{"id":101,"date":"2025-08-11T16:54:27","date_gmt":"2025-08-11T16:54:27","guid":{"rendered":"https:\/\/www.ebi.ac.uk\/research\/saez\/?page_id=101"},"modified":"2025-11-25T22:01:30","modified_gmt":"2025-11-25T22:01:30","slug":"selected-publications","status":"publish","type":"page","link":"https:\/\/www.ebi.ac.uk\/research\/saez\/selected-publications\/","title":{"rendered":"Selected publications"},"content":{"rendered":"\n

See https:\/\/saezlab.org\/publications\/<\/a> for a full list of publications. Our selected recent highlights are below. <\/p>\n\n\n\n

\n
\n\n<\/div>\n<\/div>\n<\/div>\n\n\n\n

Unifying multi-sample network inference from prior knowledge and omics data with CORNETO.<\/a><\/h3>\n\n\n\n

Rodriguez-Mier, P., Garrido-Rodriguez, M., Gabor, A., Saez-Rodriguez J.<\/p>\n\n\n\n

Nat Mach Intell, 2025<\/p>\n\n\n\n

doi:10.1038\/s42256-025-01069-9<\/p>\n\n\n\n

Comprehensive evaluation of phosphoproteomic-based kinase activity inference.<\/a><\/h3>\n\n\n\n

M\u00fcller-Dott S, Jaehnig EJ, Munchic KP, Jiang W, Yaron-Barir TM, Savage SR, Garrido-Rodriguez M, Johnson JL, Lussana A, Petsalaki E, Lei JT, Dugourd A, Krug K, Cantley LC, Mani DR, Zhang B, Saez-Rodriguez J.<\/p>\n\n\n\n

Nat Commun, 2025<\/p>\n\n\n\n

doi:10.1038\/s41467-025-59779-y.<\/p>\n\n\n\n

Learning tissue representation by identification of persistent local patterns in spatial omics data.<\/a><\/h3>\n\n\n\n

Tanevski J, Vulliard L, Ibarra-Arellano MA, Schapiro D, Hartmann FJ, Saez-Rodriguez J.<\/p>\n\n\n\n

Nat Commun, 2025<\/p>\n\n\n\n

doi:10.1038\/s41467-025-59448-0.<\/p>\n\n\n\n

A platform for the biomedical application of large language models.<\/a><\/h3>\n\n\n\n

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.<\/p>\n\n\n\n

Nat Biotechnol, 2025<\/p>\n\n\n\n

doi:10.1038\/s41587-024-02534-3.<\/p>\n\n\n\n

Cell type mapping reveals tissue niches and interactions in subcortical multiple sclerosis lesions.<\/a><\/h3>\n\n\n\n

Lerma-Martin C, Badia-I-Mompel P, Ramirez Flores RO, Sekol P, Sch\u00e4fer PSL, Riedl CJ, Hofmann A, Th\u00e4wel T, W\u00fcnnemann F, Ibarra-Arellano MA, Trobisch T, Eisele P, Schapiro D, Haeussler M, Hametner S, Saez-Rodriguez J, Schirmer L.<\/p>\n\n\n\n

Nat Neurosci, 2024<\/p>\n\n\n\n

doi:10.1038\/s41593-024-01796-z.<\/p>\n\n\n\n

LIANA+ provides an all-in-one framework for cell-cell communication inference.<\/a><\/h3>\n\n\n\n

Dimitrov D, Sch\u00e4fer PSL, Farr E, Rodriguez-Mier P, Lobentanzer S, Badia-I-Mompel P, Dugourd A, Tanevski J, Ramirez Flores RO, Saez-Rodriguez J.<\/p>\n\n\n\n

Nat Cell Biol, 2024<\/p>\n\n\n\n

doi:10.1038\/s41556-024-01469-w.<\/p>\n\n\n\n

Molecular causality in the advent of foundation models.<\/a><\/h3>\n\n\n\n

Lobentanzer S, Rodriguez-Mier P, Bauer S, Saez-Rodriguez J.<\/p>\n\n\n\n

Mol Syst Biol, 2024<\/p>\n\n\n\n

doi:10.1038\/s44320-024-00041-w.<\/p>\n\n\n\n

DOT: a flexible multi-objective optimization framework for transferring features across single-cell and spatial omics.<\/a><\/h3>\n\n\n\n

Rahimi A, Vale-Silva LA, F\u00e4lth Savitski M, Tanevski J, Saez-Rodriguez J.<\/p>\n\n\n\n

Nat Commun, 2024<\/p>\n\n\n\n

doi:10.1038\/s41467-024-48868-z.<\/p>\n\n\n\n

Network integration of thermal proteome profiling with multi-omics data decodes PARP inhibition.<\/a><\/h3>\n\n\n\n

