OmniPath

A collection of literature-curated human and rodent signalling pathways. Aggregates over 50 sources in total, ~ 32 for PPIs including SigNOR and BioGRID.

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OmniPath: guidelines and gateway for literature-curated signaling pathway resources
PMID: 27898060

metasource: BiŌkeanós-Medsourcing
version: 0.0.1:2022-11-04T13:34:25.975929

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http://dx.doi.org/10.1038/nmeth.4077

metasource: bio.tools
version: extracted_at: 2022-11-04T11:25:45.043584

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• OmniPath: guidelines and gateway for literature-curated signaling pathway resources PubMed citations: 129.

  129 articles citing: OmniPath: guidelines and gateway for literature-curated signaling pathway resources

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  Computational analyses of mechanism of action (MoA): data, methods and integration. PMID:35360890

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  Deciphering tissue structure and function using spatial transcriptomics. PMID:35273328

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  Computational Models for Clinical Applications in Personalized Medicine-Guidelines and Recommendations for Data Integration and Model Validation. PMID:35207655

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  Network Pharmacology Integrated Molecular Docking Revealed the Mechanism of Jianpi Yiqi Taohua Decoction Against Ulcerative Colitis. PMID:35173140

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  FUNKI: Interactive functional footprint-based analysis of omics data. PMID:35134857

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  Extracellular vesicles produced by the human commensal gut bacterium Bacteroides thetaiotaomicron affect host immune pathways in a cell-type specific manner that are altered in inflammatory bowel disease. PMID:35064769

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  Bioengineered models of Parkinson's disease using patient-derived dopaminergic neurons exhibit distinct biological profiles in a 3D microenvironment. PMID:35044538

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  The use of machine learning to discover regulatory networks controlling biological systems. PMID:35016036

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  Cytochrome b561 Serves as a Potential Prognostic Biomarker and Target for Breast Cancer. PMID:35002301

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  Single-cell transcriptome atlas of human mesenchymal stem cells exploring cellular heterogeneity. PMID:34965030

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  Network analytics for drug repurposing in COVID-19. PMID:34864885

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  Identification of Intercellular Signaling Changes Across Conditions and Their Influence on Intracellular Signaling Response From Multiple Single-Cell Datasets. PMID:34858473

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  Chromatin Accessibility and Transcriptomic Alterations in Murine Ovarian Granulosa Cells upon Deoxynivalenol Exposure. PMID:34831041

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  Immune Infiltration-Related Signature Predicts Risk Stratification and Immunotherapy Efficacy in Grade II and III Gliomas. PMID:34805164

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  ProteomicsDB: toward a FAIR open-source resource for life-science research. PMID:34791421

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  Bioinformatics approach to identify common gene signatures of patients with coronavirus 2019 and lung adenocarcinoma. PMID:34775559

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  Network analysis reveals rare disease signatures across multiple levels of biological organization. PMID:34753928

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  PaIRKAT: A pathway integrated regression-based kernel association test with applications to metabolomics and COPD phenotypes. PMID:34679079

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  COVID19 Disease Map, a computational knowledge repository of virus-host interaction mechanisms. PMID:34664389

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  Proteogenomic characterization of pancreatic ductal adenocarcinoma. PMID:34534465

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  Exosomes Secreted by Adipose-Derived Stem Cells Following FK506 Stimulation Reduce Autophagy of Macrophages in Spine after Nerve Crush Injury. PMID:34502537

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  Inflammatory gene expression profiling in peripheral blood from patients with Alzheimer's disease reveals key pathways and hub genes with potential diagnostic utility: a preliminary study. PMID:34484988

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  Identification of Immune-Related Genes in Sepsis due to Community-Acquired Pneumonia. PMID:34484417

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  Expanding the potential genes of inborn errors of immunity through protein interactions. PMID:34391382

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  Comprior: facilitating the implementation and automated benchmarking of prior knowledge-based feature selection approaches on gene expression data sets. PMID:34384353

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  NetControl4BioMed: A web-based platform for controllability analysis of protein-protein interaction networks. PMID:34352070

