WikiPathways
Names
More detailed information about this field from each metasource.
WikiPathways
metasource: Fairsharing.org
version: FAIRsharing.org: WikiPathways; WikiPathways; DOI: https://doi.org/10.25504/FAIRsharing.1x53qk; Last edited: March 19, 2021, 11:17 a.m.; Last accessed: Jan 03 2022 7:05 p.m.
metasource: Biontology / Bioportal
version: extracted_at: 2022-11-04T11:10:15.597147, http://bioportal.bioontology.org/ontologies/WIKIPATHWAYS
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657
metasource: re3data.org
version: re3data.org: WikiPathways; editing status 2021-09-09; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R31NJMRO last accessed: 2022-11-04
metasource: bio.tools
version: extracted_at: 2022-11-04T11:24:43.813232
WIKIPATHWAYS
metasource: Biontology / Bioportal
version: extracted_at: 2022-11-04T11:10:15.597147, http://bioportal.bioontology.org/ontologies/WIKIPATHWAYS
wikipathways
metasource: bio.tools
version: extracted_at: 2022-11-04T11:24:43.813232
Names
More detailed information about this field from each metasource.
WikiPathways
metasource: Fairsharing.orgversion: FAIRsharing.org: WikiPathways; WikiPathways; DOI: https://doi.org/10.25504/FAIRsharing.1x53qk; Last edited: March 19, 2021, 11:17 a.m.; Last accessed: Jan 03 2022 7:05 p.m.
metasource: Biontology / Bioportal
version: extracted_at: 2022-11-04T11:10:15.597147, http://bioportal.bioontology.org/ontologies/WIKIPATHWAYS
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657
metasource: re3data.org
version: re3data.org: WikiPathways; editing status 2021-09-09; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R31NJMRO last accessed: 2022-11-04
metasource: bio.tools
version: extracted_at: 2022-11-04T11:24:43.813232
WIKIPATHWAYS
metasource: Biontology / Bioportalversion: extracted_at: 2022-11-04T11:10:15.597147, http://bioportal.bioontology.org/ontologies/WIKIPATHWAYS
wikipathways
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:24:43.813232
Other names: WIKIPATHWAYS, wikipathways
Names
More detailed information about this field from each metasource.
WikiPathways
metasource: Fairsharing.orgversion: FAIRsharing.org: WikiPathways; WikiPathways; DOI: https://doi.org/10.25504/FAIRsharing.1x53qk; Last edited: March 19, 2021, 11:17 a.m.; Last accessed: Jan 03 2022 7:05 p.m.
metasource: Biontology / Bioportal
version: extracted_at: 2022-11-04T11:10:15.597147, http://bioportal.bioontology.org/ontologies/WIKIPATHWAYS
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657
metasource: re3data.org
version: re3data.org: WikiPathways; editing status 2021-09-09; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R31NJMRO last accessed: 2022-11-04
metasource: bio.tools
version: extracted_at: 2022-11-04T11:24:43.813232
WIKIPATHWAYS
metasource: Biontology / Bioportalversion: extracted_at: 2022-11-04T11:10:15.597147, http://bioportal.bioontology.org/ontologies/WIKIPATHWAYS
wikipathways
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:24:43.813232
WikiPathways is an open, collaborative platform dedicated to the curation of biological pathways. WikiPathways was established to facilitate the contribution and maintenance of pathway information by the biology community.
Description
More detailed information about this field from each metasource.
WikiPathways is an open, collaborative platform dedicated to the curation of biological pathways. WikiPathways was established to facilitate the contribution and maintenance of pathway information by the biology community.
metasource: Fairsharing.orgversion: FAIRsharing.org: WikiPathways; WikiPathways; DOI: https://doi.org/10.25504/FAIRsharing.1x53qk; Last edited: March 19, 2021, 11:17 a.m.; Last accessed: Jan 03 2022 7:05 p.m.
The WP ontology for WikiPathways.
metasource: Biontology / Bioportalversion: extracted_at: 2022-11-04T11:10:15.597147, http://bioportal.bioontology.org/ontologies/WIKIPATHWAYS
WikiPathways (wikipathways.org) captures the collective knowledge represented in biological pathways. By providing a database in a curated, machine readable way, omics data analysis and visualization is enabled. WikiPathways and other pathway databases are used to analyze experimental data by research groups in many fields. Due to the open and collaborative nature of the WikiPathways platform, our content keeps growing and is getting more accurate, making WikiPathways a reliable and rich pathway database. Previously, however, the focus was primarily on genes and proteins, leaving many metabolites with only limited annotation. Recent curation efforts focused on improving the annotation of metabolism and metabolic pathways by associating unmapped metabolites with database identifiers and providing more detailed interaction knowledge. Here, we report the outcomes of the continued growth and curation efforts, such as a doubling of the number of annotated metabolite nodes in WikiPathways. Furthermore, we introduce an OpenAPI documentation of our web services and the FAIR (Findable, Accessible, Interoperable and Reusable) annotation of resources to increase the interoperability of the knowledge encoded in these pathways and experimental omics data. New search options, monthly downloads, more links to metabolite databases, and new portals make pathway knowledge more effortlessly accessible to individual researchers and research communities.
metasource: Nucleic Acid Research database catalogueversion: extracted_at: 2022-11-04T11:16:25.468657
WikiPathways was established to facilitate the contribution and maintenance of pathway information by the biology community. WikiPathways is an open, collaborative platform dedicated to the curation of biological pathways. WikiPathways thus presents a new model for pathway databases that enhances and complements ongoing efforts, such as KEGG, Reactome and Pathway Commons. Building on the same MediaWiki software that powers Wikipedia, we added a custom graphical pathway editing tool and integrated databases covering major gene, protein, and small-molecule systems. The familiar web-based format of WikiPathways greatly reduces the barrier to participate in pathway curation. More importantly, the open, public approach of WikiPathways allows for broader participation by the entire community, ranging from students to senior experts in each field. This approach also shifts the bulk of peer review, editorial curation, and maintenance to the community.
metasource: re3data.orgversion: re3data.org: WikiPathways; editing status 2021-09-09; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R31NJMRO last accessed: 2022-11-04
WikiPathways is a database of biological pathways maintained by and for the scientific community.
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:24:43.813232
Webpage:
http://wikipathways.orgWebpage
More detailed information about this field from each metasource.
http://wikipathways.org
metasource: Fairsharing.orgversion: FAIRsharing.org: WikiPathways; WikiPathways; DOI: https://doi.org/10.25504/FAIRsharing.1x53qk; Last edited: March 19, 2021, 11:17 a.m.; Last accessed: Jan 03 2022 7:05 p.m.
metasource: re3data.org
version: re3data.org: WikiPathways; editing status 2021-09-09; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R31NJMRO last accessed: 2022-11-04
http://www.wikipathways.org/
metasource: Biontology / Bioportalversion: extracted_at: 2022-11-04T11:10:15.597147, http://bioportal.bioontology.org/ontologies/WIKIPATHWAYS
http://wikipathways.org/
metasource: Nucleic Acid Research database catalogueversion: extracted_at: 2022-11-04T11:16:25.468657
http://www.wikipathways.org
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:24:43.813232
Licence:
Name: Creative Commons Attribution 3.0 Unported (CC BY 3.0)Licence name
More detailed information about this field from each metasource.
Creative Commons Attribution 3.0 Unported (CC BY 3.0)
metasource: Fairsharing.orgversion: FAIRsharing.org: WikiPathways; WikiPathways; DOI: https://doi.org/10.25504/FAIRsharing.1x53qk; Last edited: March 19, 2021, 11:17 a.m.; Last accessed: Jan 03 2022 7:05 p.m.
CC0
metasource: re3data.orgversion: re3data.org: WikiPathways; editing status 2021-09-09; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R31NJMRO last accessed: 2022-11-04
Apache-2.0
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:24:43.813232
Licence URL
More detailed information about this field from each metasource.
https://creativecommons.org/licenses/by/3.0/
metasource: Fairsharing.orgversion: FAIRsharing.org: WikiPathways; WikiPathways; DOI: https://doi.org/10.25504/FAIRsharing.1x53qk; Last edited: March 19, 2021, 11:17 a.m.; Last accessed: Jan 03 2022 7:05 p.m.
https://creativecommons.org/publicdomain/zero/1.0/
metasource: re3data.orgversion: re3data.org: WikiPathways; editing status 2021-09-09; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R31NJMRO last accessed: 2022-11-04
Publications:
(11)
Publications
More detailed information about this field from each metasource.
WikiPathways: pathway editing for the people
PMID: 18651794
metasource: Fairsharing.org
version: FAIRsharing.org: WikiPathways; WikiPathways; DOI: https://doi.org/10.25504/FAIRsharing.1x53qk; Last edited: March 19, 2021, 11:17 a.m.; Last accessed: Jan 03 2022 7:05 p.m.
WikiPathways: building research communities on biological pathways
PMID: 22096230
metasource: Fairsharing.org
version: FAIRsharing.org: WikiPathways; WikiPathways; DOI: https://doi.org/10.25504/FAIRsharing.1x53qk; Last edited: March 19, 2021, 11:17 a.m.; Last accessed: Jan 03 2022 7:05 p.m.
WikiPathways: capturing the full diversity of pathway knowledge
PMID: 26481357
metasource: Fairsharing.org
version: FAIRsharing.org: WikiPathways; WikiPathways; DOI: https://doi.org/10.25504/FAIRsharing.1x53qk; Last edited: March 19, 2021, 11:17 a.m.; Last accessed: Jan 03 2022 7:05 p.m.
WikiPathways: connecting communities
PMID: 33211851
metasource: Fairsharing.org
version: FAIRsharing.org: WikiPathways; WikiPathways; DOI: https://doi.org/10.25504/FAIRsharing.1x53qk; Last edited: March 19, 2021, 11:17 a.m.; Last accessed: Jan 03 2022 7:05 p.m.
Mining biological pathways using WikiPathways web services
PMID: 19649250
metasource: Fairsharing.org
version: FAIRsharing.org: WikiPathways; WikiPathways; DOI: https://doi.org/10.25504/FAIRsharing.1x53qk; Last edited: March 19, 2021, 11:17 a.m.; Last accessed: Jan 03 2022 7:05 p.m.
https://scholia.toolforge.org/topic/Q7999828
metasource: Biontology / Bioportal
version: extracted_at: 2022-11-04T11:10:15.597147, http://bioportal.bioontology.org/ontologies/WIKIPATHWAYS
https://doi.org/10.1093/nar/gkaa1024
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657
http://dx.doi.org/10.1093/nar/gkv1024
metasource: bio.tools
version: extracted_at: 2022-11-04T11:24:43.813232
http://dx.doi.org/10.1371/journal.pone.0006447
metasource: bio.tools
version: extracted_at: 2022-11-04T11:24:43.813232
http://dx.doi.org/10.1093/NAR/GKAA1024
metasource: bio.tools
version: extracted_at: 2022-11-04T11:24:43.813232
http://dx.doi.org/10.1093/NAR/GKX1064
metasource: bio.tools
version: extracted_at: 2022-11-04T11:24:43.813232
Publications
More detailed information about this field from each metasource.
WikiPathways: pathway editing for the people
PMID: 18651794
metasource: Fairsharing.org
version: FAIRsharing.org: WikiPathways; WikiPathways; DOI: https://doi.org/10.25504/FAIRsharing.1x53qk; Last edited: March 19, 2021, 11:17 a.m.; Last accessed: Jan 03 2022 7:05 p.m.
WikiPathways: building research communities on biological pathways
PMID: 22096230
metasource: Fairsharing.org
version: FAIRsharing.org: WikiPathways; WikiPathways; DOI: https://doi.org/10.25504/FAIRsharing.1x53qk; Last edited: March 19, 2021, 11:17 a.m.; Last accessed: Jan 03 2022 7:05 p.m.
WikiPathways: capturing the full diversity of pathway knowledge
PMID: 26481357
metasource: Fairsharing.org
version: FAIRsharing.org: WikiPathways; WikiPathways; DOI: https://doi.org/10.25504/FAIRsharing.1x53qk; Last edited: March 19, 2021, 11:17 a.m.; Last accessed: Jan 03 2022 7:05 p.m.
WikiPathways: connecting communities
PMID: 33211851
metasource: Fairsharing.org
version: FAIRsharing.org: WikiPathways; WikiPathways; DOI: https://doi.org/10.25504/FAIRsharing.1x53qk; Last edited: March 19, 2021, 11:17 a.m.; Last accessed: Jan 03 2022 7:05 p.m.
Mining biological pathways using WikiPathways web services
PMID: 19649250
metasource: Fairsharing.org
version: FAIRsharing.org: WikiPathways; WikiPathways; DOI: https://doi.org/10.25504/FAIRsharing.1x53qk; Last edited: March 19, 2021, 11:17 a.m.; Last accessed: Jan 03 2022 7:05 p.m.
https://scholia.toolforge.org/topic/Q7999828
metasource: Biontology / Bioportalversion: extracted_at: 2022-11-04T11:10:15.597147, http://bioportal.bioontology.org/ontologies/WIKIPATHWAYS
https://doi.org/10.1093/nar/gkaa1024
metasource: Nucleic Acid Research database catalogueversion: extracted_at: 2022-11-04T11:16:25.468657
http://dx.doi.org/10.1093/nar/gkv1024
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:24:43.813232
http://dx.doi.org/10.1371/journal.pone.0006447
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:24:43.813232
http://dx.doi.org/10.1093/NAR/GKAA1024
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:24:43.813232
http://dx.doi.org/10.1093/NAR/GKX1064
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:24:43.813232
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WikiPathways: pathway editing for the people
PubMed citations: 273.
