease semantic integration. PMID:22080554
GeneWeaver: a web-based system for integrative functional genomics. PMID:22080549
Expression2Kinases: mRNA profiling linked to multiple upstream regulatory layers. PMID:22080467
The Mouse Genome Database (MGD): comprehensive resource for genetics and genomics of the laboratory mouse. PMID:22075990
FungiDB: an integrated functional genomics database for fungi. PMID:22064857
PomBase: a comprehensive online resource for fission yeast. PMID:22039153
Heat shock partially dissociates the overlapping modules of the yeast protein-protein interaction network: a systems level model of adaptation. PMID:22022244
BioPAX support in CellDesigner. PMID:22021903
The transcriptome of the novel dinoflagellate Oxyrrhis marina (Alveolata: Dinophyceae): response to salinity examined by 454 sequencing. PMID:22014029
The Reactome BioMart. PMID:22012987
Direct iterative protein profiling (DIPP) - an innovative method for large-scale protein detection applied to budding yeast mitosis. PMID:21997732
Genes2WordCloud: a quick way to identify biological themes from gene lists and free text. PMID:21995939
Towards Viral Genome Annotation Standards, Report from the 2010 NCBI Annotation Workshop. PMID:21994619
Prioritizing human cancer microRNAs based on genes' functional consistency between microRNA and cancer. PMID:21976726
Functional analysis beyond enrichment: non-redundant reciprocal linkage of genes and biological terms. PMID:21949701
Quantification of protein group coherence and pathway assignment using functional association. PMID:21929787
Oxidative injury is a common consequence of BMPR2 mutations. PMID:21904662
Minimum information about a bioactive entity (MIABE). PMID:21878981
Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. PMID:21873635
Integrating systems biology models and biomedical ontologies. PMID:21835028
How the gene ontology evolves. PMID:21819553
Dynamics of nuclear matrix proteome during embryonic development in Drosophila melanogaster. PMID:21799256
Genome-scale phylogenetic function annotation of large and diverse protein families. PMID:21784873
COLOMBOS: access port for cross-platform bacterial expression compendia. PMID:21779320
Transcriptome profiling and insilico analysis of Gynostemma pentaphyllum using a next generation sequencer. PMID:21769605
Reactome pathway analysis to enrich biological discovery in proteomics data sets. PMID:21751369
Systematic approaches towards the development of host-directed antiviral therapeutics. PMID:21747723
Therapy-, gender- and race-specific microRNA markers, target genes and networks related to glioblastoma recurrence and survival. PMID:21737610
Generation and analysis of expressed sequence tags from the bone marrow of Chinese Sika deer. PMID:21681423
MarkUs: a server to navigate sequence-structure-function space. PMID:21672961
The Gene3D Web Services: a platform for identifying, annotating and comparing structural domains in protein sequences. PMID:21646335
A protein network-guided screen for cell cycle regulators in Drosophila. PMID:21548953
Ontologies and standards in bioscience research: for machine or for human. PMID:21519400
UniProt Knowledgebase: a hub of integrated protein data. PMID:21447597
Exploration of plant genomes in the FLAGdb++ environment. PMID:21447150
The representation of heart development in the gene ontology. PMID:21419760
Gene discovery in Triatoma infestans. PMID:21418565
Using computational predictions to improve literature-based Gene Ontology annotations: a feasibility study. PMID:21411447
Diverse roles and interactions of the SWI/SNF chromatin remodeling complex revealed using global approaches. PMID:21408204
Disease and phenotype data at Ensembl. PMID:21400687
Autism candidate genes via mouse phenomics. PMID:21397722
GOChase-II: correcting semantic inconsistencies from Gene Ontology-based annotations for gene products. PMID:21342572
The what, where, how and why of gene ontology--a primer for bioinformaticians. PMID:21330331
Quantifying protein function specificity in the gene ontology. PMID:21304708
Dr. PIAS: an integrative system for assessing the druggability of protein-protein interactions. PMID:21303559
The Mouse Tumor Biology Database (MTB): a central electronic resource for locating and integrating mouse tumor pathology data. PMID:21282667
Ubiquitin-proteasome genes as targets for modulation of cisplatin sensitivity in fission yeast. PMID:21247416
Logical development of the cell ontology. PMID:21208450
Execution of the meiotic noncoding RNA expression program and the onset of gametogenesis in yeast require the conserved exosome subunit Rrp6. PMID:21149693
Correlating traits of gene retention, sequence divergence, duplicability and essentiality in vertebrates, arthropods, and fungi. PMID:21148284
Gerontome: a web-based database server for aging-related genes and analysis pipelines. PMID:21143804
IntelliGO: a new vector-based semantic similarity measure including annotation origin. PMID:21122125
Computational biology for ageing. PMID:21115530
Entrez Gene: gene-centered information at NCBI. PMID:21115458
EcoCyc: a comprehensive database of Escherichia coli biology. PMID:21097882
Chondrogenic differentiation of human bone marrow-derived mesenchymal stem cells in self-gelling alginate discs reveals novel chondrogenic signature gene clusters. PMID:21087199
AgBase: supporting functional modeling in agricultural organisms. PMID:21075795
Molecular and physiological responses to juvenile traumatic brain injury: focus on growth and metabolism. PMID:21071915
ConsensusPathDB: toward a more complete picture of cell biology. PMID:21071422
CIPRO 2.5: Ciona intestinalis protein database, a unique integrated repository of large-scale omics data, bioinformatic analyses and curated annotation, with user rating and reviewing functionality. PMID:21071393
Reactome: a database of reactions, pathways and biological processes. PMID:21067998
The mouse Gene Expression Database (GXD): 2011 update. PMID:21062809
Human and chicken TLR pathways: manual curation and computer-based orthology analysis. PMID:21052677
The Mouse Genome Database (MGD): premier model organism resource for mammalian genomics and genetics. PMID:21051359
Community cyberinfrastructure for Advanced Microbial Ecology Research and Analysis: the CAMERA resource. PMID:21045053
DroID 2011: a comprehensive, integrated resource for protein, transcription factor, RNA and gene interactions for Drosophila. PMID:21036869
ZFIN: enhancements and updates to the Zebrafish Model Organism Database. PMID:21036866
The BRENDA Tissue Ontology (BTO): the first all-integrating ontology of all organisms for enzyme sources. PMID:21030441
OrthoDB: the hierarchical catalog of eukaryotic orthologs in 2011. PMID:20972218
TcoF-DB: dragon database for human transcription co-factors and transcription factor interacting proteins. PMID:20965969
ProFITS of maize: a database of protein families involved in the transduction of signalling in the maize genome. PMID:20955618
KUPS: constructing datasets of interacting and non-interacting protein pairs with associated attributions. PMID:20952400
ViralZone: a knowledge resource to understand virus diversity. PMID:20947564
The Protein Ontology: a structured representation of protein forms and complexes. PMID:20935045
MatrixDB, the extracellular matrix interaction database. PMID:20852260
IDOMAL: an ontology for malaria. PMID:20698959
Protein kinase target discovery from genome-wide messenger RNA expression profiling. PMID:20687179
The systematic annotation of the three main GPCR families in Reactome. PMID:20671204
Somatic polyploidy promotes cell function under stress and energy depletion: evidence from tissue-specific mammal transcriptome. PMID:20625914
TabSQL: a MySQL tool to facilitate mapping user data to public databases. PMID:20573251
Nuclear matrix proteome analysis of Drosophila melanogaster. PMID:20530634
Ontologies in quantitative biology: a basis for comparison, integration, and discovery. PMID:20520843
A MOD(ern) perspective on literature curation. PMID:20221640
PANTHER version 7: improved phylogenetic trees, orthologs and collaboration with the Gene Ontology Consortium. PMID:20015972
The 2010 Nucleic Acids Research Database Issue and online Database Collection: a community of data resources. PMID:19965766
WormBase: a comprehensive resource for nematode research PubMed citations: 218.

