Saez-Rodriguez Group

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

Maier et al. Nucleic Acids Res, 2024

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

Paton et al. Nucleic Acids Res, 2024

Molecular causality in the advent of foundation models.

Lobentanzer et al. Mol Syst Biol, 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

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

Multiscale networks in multiple sclerosis.

Kennedy et al. Plos Comput Biol, 2024

Complementing Cell Taxonomies with a Multicellular Analysis of Tissues.

Ramirez et al. Physiology (Bethesda), 2024

Collaborative effect of Csnk1a1 haploinsufficiency and mutant p53 in Myc induction can promote leukemic transformation.

Fuchs et al. Blood Adv, 2024

A network-based transcriptomic landscape of HepG2 cells uncovering causal gene-cytotoxicity interactions underlying drug-induced liver injury.

Wijaya et al. Toxicol Sci, 2024

Profiling the heterogeneity of colorectal cancer consensus molecular subtypes using spatial transcriptomics.

Valdeolivas et al. NPJ Precis Oncol, 2024

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

Ghasemi et al. Nat Commun, 2024

Metabolic Communication by SGLT2 Inhibition.

Billing et al. Circulation, 2023

Predicting disease severity in multiple sclerosis using multimodal data and machine learning.

Andorra et al. J Neurol, 2023

Spatial transcriptomics of B cell and T cell receptors reveals lymphocyte clonal dynamics.

Engblom et al. Science, 2023

Mapping cardiac remodeling in chronic kidney disease.

Kaesler et al. Sci Adv, 2023

Multicellular factor analysis of single-cell data for a tissue-centric understanding of disease.

Ramirez et al. Elife, 2023

Expanding the coverage of regulons from high-confidence prior knowledge for accurate estimation of transcription factor activities.

Müller-Dott et al. Nucleic Acids Res, 2023

A machine learning and directed network optimization approach to uncover TP53 regulatory patterns.

Triantafyllidis et al. iScience, 2023