273 articles citing: WikiPathways: pathway editing for the people
Challenges and Limitations of Biological Network Analysis. PMID:35892929
Tumor treating fields affect mesothelioma cell proliferation by exerting histotype-dependent cell cycle checkpoint activations and transcriptional modulations. PMID:35840560
Individualized discovery of rare cancer drivers in global network context. PMID:35593700
DAVID: a web server for functional enrichment analysis and functional annotation of gene lists (2021 update). PMID:35325185
Pathway Analysis for Cancer Research and Precision Oncology Applications. PMID:35230687
Structurally-discovered KLF4 variants accelerate and stabilize reprogramming to pluripotency. PMID:35106457
Overexpression of microRNAs miR-25-3p, miR-185-5p and miR-132-3p in Late Onset Fetal Growth Restriction, Validation of Results and Study of the Biochemical Pathways Involved. PMID:35008715
RNA sequencing of glioblastoma tissue slice cultures reveals the effects of treatment at the transcriptional level. PMID:34923780
RDFizing the biosynthetic pathway of E.coli O-antigen to enable semantic sharing of microbiology data. PMID:34809564
CyFi-MAP: an interactive pathway-based resource for cystic fibrosis. PMID:34782688
Identification of common microRNA between COPD and non-small cell lung cancer through pathway enrichment analysis. PMID:34635059
A Chinese host genetic study discovered IFNs and causality of laboratory traits on COVID-19 severity. PMID:34608450
Using BioPAX-Parser (BiP) to enrich lists of genes or proteins with pathway data. PMID:34592927
A highly multiplexed quantitative phosphosite assay for biology and preclinical studies. PMID:34569154
Identification of Immune-Related Risk Signatures for the Prognostic Prediction in Oral Squamous Cell Carcinoma. PMID:34497859
Identifying molecular insight of synergistic complexities for SARS-CoV-2 infection with pre-existing type 2 diabetes. PMID:34340124
Transcriptomic changes in peripheral blood mononuclear cells with weight loss: systematic literature review and primary data synthesis. PMID:34281497
Systems Biomedicine of Primary and Metastatic Colorectal Cancer Reveals Potential Therapeutic Targets. PMID:34249670
Metabolomic and transcriptomic profiling of adult mice and larval zebrafish leptin mutants reveal a common pattern of changes in metabolites and signaling pathways. PMID:34233759
snpXplorer: a web application to explore human SNP-associations and annotate SNP-sets. PMID:34048563
PhenCards: a data resource linking human phenotype information to biomedical knowledge. PMID:34034817
Multiomic Big Data Analysis Challenges: Increasing Confidence in the Interpretation of Artificial Intelligence Assessments. PMID:34029068
Elevated dimethylarginine, ATP, cytokines, metabolic remodeling involving tryptophan metabolism and potential microglial inflammation characterize primary open angle glaucoma. PMID:33963197
Multi-Staged Data-Integrated Multi-Omics Analysis for Symptom Science Research. PMID:33827270
Adjunct N-Acetylcysteine Treatment in Hospitalized Patients With HIV-Associated Tuberculosis Dampens the Oxidative Stress in Peripheral Blood: Results From the RIPENACTB Study Trial. PMID:33613521
High-throughput phenotypic screen and transcriptional analysis identify new compounds and targets for macrophage reprogramming. PMID:33536439
CHOmics: A web-based tool for multi-omics data analysis and interactive visualization in CHO cell lines. PMID:33351794
Microbiomes for All. PMID:33281791
WikiPathways: connecting communities. PMID:33211851
Pathway information extracted from 25 years of pathway figures. PMID:33168034
Systems analysis of avascular necrosis of femoral head using integrative data analysis and literature mining delineates pathways associated with disease. PMID:33093559
Finding disease modules for cancer and COVID-19 in gene co-expression networks with the Core&Peel method. PMID:33077837
Maternal-fetal genetic interactions, imprinting, and risk of placental abruption. PMID:32972274
Transcriptomics predicts compound synergy in drug and natural product treated glioblastoma cells. PMID:32946518
Detecting qualitative changes in biological systems. PMID:32424123
Effect of VCP modulators on gene expression profiles of retinal ganglion cells in an acute injury mouse model. PMID:32144342
Exploring Integrative Analysis Using the BioMedical Evidence Graph. PMID:32097025
TGF-ß1 Induces Changes in the Energy Metabolism of White Adipose Tissue-Derived Human Adult Mesenchymal Stem/Stromal Cells In Vitro. PMID:32046088
PCOSBase: a manually curated database of polycystic ovarian syndrome. PMID:31725861
Pathway Commons 2019 Update: integration, analysis and exploration of pathway data. PMID:31647099
Identifying significantly impacted pathways: a comprehensive review and assessment. PMID:31597578
modEnrichr: a suite of gene set enrichment analysis tools for model organisms. PMID:31069376
Genes with High Network Connectivity Are Enriched for Disease Heritability. PMID:31051114
Connecting Western and Eastern Medicine from an Energy Perspective. PMID:30917563
A Genome-Wide Analysis of the Penumbral Volume in Inbred Mice following Middle Cerebral Artery Occlusion. PMID:30911049
Automated exploration of gene ontology term and pathway networks with ClueGO-REST. PMID:30847467
Shared Gene Expression Between Multiple Sclerosis and Ischemic Stroke. PMID:30809253
Leveraging chromatin accessibility for transcriptional regulatory network inference in T Helper 17 Cells. PMID:30696696
Introducing WikiPathways as a Data-Source to Support Adverse Outcome Pathways for Regulatory Risk Assessment of Chemicals and Nanomaterials. PMID:30622555
Comparison of the effects of pachymic acid, moronic acid and hydrocortisone on the polysome loading of RNAs in lipopolysaccharide-treated THP-1 macrophages. PMID:30414015
Specificity of the osmotic stress response in Candida albicans highlighted by quantitative proteomics. PMID:30262823
Glucose and lipid-related biomarkers and the antidepressant response to infliximab in patients with treatment-resistant depression. PMID:30249443
Shared Biological Pathways Between Alzheimer's Disease and Ischemic Stroke. PMID:30245614
ESCC ATLAS: A population wide compendium of biomarkers for Esophageal Squamous Cell Carcinoma. PMID:30143675
Podocyte-Specific Induction of Krüppel-Like Factor 15 Restores Differentiation Markers and Attenuates Kidney Injury in Proteinuric Kidney Disease. PMID:30143559
Comprehensive profiling of transcriptional networks specific for lactogenic differentiation of HC11 mammary epithelial stem-like cells. PMID:30082875
Network Rewiring in Cancer: Applications to Melanoma Cell Lines and the Cancer Genome Atlas Patients. PMID:30042785
DeCoST: A New Approach in Drug Repurposing From Control System Theory. PMID:29922160
EviNet: a web platform for network enrichment analysis with flexible definition of gene sets. PMID:29893885
New perspectives: systems medicine in cardiovascular disease. PMID:29699591
BIOPYDB: A Dynamic Human Cell Specific Biochemical Pathway Database with Advanced Computational Analyses Platform. PMID:29547394
Cross-sectional serum metabolomic study of multiple forms of muscular dystrophy. PMID:29441734
Evaluation and comparison of bioinformatic tools for the enrichment analysis of metabolomics data. PMID:29291722
Ensemble Modeling Approach Targeting Heterogeneous RNA-Seq data: Application to Melanoma Pseudogenes. PMID:29229974
Differential prioritization of therapies to subtypes of triple negative breast cancer using a systems medicine method. PMID:29190967
Computational systems biology approaches for Parkinson's disease. PMID:29185073
WikiPathways: a multifaceted pathway database bridging metabolomics to other omics research. PMID:29136241
PAGER 2.0: an update to the pathway, annotated-list and gene-signature electronic repository for Human Network Biology. PMID:29126216
Chemical Similarity Enrichment Analysis (ChemRICH) as alternative to biochemical pathway mapping for metabolomic datasets. PMID:29109515
Mammalian γ2 AMPK regulates intrinsic heart rate. PMID:29097735
Systematic integration of biomedical knowledge prioritizes drugs for repurposing. PMID:28936969
Chemoradiotherapy Resistance in Colorectal Cancer Cells is Mediated by Wnt/β-catenin Signaling. PMID:28811361
Detection of gene-environment interactions in the presence of linkage disequilibrium and noise by using genetic risk scores with internal weights from elastic net regression. PMID:28606108
Induction of senescence in primary glioblastoma cells by serum and TGFβ. PMID:28526854
A Pathway-Centered Analysis of Pig Domestication and Breeding in Eurasia. PMID:28500056
WikiGenomes: an open web application for community consumption and curation of gene annotation data in Wikidata. PMID:28365742
A Review of Bioinformatics Tools for Bio-Prospecting from Metagenomic Sequence Data. PMID:28321234
Connecting the Human Variome Project to nutrigenomics. PMID:28300226
A Comprehensive Gene Expression Meta-analysis Identifies Novel Immune Signatures in Rheumatoid Arthritis Patients. PMID:28210261
Uncovering stem cell differentiation factors for salivary gland regeneration by quantitative analysis of differential proteomes. PMID:28158262
Role of Mitochondrial Metabolism in the Control of Early Lineage Progression and Aging Phenotypes in Adult Hippocampal Neurogenesis. PMID:28111078
Global open data management in metabolomics. PMID:28092796
Proteome Profile of Starch Granules Purified from Rice (Oryza sativa) Endosperm. PMID:27992503
An Integrative Analysis of Preeclampsia Based on the Construction of an Extended Composite Network Featuring Protein-Protein Physical Interactions and Transcriptional Relationships. PMID:27802351
Hepatic transcriptome implications for palm fruit juice deterrence of type 2 diabetes mellitus in young male Nile rats. PMID:27795741
Long Term Culture of the A549 Cancer Cell Line Promotes Multilamellar Body Formation and Differentiation towards an Alveolar Type II Pneumocyte Phenotype. PMID:27792742
Analyzing gene expression profiles in dilated cardiomyopathy via bioinformatics methods. PMID:27737314
XMetDB: an open access database for xenobiotic metabolism. PMID:27651835
Subpathway-CorSP: Identification of metabolic subpathways via integrating expression correlations and topological features between metabolites and genes of interest within pathways. PMID:27625019
Pathway-Informed Classification System (PICS) for Cancer Analysis Using Gene Expression Data. PMID:27486299
Human Prostate Cancer Hallmarks Map. PMID:27476486
Community-Reviewed Biological Network Models for Toxicology and Drug Discovery Applications. PMID:27429547
Evaluating biomarkers to model cancer risk post cosmic ray exposure. PMID:27345199
Epigenomics of Total Acute Sleep Deprivation in Relation to Genome-Wide DNA Methylation Profiles and RNA Expression. PMID:27310475
Crowdsourcing the nodulation gene network discovery environment. PMID:27230384
Glucocorticoid receptor isoforms direct distinct mitochondrial programs to regulate ATP production. PMID:27226058
The systems biology format converter. PMID:27044654
Utilizing a structural meta-ontology for family-based quality assurance of the BioPortal ontologies. PMID:26988001
Gene expression profiling identifies candidate biomarkers for active and latent tuberculosis. PMID:26818387
Transcriptional profiling revealed the anti-proliferative effect of MFN2 deficiency and identified risk factors in lung adenocarcinoma. PMID:26733181
Collagen Type I Improves the Differentiation of Human Embryonic Stem Cells towards Definitive Endoderm. PMID:26713616
Genomic profiling screens small molecules of metastatic prostate carcinoma. PMID:26622681
Database resources of the National Center for Biotechnology Information. PMID:26615191
Aging Chart: a community resource for rapid exploratory pathway analysis of age-related processes. PMID:26602690
NDEx, the Network Data Exchange. PMID:26594663
Analyzing alternative splicing data of splice junction arrays from Parkinson patients' leukocytes before and after deep brain stimulation as compared with control donors. PMID:26484282
WikiPathways: capturing the full diversity of pathway knowledge. PMID:26481357
Virtual pathway explorer (viPEr) and pathway enrichment analysis tool (PEANuT): creating and analyzing focus networks to identify cross-talk between molecules and pathways. PMID:26467653
Systematic analysis of somatic mutations impacting gene expression in 12 tumour types. PMID:26436532
Visualizing genome and systems biology: technologies, tools, implementation techniques and trends, past, present and future. PMID:26309733
Single-Cell RNA-Seq with Waterfall Reveals Molecular Cascades underlying Adult Neurogenesis. PMID:26299571
Using prior knowledge from cellular pathways and molecular networks for diagnostic specimen classification. PMID:26141830
NET-GE: a novel NETwork-based Gene Enrichment for detecting biological processes associated to Mendelian diseases. PMID:26110971
Tools for visualization and analysis of molecular networks, pathways, and -omics data. PMID:26082651
Targeting PBK/TOPK decreases growth and survival of glioma initiating cells in vitro and attenuates tumor growth in vivo. PMID:26081429
PAGER: constructing PAGs and new PAG-PAG relationships for network biology. PMID:26072489
Defining bacterial regulons using ChIP-seq. PMID:26032817
BioMiner: Paving the Way for Personalized Medicine. PMID:26005322
VISIONET: intuitive visualisation of overlapping transcription factor networks, with applications in cardiogenic gene discovery. PMID:25929466
miR-200 promotes the mesenchymal to epithelial transition by suppressing multiple members of the Zeb2 and Snail1 transcriptional repressor complexes. PMID:25798844
Comparison of human cell signaling pathway databases--evolution, drawbacks and challenges. PMID:25632107
Biomarkers of NAFLD progression: a lipidomics approach to an epidemic. PMID:25598080
ReNE: a cytoscape plugin for regulatory network enhancement. PMID:25541727
Proteomic profiling of salivary gland after nonviral gene transfer mediated by conventional plasmids and minicircles. PMID:25414909
Database resources of the National Center for Biotechnology Information. PMID:25398906
Fine-mapping the 2q37 and 17q11.2-q22 loci for novel genes and sequence variants associated with a genetic predisposition to prostate cancer. PMID:25335771
Gene expression profiling of biological pathway alterations by radiation exposure. PMID:25276823
Mechanosensitive kinases regulate stiffness-induced cardiomyocyte maturation. PMID:25236849
