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Bioactivity Profile Similarities to Expand the Repertoire of COVID-19 Drugs.
J Chem Inf Model. 2020 Dec 28;60(12):5730-5734. doi: 10.1021/acs.jcim.0c00420. Epub 2020 Jul 16.
J Chem Inf Model. 2020.
PMID: 32672454
Bioactivity descriptors for uncharacterized chemical compounds.
Bertoni M, Duran-Frigola M, Badia-I-Mompel P, Pauls E, Orozco-Ruiz M, Guitart-Pla O, Alcalde V, Diaz VM, Berenguer-Llergo A, Brun-Heath I, Villegas N, de Herreros AG, Aloy P.
Bertoni M, et al. Among authors: badia i mompel p.
Nat Commun. 2021 Jun 24;12(1):3932. doi: 10.1038/s41467-021-24150-4.
Nat Commun. 2021.
PMID: 34168145
Free PMC article.
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A community challenge for a pancancer drug mechanism of action inference from perturbational profile data.
Douglass EF Jr, Allaway RJ, Szalai B, Wang W, Tian T, Fernández-Torras A, Realubit R, Karan C, Zheng S, Pessia A, Tanoli Z, Jafari M, Wan F, Li S, Xiong Y, Duran-Frigola M, Bertoni M, Badia-I-Mompel P, Mateo L, Guitart-Pla O, Chung V; DREAM CTD-squared Pancancer Drug Activity Challenge Consortium; Tang J, Zeng J, Aloy P, Saez-Rodriguez J, Guinney J, Gerhard DS, Califano A.
Douglass EF Jr, et al. Among authors: badia i mompel p.
Cell Rep Med. 2022 Jan 18;3(1):100492. doi: 10.1016/j.xcrm.2021.100492. eCollection 2022 Jan 18.
Cell Rep Med. 2022.
PMID: 35106508
Free PMC article.
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Molecular consequences of SARS-CoV-2 liver tropism.
Wanner N, Andrieux G, Badia-I-Mompel P, Edler C, Pfefferle S, Lindenmeyer MT, Schmidt-Lauber C, Czogalla J, Wong MN, Okabayashi Y, Braun F, Lütgehetmann M, Meister E, Lu S, Noriega MLM, Günther T, Grundhoff A, Fischer N, Bräuninger H, Lindner D, Westermann D, Haas F, Roedl K, Kluge S, Addo MM, Huber S, Lohse AW, Reiser J, Ondruschka B, Sperhake JP, Saez-Rodriguez J, Boerries M, Hayek SS, Aepfelbacher M, Scaturro P, Puelles VG, Huber TB.
Wanner N, et al. Among authors: badia i mompel p.
Nat Metab. 2022 Mar;4(3):310-319. doi: 10.1038/s42255-022-00552-6. Epub 2022 Mar 28.
Nat Metab. 2022.
PMID: 35347318
Free PMC article.
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Expanding the coverage of regulons from high-confidence prior knowledge for accurate estimation of transcription factor activities.
Müller-Dott S, Tsirvouli E, Vazquez M, Ramirez Flores RO, Badia-I-Mompel P, Fallegger R, Türei D, Lægreid A, Saez-Rodriguez J.
Müller-Dott S, et al. Among authors: badia i mompel p.
Nucleic Acids Res. 2023 Nov 10;51(20):10934-10949. doi: 10.1093/nar/gkad841.
Nucleic Acids Res. 2023.
PMID: 37843125
Free PMC article.
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Gene regulatory network inference in the era of single-cell multi-omics.
Badia-I-Mompel P, Wessels L, Müller-Dott S, Trimbour R, Ramirez Flores RO, Argelaguet R, Saez-Rodriguez J.
Badia-I-Mompel P, et al.
Nat Rev Genet. 2023 Nov;24(11):739-754. doi: 10.1038/s41576-023-00618-5. Epub 2023 Jun 26.
Nat Rev Genet. 2023.
PMID: 37365273
Review.
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Best practices for single-cell analysis across modalities.
Heumos L, Schaar AC, Lance C, Litinetskaya A, Drost F, Zappia L, Lücken MD, Strobl DC, Henao J, Curion F; Single-cell Best Practices Consortium; Schiller HB, Theis FJ.
Heumos L, et al.
Nat Rev Genet. 2023 Aug;24(8):550-572. doi: 10.1038/s41576-023-00586-w. Epub 2023 Mar 31.
Nat Rev Genet. 2023.
PMID: 37002403
Free PMC article.
Review.
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decoupleR: ensemble of computational methods to infer biological activities from omics data.
Badia-I-Mompel P, Vélez Santiago J, Braunger J, Geiss C, Dimitrov D, Müller-Dott S, Taus P, Dugourd A, Holland CH, Ramirez Flores RO, Saez-Rodriguez J.
Badia-I-Mompel P, et al.
Bioinform Adv. 2022 Mar 8;2(1):vbac016. doi: 10.1093/bioadv/vbac016. eCollection 2022.
Bioinform Adv. 2022.
PMID: 36699385
Free PMC article.
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