Saez-Rodriguez Group

Systems Biomedicine

A microfluidic Braille valve platform for on-demand production, combinatorial screening and sorting of chemically distinct droplets.

Utharala et al. Nat Protoc, 2022

Spatial multi-omic map of human myocardial infarction.

Kuppe, Ramirez Flores, Li, et al. Nature, 2022

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

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

Combi-seq for multiplexed transcriptome-based profiling of drug combinations using deterministic barcoding in single-cell droplets.

Mathur, Szalai, et al. Nat Commun, 2022

Imbalanced gut microbiota fuels hepatocellular carcinoma development by shaping the hepatic inflammatory microenvironment.

Schneider et al. Nat Commun, 2022

Cancer-associated fibroblasts require proline synthesis by PYCR1 for the deposition of pro-tumorigenic extracellular matrix.

Kay et al. Nat Metab, 2022

Comparison of methods and resources for cell-cell communication inference from single-cell RNA-Seq data.

Dimitrov et al. Nat Commun, 2022

Reducing lipid bilayer stress by monounsaturated fatty acids protects renal proximal tubules in diabetes.

Pérez-Martí et al. Elife, 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

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

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

SysMod: the ISCB community for data-driven computational modelling and multi-scale analysis of biological systems.

Dräger et al. Bioinformatics, 2021

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

Callegaro et al. Arch Toxicol, 2021

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

Mazein et al. Brief Bioinform, 2021

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

Bernardo-Faura et al. Genome Med, 2021

A comprehensive database for integrated analysis of omics data in autoimmune diseases.

Martorell-Marugán et al. Bmc Bioinformatics, 2021

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

Rodrigues et al. Arch Toxicol, 2021

Deep spatial profiling of human COVID-19 brains reveals neuroinflammation with distinct microanatomical microglia-T-cell interactions.

Schwabenland et al. Immunity, 2021

Advances in systems biology modeling: 10 years of crowdsourcing DREAM challenges.

Meyer et al. Cell Syst, 2021

Integration of temporal single cell cellular stress response activity with logic-ODE modeling reveals activation of ATF4-CHOP axis as a critical predictor of drug-induced liver injury.

Wijaya et al. Biochem Pharmacol, 2021