218 articles citing: WormBase: a comprehensive resource for nematode research

The Replica Set Method is a Robust, Accurate, and High-Throughput Approach for Assessing and Comparing Lifespan in C. elegans Experiments. PMID:35821830
Structure-Based Bioisosterism Design, Synthesis, Biological Evaluation and In Silico Studies of Benzamide Analogs as Potential Anthelmintics. PMID:35566007
WormBase in 2022-data, processes, and tools for analyzing Caenorhabditis elegans. PMID:35134929
Amphioxus muscle transcriptomes reveal vertebrate-like myoblast fusion genes and a highly conserved role of insulin signalling in the metabolism of muscle. PMID:35105312
Root-knot nematodes (Meloidogyne spp.) a threat to agriculture in Mexico: biology, current control strategies, and perspectives. PMID:34989897
Mutation rate and spectrum in obligately outcrossing Caenorhabditis elegans mutation accumulation lines subjected to RNAi-induced knockdown of the mismatch repair gene msh-2. PMID:34849777
X-treme loss of sequence diversity linked to neo-X chromosomes in filarial nematodes. PMID:34705823
Analysis of Major Depression Risk Genes Reveals Evolutionary Conservation, Shared Phenotypes, and Extensive Genetic Interactions. PMID:34335334
MitoTox: a comprehensive mitochondrial toxicity database. PMID:34266386
Efficient collection of a large number of mutations by mutagenesis of DNA damage response defective animals. PMID:33828169
Effector and regulator: Diverse functions of C. elegans C-type lectin-like domain proteins. PMID:33793670
Uncovering the genetic blueprint of the C. elegans nervous system. PMID:33318182
Long-read RNA sequencing of human and animal filarial parasites improves gene models and discovers operons. PMID:33196647
Deciphering cell-cell interactions and communication from gene expression. PMID:33168968
Single-cell RNA profiling links ncRNAs to spatiotemporal gene expression during C. elegans embryogenesis. PMID:33139759
From whole-mount to single-cell spatial assessment of gene expression in 3D. PMID:33097816
CrustyBase: an interactive online database for crustacean transcriptomes. PMID:32928113
A functionally defined high-density NRF2 interactome reveals new conditional regulators of ARE transactivation. PMID:32911434
Adaptation of pine wood nematode Bursaphelenchus xylophilus to β-pinene stress. PMID:32660425
Automated generation of gene summaries at the Alliance of Genome Resources. PMID:32559296
Novel deletion alleles of a C. elegans gene C38D4.9, named as tm4476 and tm4561. PMID:32550349
More Than One-to-Four via 2R: Evidence of an Independent Amphioxus Expansion and Two-Gene Ancestral Vertebrate State for MyoD-Related Myogenic Regulatory Factors (MRFs). PMID:32520990
Genetic and functional diversification of chemosensory pathway receptors in mosquito-borne filarial nematodes. PMID:32511224
Hypoxic response regulators RHY-1 and EGL-9/PHD promote longevity through a VHL-1-independent transcriptional response. PMID:32399915
A Whole Genome Re-Sequencing Based GWA Analysis Reveals Candidate Genes Associated with Ivermectin Resistance in Haemonchus contortus. PMID:32231078
Text mining meets community curation: a newly designed curation platform to improve author experience and participation at WormBase. PMID:32185395
The Genome of Setaria digitata: A Cattle Nematode Closely Related to Human Filarial Parasites. PMID:32022853
Microtubule plus-end dynamics link wound repair to the innate immune response. PMID:31995031
A Genetic Model of the Connectome. PMID:31806491
Uncovering the Transcriptional Correlates of Hub Connectivity in Neural Networks. PMID:31379515
EPIC: software toolkit for elution profile-based inference of protein complexes. PMID:31308550
Sharing Programming Resources Between Bio* Projects. PMID:31278684
Mutational Landscape of Spontaneous Base Substitutions and Small Indels in Experimental Caenorhabditis elegans Populations of Differing Size. PMID:31110155
Environmental and Evolutionary Drivers of the Modular Gene Regulatory Network Underlying Phenotypic Plasticity for Stress Resistance in the Nematode Caenorhabditis remanei. PMID:30679247
An analog of glibenclamide selectively enhances autophagic degradation of misfolded α1-antitrypsin Z. PMID:30673724
Toxic Effects of Size-tunable Gold Nanoparticles on Caenorhabditis elegans Development and Gene Regulation. PMID:30323250
POSTAR2: deciphering the post-transcriptional regulatory logics. PMID:30239819
OpenWorm: overview and recent advances in integrative biological simulation of Caenorhabditis elegans. PMID:30201845
c302: a multiscale framework for modelling the nervous system of Caenorhabditis elegans. PMID:30201842
Discovery of genomic intervals that underlie nematode responses to benzimidazoles. PMID:29601575
Hub connectivity, neuronal diversity, and gene expression in the Caenorhabditis elegans connectome. PMID:29432412
Inferring ontology graph structures using OWL reasoning. PMID:29304741
Triage by ranking to support the curation of protein interactions. PMID:29220432
Hsp90-downregulation influences the heat-shock response, innate immune response and onset of oocyte development in nematodes. PMID:29078207
Novel functions for the RNA-binding protein ETR-1 in Caenorhabditis elegans reproduction and engulfment of germline apoptotic cell corpses. PMID:28648844
Genomic introgression mapping of field-derived multiple-anthelmintic resistance in Teladorsagia circumcincta. PMID:28644839
Naming CRISPR alleles: endonuclease-mediated mutation nomenclature across species. PMID:28589392
Signatures of co-evolutionary host-pathogen interactions in the genome of the entomopathogenic nematode Steinernema carpocapsae. PMID:28446150
The anatomy of phenotype ontologies: principles, properties and applications. PMID:28387809
An ontology-based search engine for digital reconstructions of neuronal morphology. PMID:28337675
The Bright Fluorescent Protein mNeonGreen Facilitates Protein Expression Analysis In Vivo. PMID:28108553
Mitochondrial Mutation Rate, Spectrum and Heteroplasmy in Caenorhabditis elegans Spontaneous Mutation Accumulation Lines of Differing Population Size. PMID:28087770
Genomic Scars Generated by Polymerase Theta Reveal the Versatile Mechanism of Alternative End-Joining. PMID:27755535
Revisiting the Phylogeny of the Animal Formins: Two New Subtypes, Relationships with Multiple Wing Hairs Proteins, and a Lost Human Formin. PMID:27695129
Predicting essential proteins based on subcellular localization, orthology and PPI networks. PMID:27586883
The Genetic Basis of Natural Variation in Caenorhabditis elegans Telomere Length. PMID:27449056
The nonessentiality of essential genes in yeast provides therapeutic insights into a human disease. PMID:27440870
Recent Duplication and Functional Divergence in Parasitic Nematode Levamisole-Sensitive Acetylcholine Receptors. PMID:27415016