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  A computational and structural analysis of germline and somatic variants affecting the DDR mechanism, and their impact on human diseases. PMID:34253785

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  Assembling Disease Networks From Causal Interaction Resources. PMID:34178043

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  New insights into the mechanisms underlying 5-fluorouracil-induced intestinal toxicity based on transcriptomic and metabolomic responses in human intestinal organoids. PMID:34151400

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  Genome-scale mechanistic modeling of signaling pathways made easy: A bioconductor/cytoscape/web server framework for the analysis of omic data. PMID:34136096

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  Network module-based drug repositioning for pulmonary arterial hypertension. PMID:34132494

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  PAX2GRAPHML: a Python library for large-scale regulation network analysis using BIOPAX. PMID:34128961

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  Target identification among known drugs by deep learning from heterogeneous networks. PMID:34123272

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  Computational Biology and Machine Learning Approaches to Understand Mechanistic Microbiome-Host Interactions. PMID:34046017

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  A 3D system to model human pancreas development and its reference single-cell transcriptome atlas identify signaling pathways required for progenitor expansion. PMID:34035279

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  From multi-omics integration towards novel genomic interaction networks to identify key cancer cell line characteristics. PMID:34006939

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  VB10, a new blood biomarker for differential diagnosis and recovery monitoring of acute viral and bacterial infections. PMID:33906069

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  Bioinformatic Analysis of Key Genes and Pathways Related to Keloids. PMID:33860039

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  History and Future Perspectives on the Discipline of Quantitative Systems Pharmacology Modeling and Its Applications. PMID:33841175

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  Bioinformatic Analysis of Structure and Function of LIM Domains of Human Zyxin Family Proteins. PMID:33808029

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  A Detailed Catalogue of Multi-Omics Methodologies for Identification of Putative Biomarkers and Causal Molecular Networks in Translational Cancer Research. PMID:33802234

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  Histamine, Metabolic Remodelling and Angiogenesis: A Systems Level Approach. PMID:33799732

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  Integrated intra- and intercellular signaling knowledge for multicellular omics analysis. PMID:33749993

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  Single-Cell Analysis Reveals Characterization of Infiltrating T Cells in Moderately Differentiated Colorectal Cancer. PMID:33584715

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  Proteogenomic and metabolomic characterization of human glioblastoma. PMID:33577785

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  Individualized interactomes for network-based precision medicine in hypertrophic cardiomyopathy with implications for other clinical pathophenotypes. PMID:33558530

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  ViralLink: An integrated workflow to investigate the effect of SARS-CoV-2 on intracellular signalling and regulatory pathways. PMID:33534793

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  GeneWalk identifies relevant gene functions for a biological context using network representation learning. PMID:33526072

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  Causal integration of multi-omics data with prior knowledge to generate mechanistic hypotheses. PMID:33502086

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  A regularized functional regression model enabling transcriptome-wide dosage-dependent association study of cancer drug response. PMID:33493149

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  Gene co-expression in the interactome: moving from correlation toward causation via an integrated approach to disease module discovery. PMID:33479222

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  Large-scale regulatory and signaling network assembly through linked open data. PMID:33459761

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  Multiscale Regulation of the Intervertebral Disc: Achievements in Experimental, In Silico, and Regenerative Research. PMID:33445782

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  Bioinformatics analysis of common key genes and pathways of intracranial, abdominal, and thoracic aneurysms. PMID:33407182

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  The status of causality in biological databases: data resources and data retrieval possibilities to support logical modeling. PMID:33378765

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  Identification of Interleukin-9 Producing Immune Cells in Endometrial Carcinoma and Establishment of a Prognostic Nomogram. PMID:33329510

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  Heterogeneous bone-marrow stromal progenitors drive myelofibrosis via a druggable alarmin axis. PMID:33301706

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  Network and pathway expansion of genetic disease associations identifies successful drug targets. PMID:33262371

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  Inhibition of 3-phosphoinositide-dependent protein kinase 1 (PDK1) can revert cellular senescence in human dermal fibroblasts. PMID:33229519