Qrator: a web-based curation tool for glycan structures. PMID:25165068
Identification of genes in HepG2 cells that respond to DNA methylation and histone deacetylation inhibitor treatment. PMID:25120605
e!DAL--a framework to store, share and publish research data. PMID:24958009
LINCS Canvas Browser: interactive web app to query, browse and interrogate LINCS L1000 gene expression signatures. PMID:24906883
The Zebrafish GenomeWiki: a crowdsourcing approach to connect the long tail for zebrafish gene annotation. PMID:24578356
Utility of network integrity methods in therapeutic target identification. PMID:24550933
Pathway analysis for drug repositioning based on public database mining. PMID:24460210
Systems toxicology: from basic research to risk assessment. PMID:24446777
A provisional gene regulatory atlas for mouse heart development. PMID:24421884
CyTargetLinker: a cytoscape app to integrate regulatory interactions in network analysis. PMID:24340000
WikiPathways for plants: a community pathway curation portal and a case study in rice and arabidopsis seed development networks. PMID:24280312
Database resources of the National Center for Biotechnology Information. PMID:24259429
A Signaling Network of Thyroid-Stimulating Hormone. PMID:24255551
SMPDB 2.0: big improvements to the Small Molecule Pathway Database. PMID:24203708
Path2Models: large-scale generation of computational models from biochemical pathway maps. PMID:24180668
On Crowd-verification of Biological Networks. PMID:24151423
Toward an integrated software platform for systems pharmacology. PMID:24150748
LIN28B promotes growth and tumorigenesis of the intestinal epithelium via Let-7. PMID:24142874
Methods and approaches in the topology-based analysis of biological pathways. PMID:24133454
Using random walks to identify cancer-associated modules in expression data. PMID:24128261
Pathways of Toxicity. PMID:24127042
Wikis and collaborative writing applications in health care: a scoping review. PMID:24103318
NaviCell: a web-based environment for navigation, curation and maintenance of large molecular interaction maps. PMID:24099179
Integrated enrichment analysis of variants and pathways in genome-wide association studies indicates central role for IL-2 signaling genes in type 1 diabetes, and cytokine signaling genes in Crohn's disease. PMID:24098138
Genome-wide gene expression profiling of stress response in a spinal cord clip compression injury model. PMID:23984903
A genome-wide siRNA screen identifies proteasome addiction as a vulnerability of basal-like triple-negative breast cancer cells. PMID:23948298
Pathprinting: An integrative approach to understand the functional basis of disease. PMID:23890051
Consensus and conflict cards for metabolic pathway databases. PMID:23803311
Small RNA sequencing-microarray analyses in Parkinson leukocytes reveal deep brain stimulation-induced splicing changes that classify brain region transcriptomes. PMID:23717260
Proteomic signatures of acquired letrozole resistance in breast cancer: suppressed estrogen signaling and increased cell motility and invasiveness. PMID:23704778
WEB-based GEne SeT AnaLysis Toolkit (WebGestalt): update 2013. PMID:23703215
GeneSetDB: A comprehensive meta-database, statistical and visualisation framework for gene set analysis. PMID:23650583
CMS: a web-based system for visualization and analysis of genome-wide methylation data of human cancers. PMID:23630576
Transcriptional signatures related to glucose and lipid metabolism predict treatment response to the tumor necrosis factor antagonist infliximab in patients with treatment-resistant depression. PMID:23624296
A zebrafish high throughput screening system used for Staphylococcus epidermidis infection marker discovery. PMID:23586901
Enrichr: interactive and collaborative HTML5 gene list enrichment analysis tool. PMID:23586463
A randomised controlled phase II trial of pre-operative celecoxib treatment reveals anti-tumour transcriptional response in primary breast cancer. PMID:23566419
PathVisio-Faceted Search: an exploration tool for multi-dimensional navigation of large pathways. PMID:23547033
A pathway approach to investigate the function and regulation of SREBPs. PMID:23516131
Systems biology approaches for discovering biomarkers for traumatic brain injury. PMID:23510232
Transcriptome analysis of Inbred Long Sleep and Inbred Short Sleep mice. PMID:23433184
Chapter 3: Small molecules and disease. PMID:23300405
IntPath--an integrated pathway gene relationship database for model organisms and important pathogens. PMID:23282057
Database resources of the National Center for Biotechnology Information. PMID:23193264
Pathway Distiller - multisource biological pathway consolidation. PMID:23134636
A travel guide to Cytoscape plugins. PMID:23132118
Jointly creating digital abstracts: dealing with synonymy and polysemy. PMID:23110757
EnrichNet: network-based gene set enrichment analysis. PMID:22962466
The Cell Collective: toward an open and collaborative approach to systems biology. PMID:22871178
Integrating literature-constrained and data-driven inference of signalling networks. PMID:22734019
Public domain databases for medicinal chemistry. PMID:22731701
WikiCell: a unified resource platform for human transcriptomics research. PMID:22702248
Using the reactome database. PMID:22700314
Savant Genome Browser 2: visualization and analysis for population-scale genomics. PMID:22638571
MetaMapp: mapping and visualizing metabolomic data by integrating information from biochemical pathways and chemical and mass spectral similarity. PMID:22591066
Linking genes to diseases with a SNPedia-Gene Wiki mashup. PMID:22541597
Identification and pathway analysis of microRNAs with no previous involvement in breast cancer. PMID:22438871
Proteomic analysis of acquired tamoxifen resistance in MCF-7 cells reveals expression signatures associated with enhanced migration. PMID:22417809
Aggregating data for computational toxicology applications: The U.S. Environmental Protection Agency (EPA) Aggregated Computational Toxicology Resource (ACToR) System. PMID:22408426
A systems approach identifies HIPK2 as a key regulator of kidney fibrosis. PMID:22406746
Comparative analysis and assessment of M. tuberculosis H37Rv protein-protein interaction datasets. PMID:22369691
Nutrigenetics, nutrigenomics, and selenium. PMID:22303312
Effect of serum amyloid A1 treatment on global gene expression in THP-1-derived macrophages. PMID:22228103
Measuring passive myocardial stiffness in Drosophila melanogaster to investigate diastolic dysfunction. PMID:22225769
PathVisio-Validator: a rule-based validation plugin for graphical pathway notations. PMID:22199389
Meeting report from the first meetings of the Computational Modeling in Biology Network (COMBINE). PMID:22180826
Mining the Gene Wiki for functional genomic knowledge. PMID:22165947
Database resources of the National Center for Biotechnology Information. PMID:22140104
PathVar: analysis of gene and protein expression variance in cellular pathways using microarray data. PMID:22123829
hiPathDB: a human-integrated pathway database with facile visualization. PMID:22123737
The Stem Cell Discovery Engine: an integrated repository and analysis system for cancer stem cell comparisons. PMID:22121217
INOH: ontology-based highly structured database of signal transduction pathways. PMID:22120663
Capture of microRNA-bound mRNAs identifies the tumor suppressor miR-34a as a regulator of growth factor signaling. PMID:22102825
WikiPathways: building research communities on biological pathways. PMID:22096230
Software for systems biology: from tools to integrated platforms. PMID:22048662
Critical assessment of human metabolic pathway databases: a stepping stone for future integration. PMID:21999653
Tools and collaborative environments for bioinformatics research. PMID:21984743
3DSwap: curated knowledgebase of proteins involved in 3D domain swapping. PMID:21959866
A network-based gene-weighting approach for pathway analysis. PMID:21894192
Exploring pathway interactions in insulin resistant mouse liver. PMID:21843341
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
Integrative computational biology for cancer research. PMID:21691773
The Biological Connection Markup Language: a SBGN-compliant format for visualization, filtering and analysis of biological pathways. PMID:21653523
CoPub update: CoPub 5.0 a text mining system to answer biological questions. PMID:21622961
Relating protein adduction to gene expression changes: a systems approach. PMID:21594272
Social engineering for virtual 'big science' in systems biology. PMID:21587248
Extending biochemical databases by metabolomic surveys. PMID:21566124
Molecular aspect of good eating quality formation in Japonica rice. PMID:21494675
Answering biological questions: querying a systems biology database for nutrigenomics. PMID:21437033
Human papillomavirus deregulates the response of a cellular network comprising of chemotactic and proinflammatory genes. PMID:21423754
Current trends and new challenges of databases and web applications for systems driven biological research. PMID:21423387
A method for visualization of "omic" datasets for sphingolipid metabolism to predict potentially interesting differences. PMID:21415121
Network-based pipeline for analyzing MS data: an application toward liver cancer. PMID:21410269
Assessing quality and completeness of human transcriptional regulatory pathways on a genome-wide scale. PMID:21356087
FNV: light-weight flash-based network and pathway viewer. PMID:21349871
MicroRNAs profiling in murine models of acute and chronic asthma: a relationship with mRNAs targets. PMID:21305051
Evolution of gene regulation of pluripotency--the case for wiki tracks at genome browsers. PMID:21190561
The Micronutrient Genomics Project: a community-driven knowledge base for micronutrient research. PMID:21189865
The PluriNetWork: an electronic representation of the network underlying pluripotency in mouse, and its applications. PMID:21179244
Reactome: a database of reactions, pathways and biological processes. PMID:21067998
PathEx: a novel multi factors based datasets selector web tool. PMID:20969778
Ten simple rules for editing Wikipedia. PMID:20941386
Signaling network of dendritic cells in response to pathogens: a community-input supported knowledgebase. PMID:20929569
Gene expression study of monocytes/macrophages during early foreign body reaction and identification of potential precursors of myofibroblasts. PMID:20886081
The BioPAX community standard for pathway data sharing. PMID:20829833
Finding the right questions: exploratory pathway analysis to enhance biological discovery in large datasets. PMID:20824171
Gene set analysis exploiting the topology of a pathway. PMID:20809931
TOPSAN: a collaborative annotation environment for structural genomics. PMID:20716366
PDBWiki: added value through community annotation of the Protein Data Bank. PMID:20624717
PathText: a text mining integrator for biological pathway visualizations. PMID:20529930
Computational tools for the interactive exploration of proteomic and structural data. PMID:20525940
AltAnalyze and DomainGraph: analyzing and visualizing exon expression data. PMID:20513647
Pathway signature and cellular differentiation in clear cell renal cell carcinoma. PMID:20502531
The mEPN scheme: an intuitive and flexible graphical system for rendering biological pathways. PMID:20478018
Construction of a large scale integrated map of macrophage pathogen recognition and effector systems. PMID:20470404
Payao: a community platform for SBML pathway model curation. PMID:20371497
Visualization of omics data for systems biology. PMID:20195258
Collaboratively charting the gene-to-phenotype network of human congenital heart defects. PMID:20193066
A community-curated consensual annotation that is continuously updated: the Bacillus subtilis centred wiki SubtiWiki. PMID:20157485
Time-resolved and tissue-specific systems analysis of the pathogenesis of insulin resistance. PMID:20098690
NetPath: a public resource of curated signal transduction pathways. PMID:20067622
The BridgeDb framework: standardized access to gene, protein and metabolite identifier mapping services. PMID:20047655
Mass-spectrometry-based metabolomics: limitations and recommendations for future progress with particular focus on nutrition research. PMID:20046865
SMPDB: The Small Molecule Pathway Database. PMID:19948758
BioGPS: an extensible and customizable portal for querying and organizing gene annotation resources. PMID:19919682
Pathway projector: web-based zoomable pathway browser using KEGG atlas and Google Maps API. PMID:19907644
Alternative splicing in the differentiation of human embryonic stem cells into cardiac precursors. PMID:19893621
HPD: an online integrated human pathway database enabling systems biology studies. PMID:19811689
Automated seeding of specialised wiki knowledgebases with BioKb. PMID:19758431
The Gene Wiki: community intelligence applied to human gene annotation. PMID:19755503
Mining biological pathways using WikiPathways web services. PMID:19649250
Pathway databases and tools for their exploitation: benefits, current limitations and challenges. PMID:19638971
Use of GenMAPP and MAPPFinder to analyse pathways involved in chickens infected with the protozoan parasite Eimeria. PMID:19615120
WebLab: a data-centric, knowledge-sharing bioinformatic platform. PMID:19465388
Science wikinomics. Mass networking through the web creates new forms of scientific collaboration. PMID:19415079
Seeking health information online: does Wikipedia matter? PMID:19390105
Metagenome annotation using a distributed grid of undergraduate students. PMID:19067492
Bioinformatics for the NuGO proof of principle study: analysis of gene expression in muscle of ApoE3*Leiden mice on a high-fat diet using PathVisio. PMID:19034557
Bioinformatic interrogation of expression array data to identify nutritionally regulated genes potentially modulated by DNA methylation. PMID:19034551
The role of bioinformatics in pathway curation. PMID:19034548
SNPLogic: an interactive single nucleotide polymorphism selection, annotation, and prioritization system. PMID:18984625
PLoS Biology at 5: the future is open access. PMID:18959486
Search extension transforms Wiki into a relational system: a case for flavonoid metabolite database. PMID:18822113
Presenting and exploring biological pathways with PathVisio. PMID:18817533 -
WikiPathways: building research communities on biological pathways
PubMed citations: 247.