Hitting two birds with one stone: The unforeseen consequences of nested gene knockouts in Caenorhabditis elegans. PMID:27386165
Nuclear import sequence identification in hOAS3 protein. PMID:27379722
neXtA5: accelerating annotation of articles via automated approaches in neXtProt. PMID:27374119
Diversity, evolution and medical applications of insect antimicrobial peptides. PMID:27160593
Ancient horizontal transfers of retrotransposons between birds and ancestors of human pathogenic nematodes. PMID:27097561
Unbiased identification of substrates of protein tyrosine phosphatase ptp-3 in C. elegans. PMID:27067626
Identification of a dTDP-rhamnose biosynthetic pathway that oscillates with the molting cycle in Caenorhabditis elegans. PMID:27009306
The Paired-box protein PAX-3 regulates the choice between lateral and ventral epidermal cell fates in C. elegans. PMID:26953187
Overlapping cell population expression profiling and regulatory inference in C. elegans. PMID:26926147
Mutagenesis of GATA motifs controlling the endoderm regulator elt-2 reveals distinct dominant and secondary cis-regulatory elements. PMID:26896592
Micro-proteomics with iterative data analysis: Proteome analysis in C. elegans at the single worm level. PMID:26552604
Identification of Predictive Cis-Regulatory Elements Using a Discriminative Objective Function and a Dynamic Search Space. PMID:26465884
HES-Mediated Repression of Pten in Caenorhabditis elegans. PMID:26438299
Expression profile of a Caenorhabditis elegans model of adult neuronal ceroid lipofuscinosis reveals down regulation of ubiquitin E3 ligase components. PMID:26395859
A New Player in the Spermiogenesis Pathway of Caenorhabditis elegans. PMID:26333688
Nonconsensus Protein Binding to Repetitive DNA Sequence Elements Significantly Affects Eukaryotic Genomes. PMID:26285121
Transcriptome Analysis of the Emerald Ash Borer (EAB), Agrilus planipennis: De Novo Assembly, Functional Annotation and Comparative Analysis. PMID:26244979
The Convergence of Systems and Reductionist Approaches in Complex Trait Analysis. PMID:26140590
Identification of Wnt Pathway Target Genes Regulating the Division and Differentiation of Larval Seam Cells and Vulval Precursor Cells in Caenorhabditis elegans. PMID:26048561
Illumina Synthetic Long Read Sequencing Allows Recovery of Missing Sequences even in the "Finished" C. elegans Genome. PMID:26039588
Future translational applications from the contemporary genomics era: a scientific statement from the American Heart Association. PMID:25882488
Rice husks and their hydrochars cause unexpected stress response in the nematode Caenorhabditis elegans: reduced transcription of stress-related genes. PMID:25877903
Metabotropic Glutamate Receptors: MODULATORS OF CONTEXT-DEPENDENT FEEDING BEHAVIOUR IN C. ELEGANS. PMID:25869139
Similarity-based search of model organism, disease and drug effect phenotypes. PMID:25763178
Using EMBL-EBI Services via Web Interface and Programmatically via Web Services. PMID:25501941
The integrin-adhesome is required to maintain muscle structure, mitochondrial ATP production, and movement forces in Caenorhabditis elegans. PMID:25491313
A chaperome subnetwork safeguards proteostasis in aging and neurodegenerative disease. PMID:25437566
An RNAi-based suppressor screen identifies interactors of the Myt1 ortholog of Caenorhabditis elegans. PMID:25298536
The transgenerational effects of heat stress in the nematode Caenorhabditis remanei are negative and rapidly eliminated under direct selection for increased stress resistance in larvae. PMID:25283346
OrthoClust: an orthology-based network framework for clustering data across multiple species. PMID:25249401
A set of structural features defines the cis-regulatory modules of antenna-expressed genes in Drosophila melanogaster. PMID:25153327
Starvation-response may not involve Atg1-dependent autophagy induction in non-unikont parasites. PMID:25059978
MORPHIN: a web tool for human disease research by projecting model organism biology onto a human integrated gene network. PMID:24861622
Phenotype ontologies and cross-species analysis for translational research. PMID:24699242
Nematode phospholipid metabolism: an example of closing the genome-structure-function circle. PMID:24685202
COMPARTMENTS: unification and visualization of protein subcellular localization evidence. PMID:24573882
Use of an activated beta-catenin to identify Wnt pathway target genes in caenorhabditis elegans, including a subset of collagen genes expressed in late larval development. PMID:24569038
Comparative RNAi screens in C. elegans and C. briggsae reveal the impact of developmental system drift on gene function. PMID:24516395
Gamete-type dependent crossover interference levels in a defined region of Caenorhabditis elegans chromosome V. PMID:24240780
Integrating in silico resources to map a signaling network. PMID:24233784
Tripal v1.1: a standards-based toolkit for construction of online genetic and genomic databases. PMID:24163125
Advances in understanding the complex mechanisms of DNA interstrand cross-link repair. PMID:24086043
Toward 959 nematode genomes. PMID:24058822
WormBase: Annotating many nematode genomes. PMID:24058818
Cell interactions and patterned intercalations shape and link epithelial tubes in C. elegans. PMID:24039608
The genome and developmental transcriptome of the strongylid nematode Haemonchus contortus. PMID:23985341
Genome-wide modeling of complex phenotypes in Caenorhabditis elegans and Drosophila melanogaster. PMID:23984798
Discovery of anthelmintic drug targets and drugs using chokepoints in nematode metabolic pathways. PMID:23935495
Adaptive and specialised transcriptional responses to xenobiotic stress in Caenorhabditis elegans are regulated by nuclear hormone receptors. PMID:23922869
New role for DCR-1/dicer in Caenorhabditis elegans innate immunity against the highly virulent bacterium Bacillus thuringiensis DB27. PMID:23918784
Cloud-based uniform ChIP-Seq processing tools for modENCODE and ENCODE. PMID:23875683
An integrative, translational approach to understanding rare and orphan genetically based diseases. PMID:23853703
GoSynthetic database tool to analyse natural and engineered molecular processes. PMID:23813641
A comparative analysis of transcription factor expression during metazoan embryonic development. PMID:23799133
SARM is required for neuronal injury and cytokine production in response to central nervous system viral infection. PMID:23749635
Identification of a tissue-selective heat shock response regulatory network. PMID:23637632
The transcription start site landscape of C. elegans. PMID:23636945
Genome-Wide RNAi Longevity Screens in Caenorhabditis elegans. PMID:23633911
C. elegans GATA factors EGL-18 and ELT-6 function downstream of Wnt signaling to maintain the progenitor fate during larval asymmetric divisions of the seam cells. PMID:23633508
