Saez-Rodriguez Group

decoupleR: Ensemble of computational methods to infer biological activities from omics data

Badia-i-Mompel et al. Bioinformatics Advances, 2022

Mapping the epithelial-immune cell interactome upon infection in the gut and the upper airways.

Poletti et al. NPJ Syst Biol Appl, 2022

Explainable multiview framework for dissecting spatial relationships from highly multiplexed data.

Tanevski et al. Genome Biol, 2022

Computational drug repurposing against SARS-CoV-2 reveals plasma membrane cholesterol depletion as key factor of antiviral drug activity.

Barsi et al. Plos Comput Biol, 2022

Molecular consequences of SARS-CoV-2 liver tropism.

Wanner et al. Nat Metab, 2022

Deficiency of myeloid PHD proteins aggravates atherogenesis via macrophage apoptosis and paracrine fibrotic signalling.

van et al. Cardiovasc Res, 2022

Experimental and computational technologies to dissect the kidney at the single-cell level.

Kuppe et al. Nephrol Dial Transplant, 2022

Patient-specific Boolean models of signalling networks guide personalised treatments.

Montagud et al. Elife, 2022

The spatial transcriptomic landscape of the healing mouse intestine following damage.

Parigi et al. Nat Commun, 2022

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

Hernansaiz-Ballesteros et al. Bioinformatics, 2022

Two heads are better than one: current landscape of integrating QSP and machine learning : An ISoP QSP SIG white paper by the working group on the integration of quantitative systems pharmacology and machine learning.

Zhang et al. J Pharmacokinet Pharmacodyn, 2022

A community challenge for a pancancer drug mechanism of action inference from perturbational profile data.

Douglass et al. Cell Rep Med, 2022

Stabilization but No Functional Influence of HIF-1α Expression in the Intestinal Epithelium during Salmonella Typhimurium Infection.

Robrahn et al. Infect Immun, 2022

COVID-19 Disease Map, a computational knowledge repository of virus-host interaction mechanisms.

Ostaszewski et al. Mol Syst Biol, 2021

MAGED2 controls vasopressin-induced aquaporin-2 expression in collecting duct cells.

Reusch et al. J Proteomics, 2021

The human hepatocyte TXG-MAPr: gene co-expression network modules to support mechanism-based risk assessment.

Callegaro et al. Arch Toxicol, 2021

Systems approach reveals distinct and shared signaling networks of the four PGE2 receptors in T cells.

Lone et al. Sci Signal, 2021

Cell-to-cell and type-to-type heterogeneity of signaling networks: insights from the crowd.

Gabor et al. Mol Syst Biol, 2021

SREBP1-induced fatty acid synthesis depletes macrophages antioxidant defences to promote their alternative activation.

Bidault et al. Nat Metab, 2021

Medial Arterial Calcification: JACC State-of-the-Art Review.

Lanzer et al. J Am Coll Cardiol, 2021

Reusability and composability in process description maps: RAS-RAF-MEK-ERK signalling.

Mazein et al. Brief Bioinform, 2021

Transcriptomic Cross-Species Analysis of Chronic Liver Disease Reveals Consistent Regulation Between Humans and Mice.

Holland et al. Hepatol Commun, 2021

Partial Inhibition of the 6-Phosphofructo-2-Kinase/Fructose-2,6-Bisphosphatase-3 (PFKFB3) Enzyme in Myeloid Cells Does Not Affect Atherosclerosis.

Tillie et al. Front Cell Dev Biol, 2021

Prediction of combination therapies based on topological modeling of the immune signaling network in multiple sclerosis.

Bernardo-Faura et al. Genome Med, 2021

Contextualization of causal regulatory networks from toxicogenomics data applied to drug-induced liver injury.

Trairatphisan et al. Toxicol Lett, 2021