247 articles citing: WikiPathways: building research communities on biological pathways
Identification of Differentially Expressed Long Noncoding RNAs as Functional Biomarkers and Construction of Function Enrichment Network in Oral Squamous Cell Carcinoma. PMID:35795287
A pan-cancer survey of cell line tumor similarity by feature-weighted molecular profiles. PMID:35475239
Single-cell transcriptomics identifies Mcl-1 as a target for senolytic therapy in cancer. PMID:35449130
Stat5b inhibition blocks proliferation and tumorigenicity of glioblastoma stem cells derived from a de novo murine brain cancer model. PMID:35411230
An In Vivo Inflammatory Loop Potentiates KRAS Blockade. PMID:35327394
Pathway Analysis for Cancer Research and Precision Oncology Applications. PMID:35230687
Plants Metabolome Study: Emerging Tools and Techniques. PMID:34834772
Trends in the Application of "Omics" to Ecotoxicology and Stress Ecology. PMID:34680873
Recipient APOL1 risk alleles associate with death-censored renal allograft survival and rejection episodes. PMID:34499625
Identification of CCNB2 as A Potential Non-Invasive Breast Cancer Biomarker in Peripheral Blood Mononuclear Cells Using The Systems Biology Approach. PMID:34455715
PathExNET: A tool for extracting pathway expression networks from gene expression statistics. PMID:34429851
Dietary omega-3 fatty acid intake impacts peripheral blood DNA methylation -anti-inflammatory effects and individual variability in a pilot study. PMID:34411715
Identification of Nrf2-responsive microRNA networks as putative mediators of myocardial reductive stress. PMID:34099738
Integration of summary data from GWAS and eQTL studies identified novel risk genes for coronary artery disease. PMID:33725943
A Meta-Analysis of the Effects of High-LET Ionizing Radiations in Human Gene Expression. PMID:33546472
Inhibition of Gli2 suppresses tumorigenicity in glioblastoma stem cells derived from a de novo murine brain cancer model. PMID:33414520
TMEA: A Thermodynamically Motivated Framework for Functional Characterization of Biological Responses to System Acclimation. PMID:33286800
WikiPathways: connecting communities. PMID:33211851
Integrated transcriptome meta-analysis of pancreatic ductal adenocarcinoma and matched adjacent pancreatic tissues. PMID:33194391
Dynamic remodelling of the human host cell proteome and phosphoproteome upon enterovirus infection. PMID:32859902
Genes Involved in Energy Metabolism Are Differentially Expressed During the Day-Night Cycle in Murine Retinal Pigment Epithelium. PMID:32460311
Extending the small-molecule similarity principle to all levels of biology with the Chemical Checker. PMID:32440005
The Molecular Processes in the Trabecular Meshwork After Exposure to Corticosteroids and in Corticosteroid-Induced Ocular Hypertension. PMID:32305042
Visualizing metabolic network dynamics through time-series metabolomic data. PMID:32245365
Investigating global gene expression changes in a murine model of cherubism. PMID:32165349
Effect of VCP modulators on gene expression profiles of retinal ganglion cells in an acute injury mouse model. PMID:32144342
Sexual-dimorphism in human immune system aging. PMID:32029736
Graph-based information diffusion method for prioritizing functionally related genes in protein-protein interaction networks. PMID:31797617
Discovery of disease- and drug-specific pathways through community structures of a literature network. PMID:31738408
PathBank: a comprehensive pathway database for model organisms. PMID:31602464
Genomic alterations in high-risk chronic lymphocytic leukemia frequently affect cell cycle key regulators and NOTCH1-regulated transcription. PMID:31467127
IRNdb: the database of immunologically relevant non-coding RNAs. PMID:31414702
Comprehensive bioinformatics analysis of trabecular meshwork gene expression data to unravel the molecular pathogenesis of primary open-angle glaucoma. PMID:31197946
Genetic Predisposition for Immune System, Hormone, and Metabolic Dysfunction in Myalgic Encephalomyelitis/Chronic Fatigue Syndrome: A Pilot Study. PMID:31179255
Identification of Cholecystokinin by Genome-Wide Profiling as Potential Mediator of Serotonin-Dependent Behavioral Effects of Maternal Separation in the Amygdala. PMID:31133792
Integration of Multiple Data Sources for Gene Network Inference Using Genetic Perturbation Data. PMID:31009236
Metabopolis: scalable network layout for biological pathway diagrams in urban map style. PMID:30991966
Pathway enrichment analysis and visualization of omics data using g:Profiler, GSEA, Cytoscape and EnrichmentMap. PMID:30664679
Determination of host proteins composing the microenvironment of coronavirus replicase complexes by proximity-labeling. PMID:30632963
Network spectra for drug-target identification in complex diseases: new guns against old foes. PMID:30596144
Cooperative interaction among BMAL1, HSF1, and p53 protects mammalian cells from UV stress. PMID:30480104
C/VDdb: A multi-omics expression profiling database for a knowledge-driven approach in cardiovascular disease (CVD). PMID:30419069
SyNDI: synchronous network data integration framework. PMID:30400817
Computational discovery of dynamic cell line specific Boolean networks from multiplex time-course data. PMID:30372442
Microvesicles from malaria-infected red blood cells activate natural killer cells via MDA5 pathway. PMID:30286211
Large-scale meta-analysis highlights the hypothalamic-pituitary-gonadal axis in the genetic regulation of menstrual cycle length. PMID:30202859
Adaptive Evolution of Animal Proteins over Development: Support for the Darwin Selection Opportunity Hypothesis of Evo-Devo. PMID:30184095
A proteomic signature that reflects pancreatic beta-cell function. PMID:30161145
NetControl4BioMed: a pipeline for biomedical data acquisition and analysis of network controllability. PMID:30066633
Network Rewiring in Cancer: Applications to Melanoma Cell Lines and the Cancer Genome Atlas Patients. PMID:30042785
Phenotype-driven gene prioritization for rare diseases using graph convolution on heterogeneous networks. PMID:29980210
Oct4 regulates the embryonic axis and coordinates exit from pluripotency and germ layer specification in the mouse embryo. PMID:29915126
Anti-tumoral effects of exercise on hepatocellular carcinoma growth. PMID:29761175
Signalling maps in cancer research: construction and data analysis. PMID:29688383
A personalized, multiomics approach identifies genes involved in cardiac hypertrophy and heart failure. PMID:29507758
From correlation to causation: analysis of metabolomics data using systems biology approaches. PMID:29503602
Data processing, multi-omic pathway mapping, and metabolite activity analysis using XCMS Online. PMID:29494574
RaMP: A Comprehensive Relational Database of Metabolomics Pathways for Pathway Enrichment Analysis of Genes and Metabolites. PMID:29470400
Ribonuclease inhibitor 1 regulates erythropoiesis by controlling GATA1 translation. PMID:29408805
The extent of ribosome queuing in budding yeast. PMID:29377894
Genome-Wide Methylation Patterns in Androgen-Independent Prostate Cancer Cells: A Comprehensive Analysis Combining MeDIP-Bisulfite, RNA, and microRNA Sequencing Data. PMID:29324665
Addition of carbonic anhydrase 9 inhibitor SLC-0111 to temozolomide treatment delays glioblastoma growth in vivo. PMID:29263302
Gene Network Analysis of Interstitial Macrophages After Treatment with Induced Pluripotent Stem Cells Secretome (iPSC-cm) in the Bleomycin Injured Rat Lung. PMID:29256173
Null diffusion-based enrichment for metabolomics data. PMID:29211807
A Comparative Proteome Profile of Female Mouse Gonads Suggests a Tight Link between the Electron Transport Chain and Meiosis Initiation. PMID:29158290
Trichloroethylene metabolite S-(1,2-dichlorovinyl)-l-cysteine induces lipid peroxidation-associated apoptosis via the intrinsic and extrinsic apoptosis pathways in a first-trimester placental cell line. PMID:29129777
The UCSC Genome Browser database: 2018 update. PMID:29106570
LiverWiki: a wiki-based database for human liver. PMID:29029599
The ESRP1-GPR137 axis contributes to intestinal pathogenesis. PMID:28975893
Integrative Systems Biology Investigation of Fabry Disease. PMID:28933415
The chromatin accessibility signature of human immune aging stems from CD8+ T cells. PMID:28904110
Gene expression associated with suicide attempts in US veterans. PMID:28872639
Advances in metabolome information retrieval: turning chemistry into biology. Part II: biological information recovery. PMID:28842777
Logic programming reveals alteration of key transcription factors in multiple myeloma. PMID:28835615
Decoding the complex genetic causes of heart diseases using systems biology. PMID:28509974
Establishment of a Strong Link Between Smoking and Cancer Pathogenesis through DNA Methylation Analysis. PMID:28500316
Pathview Web: user friendly pathway visualization and data integration. PMID:28482075
Neurons and neuronal activity control gene expression in astrocytes to regulate their development and metabolism. PMID:28462931
PIF* promotes brain re-myelination locally while regulating systemic inflammation- clinically relevant multiple sclerosis M.smegmatis model. PMID:28423529
Tracking the evolution of 3D gene organization demonstrates its connection to phenotypic divergence. PMID:28369658
Drug-screening and genomic analyses of HER2-positive breast cancer cell lines reveal predictors for treatment response. PMID:28356768
Detection of Pathways Affected by Positive Selection in Primate Lineages Ancestral to Humans. PMID:28333345
The Transcriptome of the Zebrafish Embryo After Chemical Exposure: A Meta-Analysis. PMID:28329862
A Review of Bioinformatics Tools for Bio-Prospecting from Metagenomic Sequence Data. PMID:28321234
Bayesian model of signal rewiring reveals mechanisms of gene dysregulation in acquired drug resistance in breast cancer. PMID:28288164
A Web Tool for Generating High Quality Machine-readable Biological Pathways. PMID:28287524
Avoiding the pitfalls of gene set enrichment analysis with SetRank. PMID:28259142
Systematic analyses of drugs and disease indications in RepurposeDB reveal pharmacological, biological and epidemiological factors influencing drug repositioning. PMID:28200013
Establishment of a integrative multi-omics expression database CKDdb in the context of chronic kidney disease (CKD). PMID:28079125
Impaired liver regeneration in aged mice can be rescued by silencing Hippo core kinases MST1 and MST2. PMID:27940445
MicroScope in 2017: an expanding and evolving integrated resource for community expertise of microbial genomes. PMID:27899624
Biomolecular Network-Based Synergistic Drug Combination Discovery. PMID:27891522
Systems Biomedicine of Rabies Delineates the Affected Signaling Pathways. PMID:27872612
The Modular Adaptive Ribosome. PMID:27812193
Multi-OMIC profiling of survival and metabolic signaling networks in cells subjected to photodynamic therapy. PMID:27803950
Hepatic transcriptome implications for palm fruit juice deterrence of type 2 diabetes mellitus in young male Nile rats. PMID:27795741
Long Term Culture of the A549 Cancer Cell Line Promotes Multilamellar Body Formation and Differentiation towards an Alveolar Type II Pneumocyte Phenotype. PMID:27792742
Analyzing gene expression profiles in dilated cardiomyopathy via bioinformatics methods. PMID:27737314
Genome sequence of the basal haplorrhine primate Tarsius syrichta reveals unusual insertions. PMID:27708261
Increasing rigor in NMR-based metabolomics through validated and open source tools. PMID:27643760
Identification of miRNAs Potentially Involved in Bronchiolitis Obliterans Syndrome: A Computational Study. PMID:27564214
New insights in Rett syndrome using pathway analysis for transcriptomics data. PMID:27517371
Bioinformatic prediction of transcription factor binding sites at promoter regions of genes for photoperiod and vernalization responses in model and temperate cereal plants. PMID:27503086
Prediction of scaffold proteins based on protein interaction and domain architectures. PMID:27490120
PreImplantation factor (PIF) therapy provides comprehensive protection against radiation induced pathologies. PMID:27449294
Clinical Metabolomics: The New Metabolic Window for Inborn Errors of Metabolism Investigations in the Post-Genomic Era. PMID:27447622
Expression and methylation patterns partition luminal-A breast tumors into distinct prognostic subgroups. PMID:27386846
The harmonizome: a collection of processed datasets gathered to serve and mine knowledge about genes and proteins. PMID:27374120
Transcriptome Alterations In X-Irradiated Human Gingiva Fibroblasts. PMID:27356049
Using the Semantic Web for Rapid Integration of WikiPathways with Other Biological Online Data Resources. PMID:27336457
BioASF: a framework for automatically generating executable pathway models specified in BioPAX. PMID:27307645
MyoD reprogramming requires Six1 and Six4 homeoproteins: genome-wide cis-regulatory module analysis. PMID:27302134
Immune signatures and disorder-specific patterns in a cross-disorder gene expression analysis. PMID:27151072
Supporting community annotation and user collaboration in the integrated microbial genomes (IMG) system. PMID:27118214
Screening for genes and subnetworks associated with pancreatic cancer based on the gene expression profile. PMID:27035224
Trichlorobenzene-substituted azaaryl compounds as novel FGFR inhibitors exhibiting potent antitumor activity in bladder cancer cells in vitro and in vivo. PMID:27029060
Systems psychopharmacology: A network approach to developing novel therapies. PMID:27014599
DNA Damage Response Is Involved in the Developmental Toxicity of Mebendazole in Zebrafish Retina. PMID:27014071
miTALOS v2: Analyzing Tissue Specific microRNA Function. PMID:26998997
Progress in low-resolution ab initio phasing with CrowdPhase. PMID:26960132