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  Virtual screening and network pharmacology-based synergistic mechanism identification of multiple components contained in Guanxin V against coronary artery disease. PMID:33187508

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  FunRes: resolving tissue-specific functional cell states based on a cell-cell communication network model. PMID:33179736

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  Preclinical validation of therapeutic targets predicted by tensor factorization on heterogeneous graphs. PMID:33106501

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  The tissue proteome in the multi-omic landscape of kidney disease. PMID:33028957

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  Genome-Wide Identification of RNA Editing Sites Affecting Intramuscular Fat in Pigs. PMID:32927662

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  Significance of hub genes and immune cell infiltration identified by bioinformatics analysis in pelvic organ prolapse. PMID:32874785

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  Footprint-based functional analysis of multiomic data. PMID:32685770

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  Toward Systems Biomarkers of Response to Immune Checkpoint Blockers. PMID:32670886

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  GLIDE: combining local methods and diffusion state embeddings to predict missing interactions in biological networks. PMID:32657369

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  Understanding the Mechanism of Cell Death in Gemcitabine Resistant Pancreatic Ductal Adenocarcinoma: A Systems Biology Approach. PMID:32655287

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  Network determinants of cardiovascular calcification and repositioned drug treatments. PMID:32638415

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  The Minimum Information about a Molecular Interaction CAusal STatement (MI2CAST). PMID:32637990

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  Integrated pharmaco-proteogenomics defines two subgroups in isocitrate dehydrogenase wild-type glioblastoma with prognostic and therapeutic opportunities. PMID:32620753

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  ULK1 and ULK2 are less redundant than previously thought: computational analysis uncovers distinct regulation and functions of these autophagy induction proteins. PMID:32616830

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  Converting networks to predictive logic models from perturbation signalling data with CellNOpt. PMID:32516357

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  Can We Assume the Gene Expression Profile as a Proxy for Signaling Network Activity? PMID:32503292

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  MicrobioLink: An Integrated Computational Pipeline to Infer Functional Effects of Microbiome-Host Interactions. PMID:32455748

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  Setting the basis of best practices and standards for curation and annotation of logical models in biology-highlights of the [BC]2 2019 CoLoMoTo/SysMod Workshop. PMID:32313939

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  Big data in IBD: big progress for clinical practice. PMID:32111636

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  Patient-specific logic models of signaling pathways from screenings on cancer biopsies to prioritize personalized combination therapies. PMID:32073727

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  Proteogenomic Characterization of Endometrial Carcinoma. PMID:32059776

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  Genomic Features and Clinical Characteristics of Adolescents and Young Adults With Cholangiocarcinoma. PMID:32010606

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  Stabilized Reconstruction of Signaling Networks from Single-Cell Cue-Response Data. PMID:31988302

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  Dysregulated mesenchymal PDGFR-β drives kidney fibrosis. PMID:31943786

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  A pipeline to create predictive functional networks: application to the tumor progression of hepatocellular carcinoma. PMID:31937236

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  The Impact of Pathway Database Choice on Statistical Enrichment Analysis and Predictive Modeling. PMID:31824580

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  Metabolic rewiring of the hypertensive kidney. PMID:31822592

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  NicheNet: modeling intercellular communication by linking ligands to target genes. PMID:31819264

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  The functional landscape of the human phosphoproteome. PMID:31819260

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  Impact of negative lymph nodes on colon cancer survival and exploring relevant transcriptomics differences through real-world data analyses. PMID:31807507

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  From expression footprints to causal pathways: contextualizing large signaling networks with CARNIVAL. PMID:31728204

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  SigHotSpotter: scRNA-seq-based computational tool to control cell subpopulation phenotypes for cellular rejuvenation strategies. PMID:31697324

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  SIGNOR 2.0, the SIGnaling Network Open Resource 2.0: 2019 update. PMID:31665520

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  ProteomicsDB: a multi-omics and multi-organism resource for life science research. PMID:31665479

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  Signal flow control of complex signaling networks. PMID:31582789