Systematic analysis of experimental phenotype data reveals gene functions. PMID:23626672
Genome-wide microarrray analysis reveals roles for the REF-1 family member HLH-29 in ferritin synthesis and peroxide stress response. PMID:23533643
Integrative analysis of C. elegans modENCODE ChIP-seq data sets to infer gene regulatory interactions. PMID:23531767
Identification of neuropeptides, flp-1 and flp-12 targeting neuromuscular system of rice root knot nematode (RRKN) Meloidogyne graminicola. PMID:23520432
Premature sperm activation and defective spermatogenesis caused by loss of spe-46 function in Caenorhabditis elegans. PMID:23483899
Incorporating genomics into the toolkit of nematology. PMID:23482088
Roles of the developmental regulator unc-62/Homothorax in limiting longevity in Caenorhabditis elegans. PMID:23468654
STOP using just GO: a multi-ontology hypothesis generation tool for high throughput experimentation. PMID:23409969
The transcriptome of the invasive eel swimbladder nematode parasite Anguillicola crassus. PMID:23394720
Identification of DVA interneuron regulatory sequences in Caenorhabditis elegans. PMID:23383017
Using genome-wide expression profiling to define gene networks relevant to the study of complex traits: from RNA integrity to network topology. PMID:23195313
CooVar: co-occurring variant analyzer. PMID:23116482
System wide analysis of the evolution of innate immunity in the nematode model species Caenorhabditis elegans and Pristionchus pacificus. PMID:23028509
Nematode-bacterium symbioses--cooperation and conflict revealed in the "omics" age. PMID:22983035
Comparative genomics of eukaryotic small nucleolar RNAs reveals deep evolutionary ancestry amidst ongoing intragenomic mobility. PMID:22978381
oPOSSUM-3: advanced analysis of regulatory motif over-representation across genes or ChIP-Seq datasets. PMID:22973536
A genome-wide RNAi screen for enhancers of par mutants reveals new contributors to early embryonic polarity in Caenorhabditis elegans. PMID:22887819
Meiotic development in Caenorhabditis elegans. PMID:22872477
Reverse engineering biomolecular systems using -omic data: challenges, progress and opportunities. PMID:22833495
A survey of putative secreted and transmembrane proteins encoded in the C. elegans genome. PMID:22823938
Computational tools for comparative phenomics: the role and promise of ontologies. PMID:22814867
Divergent gene expression in the conserved dauer stage of the nematodes Pristionchus pacificus and Caenorhabditis elegans. PMID:22712530
Duplicate gene enrichment and expression pattern diversification in multicellularity. PMID:22645319
GPSy: a cross-species gene prioritization system for conserved biological processes--application in male gamete development. PMID:22570409
Linking proteins to signaling pathways for experiment design and evaluation. PMID:22558382
Multidimensional regulation of gene expression in the C. elegans embryo. PMID:22508763
The diversification of the LIM superclass at the base of the metazoa increased subcellular complexity and promoted multicellular specialization. PMID:22438907
Tetrahymena Genome Database Wiki: a community-maintained model organism database. PMID:22434841
Considerations for creating and annotating the budding yeast Genome Map at SGD: a progress report. PMID:22434826
A new database (GCD) on genome composition for eukaryote and prokaryote genome sequences and their initial analyses. PMID:22417913
RHGF-2 is an essential Rho-1 specific RhoGEF that binds to the multi-PDZ domain scaffold protein MPZ-1 in Caenorhabditis elegans. PMID:22363657
A genome-wide collection of Mos1 transposon insertion mutants for the C. elegans research community. PMID:22347378
A differential sequencing-based analysis of the C. elegans noncoding transcriptome. PMID:22345127
Evidence for centromere drive in the holocentric chromosomes of Caenorhabditis. PMID:22291967
CCDC-55 is required for larval development and distal tip cell migration in Caenorhabditis elegans. PMID:22285439
Whole-genome sequence of Schistosoma haematobium. PMID:22246508
Amplification of siRNA in Caenorhabditis elegans generates a transgenerational sequence-targeted histone H3 lysine 9 methylation footprint. PMID:22231482
Evolution of biological interaction networks: from models to real data. PMID:22204388
Nematode.net update 2011: addition of data sets and tools featuring next-generation sequencing data. PMID:22139919
MOPED: Model Organism Protein Expression Database. PMID:22139914
Construction and analysis of an integrated regulatory network derived from high-throughput sequencing data. PMID:22125477
The UniProt-GO Annotation database in 2011. PMID:22123736
Analysis of microRNA expression and function. PMID:22118279
Dissection of genetic pathways in C. elegans. PMID:22118276
modMine: flexible access to modENCODE data. PMID:22080565
GeneWeaver: a web-based system for integrative functional genomics. PMID:22080549
Organic carbon source in formulated sediments influences life traits and gene expression of Caenorhabditis elegans. PMID:22080434
Multiple phenotypes resulting from a mutagenesis screen for pharynx muscle mutations in Caenorhabditis elegans. PMID:22073173
WormBase 2012: more genomes, more data, new website. PMID:22067452
Ensembl Genomes: an integrative resource for genome-scale data from non-vertebrate species. PMID:22067447
959 Nematode Genomes: a semantic wiki for coordinating sequencing projects. PMID:22058131
Ortho2ExpressMatrix--a web server that interprets cross-species gene expression data by gene family information. PMID:21970648
Tripal: a construction toolkit for online genome databases. PMID:21959868
Comparative analysis of serine/arginine-rich proteins across 27 eukaryotes: insights into sub-family classification and extent of alternative splicing. PMID:21935421
BioMart Central Portal: an open database network for the biological community. PMID:21930507
BioMart: a data federation framework for large collaborative projects. PMID:21930506
Rational design of temperature-sensitive alleles using computational structure prediction. PMID:21912654
Rapid mapping and identification of mutations in Caenorhabditis elegans by restriction site-associated DNA mapping and genomic interval pull-down sequencing. PMID:21900274
The transcriptome of Trichuris suis--first molecular insights into a parasite with curative properties for key immune diseases of humans. PMID:21887281
Large-Scale Analysis of Gene Expression and Connectivity in the Rodent Brain: Insights through Data Integration. PMID:21863139
Evolutionary patterns of recently emerged animal duplogs. PMID:21859807
Evolution of the Max and Mlx networks in animals. PMID:21859806
Structural and functional evaluation of C. elegans filamins FLN-1 and FLN-2. PMID:21799850
