Publications
OmniPath: integrated knowledgebase for multi-omics analysis.
2025
Türei D, Schaul J, Palacio-Escat N, Bohár B, Bai Y, Ceccarelli F, Çevrim E, Daley M, Darcan M, Dimitrov D et al.
Nucleic acids research
A cross-study transcriptional patient map of heart failure defines conserved multicellular coordination in cardiac remodeling.
2025
Lanzer JD, Ramirez Flores RO, Liñares Blanco J, Steier M, Rangrez AY, Frey N, Saez-Rodriguez J
Nature communications
Unifying multi-sample network inference from prior knowledge and omics data with CORNETO
2025
Pablo Rodriguez-Mier, Martin Garrido-Rodriguez, Attila Gabor, Julio Saez-Rodriguez
Nature Machine Intelligence
Dynamic multi-omics and mechanistic modeling approach uncovers novel mechanisms of kidney fibrosis progression.
2025
Tuechler N, Burtscher ML, Garrido-Rodriguez M, Khan MM, Türei D, Tischer C, Kaspar S, Schwarz JJ, Stein F, Rettel M et al.
Molecular systems biology
Comprehensive evaluation of phosphoproteomic-based kinase activity inference.
2025
Müller-Dott S, Jaehnig EJ, Munchic KP, Jiang W, Yaron-Barir TM, Savage SR, Garrido-Rodriguez M, Johnson JL, Lussana A, Petsalaki E et al.
Nature communications
A platform for the biomedical application of large language models.
2025
Lobentanzer S, Feng S, Bruderer N, Maier A, BioChatter Consortium, Wang C, Baumbach J, Abreu-Vicente J, Krehl N, Ma Q et al.
Nature biotechnology
Cell type mapping reveals tissue niches and interactions in subcortical multiple sclerosis lesions.
2024
Lerma-Martin C, Badia-I-Mompel P, Ramirez Flores RO, Sekol P, Schäfer PSL, Riedl CJ, Hofmann A, Thäwel T, Wünnemann F, Ibarra-Arellano MA et al.
Nature neuroscience
LIANA+ provides an all-in-one framework for cell-cell communication inference.
2024
Dimitrov D, Schäfer PSL, Farr E, Rodriguez-Mier P, Lobentanzer S, Badia-I-Mompel P, Dugourd A, Tanevski J, Ramirez Flores RO, Saez-Rodriguez J
Nature cell biology
DOT: a flexible multi-objective optimization framework for transferring features across single-cell and spatial omics
2024
Arezou Rahimi, Luis A. Vale-Silva, Maria Fälth Savitski, Jovan Tanevski, Julio Saez-Rodriguez
Nature Communications
Network integration of thermal proteome profiling with multi-omics data decodes PARP inhibition.
2024
Burtscher ML, Gade S, Garrido-Rodriguez M, Rutkowska A, Werner T, Eberl HC, Petretich M, Knopf N, Zirngibl K, Grandi P et al.
Molecular systems biology
Multicellular factor analysis of single-cell data for a tissue-centric understanding of disease
2023
Ricardo Omar Ramirez Flores, Jan David Lanzer, Daniel Dimitrov, Britta Velten, Julio Saez-Rodriguez
eLife
Expanding the coverage of regulons from high-confidence prior knowledge for accurate estimation of transcription factor activities
2023
Sophia Müller-Dott, Eirini Tsirvouli, Miguel Vazquez, Ricardo O Ramirez Flores, Pau Badia-i-Mompel, Robin Fallegger, Dénes Türei, Astrid Lægreid, Julio Saez-Rodriguez
Nucleic Acids Research
Democratizing knowledge representation with BioCypher.
2023
Lobentanzer S, Aloy P, Baumbach J, Bohar B, Carey VJ, Charoentong P, Danhauser K, Doğan T, Dreo J, Dunham I et al.
Nature biotechnology
Spatial multi-omic map of human myocardial infarction.
2022
Kuppe C, Ramirez Flores RO, Li Z, Hayat S, Levinson RT, Liao X, Hannani MT, Tanevski J, Wünnemann F, Nagai JS et al.
Comparison of methods and resources for cell-cell communication inference from single-cell RNA-Seq data.
2022
Dimitrov D, Türei D, Garrido-Rodriguez M, Burmedi PL, Nagai JS, Boys C, Ramirez Flores RO, Kim H, Szalai B, Costa IG et al.
Nature communications
Integrated intra- and intercellular signaling knowledge for multicellular omics analysis.
2021
Türei D, Valdeolivas A, Gul L, Palacio-Escat N, Klein M, Ivanova O, Ölbei M, Gábor A, Theis F, Módos D et al.
Molecular systems biology
Causal integration of multi-omics data with prior knowledge to generate mechanistic hypotheses.
2021
Dugourd A, Kuppe C, Sciacovelli M, Gjerga E, Gabor A, Emdal KB, Vieira V, Bekker-Jensen DB, Kranz J, Bindels EMJ et al.
Molecular systems biology
Robustness and applicability of transcription factor and pathway analysis tools on single-cell RNA-seq data.
2020
Holland CH, Tanevski J, Perales-Patón J, Gleixner J, Kumar MP, Mereu E, Joughin BA, Stegle O, Lauffenburger DA, Heyn H et al.
Genome biology
Community assessment to advance computational prediction of cancer drug combinations in a pharmacogenomic screen.
2019
Menden MP, Wang D, Mason MJ, Szalai B, Bulusu KC, Guan Y, Yu T, Kang J, Jeon M, Wolfinger R et al.
Nature communications
A Landscape of Pharmacogenomic Interactions in Cancer.
2016
Iorio F, Knijnenburg TA, Vis DJ, Bignell GR, Menden MP, Schubert M, Aben N, Gonçalves E, Barthorpe S, Lightfoot H et al.
Inferring causal molecular networks: empirical assessment through a community-based effort.
2016
Hill SM, Heiser LM, Cokelaer T, Unger M, Nesser NK, Carlin DE, Zhang Y, Sokolov A, Paull EO, Wong CK et al.