Complementary Post Transcriptional Regulatory Information is Detected by PUNCH-P and Ribosome Profiling. PMID:26898226
Translational bioinformatics in the era of real-time biomedical, health care and wellness data streams. PMID:26876889
Selectivity profiling of BCRP versus P-gp inhibition: from automated collection of polypharmacology data to multi-label learning. PMID:26855674
Transcriptional Analysis of T Cells Resident in Human Skin. PMID:26824609
Advanced Running Performance by Genetic Predisposition in Male Dummerstorf Marathon Mice (DUhTP) Reveals Higher Sterol Regulatory Element-Binding Protein (SREBP) Related mRNA Expression in the Liver and Higher Serum Levels of Progesterone. PMID:26799318
Collagen Type I Improves the Differentiation of Human Embryonic Stem Cells towards Definitive Endoderm. PMID:26713616
Constructing a molecular interaction network for thyroid cancer via large-scale text mining of gene and pathway events. PMID:26679379
AnGeLi: A Tool for the Analysis of Gene Lists from Fission Yeast. PMID:26635866
Genomic profiling screens small molecules of metastatic prostate carcinoma. PMID:26622681
Analysis of volatile organic compounds in exhaled breath to diagnose ventilator-associated pneumonia. PMID:26608483
Aging Chart: a community resource for rapid exploratory pathway analysis of age-related processes. PMID:26602690
Therapeutic target database update 2016: enriched resource for bench to clinical drug target and targeted pathway information. PMID:26578601
The homeoprotein DLX3 and tumor suppressor p53 co-regulate cell cycle progression and squamous tumor growth. PMID:26522723
WikiPathways: capturing the full diversity of pathway knowledge. PMID:26481357
The eNanoMapper database for nanomaterial safety information. PMID:26425413
Targeting Mortalin by Embelin Causes Activation of Tumor Suppressor p53 and Deactivation of Metastatic Signaling in Human Breast Cancer Cells. PMID:26376435
PathwayMatrix: visualizing binary relationships between proteins in biological pathways. PMID:26361499
ConTour: Data-Driven Exploration of Multi-Relational Datasets for Drug Discovery. PMID:26356902
Serum N-glycan analysis in breast cancer patients--Relation to tumour biology and clinical outcome. PMID:26321095
Integration of extracellular RNA profiling data using metadata, biomedical ontologies and Linked Data technologies. PMID:26320941
Escher: A Web Application for Building, Sharing, and Embedding Data-Rich Visualizations of Biological Pathways. PMID:26313928
In vivo hematopoietic Myc activation directs a transcriptional signature in endothelial cells within the bone marrow microenvironment. PMID:26308666
Advances in computational approaches for prioritizing driver mutations and significantly mutated genes in cancer genomes. PMID:26307061
Meta-analysis of shared genetic architecture across ten pediatric autoimmune diseases. PMID:26301688
Automatically visualise and analyse data on pathways using PathVisioRPC from any programming environment. PMID:26298294
YAP1 Exerts Its Transcriptional Control via TEAD-Mediated Activation of Enhancers. PMID:26295846
Integrative network-based analysis of mRNA and microRNA expression in 1,25-dihydroxyvitamin D3-treated cancer cells. PMID:26276506
The Histone-Deacetylase-Inhibitor Suberoylanilide Hydroxamic Acid Promotes Dental Pulp Repair Mechanisms Through Modulation of Matrix Metalloproteinase-13 Activity. PMID:26264761
Transcriptomic Analysis of Metabolic Pathways in Milkfish That Respond to Salinity and Temperature Changes. PMID:26263550
Human metabolic atlas: an online resource for human metabolism. PMID:26209309
Atlas of Cancer Signalling Network: a systems biology resource for integrative analysis of cancer data with Google Maps. PMID:26192618
Using gene expression signatures to identify novel treatment strategies in gulf war illness. PMID:26156520
Time-course gene profiling and networks in demethylated retinoblastoma cell line. PMID:26143641
Whole transcriptome analysis reveals changes in expression of immune-related genes during and after bleaching in a reef-building coral. PMID:26064625
Inference of Evolutionary Forces Acting on Human Biological Pathways. PMID:25971280
Pathways with PathWhiz. PMID:25934797
Identification of sample-specific regulations using integrative network level analysis. PMID:25928379
A new CRB1 rat mutation links Müller glial cells to retinal telangiectasia. PMID:25878282
Genistein exerts anti-leukemic effects on genetically different acute myeloid leukemia cell lines by inhibiting protein synthesis and cell proliferation while inducing apoptosis - molecular insights from an iTRAQ™ quantitative proteomics study. PMID:25859554
Expression quantitative trait loci (eQTLs) in microRNA genes are enriched for schizophrenia and bipolar disorder association signals. PMID:25817407
Analytical methods in untargeted metabolomics: state of the art in 2015. PMID:25798438
Phenotype specific analyses reveal distinct regulatory mechanism for chronically activated p53. PMID:25790137
Toxicogenomics profiling of bone marrow from rats treated with topotecan in combination with oxaliplatin: a mechanistic strategy to inform combination toxicity. PMID:25729387
PathCards: multi-source consolidation of human biological pathways. PMID:25725062
PathVisio 3: an extendable pathway analysis toolbox. PMID:25706687
Network representations of immune system complexity. PMID:25625853
Prediction of signaling cross-talks contributing to acquired drug resistance in breast cancer cells by Bayesian statistical modeling. PMID:25599599
ENViz: a Cytoscape App for integrated statistical analysis and visualization of sample-matched data with multiple data types. PMID:25577435
Proceedings of the Thirteenth Annual UT- KBRIN Bioinformatics Summit 2014. PMID:25571995
Insulin resistance and white adipose tissue inflammation are uncoupled in energetically challenged Fsp27-deficient mice. PMID:25565658
Improving collaboration by standardization efforts in systems biology. PMID:25538939
The application of the open pharmacological concepts triple store (open PHACTS) to support drug discovery research. PMID:25522365
Analysis of RNAseq datasets from a comparative infectious disease zebrafish model using GeneTiles bioinformatics. PMID:25503064
White adipose tissue reference network: a knowledge resource for exploring health-relevant relations. PMID:25466819
Transcriptional profiling of the spleen in progressive visceral leishmaniasis reveals mixed expression of type 1 and type 2 cytokine-responsive genes. PMID:25424735
Targets and candidate agents for type 2 diabetes treatment with computational bioinformatics approach. PMID:25401107
A network biology workflow to study transcriptomics data of the diabetic liver. PMID:25399255
Comparative analysis of the domestic cat genome reveals genetic signatures underlying feline biology and domestication. PMID:25385592
Current advances in systems and integrative biology. PMID:25379142
MiR-101 induces senescence and prevents apoptosis in the background of DNA damage in MCF7 cells. PMID:25353636
EpilepsyGene: a genetic resource for genes and mutations related to epilepsy. PMID:25324312
In-vivo fusion of human cancer and hamster stromal cells permanently transduces and transcribes human DNA. PMID:25259521
Network signatures link hepatic effects of anti-diabetic interventions with systemic disease parameters. PMID:25204982
Biological network exploration with Cytoscape 3. PMID:25199793
Identification of the transcription factor ZEB1 as a central component of the adipogenic gene regulatory network. PMID:25163748
STATdb: a specialised resource for the STATome. PMID:25157689
Network biology in medicine and beyond. PMID:25140061
Identification of genes in HepG2 cells that respond to DNA methylation and histone deacetylation inhibitor treatment. PMID:25120605
Lean Big Data integration in systems biology and systems pharmacology. PMID:25109570
Annotation of functional variation within non-MHC MS susceptibility loci through bioinformatics analysis. PMID:25030428
Metabolic adaptation and protein complexes in prokaryotes. PMID:24957769
Proteomics analysis of the non-muscle myosin heavy chain IIa-enriched actin-myosin complex reveals multiple functions within the podocyte. PMID:24949636
CrowdPhase: crowdsourcing the phase problem. PMID:24914965
Alkemio: association of chemicals with biomedical topics by text and data mining. PMID:24838570
R-based software for the integration of pathway data into bioinformatic algorithms. PMID:24833336
The Longissimus and Semimembranosus muscles display marked differences in their gene expression profiles in pig. PMID:24809746
Principles and methods of integrative genomic analyses in cancer. PMID:24759209
Systems-level analysis of innate immunity. PMID:24655298
enRoute: dynamic path extraction from biological pathway maps for exploring heterogeneous experimental datasets. PMID:24564375
Integrated Bio-Search: challenges and trends for the integration, search and comprehensive processing of biological information. PMID:24564249
PathNER: a tool for systematic identification of biological pathway mentions in the literature. PMID:24555844
Systems toxicology: from basic research to risk assessment. PMID:24446777
A provisional gene regulatory atlas for mouse heart development. PMID:24421884
POMO--Plotting Omics analysis results for Multiple Organisms. PMID:24365393
CyTargetLinker: a cytoscape app to integrate regulatory interactions in network analysis. PMID:24340000
ROS stress resets circadian clocks to coordinate pro-survival signals. PMID:24312621
Novel insights into embryonic stem cell self-renewal revealed through comparative human and mouse systems biology networks. PMID:24307629
WikiPathways for plants: a community pathway curation portal and a case study in rice and arabidopsis seed development networks. PMID:24280312
miRBase: annotating high confidence microRNAs using deep sequencing data. PMID:24275495
The Reactome pathway knowledgebase. PMID:24243840
Integrating in silico resources to map a signaling network. PMID:24233784
A systematic analysis of a mi-RNA inter-pathway regulatory motif. PMID:24152805
RiceWiki: a wiki-based database for community curation of rice genes. PMID:24136999
Pathways of Toxicity. PMID:24127042
Integrated enrichment analysis of variants and pathways in genome-wide association studies indicates central role for IL-2 signaling genes in type 1 diabetes, and cytokine signaling genes in Crohn's disease. PMID:24098138
Entourage: visualizing relationships between biological pathways using contextual subsets. PMID:24051820
Discovering causal pathways linking genomic events to transcriptional states using Tied Diffusion Through Interacting Events (TieDIE). PMID:23986566
Genome-wide gene expression profiling of stress response in a spinal cord clip compression injury model. PMID:23984903
Dizeez: an online game for human gene-disease annotation. PMID:23951102
Bioinformatics for spermatogenesis: annotation of male reproduction based on proteomics. PMID:23852026
Integrating pathways of Parkinson's disease in a molecular interaction map. PMID:23832570
Modeling approaches for qualitative and semi-quantitative analysis of cellular signaling networks. PMID:23803171
NOA: a cytoscape plugin for network ontology analysis. PMID:23749961
The UCSC Interaction Browser: multidimensional data views in pathway context. PMID:23748957
Review: toxicometabolomics. PMID:23722930
Microarray analyses reveal novel targets of exercise-induced stress resistance in the dorsal raphe nucleus. PMID:23717271
Integrating murine gene expression studies to understand obstructive lung disease due to chronic inhaled endotoxin. PMID:23675439
Towards the collaborative curation of the registry underlying Identifiers.org. PMID:23584831
Renoprotective effect of combined inhibition of angiotensin-converting enzyme and histone deacetylase. PMID:23559582
A pathway approach to investigate the function and regulation of SREBPs. PMID:23516131
The immediate early gene product EGR1 and polycomb group proteins interact in epigenetic programming during chondrogenesis. PMID:23483971
Community intelligence in knowledge curation: an application to managing scientific nomenclature. PMID:23451119
Transcriptome analysis of Inbred Long Sleep and Inbred Short Sleep mice. PMID:23433184
Visualizing multidimensional cancer genomics data. PMID:23363777
Enhancing the utility of Proteomics Signature Profiling (PSP) with Pathway Derived Subnets (PDSs), performance analysis and specialised ontologies. PMID:23324392
The Internet as Scientific Knowledge Base: Navigating the Chem-Bio Space. PMID:23293679
PANTHER in 2013: modeling the evolution of gene function, and other gene attributes, in the context of phylogenetic trees. PMID:23193289
Molecular pathways involved in prostate carcinogenesis: insights from public microarray datasets. PMID:23185449
Visual analysis of transcriptome data in the context of anatomical structures and biological networks. PMID:23162564
PRGdb 2.0: towards a community-based database model for the analysis of R-genes in plants. PMID:23161682
RNApathwaysDB--a database of RNA maturation and decay pathways. PMID:23155061
The ConsensusPathDB interaction database: 2013 update. PMID:23143270
Jointly creating digital abstracts: dealing with synonymy and polysemy. PMID:23110757
MetNet Online: a novel integrated resource for plant systems biology. PMID:23066841
IPAD: the Integrated Pathway Analysis Database for Systematic Enrichment Analysis. PMID:23046449
Multi-edge gene set networks reveal novel insights into global relationships between biological themes. PMID:23028852
Bilberries potentially alleviate stress-related retinal gene expression induced by a high-fat diet in mice. PMID:22993483 -
WikiPathways: capturing the full diversity of pathway knowledge
PubMed citations: 196.