Reactome pathway analysis to enrich biological discovery in proteomics data sets. PMID:21751369
New structural and functional contexts of the Dx[DN]xDG linear motif: insights into evolution of calcium-binding proteins. PMID:21720552
The Strategies WDK: a graphical search interface and web development kit for functional genomics databases. PMID:21705364
Using C. elegans for antimicrobial drug discovery. PMID:21686092
DARIO: a ncRNA detection and analysis tool for next-generation sequencing experiments. PMID:21622957
Determining the sub-cellular localization of proteins within Caenorhabditis elegans body wall muscle. PMID:21611156
A comprehensive analysis of gene expression changes provoked by bacterial and fungal infection in C. elegans. PMID:21602919
Signalogs: orthology-based identification of novel signaling pathway components in three metazoans. PMID:21559328
Methods and strategies for gene structure curation in WormBase. PMID:21543339
A high-resolution C. elegans essential gene network based on phenotypic profiling of a complex tissue. PMID:21529718
Nematodes: the worm and its relatives. PMID:21526226
Ontologies and standards in bioscience research: for machine or for human. PMID:21519400
Major prospects for exploring canine vector borne diseases and novel intervention methods using 'omic technologies. PMID:21489242
Profiling a Caenorhabditis elegans behavioral parametric dataset with a supervised K-means clustering algorithm identifies genetic networks regulating locomotion. PMID:21376755
Meet me halfway: when genomics meets structural bioinformatics. PMID:21350909
Revealing developmental networks by comparative transcriptomics. PMID:21326891
A statistical framework for modeling gene expression using chromatin features and application to modENCODE datasets. PMID:21324173
Worm Phenotype Ontology: integrating phenotype data within and beyond the C. elegans community. PMID:21261995
HIF-1 modulates longevity and healthspan in a temperature-dependent manner. PMID:21241450
TbUNC119 and its binding protein complex are essential for propagation, motility, and morphogenesis of Trypanosoma brucei procyclic form cells. PMID:21203515
Integrative analysis of the Caenorhabditis elegans genome by the modENCODE project. PMID:21177976
Genome-wide analysis of alternative splicing in Caenorhabditis elegans. PMID:21177968
The BioGRID Interaction Database: 2011 update. PMID:21071413
RBPDB: a database of RNA-binding specificities. PMID:21036867
Scaffolding a Caenorhabditis nematode genome with RNA-seq. PMID:20980554
The HUDSEN Atlas: a three-dimensional (3D) spatial framework for studying gene expression in the developing human brain. PMID:20979583
genenames.org: the HGNC resources in 2011. PMID:20929869
DAnCER: disease-annotated chromatin epigenetics resource. PMID:20876685
Identification and characterization of a serine protease inhibitor with two trypsin inhibitor-like domains from the human hookworm Ancylostoma duodenale. PMID:20852886
Bacteria, yeast, worms, and flies: exploiting simple model organisms to investigate human mitochondrial diseases. PMID:20818735
FLN-1/filamin is required for maintenance of actin and exit of fertilized oocytes from the spermatheca in C. elegans. PMID:20707996
Genomic information infrastructure after the deluge. PMID:20670392
The landscape of C. elegans 3'UTRs. PMID:20522740
SOBA: sequence ontology bioinformatics analysis. PMID:20494974
The case for cloud computing in genome informatics. PMID:20441614
Nuclear hormone receptors in nematodes: evolution and function. PMID:20438802
Targeted gene deletions in C. elegans using transposon excision. PMID:20418868
Drug target prediction and prioritization: using orthology to predict essentiality in parasite genomes. PMID:20361874
WormBase: a modern Model Organism Information Resource PubMed citations: 114.

114 articles citing: WormBase: a modern Model Organism Information Resource

Single-molecule FISH in C. elegans embryos reveals early embryonic expression dynamics of par-2 , lgl-1 and chin-1 and possible differences between hyper-diverged strains. PMID:35903776
Mode of action of fluopyram in plant-parasitic nematodes. PMID:35831379
The impact of species-wide gene expression variation on Caenorhabditis elegans complex traits. PMID:35710766
CaveCrawler: an interactive analysis suite for cavefish bioinformatics. PMID:35708643
Differential regulation of degradation and immune pathways underlies adaptation of the ectosymbiotic nematode Laxus oneistus to oxic-anoxic interfaces. PMID:35697683
Endomitosis controls tissue-specific gene expression during development. PMID:35609035
Defining characteristics and conservation of poorly annotated genes in Caenorhabditis elegans using WormCat 2.0. PMID:35587742
The gut efflux pump MRP-1 exports oxidized glutathione as a danger signal that stimulates behavioral immunity and aversive learning. PMID:35513700
Critical contribution of 3' non-seed base pairing to the in vivo function of the evolutionarily conserved let-7a microRNA. PMID:35476978
Intraspecific de novo gene birth revealed by presence-absence variant genes in Caenorhabditis elegans. PMID:35464238
Tandem Exon Duplications Expanding the Alternative Splicing Repertoire. PMID:35441045
SwissBioPics-an interactive library of cell images for the visualization of subcellular location data. PMID:35411389
Rectifying nematode names. PMID:35380660
Making biological knowledge useful for humans and machines. PMID:35380659
Chromosome-Level Reference Genomes for Two Strains of Caenorhabditis briggsae: An Improved Platform for Comparative Genomics. PMID:35348662
Genomic architecture of 5S rDNA cluster and its variations within and between species. PMID:35346033
Nematode chromosomes. PMID:35323874
Identification and characterization of Crumbs polarity complex proteins in Caenorhabditis elegans. PMID:35247383
A High-Throughput Phenotypic Screen of the 'Pandemic Response Box' Identifies a Quinoline Derivative with Significant Anthelmintic Activity. PMID:35215369
ERM-1 Phosphorylation and NRFL-1 Redundantly Control Lumen Formation in the C. elegans Intestine. PMID:35198555
Post-insemination selection dominates pre-insemination selection in driving rapid evolution of male competitive ability. PMID:35157717
WormBase in 2022-data, processes, and tools for analyzing Caenorhabditis elegans. PMID:35134929
Distinct mechanoreceptor pezo-1 isoforms modulate food intake in the nematode Caenorhabditis elegans. PMID:35100363
Formation and function of dauer ascarosides in the nematodes Caenorhabditis briggsae and Caenorhabditis elegans. PMID:35094091
Evolution of DNA Methylation Across Ecdysozoa. PMID:35089376
Caenorhabditis elegans transposable elements harbor diverse transcription factor DNA-binding sites. PMID:35088854
A simple guide to de novo transcriptome assembly and annotation. PMID:35076693
