Converting networks to predictive logic models from perturbation signalling data with CellNOpt
Gjerga E Bioinformatics, 2020
Stratification and prediction of drug synergy based on target functional similarity
Yang M npj Systems Biology and Applications, 2020
CELLector: Genomics Guided Selection of Cancer in vitro Models
Najgebauer H Cell Systems, 2020
Patient‐specific logic models of signaling pathways from screenings on cancer biopsies to prioritize personalized combination therapies
Eduati F Molecular systems biology, 2020
Robustness and applicability of transcription factor and pathway analysis tools on single-cell RNA-seq data
Holland CH Genome Biology, 2020
Dysregulated mesenchymal PDGFR-β drives kidney fibrosis
Buhl E EMBO Mol Med, 2020
Personalized signaling models for personalized treatments
Saez‐Rodriguez J Mol Syst Biol, 2020
Quantitative Systems Toxicology Modeling To Address Key Safety Questions in Drug Development: A Focus of the TransQST Consortium
Ferreira S Chem Res Toxicol, 2020
Bringing data from curated pathway resources to Cytoscape with OmniPath
Ceccarelli F Bioinformatics, 2019
Kinetic modelling of quantitative proteome data predicts metabolic reprogramming of liver cancer
Berndt N British Journal of Cancer , 2019
Metabolic rewiring of the hypertensive kidney
Rinschen M Science Signaling, 2019
Influence of Liver Fibrosis on Lobular Zonation
Ghallab A MDPI cells, 2019
A Functional Landscape of CKD Entities From Public Transcriptomic Data
Tajti F Kidney International Reports, 2019
From expression footprints to causal pathways: contextualizing large signaling networks with CARNIVAL
Liu A npj Systems Biology and Applications, 2019
Modeling Cell-Cell Interactions from Spatial Molecular Data with Spatial Variance Component Analysis
Arnol D Cell reports, 2019
Signatures of cell death and proliferation in perturbation transcriptomics data—from confounding factor to effective prediction
Szalai B Nucleic Acids Research, 2019
Transfer of regulatory knowledge from human to mouse for functional genomic analysis.
Holland CH Biochim Biophys Acta Gene Regul Mech, 2019
Reproducible biomedical benchmarking in the cloud: lessons from crowd-sourced data challenges.
Ellrott K Genome Biol, 2019
Assessment of network module identification across complex diseases.
Choobdar S Nat Methods, 2019
Novel plasma peptide markers involved in the pathology of CKD identified using mass spectrometric approach.
Gajjala PR J Mol Med (Berl), 2019
Elucidating essential kinases of endothelin signalling by logic modelling of phosphoproteomics data.
Schäfer A Mol Syst Biol, 2019
Benchmark and integration of resources for the estimation of human transcription factor activities.
Garcia-Alonso L Genome Res, 2019
Network pharmacology modeling identifies synergistic Aurora B and ZAK interaction in triple-negative breast cancer.
Tang J NPJ Syst Biol Appl, 2019
Community assessment to advance computational prediction of cancer drug combinations in a pharmacogenomic screen.
Menden MP Nat Commun, 2019
Functional linkage of gene fusions to cancer cell fitness assessed by pharmacological and CRISPR-Cas9 screening.
Picco G Nat Commun, 2019