196 articles citing: WikiPathways: capturing the full diversity of pathway knowledge
Getting Started with LINCS Datasets and Tools. PMID:35876555
Pan-sarcoma characterization of lncRNAs in the crosstalk of EMT and tumour immunity identifies distinct clinical outcomes and potential implications for immunotherapy. PMID:35842562
Genome-wide Meta-analysis Reveals New Gene Signatures and Potential Drug Targets of Hypertension. PMID:35811894
Studying Metabolism by NMR-Based Metabolomics. PMID:35573745
De novo identification of maximally deregulated subnetworks based on multi-omics data with DeRegNet. PMID:35439941
Understanding signaling and metabolic paths using semantified and harmonized information about biological interactions. PMID:35436299
OmicsView: Omics data analysis through interactive visual analytics. PMID:35356547
Pathway Analysis for Cancer Research and Precision Oncology Applications. PMID:35230687
The m6A(m)-independent role of FTO in regulating WNT signaling pathways. PMID:35169043
In Silico Investigation of the Biological Implications of Complex DNA Damage with Emphasis in Cancer Radiotherapy through a Systems Biology Approach. PMID:34946681
Gene Ontology Enrichment Analysis of Renal Agenesis: Improving Prenatal Molecular Diagnosis. PMID:34899145
Insilico Functional Analysis of Genome-Wide Dataset From 17,000 Individuals Identifies Candidate Malaria Resistance Genes Enriched in Malaria Pathogenic Pathways. PMID:34868193
Association of low-frequency and rare coding variants with information processing speed. PMID:34864818
Network Biology Approaches to Achieve Precision Medicine in Inflammatory Bowel Disease. PMID:34745229
NDEx: Accessing Network Models and Streamlining Network Biology Workflows. PMID:34570431
Intratumoral injection of caerin 1.1 and 1.9 peptides increases the efficacy of vaccinated TC-1 tumor-bearing mice with PD-1 blockade by modulating macrophage heterogeneity and the activation of CD8+ T cells in the tumor microenvironment. PMID:34429969
Dietary omega-3 fatty acid intake impacts peripheral blood DNA methylation -anti-inflammatory effects and individual variability in a pilot study. PMID:34411715
E-type prostanoid receptor 4 drives resolution of intestinal inflammation by blocking epithelial necroptosis. PMID:34239062
PIAS2-mediated blockade of IFN-β signaling: a basis for sporadic Parkinson disease dementia. PMID:34234281
CROssBAR: comprehensive resource of biomedical relations with knowledge graph representations. PMID:34181736
Plasma Protein Biomarkers Associated with Higher Ovarian Cancer Risk in BRCA1/2 Carriers. PMID:34064977
Genetic underpinnings of sociability in the general population. PMID:34054130
IDSM ChemWebRDF: SPARQLing small-molecule datasets. PMID:33980298
Systematic Analysis of the Transcriptome Profiles and Co-Expression Networks of Tumour Endothelial Cells Identifies Several Tumour-Associated Modules and Potential Therapeutic Targets in Hepatocellular Carcinoma. PMID:33917186
The microRNA analysis portal is a next-generation tool for exploring and analyzing miRNA-focused data in the literature. PMID:33903708
Investigating Molecular Determinants of Cancer Cell Resistance to Ionizing Radiation Through an Integrative Bioinformatics Approach. PMID:33898418
An EPIC predictor of gestational age and its application to newborns conceived by assisted reproductive technologies. PMID:33875015
Genomic insights into population history and biological adaptation in Oceania. PMID:33854233
Chronic Alcohol Use Induces Molecular Genetic Changes in the Dorsomedial Thalamus of People with Alcohol-Related Disorders. PMID:33805312
A Streamlined Approach to Pathway Analysis from RNA-Sequencing Data. PMID:33802642
Identification of high-dimensional omics-derived predictors for tumor growth dynamics using machine learning and pharmacometric modeling. PMID:33792207
Elucidation of Novel Therapeutic Targets for Breast Cancer with ESR1-CCDC170 Fusion. PMID:33557149
Long tracks of homozygosity predict the severity of alcohol use disorders in an American Indian population. PMID:33398086
System, Method and Software for Calculation of a Cannabis Drug Efficiency Index for the Reduction of Inflammation. PMID:33396562
The status of causality in biological databases: data resources and data retrieval possibilities to support logical modeling. PMID:33378765
Embryonic Stem Cell Differentiation Is Regulated by SET through Interactions with p53 and β-Catenin. PMID:33296674
A powerful method for pleiotropic analysis under composite null hypothesis identifies novel shared loci between Type 2 Diabetes and Prostate Cancer. PMID:33290408
The mechanisms of skeletal muscle atrophy in response to transient knockdown of the vitamin D receptor in vivo. PMID:33258480
WikiPathways: connecting communities. PMID:33211851
Bioinformatics Analysis Discovers Microtubular Tubulin Beta 6 Class V (TUBB6) as a Potential Therapeutic Target in Glioblastoma. PMID:33193654
Pathway information extracted from 25 years of pathway figures. PMID:33168034
A practical guide to mechanistic systems modeling in biology using a logic-based approach. PMID:33064138
Transcriptomics predicts compound synergy in drug and natural product treated glioblastoma cells. PMID:32946518
A novel single-cell based method for breast cancer prognosis. PMID:32833968
Combination of the PI3K inhibitor Idelalisib with the conventional cytostatics cytarabine and dexamethasone leads to changes in pathway activation that induce anti-proliferative effects in B lymphoblastic leukaemia cell lines. PMID:32817744
Overexpression of the vitamin D receptor (VDR) induces skeletal muscle hypertrophy. PMID:32771696
Gene mapping and functional annotation of GWAS of oral ulcers using FUMA software. PMID:32699208
Meta-Analysis of the Alzheimer's Disease Human Brain Transcriptome and Functional Dissection in Mouse Models. PMID:32668255
Dynamic rewiring of the human interactome by interferon signaling. PMID:32539747
Role of microRNA 690 in Mediating Angiotensin II Effects on Inflammation and Endoplasmic Reticulum Stress. PMID:32466437
Genes Involved in Energy Metabolism Are Differentially Expressed During the Day-Night Cycle in Murine Retinal Pigment Epithelium. PMID:32460311
PathwayPCA: an R/Bioconductor Package for Pathway Based Integrative Analysis of Multi-Omics Data. PMID:32430990
Comprehensive Immunoprofiling of Pediatric Zika Reveals Key Role for Monocytes in the Acute Phase and No Effect of Prior Dengue Virus Infection. PMID:32348760
BioHackathon 2015: Semantics of data for life sciences and reproducible research. PMID:32308977
The Molecular Processes in the Trabecular Meshwork After Exposure to Corticosteroids and in Corticosteroid-Induced Ocular Hypertension. PMID:32305042
Transcriptional profiling and therapeutic targeting of oxidative stress in neuroinflammation. PMID:32284594
Investigating global gene expression changes in a murine model of cherubism. PMID:32165349
A framework using topological pathways for deeper analysis of transcriptome data. PMID:32138666
Assessment of the Mode of Action Underlying the Effects of GenX in Mouse Liver and Implications for Assessing Human Health Risks. PMID:32138627
Machine Learning and Bioinformatics Models to Identify Pathways that Mediate Influences of Welding Fumes on Cancer Progression. PMID:32066756
Common genetic substrates of alcohol and substance use disorder severity revealed by pleiotropy detection against GWAS catalog in two populations. PMID:32027075
Stratifying cellular metabolism during weight loss: an interplay of metabolism, metabolic flexibility and inflammation. PMID:32015415
Developmentally Engineered Callus Organoid Bioassemblies Exhibit Predictive In Vivo Long Bone Healing. PMID:31993293
Genome wide association study of incomplete hippocampal inversion in adolescents. PMID:31990937
Circulating miRNAs and Risk of Sudden Death in Patients With Coronary Heart Disease. PMID:31971908
Whole-Genome Sequencing of Finnish Type 1 Diabetic Siblings Discordant for Kidney Disease Reveals DNA Variants associated with Diabetic Nephropathy. PMID:31919106
Proteostasis regulators modulate proteasomal activity and gene expression to attenuate multiple phenotypes in Fabry disease. PMID:31899485
RNA Sequencing of Collecting Duct Renal Cell Carcinoma Suggests an Interaction between miRNA and Target Genes and a Predominance of Deregulated Solute Carrier Genes. PMID:31878355
A Bioinformatic Approach for the Identification of Molecular Determinants of Resistance/Sensitivity to Cancer Thermotherapy. PMID:31814876
Multi-trait genome-wide association study identifies new loci associated with optic disc parameters. PMID:31798171
ADGRL4/ELTD1 Silencing in Endothelial Cells Induces ACLY and SLC25A1 and Alters the Cellular Metabolic Profile. PMID:31775252
Hypergraph-based connectivity measures for signaling pathway topologies. PMID:31652258
Universal concept signature analysis: genome-wide quantification of new biological and pathological functions of genes and pathways. PMID:31631213
Genomic alterations in high-risk chronic lymphocytic leukemia frequently affect cell cycle key regulators and NOTCH1-regulated transcription. PMID:31467127
Data-driven characterization of molecular phenotypes across heterogeneous sample collections. PMID:31329928
Ileal interposition surgery targets the hepatic TGF-β pathway, influencing gluconeogenesis and mitochondrial bioenergetics in the UCD-T2DM rat model of diabetes. PMID:31307210
Simultaneous Enrichment Analysis of all Possible Gene-sets: Unifying Self-Contained and Competitive Methods. PMID:31297505
Genome-wide functional association networks: background, data & state-of-the-art resources. PMID:31281921
Closing the gap between formats for storing layout information in systems biology. PMID:31273380
Comprehensive bioinformatics analysis of trabecular meshwork gene expression data to unravel the molecular pathogenesis of primary open-angle glaucoma. PMID:31197946
Predicting instances of pathway ontology classes for pathway integration. PMID:31196182
Transcriptomic analysis of vitamin D responses in uterine and peripheral NK cells. PMID:31163399
Identification of Cholecystokinin by Genome-Wide Profiling as Potential Mediator of Serotonin-Dependent Behavioral Effects of Maternal Separation in the Amygdala. PMID:31133792
Adipocyte abundances of CES1, CRYAB, ENO1 and GANAB are modified in-vitro by glucose restriction and are associated with cellular remodelling during weight regain. PMID:31037987
Metabopolis: scalable network layout for biological pathway diagrams in urban map style. PMID:30991966
Elucidation of Novel Therapeutic Targets for Acute Myeloid Leukemias with RUNX1-RUNX1T1 Fusion. PMID:30959925
Bioenergetic deficits in Huntington's disease iPSC-derived neural cells and rescue with glycolytic metabolites. PMID:30768179
A network biology approach to unraveling inherited axonopathies. PMID:30737464
Stress dynamically regulates co-expression networks of glucocorticoid receptor-dependent MDD and SCZ risk genes. PMID:30696808
Introducing WikiPathways as a Data-Source to Support Adverse Outcome Pathways for Regulatory Risk Assessment of Chemicals and Nanomaterials. PMID:30622555
Epstein-Barr virus microRNAs regulate B cell receptor signal transduction and lytic reactivation. PMID:30615681
An atlas of genetic influences on osteoporosis in humans and mice. PMID:30598549
Proteins Altered by Surgical Weight Loss Highlight Biomarkers of Insulin Resistance in the Community. PMID:30580566
iDEP: an integrated web application for differential expression and pathway analysis of RNA-Seq data. PMID:30567491
ComPath: an ecosystem for exploring, analyzing, and curating mappings across pathway databases. PMID:30564458
A Curated Resource for Phosphosite-specific Signature Analysis. PMID:30563849
Analysis of the Effect of Intestinal Ischemia and Reperfusion on the Rat Neutrophils Proteome. PMID:30555831
Cooperative interaction among BMAL1, HSF1, and p53 protects mammalian cells from UV stress. PMID:30480104
SyNDI: synchronous network data integration framework. PMID:30400817
Dietary cholesterol promotes steatohepatitis related hepatocellular carcinoma through dysregulated metabolism and calcium signaling. PMID:30367044
Genomic data integration systematically biases interactome mapping. PMID:30332399
Ubiquitin ligase RNF8 suppresses Notch signaling to regulate mammary development and tumorigenesis. PMID:30222135
Clustering approaches for visual knowledge exploration in molecular interaction networks. PMID:30157777
Comprehensive innate immune profiling of chikungunya virus infection in pediatric cases. PMID:30150281
Turning omics data into therapeutic insights. PMID:30149217
Predictive classification models and targets identification for betulin derivatives as Leishmania donovani inhibitors. PMID:30120601
Immunophenotype and Transcriptome Profile of Patients With Multiple Sclerosis Treated With Fingolimod: Setting Up a Model for Prediction of Response in a 2-Year Translational Study. PMID:30090102
NetControl4BioMed: a pipeline for biomedical data acquisition and analysis of network controllability. PMID:30066633
Network Rewiring in Cancer: Applications to Melanoma Cell Lines and the Cancer Genome Atlas Patients. PMID:30042785
Exploring the cellular network of metabolic flexibility in the adipose tissue. PMID:30002738
Phenotype-driven gene prioritization for rare diseases using graph convolution on heterogeneous networks. PMID:29980210
Exploring the functional impact of alternative splicing on human protein isoforms using available annotation sources. PMID:29931155
Integrated multi-omics data analysis identifying novel drug sensitivity-associated molecular targets of hepatocellular carcinoma cells. PMID:29930714
Identification of an immune gene expression signature associated with favorable clinical features in Treg-enriched patient tumor samples. PMID:29928512
Developments in toxicogenomics: understanding and predicting compound-induced toxicity from gene expression data. PMID:29917034
Using Regularization to Infer Cell Line Specificity in Logical Network Models of Signaling Pathways. PMID:29872402
Community-driven roadmap for integrated disease maps. PMID:29688273
Navigating the disease landscape: knowledge representations for contextualizing molecular signatures. PMID:29684165
The latent geometry of the human protein interaction network. PMID:29635317
From SNPs to pathways: Biological interpretation of type 2 diabetes (T2DM) genome wide association study (GWAS) results. PMID:29617380
Serum levels of miR-320 family members are associated with clinical parameters and diagnosis in prostate cancer patients. PMID:29535815
EZH2 regulates neuroblastoma cell differentiation via NTRK1 promoter epigenetic modifications. PMID:29507419
RaMP: A Comprehensive Relational Database of Metabolomics Pathways for Pathway Enrichment Analysis of Genes and Metabolites. PMID:29470400
Redox responses are preserved across muscle fibres with differential susceptibility to aging. PMID:29438851
Cross-linking BioThings APIs through JSON-LD to facilitate knowledge exploration. PMID:29390967
B Cell-Intrinsic Role for IRF5 in TLR9/BCR-Induced Human B Cell Activation, Proliferation, and Plasmablast Differentiation. PMID:29367853
Dysregulation of miR-155-5p and miR-200-3p and the Anti-Non-Bilayer Phospholipid Arrangement Antibodies Favor the Development of Lupus in Three Novel Murine Lupus Models. PMID:29349090
Semi-supervised identification of cancer subgroups using survival outcomes and overlapping grouping information. PMID:29336210
About miRNAs, miRNA seeds, target genes and target pathways. PMID:29291020
Effects of cell-cell crosstalk on gene expression patterns in a cell model of renal cell carcinoma lung metastasis. PMID:29286165