Accumulation of Glycogen and Upregulation of LEA-1 in C. elegans daf-2(e1370) Support Stress Resistance, Not Longevity. PMID:35053361
Identifying essential genes across eukaryotes by machine learning. PMID:34859210
Ensembl Genomes 2022: an expanding genome resource for non-vertebrates. PMID:34791415
The Human Disease Ontology 2022 update. PMID:34755882
Signaling via the FLP-14/FRPR-19 neuropeptide pathway sustains nociceptive response to repeated noxious stimuli in C. elegans. PMID:34748554
A new gene on C. elegans chromosome V. PMID:34746681
ConVarT: a search engine for matching human genetic variants with variants from non-human species. PMID:34718716
Multiomic profiling of the liver across diets and age in a diverse mouse population. PMID:34666007
Phylum-Spanning Neuropeptide GPCR Identification and Prioritization: Shaping Drug Target Discovery Pipelines for Nematode Parasite Control. PMID:34659113
Identifying piRNA targets on mRNAs in C. elegans using a deep multi-head attention network. PMID:34656087
WikiNetworks: translating manually created biological pathways for topological analysis. PMID:34636843
SignaLink3: a multi-layered resource to uncover tissue-specific signaling networks. PMID:34634810
Intergenerational adaptations to stress are evolutionarily conserved, stress-specific, and have deleterious trade-offs. PMID:34622777
Primordial Germ Cell Specification in Vertebrate Embryos: Phylogenetic Distribution and Conserved Molecular Features of Preformation and Induction. PMID:34604230
Natural variation in reproductive timing and X-chromosome nondisjunction in Caenorhabditis elegans. PMID:34550364
Deletion of a putative HDA-1 binding site in the hlh-2 promoter eliminates expression in C. elegans dorsal uterine cells. PMID:34514358
Exploring the β-tubulin gene family in a benzimidazole-resistant Parascaris univalens population. PMID:34467878
Small Intestinal Levels of the Branched Short-Chain Fatty Acid Isovalerate Are Elevated during Infection with Heligmosomoides polygyrus and Can Promote Helminth Fecundity. PMID:34460289
Combinatorial Assembly of Modular Glucosides via Carboxylesterases Regulates C. elegans Starvation Survival. PMID:34460264
Modelling the functional genomics of Parkinson's disease in Caenorhabditis elegans: LRRK2 and beyond. PMID:34397087
Filtering of Data-Driven Gene Regulatory Networks Using Drosophila melanogaster as a Case Study. PMID:34394179
Diversification of the calponin family proteins by gene amplification and repeat expansion of calponin-like motifs. PMID:34333878
Identification of novel yolk ferritins unique to planarians: planarians supply aluminum rather than iron to vitellaria in egg capsules. PMID:34319433
Functionathon: a manual data mining workflow to generate functional hypotheses for uncharacterized human proteins and its application by undergraduate students. PMID:34318869
A 4D single-cell protein atlas of transcription factors delineates spatiotemporal patterning during embryogenesis. PMID:34312566
Practical High-Throughput Method to Screen Compounds for Anthelmintic Activity against Caenorhabditis elegans. PMID:34299431
Genome-scale metabolic network reconstruction of model animals as a platform for translational research. PMID:34282017
Ancestry analysis indicates two different sets of essential genes in eukaryotic model species. PMID:34279742
The tweety Gene Family: From Embryo to Disease. PMID:34262434
Metagenomics: a path to understanding the gut microbiome. PMID:34259891
Utilizing image and caption information for biomedical document classification. PMID:34252939
Tripal, a community update after 10 years of supporting open source, standards-based genetic, genomic and breeding databases. PMID:34251419
Molecular topography of an entire nervous system. PMID:34237253
Inhibition of the neuromuscular acetylcholine receptor with atracurium activates FOXO/DAF-16-induced longevity. PMID:34227219
Novel LOTUS-domain proteins are organizational hubs that recruit C. elegans Vasa to germ granules. PMID:34223818
GENCODE Pseudogenes. PMID:34165709
Schistosomiasis Drug Discovery in the Era of Automation and Artificial Intelligence. PMID:34135888
Nuclear lipid droplets and nuclear damage in Caenorhabditis elegans. PMID:34133414
WormPaths: Caenorhabditis elegans metabolic pathway annotation and visualization. PMID:34117752
Updates to HCOP: the HGNC comparison of orthology predictions tool. PMID:33959747
ZebraShare: a new venue for rapid dissemination of zebrafish mutant data. PMID:33954026
Quo Vadis Caenorhabditis elegans Metabolomics-A Review of Current Methods and Applications to Explore Metabolism in the Nematode. PMID:33947148
Rhynchophorus palmarum (Linnaeus, 1758) (Coleoptera: Curculionidae): Guarani-Kaiowá indigenous knowledge and pharmacological activities. PMID:33914744
A survey of the kinome pharmacopeia reveals multiple scaffolds and targets for the development of novel anthelmintics. PMID:33911106
Student Annotations of Published Data as a Collaboration between an Online Laboratory Course and the C. elegans Database, WormBase. PMID:33884078
Network analysis in aged C. elegans reveals candidate regulatory genes of ageing. PMID:33871732
The Nesprin-1/-2 ortholog ANC-1 regulates organelle positioning in C. elegans independently from its KASH or actin-binding domains. PMID:33860766
A draft transcriptome of a parasite Neocamacolaimus parasiticus (Camacolaimidae, Plectida). PMID:33860270
MolluscDB: a genome and transcriptome database for molluscs. PMID:33813885
Wormicloud: a new text summarization tool based on word clouds to explore the C. elegans literature. PMID:33787871
Genome-wide RNAi screen for regulators of UPRmt in Caenorhabditis elegans mutants with defects in mitochondrial fusion. PMID:33784383
Two novel loci underlie natural differences in Caenorhabditis elegans abamectin responses. PMID:33720993
Long-read sequencing and de novo genome assemblies reveal complex chromosome end structures caused by telomere dysfunction at the single nucleotide level. PMID:33693840
Transcriptome analysis of Caenorhabditis elegans lacking heme peroxidase SKPO-1 reveals an altered response to Enterococcus faecalis. PMID:33609366
An Integrated Approach to Identify New Anti-Filarial Leads to Treat River Blindness, a Neglected Tropical Disease. PMID:33466870
Streamlining data-intensive biology with workflow systems. PMID:33438730
Estimation of C. elegans cell- and tissue volumes. PMID:33426507
WormPaths: Caenorhabditis elegans metabolic pathway annotation and visualization. PMID:33398287
Comparative Transcriptomics Identifies Neuronal and Metabolic Adaptations to Hypergravity and Microgravity in Caenorhabditis elegans. PMID:33376968
Epidermal PAR-6 and PKC-3 are essential for larval development of C. elegans and organize non-centrosomal microtubules. PMID:33300872
The Gene Ontology resource: enriching a GOld mine. PMID:33290552