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  A Survey of Gene Prioritization Tools for Mendelian and Complex Human Diseases. PMID:31494632

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  Benchmarking network propagation methods for disease gene identification. PMID:31479437

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  Assessment of network module identification across complex diseases. PMID:31471613

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  Elucidating essential kinases of endothelin signalling by logic modelling of phosphoproteomics data. PMID:31464372

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  A comprehensive study on genome-wide coexpression network of KHDRBS1/Sam68 reveals its cancer and patient-specific association. PMID:31366900

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  Benchmark and integration of resources for the estimation of human transcription factor activities. PMID:31340985

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  Network pharmacology modeling identifies synergistic Aurora B and ZAK interaction in triple-negative breast cancer. PMID:31312514

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  Community assessment to advance computational prediction of cancer drug combinations in a pharmacogenomic screen. PMID:31209238

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  Analysis of the Human Kinome and Phosphatome by Mass Cytometry Reveals Overexpression-Induced Effects on Cancer-Related Signaling. PMID:31101498

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  PathMe: merging and exploring mechanistic pathway knowledge. PMID:31092193

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  Evaluating measures of association for single-cell transcriptomics. PMID:30962620

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  Identification of pharmacodynamic biomarker hypotheses through literature analysis with IBM Watson. PMID:30958864

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  Metascape provides a biologist-oriented resource for the analysis of systems-level datasets. PMID:30944313

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  Adapting Community Detection Algorithms for Disease Module Identification in Heterogeneous Biological Networks. PMID:30918511

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  PIMKL: Pathway-Induced Multiple Kernel Learning. PMID:30854223

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  CausalTAB: the PSI-MITAB 2.8 updated format for signalling data representation and dissemination. PMID:30793173

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  Embracing the Dark Side: Computational Approaches to Unveil the Functionality of Genes Lacking Biological Annotation in Drug-Induced Liver Injury. PMID:30515189

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  Adipocyte-secreted BMP8b mediates adrenergic-induced remodeling of the neuro-vascular network in adipose tissue. PMID:30478315

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  Open Targets Platform: new developments and updates two years on. PMID:30462303

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  Transcriptomic and functional network features of lung squamous cell carcinoma through integrative analysis of GEO and TCGA data. PMID:30367091

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  Bioinformatics Analysis Identifies p53 as a Candidate Prognostic Biomarker for Neuropathic Pain. PMID:30233637

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  Exploring the Mechanism of Flavonoids Through Systematic Bioinformatics Analysis. PMID:30158870

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  Reconstructing phosphorylation signalling networks from quantitative phosphoproteomic data. PMID:30072490

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  Developments in toxicogenomics: understanding and predicting compound-induced toxicity from gene expression data. PMID:29917034

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  Proteomics Versus Clinical Data and Stochastic Local Search Based Feature Selection for Acute Myeloid Leukemia Patients' Classification. PMID:29869179

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  Integrative Computational Network Analysis Reveals Site-Specific Mediators of Inflammation in Alzheimer's Disease. PMID:29551980

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  Discriminate the response of Acute Myeloid Leukemia patients to treatment by using proteomics data and Answer Set Programming. PMID:29536824

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  Phosphoproteomics-Based Profiling of Kinase Activities in Cancer Cells. PMID:29344887

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  Transcription Factor Activities Enhance Markers of Drug Sensitivity in Cancer. PMID:29229604

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  GDSCTools for mining pharmacogenomic interactions in cancer. PMID:29186349

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  From word models to executable models of signaling networks using automated assembly. PMID:29175850

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  DISNOR: a disease network open resource. PMID:29036667

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  Logic Modeling in Quantitative Systems Pharmacology. PMID:28681552

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  Drug Resistance Mechanisms in Colorectal Cancer Dissected with Cell Type-Specific Dynamic Logic Models. PMID:28381545

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  Data-driven reverse engineering of signaling pathways using ensembles of dynamic models. PMID:28166222
• http://dx.doi.org/10.1038/nmeth.4077

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protein interactions

metasource: bio.tools
version: extracted_at: 2022-11-04T11:25:45.043584

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protein interaction