Heat Failure Phenotypes Induced by Knockdown of DAPIT in Zebrafish: A New Insight into Mechanism of Dilated Cardiomyopathy. PMID:29234032
Pathway analysis of transcriptomic data shows immunometabolic effects of vitamin D. PMID:29233860
Reactome diagram viewer: data structures and strategies to boost performance. PMID:29186351
Functional mapping and annotation of genetic associations with FUMA. PMID:29184056
A Review of Pathway-Based Analysis Tools That Visualize Genetic Variants. PMID:29163640
A Comparative Proteome Profile of Female Mouse Gonads Suggests a Tight Link between the Electron Transport Chain and Meiosis Initiation. PMID:29158290
WikiPathways: a multifaceted pathway database bridging metabolomics to other omics research. PMID:29136241
Identification of cancer biomarkers of prognostic value using specific gene regulatory networks (GRN): a novel role of RAD51AP1 for ovarian and lung cancers. PMID:29126163
The UCSC Genome Browser database: 2018 update. PMID:29106570
Post-weaning epiphysiolysis causes distal femur dysplasia and foreshortened hindlimbs in fetuin-A-deficient mice. PMID:29088242
Reactome enhanced pathway visualization. PMID:29077811
Comparison of Whole Body SOD1 Knockout with Muscle-Specific SOD1 Knockout Mice Reveals a Role for Nerve Redox Signaling in Regulation of Degenerative Pathways in Skeletal Muscle. PMID:29065712
LiverWiki: a wiki-based database for human liver. PMID:29029599
Developing Tools for Analysis of Renal Genomic Data: An Invitation to Participate. PMID:28982694
Molecular mechanisms underlying gliomas and glioblastoma pathogenesis revealed by bioinformatics analysis of microarray data. PMID:28952134
A genomic screen for angiosuppressor genes in the tumor endothelium identifies a multifaceted angiostatic role for bromodomain containing 7 (BRD7). PMID:28951988
Systematic integration of biomedical knowledge prioritizes drugs for repurposing. PMID:28936969
Determinants and Regulation of Protein Turnover in Yeast. PMID:28918244
Is systems pharmacology ready to impact upon therapy development? A study on the cholesterol biosynthesis pathway. PMID:28910500
Mapping the STK4/Hippo signaling network in prostate cancer cell. PMID:28880957
Predicting the murine enterocyte metabolic response to diets that differ in lipid and carbohydrate composition. PMID:28821741
MINERVA-a platform for visualization and curation of molecular interaction networks. PMID:28725475
Logic Modeling in Quantitative Systems Pharmacology. PMID:28681552
Gene Expression Profiling in Human Lung Cells Exposed to Isoprene-Derived Secondary Organic Aerosol. PMID:28636383
p21 maintains senescent cell viability under persistent DNA damage response by restraining JNK and caspase signaling. PMID:28607003
Using ChEMBL web services for building applications and data processing workflows relevant to drug discovery. PMID:28602100
Deconstructing Olfactory Stem Cell Trajectories at Single-Cell Resolution. PMID:28506465
Interferon Receptor Signaling Pathways Regulating PD-L1 and PD-L2 Expression. PMID:28494868
Computational Analysis of Specific MicroRNA Biomarkers for Noninvasive Early Cancer Detection. PMID:28357401
The Genomic Impact of DNA CpG Methylation on Gene Expression; Relationships in Prostate Cancer. PMID:28216563
The origin of chow chows in the light of the East Asian breeds. PMID:28201986
Extracellular RNAs Are Associated With Insulin Resistance and Metabolic Phenotypes. PMID:28183786
Epigenetic profiling of human brain differential DNA methylation networks in schizophrenia. PMID:28117656
A new semisynthetic cardenolide analog 3β-[2-(1-amantadine)- 1-on-ethylamine]-digitoxigenin (AMANTADIG) affects G2/M cell cycle arrest and miRNA expression profiles and enhances proapoptotic survivin-2B expression in renal cell carcinoma cell lines. PMID:28099931
Non-Coding RNAs in Lung Cancer: Contribution of Bioinformatics Analysis to the Development of Non-Invasive Diagnostic Tools. PMID:28035947
DTNI: a novel toxicogenomics data analysis tool for identifying the molecular mechanisms underlying the adverse effects of toxic compounds. PMID:28032149
A Meta-Analysis Based Method for Prioritizing Candidate Genes Involved in a Pre-specific Function. PMID:28018423
DisGeNET: a comprehensive platform integrating information on human disease-associated genes and variants. PMID:27924018
The KDM5 family is required for activation of pro-proliferative cell cycle genes during adipocyte differentiation. PMID:27899593
XTalkDB: a database of signaling pathway crosstalk. PMID:27899583
pathDIP: an annotated resource for known and predicted human gene-pathway associations and pathway enrichment analysis. PMID:27899558
A scored human protein-protein interaction network to catalyze genomic interpretation. PMID:27892958
Global analysis of somatic structural genomic alterations and their impact on gene expression in diverse human cancers. PMID:27856756
A network of epigenetic modifiers and DNA repair genes controls tissue-specific copy number alteration preference. PMID:27831464
Multi-OMIC profiling of survival and metabolic signaling networks in cells subjected to photodynamic therapy. PMID:27803950
ATR maintains chromosomal integrity during postnatal cerebellar neurogenesis and is required for medulloblastoma formation. PMID:27803059
Open PHACTS computational protocols for in silico target validation of cellular phenotypic screens: knowing the knowns. PMID:27774140
Proteomic Analysis, Immune Dysregulation, and Pathway Interconnections with Obesity. PMID:27769113
XMetDB: an open access database for xenobiotic metabolism. PMID:27651835
Analyzing and interpreting genome data at the network level with ConsensusPathDB. PMID:27606777
Integration of targeted metabolomics and transcriptomics identifies deregulation of phosphatidylcholine metabolism in Huntington's disease peripheral blood samples. PMID:27524956
Modelling the Structure and Dynamics of Biological Pathways. PMID:27509052
Crowdsourcing and curation: perspectives from biology and natural language processing. PMID:27504010
Single-cell analyses of X Chromosome inactivation dynamics and pluripotency during differentiation. PMID:27486082
Integration and Visualization of Translational Medicine Data for Better Understanding of Human Diseases. PMID:27441714
Crowdsourcing biomedical research: leveraging communities as innovation engines. PMID:27418159
Innate immune defects in HIV permissive cell lines. PMID:27350062
CyLineUp: A Cytoscape app for visualizing data in network small multiples. PMID:27347378
Using the Semantic Web for Rapid Integration of WikiPathways with Other Biological Online Data Resources. PMID:27336457
Obese diet-induced mouse models of nonalcoholic steatohepatitis-tracking disease by liver biopsy. PMID:27326314
Glucocorticoid receptor isoforms direct distinct mitochondrial programs to regulate ATP production. PMID:27226058
Gene promoter DNA methylation patterns have a limited role in orchestrating transcriptional changes in the fetal liver in response to maternal folate depletion during pregnancy. PMID:27133805
Using biological networks to integrate, visualize and analyze genomics data. PMID:27036106
Bioinformatics Mining and Modeling Methods for the Identification of Disease Mechanisms in Neurodegenerative Disorders. PMID:26690135
Systems biology approaches to study the molecular effects of caloric restriction and polyphenols on aging processes. PMID:26608884
Lynx: a knowledge base and an analytical workbench for integrative medicine. PMID:26590263 -
WikiPathways: connecting communities
PubMed citations: 113.
113 articles citing: WikiPathways: connecting communities
STAT3 and NTRK2 Genes Predicted by the Bioinformatics Approach May Play Important Roles in the Pathogenesis of Multiple Sclerosis and Obsessive-Compulsive Disorder. PMID:35887540
Multi-Level Biological Network Analysis and Drug Repurposing Based on Leukocyte Transcriptomics in Severe COVID-19: In Silico Systems Biology to Precision Medicine. PMID:35887528
Genomic Characterization by Whole-Exome Sequencing of Hypermobility Spectrum Disorder. PMID:35886052
Immunomodulation of Pluripotent Stem Cell-Derived Mesenchymal Stem Cells in Rotator Cuff Tears Model. PMID:35884853
Shared mechanisms across the major psychiatric and neurodegenerative diseases. PMID:35882878
Empagliflozin mitigates endothelial inflammation and attenuates endoplasmic reticulum stress signaling caused by sustained glycocalyx disruption. PMID:35879337
Circulating miRNAs as Epigenetic Mediators of Periodontitis and Preeclampsia Association. PMID:35860693
Immune System Modulation by the Adjuvants Poly (I:C) and Montanide ISA 720. PMID:35844531
The heterogeneous pharmacological medical biochemical network PharMeBINet. PMID:35821017
Impaired Neurodevelopmental Genes in Slovenian Autistic Children Elucidate the Comorbidity of Autism With Other Developmental Disorders. PMID:35813072
Effective tumor cell abrogation via Venetoclax-mediated BCL-2 inhibition in KMT2A-rearranged acute B-lymphoblastic leukemia. PMID:35778418
TCGA-My: A Systematic Repository for Systems Biology of Malaysian Colorectal Cancer. PMID:35743803
miRNAs Copy Number Variations Repertoire as Hallmark Indicator of Cancer Species Predisposition. PMID:35741808
Adipocyte HIF2α functions as a thermostat via PKA Cα regulation in beige adipocytes. PMID:35672324
A Nine-Strain Bacterial Consortium Improves Portal Hypertension and Insulin Signaling and Delays NAFLD Progression In Vivo. PMID:35625927
Immune-Related Protein Interaction Network in Severe COVID-19 Patients toward the Identification of Key Proteins and Drug Repurposing. PMID:35625619
The LOTUS initiative for open knowledge management in natural products research. PMID:35616633
Integrated Network Discovery Using Multi-Proteomic Data. PMID:35612742
hECA: The cell-centric assembly of a cell atlas. PMID:35602947
A Community-Driven, Openly Accessible Molecular Pathway Integrating Knowledge on Malignant Pleural Mesothelioma. PMID:35558518
Multi-omics analysis of the cervical epithelial integrity of women using depot medroxyprogesterone acetate. PMID:35533147
Functional deficiency of succinate dehydrogenase promotes tumorigenesis and development of clear cell renal cell carcinoma through weakening of ferroptosis. PMID:35510387
Membranome 3.0: Database of single-pass membrane proteins with AlphaFold models. PMID:35481632
A Cancer Associated Fibroblasts-Related Six-Gene Panel for Anti-PD-1 Therapy in Melanoma Driven by Weighted Correlation Network Analysis and Supervised Machine Learning. PMID:35479936
Network- and enrichment-based inference of phenotypes and targets from large-scale disease maps. PMID:35473910
Postnatal Smad3 Inactivation in Murine Smooth Muscle Cells Elicits a Temporally and Regionally Distinct Transcriptional Response. PMID:35463747
Darling: A Web Application for Detecting Disease-Related Biomedical Entity Associations with Literature Mining. PMID:35454109
A Pathway-Based Genetic Score for Oxidative Stress: An Indicator of Host Vulnerability to Phthalate-Associated Adverse Neurodevelopment. PMID:35453345
On the influence of several factors on pathway enrichment analysis. PMID:35453140
PTHrP induces STAT5 activation, secretory differentiation and accelerates mammary tumor development. PMID:35440032
Combined Analysis of RRBS DNA Methylome and Transcriptome Reveal Novel Candidate Genes Related to Porcine Clostridium perfringens Type C-Induced Diarrhea. PMID:35401691
Providing Adverse Outcome Pathways from the AOP-Wiki in a Semantic Web Format to Increase Usability and Accessibility of the Content. PMID:35388368
SPCS: a spatial and pattern combined smoothing method for spatial transcriptomic expression. PMID:35380614
Functional Enrichment Analysis of Regulatory Elements. PMID:35327392
CFTR-mediated monocyte/macrophage dysfunction revealed by cystic fibrosis proband-parent comparisons. PMID:35315363
Corticosteroid sensitization drives opioid addiction. PMID:35296810
The AOP-DB RDF: Applying FAIR Principles to the Semantic Integration of AOP Data Using the Research Description Framework. PMID:35295213
Beyond AOPs: A Mechanistic Evaluation of NAMs in DART Testing. PMID:35295212
A comprehensive atlas of fetal splicing patterns in the brain of adult myotonic dystrophy type 1 patients. PMID:35274098
Spatially Annotated Single Cell Sequencing for Unraveling Intratumor Heterogeneity. PMID:35273957
DNA damage contributes to neurotoxic inflammation in Aicardi-Goutières syndrome astrocytes. PMID:35262626
Immunomodulatory potential of in vivo natural killer T (NKT) activation by NKTT320 in Mauritian-origin cynomolgus macaques. PMID:35243248
Cancer proteogenomics: current impact and future prospects. PMID:35236940
Identification of Molecular Signatures and Candidate Drugs in Vascular Dementia by Bioinformatics Analyses. PMID:35221911
A Transcriptomic Approach to Elucidate the Mechanisms of Gefitinib-Induced Toxicity in Healthy Human Intestinal Organoids. PMID:35216325
Network-Assisted Systems Biology Analysis of the Mitochondrial Proteome in a Pre-Clinical Model of Ischemia, Revascularization and Post-Conditioning. PMID:35216205
Vulnerability of Triple-Negative Breast Cancer to Saponin Formosanin C-Induced Ferroptosis. PMID:35204181
Identification of phenotype-specific networks from paired gene expression-cell shape imaging data. PMID:35197309
Down-Regulated miR-130a/b Attenuates Rhabdomyosarcoma Proliferation via PPARG. PMID:35187064
A Novel Ferroptosis-Related lncRNA Prognostic Model and Immune Infiltration Features in Skin Cutaneous Melanoma. PMID:35186949
Personalized chordoma organoids for drug discovery studies. PMID:35171675
Racial and Ethnic Differences in Genomic Profiling of Early Onset Colorectal Cancer. PMID:35134211
The Age-Specific Features and Clinical Significance of NRF2 and MAPK10 Expression in HCC Patients. PMID:35082522
BioInfograph: An Online Tool to Design and Display Multi-Panel Scientific Figure Interactively. PMID:35069687
Circadian Regulation Patterns With Distinct Immune Landscapes in Gliomas Aid in the Development of a Risk Model to Predict Prognosis and Therapeutic Response. PMID:35069579
TrpNet: Understanding Tryptophan Metabolism across Gut Microbiome. PMID:35050132
Multiplex-Heterogeneous Network-Based Capturing Potential SNP "Switches" of Pathways Associating With Diverse Disease Characteristics of Asthma. PMID:34970542
Hepatic MIR20B promotes nonalcoholic fatty liver disease by suppressing PPARA. PMID:34964438
9-ING-41, a Small Molecule Inhibitor of GSK-3β, Potentiates the Effects of Chemotherapy on Colorectal Cancer Cells. PMID:34955846
In Silico Investigation of the Biological Implications of Complex DNA Damage with Emphasis in Cancer Radiotherapy through a Systems Biology Approach. PMID:34946681
Recurring exposure to low humidity induces transcriptional and protein level changes in the vocal folds of rabbits. PMID:34921171
DNA methylation of ARHGAP30 is negatively associated with ARHGAP30 expression in lung adenocarcinoma, which reduces tumor immunity and is detrimental to patient survival. PMID:34910688
Pathway Enrichment Analysis of Microarray Data. PMID:34902127
Deep Proteomic Analysis on Biobanked Paraffine-Archived Melanoma with Prognostic/Predictive Biomarker Read-Out. PMID:34885218
A Transcriptional Signature of IL-2 Expanded Natural Killer Cells Predicts More Favorable Prognosis in Bladder Cancer. PMID:34858395
ConsensusPathDB 2022: molecular interactions update as a resource for network biology. PMID:34850110
A 3D primary human cell-based in vitro model of non-alcoholic steatohepatitis for efficacy testing of clinical drug candidates. PMID:34815444
Tackling the Biological Meaning of the Human Olfactory Bulb Dyshomeostatic Proteome across Neurological Disorders: An Integrative Bioinformatic Approach. PMID:34768771