A Database of Caenorhabditis elegans Locomotion and Body Posture Phenotypes for the Peripheral Neuropathy Model. PMID:33115980
FlyRNAi.org-the database of the Drosophila RNAi screening center and transgenic RNAi project: 2021 update. PMID:33104800
Raising the Connectome: The Emergence of Neuronal Activity and Behavior in Caenorhabditis elegans. PMID:33100971
OGEE v3: Online GEne Essentiality database with increased coverage of organisms and human cell lines. PMID:33084874
The BioGRID database: A comprehensive biomedical resource of curated protein, genetic, and chemical interactions. PMID:33070389
Protein ontology on the semantic web for knowledge discovery. PMID:33046717
The Bgee suite: integrated curated expression atlas and comparative transcriptomics in animals. PMID:33037820
The pursuit of precision mitochondrial medicine: Harnessing preclinical cellular and animal models to optimize mitochondrial disease therapeutic discovery. PMID:33006762
Large-scale RNAi screening uncovers therapeutic targets in the parasite Schistosoma mansoni. PMID:32973031
Review on the Computational Genome Annotation of Sequences Obtained by Next-Generation Sequencing. PMID:32962098
Systematic analysis of bypass suppression of essential genes. PMID:32939983
Ribosomal proteins: mutant phenotypes by the numbers and associated gene expression changes. PMID:32810425
Neuronal subclass-selective proteomic analysis in Caenorhabditis elegans. PMID:32792517
Prototypical pacemaker neurons interact with the resident microbiota. PMID:32647059
Structures of mammalian GLD-2 proteins reveal molecular basis of their functional diversity in mRNA and microRNA processing. PMID:32633758
Measuring Genome Sizes Using Read-Depth, k-mers, and Flow Cytometry: Methodological Comparisons in Beetles (Coleoptera). PMID:32601059
Automated generation of gene summaries at the Alliance of Genome Resources. PMID:32559296
The GTPase-activating protein p120RasGAP has an evolutionarily conserved "FLVR-unique" SH2 domain. PMID:32540970
PINOT: an intuitive resource for integrating protein-protein interactions. PMID:32527260
Caenorhabditis elegans PIEZO channel coordinates multiple reproductive tissues to govern ovulation. PMID:32490809
Predicting gene essentiality in Caenorhabditis elegans by feature engineering and machine-learning. PMID:32489524
Disruption of genes associated with Charcot-Marie-Tooth type 2 lead to common behavioural, cellular and molecular defects in Caenorhabditis elegans. PMID:32294113
A Whole Genome Re-Sequencing Based GWA Analysis Reveals Candidate Genes Associated with Ivermectin Resistance in Haemonchus contortus. PMID:32231078
Neuron ID dataset facilitates neuronal annotation for whole-brain activity imaging of C. elegans. PMID:32188430
Text mining meets community curation: a newly designed curation platform to improve author experience and participation at WormBase. PMID:32185395
The 27th annual Nucleic Acids Research database issue and molecular biology database collection. PMID:31906604
The Gene Ontology's Reference Genome Project: a unified framework for functional annotation across species PubMed citations: 101.

101 articles citing: The Gene Ontology's Reference Genome Project: a unified framework for functional annotation across species

Contributions of Artificial Intelligence Reported in Obstetrics and Gynecology Journals: Systematic Review. PMID:35297766
PANTHER: Making genome-scale phylogenetics accessible to all. PMID:34717010
Structure-based protein function prediction using graph convolutional networks. PMID:34039967
Proteome-Wide Analysis of Lysine 2-Hydroxyisobutyrylation in the Phytopathogenic Fungus Botrytis cinerea. PMID:33329453
Predicting functions of maize proteins using graph convolutional network. PMID:33323113
Development and validation of prognostic gene signature for basal-like breast cancer and high-grade serous ovarian cancer. PMID:32880016
Molecular genotyping, diversity studies and high-resolution molecular markers unveiled by microsatellites in Giardia duodenalis. PMID:30500829
The evolutionary signal in metagenome phyletic profiles predicts many gene functions. PMID:29991352
A descriptive marker gene approach to single-cell pseudotime inference. PMID:29939207
OmicsNet: a web-based tool for creation and visual analysis of biological networks in 3D space. PMID:29878180
Integrative genomics identifies new genes associated with severe COPD and emphysema. PMID:29566699
Metagenomic Analysis of Microbial Diversity in Landfill Lysimeter Soil of Ghazipur Landfill Site, New Delhi, India. PMID:29051248
Metagenomic Sequencing of Microbial Communities from Brackish Water of Pangong Lake of the Northwest Indian Himalayas. PMID:28982995
Global transcriptome analysis of the maize (Zea mays L.) inbred line 08LF during leaf senescence initiated by pollination-prevention. PMID:28973044
NoGOA: predicting noisy GO annotations using evidences and sparse representation. PMID:28732468
RNA target profiles direct the discovery of virulence functions for the cold-shock proteins CspC and CspE. PMID:28611217
The Biomphalaria glabrata DNA methylation machinery displays spatial tissue expression, is differentially active in distinct snail populations and is modulated by interactions with Schistosoma mansoni. PMID:28510608
Combined Administration of ASCs and BMP-12 Promotes an M2 Macrophage Phenotype and Enhances Tendon Healing. PMID:28462460
Oral immune priming with Bacillus thuringiensis induces a shift in the gene expression of Tribolium castaneum larvae. PMID:28446171
Genomic responses to the socio-sexual environment in male Drosophila melanogaster exposed to conspecific rivals. PMID:28428330
Neuropilin-1 Is Expressed on Lymphoid Tissue Residing LTi-like Group 3 Innate Lymphoid Cells and Associated with Ectopic Lymphoid Aggregates. PMID:28199847
Interspecies gene function prediction using semantic similarity. PMID:28155711
LPS-induced modules of co-expressed genes in equine peripheral blood mononuclear cells. PMID:28056766
Expansion of the Gene Ontology knowledgebase and resources. PMID:27899567
The Evidence and Conclusion Ontology (ECO): Supporting GO Annotations. PMID:27812948
Primer on the Gene Ontology. PMID:27812933
Behavioral, morphometric, and gene expression effects in adult zebrafish (Danio rerio) embryonically exposed to PFOA, PFOS, and PFNA. PMID:27710860
Functional Annotations of Paralogs: A Blessing and a Curse. PMID:27618105
MicroRNAs as biomarkers for major depression: a role for let-7b and let-7c. PMID:27483380
A draft map of the mouse pluripotent stem cell spatial proteome. PMID:26754106
COGNIZER: A Framework for Functional Annotation of Metagenomic Datasets. PMID:26561344
Single-cell RNA-seq reveals changes in cell cycle and differentiation programs upon aging of hematopoietic stem cells. PMID:26430063
