Saez-Rodriguez Group

NetworkCommons: bridging data, knowledge, and methods to build and evaluate context-specific biological networks.

Paton et al. Bioinformatics, 2025

A platform for the biomedical application of large language models.

Lobentanzer et al. Nat Biotechnol, 2025

Single-cell integration reveals metaplasia in inflammatory gut diseases.

Oliver et al. Nature, 2024

Author Correction: Community assessment of methods to deconvolve cellular composition from bulk gene expression.

White et al. Nat Commun, 2024

Cell type mapping reveals tissue niches and interactions in subcortical multiple sclerosis lesions.

Lerma-Martin et al. Nat Neurosci, 2024

PhosX: data-driven kinase activity inference from phosphoproteomics experiments.

Lussana et al. Bioinformatics, 2024

Author Correction: Compartments in medulloblastoma with extensive nodularity are connected through differentiation along the granular precursor lineage.

Ghasemi et al. Nat Commun, 2024

Single-cell transcriptomics reveal distinctive patterns of fibroblast activation in heart failure with preserved ejection fraction.

Lanzer et al. Basic Res Cardiol, 2024

LIANA+ provides an all-in-one framework for cell-cell communication inference.

Dimitrov et al. Nat Cell Biol, 2024

Community assessment of methods to deconvolve cellular composition from bulk gene expression.

White et al. Nat Commun, 2024

Assessing the impact of transcriptomics data analysis pipelines on downstream functional enrichment results.

Paton et al. Nucleic Acids Res, 2024

A single-sample workflow for joint metabolomic and proteomic analysis of clinical specimens.

Gegner et al. Clin Proteomics, 2024

Drugst.One – a plug-and-play solution for online systems medicine and network-based drug repurposing.

Maier et al. Nucleic Acids Res, 2024

Molecular causality in the advent of foundation models.

Lobentanzer et al. Mol Syst Biol, 2024

Gene regulatory networks in disease and ageing.

Unger et al. Nat Rev Nephrol, 2024

Spatially resolved multiomics on the neuronal effects induced by spaceflight in mice.

Masarapu et al. Nat Commun, 2024

DOT: a flexible multi-objective optimization framework for transferring features across single-cell and spatial omics.

Rahimi et al. Nat Commun, 2024

Opening the Black Box: Spatial Transcriptomics and the Relevance of Artificial Intelligence-Detected Prognostic Regions in High-Grade Serous Carcinoma.

Laury et al. Mod Pathol, 2024

MetalinksDB: a flexible and contextualizable resource of metabolite-protein interactions.

Farr et al. Brief Bioinform, 2024

Combining LIANA and Tensor-cell2cell to decipher cell-cell communication across multiple samples.

Baghdassarian et al. Cell Rep Methods, 2024

Network integration of thermal proteome profiling with multi-omics data decodes PARP inhibition.

Burtscher et al. Mol Syst Biol, 2024

Integrating single-cell multi-omics and prior biological knowledge for a functional characterization of the immune system.

Schäfer et al. Nat Immunol, 2024

Drug-target identification in COVID-19 disease mechanisms using computational systems biology approaches.

Niarakis et al. Front Immunol, 2024

Metrics reloaded: recommendations for image analysis validation.

Maier-Hein et al. Nat Methods, 2024

Understanding metric-related pitfalls in image analysis validation.

Reinke et al. Nat Methods, 2024