Mining plant metabolomes: Methods, applications, and perspectives. PMID:34746766
DNA Methylation Patterns in CD8+ T Cells Discern Psoriasis From Psoriatic Arthritis and Correlate With Cutaneous Disease Activity. PMID:34746142
Network Biology Approaches to Achieve Precision Medicine in Inflammatory Bowel Disease. PMID:34745229
Identification of a Putative Enhancer RNA for EGFR in Hyper-Accessible Regions in Esophageal Squamous Cell Carcinoma Cells by Analysis of Chromatin Accessibility Landscapes. PMID:34722266
Complex Portal 2022: new curation frontiers. PMID:34718729
Transcriptome changes in maternal peripheral blood during term parturition mimic perturbations preceding spontaneous preterm birth†. PMID:34686873
RGD v2.0: a major update of the ruminant functional and evolutionary genomics database. PMID:34643708
WikiNetworks: translating manually created biological pathways for topological analysis. PMID:34636843
OnTheFly2.0: a text-mining web application for automated biomedical entity recognition, document annotation, network and functional enrichment analysis. PMID:34632381
GeneTrail: A Framework for the Analysis of High-Throughput Profiles. PMID:34604304
Bioinformatics and system biology approaches to identify pathophysiological impact of COVID-19 to the progression and severity of neurological diseases. PMID:34601390
Personalised Medicine for Colorectal Cancer Using Mechanism-Based Machine Learning Models. PMID:34576133
Elevating CDCA3 Levels Enhances Tyrosine Kinase Inhibitor Sensitivity in TKI-Resistant EGFR Mutant Non-Small-Cell Lung Cancer. PMID:34572879
CTR-DB, an omnibus for patient-derived gene expression signatures correlated with cancer drug response. PMID:34570230
A highly multiplexed quantitative phosphosite assay for biology and preclinical studies. PMID:34569154
DecoPath: a web application for decoding pathway enrichment analysis. PMID:34568823
clusterProfiler 4.0: A universal enrichment tool for interpreting omics data. PMID:34557778
Therapeutic radiation exposure of the abdomen during childhood induces chronic adipose tissue dysfunction. PMID:34554929
Investigation of pharmacological mechanism of natural product using pathway fingerprints similarity based on "drug-target-pathway" heterogenous network. PMID:34544480
Investigating the Molecular Processes behind the Cell-Specific Toxicity Response to Titanium Dioxide Nanobelts. PMID:34502343
Biomolecule and Bioentity Interaction Databases in Systems Biology: A Comprehensive Review. PMID:34439912
Ten simple rules for creating reusable pathway models for computational analysis and visualization. PMID:34411100
Arabidopsis Coexpression Tool: a tool for gene coexpression analysis in Arabidopsis thaliana. PMID:34381973
Characterisation of Neurospheres-Derived Cells from Human Olfactory Epithelium. PMID:34359860
Transcriptome Profiling and Metagenomic Analysis Help to Elucidate Interactions in an Inflammation-Associated Cancer Mouse Model. PMID:34359585
The network map of Elabela signaling pathway in physiological and pathological conditions. PMID:34339006
Prediction of combination therapies based on topological modeling of the immune signaling network in multiple sclerosis. PMID:34271980
Predicting mechanism of action of novel compounds using compound structure and transcriptomic signature coembedding. PMID:34252937
E-type prostanoid receptor 4 drives resolution of intestinal inflammation by blocking epithelial necroptosis. PMID:34239062
Towards a global investigation of transcriptomic signatures through co-expression networks and pathway knowledge for the identification of disease mechanisms. PMID:34197603
Crowdsourcing assessment of maternal blood multi-omics for predicting gestational age and preterm birth. PMID:34195686
Interpreting the lipidome: bioinformatic approaches to embrace the complexity. PMID:34091802
Identification of Novel Genomic-Variant Patterns of OR56A5, OR52L1, and CTSD in Retinitis Pigmentosa Patients by Whole-Exome Sequencing. PMID:34070492
The PI3K/mTOR Pathway Is Targeted by Rare Germline Variants in Patients with Both Melanoma and Renal Cell Carcinoma. PMID:34067022
The Transcriptome of SH-SY5Y at Single-Cell Resolution: A CITE-Seq Data Analysis Workflow. PMID:34066513
Disease-specific interactome alterations via epichaperomics: the case for Alzheimer's disease. PMID:34028172
eVITTA: a web-based visualization and inference toolbox for transcriptome analysis. PMID:34019643
Defining the lineage of thermogenic perivascular adipose tissue. PMID:33846639
Chronic Alcohol Use Induces Molecular Genetic Changes in the Dorsomedial Thalamus of People with Alcohol-Related Disorders. PMID:33805312
Analysing the yeast complexome-the Complex Portal rising to the challenge. PMID:33677561
miR-582-5p Is a Tumor Suppressor microRNA Targeting the Hippo-YAP/TAZ Signaling Pathway in Non-Small Cell Lung Cancer. PMID:33670427
TOXPANEL: A Gene-Set Analysis Tool to Assess Liver and Kidney Injuries. PMID:33633572
Polygenic risk modeling with latent trait-related genetic components. PMID:33558700
Single-Cell Gene Network Analysis and Transcriptional Landscape of MYCN-Amplified Neuroblastoma Cell Lines. PMID:33525507
The 2021 Nucleic Acids Research database issue and the online molecular biology database collection. PMID:33396976 -
Mining biological pathways using WikiPathways web services
PubMed citations: 62.
62 articles citing: Mining biological pathways using WikiPathways web services
Structurally-discovered KLF4 variants accelerate and stabilize reprogramming to pluripotency. PMID:35106457
Opioid receptors signaling network. PMID:34724150
Personalised Medicine for Colorectal Cancer Using Mechanism-Based Machine Learning Models. PMID:34576133
CPA: a web-based platform for consensus pathway analysis and interactive visualization. PMID:34037798
SKI activates the Hippo pathway via LIMD1 to inhibit cardiac fibroblast activation. PMID:33847835
Combination of Ginsenosides Rb2 and Rg3 Promotes Angiogenic Phenotype of Human Endothelial Cells via PI3K/Akt and MAPK/ERK Pathways. PMID:33643049
Apple Peel and Flesh Contain Pro-neurogenic Compounds. PMID:33577796
Multi-omics integration in biomedical research - A metabolomics-centric review. PMID:33248648
An assembly of galanin-galanin receptor signaling network. PMID:33136286
Seq-ing answers: Current data integration approaches to uncover mechanisms of transcriptional regulation. PMID:32612756
Citalopram-induced pathways regulation and tentative treatment-outcome-predicting biomarkers in lymphoblastoid cell lines from depression patients. PMID:32612257
Longitudinal metabolomic analysis of plasma enables modeling disease progression in Duchenne muscular dystrophy mouse models. PMID:32025735
Thrombospondin-I is a critical modulator in non-alcoholic steatohepatitis (NASH). PMID:31891606
Pan-cancer RNA-seq data stratifies tumours by some hallmarks of cancer. PMID:31730267
Targeting Epithelial Mesenchymal Plasticity in Pancreatic Cancer: A Compendium of Preclinical Discovery in a Heterogeneous Disease. PMID:31703358
Computational identification and analysis of neurodegenerative disease associated protein kinases in hominid genomes. PMID:30258892
Computational prediction of changes in brain metabolic fluxes during Parkinson's disease from mRNA expression. PMID:30208076
Developing Tools for Analysis of Renal Genomic Data: An Invitation to Participate. PMID:28982694
Detection of gene-environment interactions in the presence of linkage disequilibrium and noise by using genetic risk scores with internal weights from elastic net regression. PMID:28606108
From chromatogram to analyte to metabolite. How to pick horses for courses from the massive web resources for mass spectral plant metabolomics. PMID:28520864
Connecting the Human Variome Project to nutrigenomics. PMID:28300226
Determination of Genetic Structure and Signatures of Selection in Three Strains of Tanzania Shorthorn Zebu, Boran and Friesian Cattle by Genome-Wide SNP Analyses. PMID:28129396
Long Term Culture of the A549 Cancer Cell Line Promotes Multilamellar Body Formation and Differentiation towards an Alveolar Type II Pneumocyte Phenotype. PMID:27792742
Use of RNA-seq to identify cardiac genes and gene pathways differentially expressed between dogs with and without dilated cardiomyopathy. PMID:27347821
Anti-inflammatory effects of alpinone 3-acetate from Alpinia japonica seeds. PMID:27137785
Using biological networks to integrate, visualize and analyze genomics data. PMID:27036106
Collagen Type I Improves the Differentiation of Human Embryonic Stem Cells towards Definitive Endoderm. PMID:26713616
Brain Transcriptomic Response to Social Eavesdropping in Zebrafish (Danio rerio). PMID:26713440
Database resources of the National Center for Biotechnology Information. PMID:26615191
WikiPathways: capturing the full diversity of pathway knowledge. PMID:26481357
A legion of potential regulatory sRNAs exists beyond the typical microRNAs microcosm. PMID:26354861
Automatically visualise and analyse data on pathways using PathVisioRPC from any programming environment. PMID:26298294
DNA microarray integromics analysis platform. PMID:26110022
Analysis and interpretation of transcriptomic data obtained from extended Warburg effect genes in patients with clear cell renal cell carcinoma. PMID:25859558
Comparison of human cell signaling pathway databases--evolution, drawbacks and challenges. PMID:25632107
Genomic adaptation of admixed dairy cattle in East Africa. PMID:25566325
Culture conditions profoundly impact phenotype in BEAS-2B, a human pulmonary epithelial model. PMID:25524072
Database resources of the National Center for Biotechnology Information. PMID:25398906
TSLP signaling pathway map: a platform for analysis of TSLP-mediated signaling. PMID:24573880
Pathway analysis for drug repositioning based on public database mining. PMID:24460210
Database resources of the National Center for Biotechnology Information. PMID:24259429
Enabling transparent and collaborative computational analysis of 12 tumor types within The Cancer Genome Atlas. PMID:24071850
Genome-wide gene expression profiling of stress response in a spinal cord clip compression injury model. PMID:23984903
IntPath--an integrated pathway gene relationship database for model organisms and important pathogens. PMID:23282057
Allele-specific FKBP5 DNA demethylation mediates gene-childhood trauma interactions. PMID:23201972
Database resources of the National Center for Biotechnology Information. PMID:23193264
WikiCell: a unified resource platform for human transcriptomics research. PMID:22702248
Comparative analysis and assessment of M. tuberculosis H37Rv protein-protein interaction datasets. PMID:22369691
Mining and integration of pathway diagrams from imaging data. PMID:22267504
Effect of serum amyloid A1 treatment on global gene expression in THP-1-derived macrophages. PMID:22228103
Database resources of the National Center for Biotechnology Information. PMID:22140104
WikiPathways: building research communities on biological pathways. PMID:22096230
Computational toxicology using the OpenTox application programming interface and Bioclipse. PMID:22075173
Extending biochemical databases by metabolomic surveys. PMID:21566124
Answering biological questions: querying a systems biology database for nutrigenomics. PMID:21437033
Network-based pipeline for analyzing MS data: an application toward liver cancer. PMID:21410269
The Micronutrient Genomics Project: a community-driven knowledge base for micronutrient research. PMID:21189865
ExprEssence--revealing the essence of differential experimental data in the context of an interaction/regulation net-work. PMID:21118483
MetNetAPI: A flexible method to access and manipulate biological network data from MetNet. PMID:21083943
Challenges of molecular nutrition research 6: the nutritional phenotype database to store, share and evaluate nutritional systems biology studies. PMID:21052526
Finding the right questions: exploratory pathway analysis to enhance biological discovery in large datasets. PMID:20824171
Computational tools for the interactive exploration of proteomic and structural data. PMID:20525940
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version: FAIRsharing.org: WikiPathways; WikiPathways; DOI: https://doi.org/10.25504/FAIRsharing.1x53qk; Last edited: March 19, 2021, 11:17 a.m.; Last accessed: Jan 03 2022 7:05 p.m.
mathematical model
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version: FAIRsharing.org: WikiPathways; WikiPathways; DOI: https://doi.org/10.25504/FAIRsharing.1x53qk; Last edited: March 19, 2021, 11:17 a.m.; Last accessed: Jan 03 2022 7:05 p.m.
pathway model
metasource: Fairsharing.org
version: FAIRsharing.org: WikiPathways; WikiPathways; DOI: https://doi.org/10.25504/FAIRsharing.1x53qk; Last edited: March 19, 2021, 11:17 a.m.; Last accessed: Jan 03 2022 7:05 p.m.
covid-19
metasource: re3data.org
version: re3data.org: WikiPathways; editing status 2021-09-09; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R31NJMRO last accessed: 2022-11-04
fair
metasource: re3data.org
version: re3data.org: WikiPathways; editing status 2021-09-09; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R31NJMRO last accessed: 2022-11-04
biological pathway
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biological process
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metabolomics
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molecular interactions, pathways and networks
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version: extracted_at: 2022-11-04T11:24:43.813232
rare diseases
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version: extracted_at: 2022-11-04T11:24:43.813232
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metasource: Fairsharing.orgversion: FAIRsharing.org: WikiPathways; WikiPathways; DOI: https://doi.org/10.25504/FAIRsharing.1x53qk; Last edited: March 19, 2021, 11:17 a.m.; Last accessed: Jan 03 2022 7:05 p.m.
mathematical model
metasource: Fairsharing.orgversion: FAIRsharing.org: WikiPathways; WikiPathways; DOI: https://doi.org/10.25504/FAIRsharing.1x53qk; Last edited: March 19, 2021, 11:17 a.m.; Last accessed: Jan 03 2022 7:05 p.m.
pathway model
metasource: Fairsharing.orgversion: FAIRsharing.org: WikiPathways; WikiPathways; DOI: https://doi.org/10.25504/FAIRsharing.1x53qk; Last edited: March 19, 2021, 11:17 a.m.; Last accessed: Jan 03 2022 7:05 p.m.
covid-19
metasource: re3data.orgversion: re3data.org: WikiPathways; editing status 2021-09-09; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R31NJMRO last accessed: 2022-11-04
fair
metasource: re3data.orgversion: re3data.org: WikiPathways; editing status 2021-09-09; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R31NJMRO last accessed: 2022-11-04
biological pathway
metasource: re3data.orgversion: re3data.org: WikiPathways; editing status 2021-09-09; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R31NJMRO last accessed: 2022-11-04
biological process
metasource: re3data.orgversion: re3data.org: WikiPathways; editing status 2021-09-09; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R31NJMRO last accessed: 2022-11-04
metabolomics
metasource: re3data.orgversion: re3data.org: WikiPathways; editing status 2021-09-09; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R31NJMRO last accessed: 2022-11-04
molecular interactions, pathways and networks
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:24:43.813232
rare diseases
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:24:43.813232
mathematical model pathway model covid-19 biological pathway biological process metabolomics molecular interactions, pathways and networks rare diseases
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