Mouse Genome Database: From sequence to phenotypes and disease models. PMID:26150326
Using Gene Ontology to describe the role of the neurexin-neuroligin-SHANK complex in human, mouse and rat and its relevance to autism. PMID:26047810
Combination of inflammation-related cytokines promotes long-term muscle stem cell expansion. PMID:25976405
Community challenges in biomedical text mining over 10 years: success, failure and the future. PMID:25935162
Transcript and protein expression decoupling reveals RNA binding proteins and miRNAs as potential modulators of human aging. PMID:25853883
INTEGRATING COMPUTATIONAL PROTEIN FUNCTION PREDICTION INTO DRUG DISCOVERY INITIATIVES. PMID:25530654
Expression profiles of long non-coding RNAs located in autoimmune disease-associated regions reveal immune cell-type specificity. PMID:25419237
UniRef clusters: a comprehensive and scalable alternative for improving sequence similarity searches. PMID:25398609
PLAZA 3.0: an access point for plant comparative genomics. PMID:25324309
Managing, analysing, and integrating big data in medical bioinformatics: open problems and future perspectives. PMID:25254202
The use of semantic similarity measures for optimally integrating heterogeneous Gene Ontology data from large scale annotation pipelines. PMID:25147557
Standardized description of scientific evidence using the Evidence Ontology (ECO). PMID:25052702
OMIT: dynamic, semi-automated ontology development for the microRNA domain. PMID:25025130
A Gpr120-selective agonist improves insulin resistance and chronic inflammation in obese mice. PMID:24997608
Protein Ontology: a controlled structured network of protein entities. PMID:24270789
Large-scale gene function analysis with the PANTHER classification system. PMID:23868073
A genome-wide integrative study of microRNAs in human liver. PMID:23758991
A semi-automated genome annotation comparison and integration scheme. PMID:23725374
A protein prioritization approach tailored for the FA/BRCA pathway. PMID:23620800
SNPranker 2.0: a gene-centric data mining tool for diseases associated SNP prioritization in GWAS. PMID:23369106
Phyletic profiling with cliques of orthologs is enhanced by signatures of paralogy relationships. PMID:23308060
PANTHER in 2013: modeling the evolution of gene function, and other gene attributes, in the context of phylogenetic trees. PMID:23193289
ProteinHistorian: tools for the comparative analysis of eukaryote protein origin. PMID:22761559
Quality of computationally inferred gene ontology annotations. PMID:22693439
Resolving the ortholog conjecture: orthologs tend to be weakly, but significantly, more similar in function than paralogs. PMID:22615551
Mining Gene Ontology Data with AGENDA. PMID:22553422
Toward community standards in the quest for orthologs. PMID:22332236
Manual GO annotation of predictive protein signatures: the InterPro approach to GO curation. PMID:22301074
Accurate evaluation and analysis of functional genomics data and methods. PMID:22268703
The impact of focused Gene Ontology curation of specific mammalian systems. PMID:22174742
The Arabidopsis Information Resource (TAIR): improved gene annotation and new tools. PMID:22140109
Proteomics plus genomics approaches in primary immunodeficiency: the case of immune dysregulation, polyendocrinopathy, enteropathy, X-linked (IPEX) syndrome. PMID:22132891
GeneSigDB: a manually curated database and resource for analysis of gene expression signatures. PMID:22110038
Saccharomyces Genome Database: the genomics resource of budding yeast. PMID:22110037
GONUTS: the Gene Ontology Normal Usage Tracking System. PMID:22110029
The Gene Ontology: enhancements for 2011. PMID:22102568
The Mouse Genome Database (MGD): comprehensive resource for genetics and genomics of the laboratory mouse. PMID:22075990
AIGO: towards a unified framework for the analysis and the inter-comparison of GO functional annotations. PMID:22054122
The dynamics and evolutionary potential of domain loss and emergence. PMID:22016574
The Reactome BioMart. PMID:22012987
New resources for functional analysis of omics data for the genus Aspergillus. PMID:21974739
Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. PMID:21873635
Reactome pathway analysis to enrich biological discovery in proteomics data sets. PMID:21751369
Systematic approaches towards the development of host-directed antiviral therapeutics. PMID:21747723
PILGRM: an interactive data-driven discovery platform for expert biologists. PMID:21653547
Representative proteomes: a stable, scalable and unbiased proteome set for sequence analysis and functional annotation. PMID:21556138
Ontologies and standards in bioscience research: for machine or for human. PMID:21519400
Inferring protein function from homology using the Princeton Protein Orthology Database (P-POD). PMID:21400696
The what, where, how and why of gene ontology--a primer for bioinformaticians. PMID:21330331
Combining modularity, conservation, and interactions of proteins significantly increases precision and coverage of protein function prediction. PMID:21171995
AgBase: supporting functional modeling in agricultural organisms. PMID:21075795
The BioGRID Interaction Database: 2011 update. PMID:21071413
Reactome: a database of reactions, pathways and biological processes. PMID:21067998
Formalization of taxon-based constraints to detect inconsistencies in annotation and ontology development. PMID:20973947
Gene regulatory network reveals oxidative stress as the underlying molecular mechanism of type 2 diabetes and hypertension. PMID:20942928
The Protein Ontology: a structured representation of protein forms and complexes. PMID:20935045
The Renal Gene Ontology Annotation Initiative. PMID:20885853
Improving disease gene prioritization using the semantic similarity of Gene Ontology terms. PMID:20823322
GIGA: a simple, efficient algorithm for gene tree inference in the genomic age. PMID:20534164
A multilevel data integration resource for breast cancer study. PMID:20525248
A MOD(ern) perspective on literature curation. PMID:20221640
Visualization of multiple alignments, phylogenies and gene family evolution. PMID:20195253
PLAZA: a comparative genomics resource to study gene and genome evolution in plants. PMID:20040540
PANTHER version 7: improved phylogenetic trees, orthologs and collaboration with the Gene Ontology Consortium. PMID:20015972
Representing ontogeny through ontology: a developmental biologist's guide to the gene ontology. PMID:19921742
The Gene Ontology in 2010: extensions and refinements. PMID:19920128
InParanoid 7: new algorithms and tools for eukaryotic orthology analysis. PMID:19892828
Computational resources in infectious disease: limitations and challenges. PMID:19855825
Semi-automated curation of protein subcellular localization: a text mining-based approach to Gene Ontology (GO) Cellular Component curation. PMID:19622167