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, F\u00e4lth-Savitski M, Saez-Rodriguez J.<\/p>\n\n\n\n

Mol Syst Biol, 2024<\/p>\n\n\n\n

doi:10.1038\/s44320-024-00025-w.<\/p>\n\n\n\n

Multicellular factor analysis of single-cell data for a tissue-centric understanding of disease.<\/a><\/h3>\n\n\n\n

Ramirez Flores RO, Lanzer JD, Dimitrov D, Velten B, Saez-Rodriguez J.<\/p>\n\n\n\n

Elife, 2023<\/p>\n\n\n\n

doi:10.7554\/elife.93161.<\/p>\n\n\n\n

Expanding the coverage of regulons from high-confidence prior knowledge for accurate estimation of transcription factor activities.<\/a><\/h3>\n\n\n\n

M\u00fcller-Dott S, Tsirvouli E, Vazquez M, Ramirez Flores RO, Badia-I-Mompel P, Fallegger R, T\u00fcrei D, L\u00e6greid A, Saez-Rodriguez J.<\/p>\n\n\n\n

Nucleic Acids Res, 2023<\/p>\n\n\n\n

doi:10.1093\/nar\/gkad841.<\/p>\n\n\n\n

Democratizing knowledge representation with BioCypher.<\/a><\/h3>\n\n\n\n

Lobentanzer S, Aloy P, Baumbach J, Bohar B, Carey VJ, Charoentong P, Danhauser K, Do\u011fan T, Dreo J, Dunham I, Farr E, Fernandez-Torras A, Gyori BM, Hartung M, Hoyt CT, Klein C, Korcsmaros T, Maier A, Mann M, Ochoa D, Pareja-Lorente E, Popp F, Preusse M, Probul N, Schwikowski B, Sen B, Strauss MT, Turei D, Ulusoy E, Waltemath D, Wodke JAH, Saez-Rodriguez J.<\/p>\n\n\n\n

Nat Biotechnol, 2023<\/p>\n\n\n\n

doi:10.1038\/s41587-023-01848-y.<\/p>\n\n\n\n

Gene regulatory network inference in the era of single-cell multi-omics.<\/a><\/h3>\n\n\n\n

Badia-I-Mompel P, Wessels L, M\u00fcller-Dott S, Trimbour R, Ramirez Flores RO, Argelaguet R, Saez-Rodriguez J.<\/p>\n\n\n\n

Nat Rev Genet, 2023<\/p>\n\n\n\n

doi:10.1038\/s41576-023-00618-5.<\/p>\n\n\n\n

<\/p>\n","protected":false},"excerpt":{"rendered":"

See https:\/\/saezlab.org\/publications\/ for a full list of publications. Our selected recent highlights are below. Unifying multi-sample network inference from prior knowledge and omics data with CORNETO. Rodriguez-Mier, P., Garrido-Rodriguez, M., Gabor, A., Saez-Rodriguez J. Nat Mach Intell, 2025…<\/p>\n","protected":false},"author":5,"featured_media":0,"parent":0,"menu_order":0,"comment_status":"closed","ping_status":"closed","template":"","meta":{"_acf_changed":false,"footnotes":""},"embl_taxonomy":[],"class_list":["post-101","page","type-page","status-publish","hentry"],"acf":[],"embl_taxonomy_terms":[],"_links":{"self":[{"href":"https:\/\/www.ebi.ac.uk\/research\/saez\/wp-json\/wp\/v2\/pages\/101","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/www.ebi.ac.uk\/research\/saez\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/www.ebi.ac.uk\/research\/saez\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/www.ebi.ac.uk\/research\/saez\/wp-json\/wp\/v2\/users\/5"}],"replies":[{"embeddable":true,"href":"https:\/\/www.ebi.ac.uk\/research\/saez\/wp-json\/wp\/v2\/comments?post=101"}],"version-history":[{"count":7,"href":"https:\/\/www.ebi.ac.uk\/research\/saez\/wp-json\/wp\/v2\/pages\/101\/revisions"}],"predecessor-version":[{"id":9211,"href":"https:\/\/www.ebi.ac.uk\/research\/saez\/wp-json\/wp\/v2\/pages\/101\/revisions\/9211"}],"wp:attachment":[{"href":"https:\/\/www.ebi.ac.uk\/research\/saez\/wp-json\/wp\/v2\/media?parent=101"}],"wp:term":[{"taxonomy":"embl_taxonomy","embeddable":true,"href":"https:\/\/www.ebi.ac.uk\/research\/saez\/wp-json\/wp\/v2\/embl_taxonomy?post=101"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}