Publications
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
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, Lei JT, Saez-Rodriguez J
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, Lemberger T, Saez-Rodriguez J
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, Schirmer L
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
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, Bergamini G, Bantscheff M, Saez-Rodriguez J
Molecular systems biology
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, Farr E, Fernandez-Torras A, Gyori BM, Saez-Rodriguez J
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, Halder M, Schumacher D, Menzel S, Kramann R
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, Valdeolivas A, Dugourd A, Saez-Rodriguez J
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, Korcsmáros T, Saez-Rodriguez J
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, Costa ASH, Sousa A, Beltrao P, Saez-Rodriguez J
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, Szalai B, Saez-Rodriguez J
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, Nguyen T, Zaslavskiy M, Saez-Rodriguez J
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, Cokelaer T, Greninger P, van Dyk E, Chang H, de Silva H, Heyn H, Deng X, Egan RK, Liu Q, Mironenko T
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, Graim K, Bivol A, Wang H, Zhu F, Afsari B, Danilova LV, Favorov AV, Lee WS, Taylor D, Hu CW