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Community assessment of methods to deconvolve cellular composition from bulk gene expression.
White BS, de Reyniès A, Newman AM, Waterfall JJ, Lamb A, Petitprez F, Lin Y, Yu R, Guerrero-Gimenez ME, Domanskyi S, Monaco G, Chung V, Banerjee J, Derrick D, Valdeolivas A, Li H, Xiao X, Wang S, Zheng F, Yang W, Catania CA, Lang BJ, Bertus TJ, Piermarocchi C, Caruso FP, Ceccarelli M, Yu T, Guo X, Bletz J, Coller J, Maecker H, Duault C, Shokoohi V, Patel S, Liliental JE, Simon S; Tumor Deconvolution DREAM Challenge consortium; Saez-Rodriguez J, Heiser LM, Guinney J, Gentles AJ. White BS, et al. Among authors: valdeolivas a. Nat Commun. 2024 Aug 27;15(1):7362. doi: 10.1038/s41467-024-50618-0. Nat Commun. 2024. PMID: 39191725 Free PMC article.
Contextual AI models for single-cell protein biology.
Li MM, Huang Y, Sumathipala M, Liang MQ, Valdeolivas A, Ananthakrishnan AN, Liao K, Marbach D, Zitnik M. Li MM, et al. Among authors: valdeolivas a. Nat Methods. 2024 Aug;21(8):1546-1557. doi: 10.1038/s41592-024-02341-3. Epub 2024 Jul 22. Nat Methods. 2024. PMID: 39039335 Free PMC article.
Tumor-agnostic transcriptome-based classifier identifies spatial infiltration patterns of CD8+T cells in the tumor microenvironment and predicts clinical outcome in early-phase and late-phase clinical trials.
Roller A, Davydov II, Schwalie PC, Serrano-Serrano ML, Heller A, Staedler N, Ferreira CS, Dietmann G, Klaman I, Valdeolivas A, Korski K, Cannarile MA. Roller A, et al. Among authors: valdeolivas a. J Immunother Cancer. 2024 Apr 22;12(4):e008185. doi: 10.1136/jitc-2023-008185. J Immunother Cancer. 2024. PMID: 38649280 Free PMC article.
Drug-target identification in COVID-19 disease mechanisms using computational systems biology approaches.
Niarakis A, Ostaszewski M, Mazein A, Kuperstein I, Kutmon M, Gillespie ME, Funahashi A, Acencio ML, Hemedan A, Aichem M, Klein K, Czauderna T, Burtscher F, Yamada TG, Hiki Y, Hiroi NF, Hu F, Pham N, Ehrhart F, Willighagen EL, Valdeolivas A, Dugourd A, Messina F, Esteban-Medina M, Peña-Chilet M, Rian K, Soliman S, Aghamiri SS, Puniya BL, Naldi A, Helikar T, Singh V, Fernández MF, Bermudez V, Tsirvouli E, Montagud A, Noël V, Ponce-de-Leon M, Maier D, Bauch A, Gyori BM, Bachman JA, Luna A, Piñero J, Furlong LI, Balaur I, Rougny A, Jarosz Y, Overall RW, Phair R, Perfetto L, Matthews L, Rex DAB, Orlic-Milacic M, Gomez LCM, De Meulder B, Ravel JM, Jassal B, Satagopam V, Wu G, Golebiewski M, Gawron P, Calzone L, Beckmann JS, Evelo CT, D'Eustachio P, Schreiber F, Saez-Rodriguez J, Dopazo J, Kuiper M, Valencia A, Wolkenhauer O, Kitano H, Barillot E, Auffray C, Balling R, Schneider R; COVID-19 Disease Map Community. Niarakis A, et al. Among authors: valdeolivas a. Front Immunol. 2024 Feb 13;14:1282859. doi: 10.3389/fimmu.2023.1282859. eCollection 2023. Front Immunol. 2024. PMID: 38414974 Free PMC article.
Profiling the heterogeneity of colorectal cancer consensus molecular subtypes using spatial transcriptomics.
Valdeolivas A, Amberg B, Giroud N, Richardson M, Gálvez EJC, Badillo S, Julien-Laferrière A, Túrós D, Voith von Voithenberg L, Wells I, Pesti B, Lo AA, Yángüez E, Das Thakur M, Bscheider M, Sultan M, Kumpesa N, Jacobsen B, Bergauer T, Saez-Rodriguez J, Rottenberg S, Schwalie PC, Hahn K. Valdeolivas A, et al. NPJ Precis Oncol. 2024 Jan 10;8(1):10. doi: 10.1038/s41698-023-00488-4. NPJ Precis Oncol. 2024. PMID: 38200223 Free PMC article.
Mapping the epithelial-immune cell interactome upon infection in the gut and the upper airways.
Poletti M, Treveil A, Csabai L, Gul L, Modos D, Madgwick M, Olbei M, Bohar B, Valdeolivas A, Turei D, Verstockt B, Triana S, Alexandrov T, Saez-Rodriguez J, Stanifer ML, Boulant S, Korcsmaros T. Poletti M, et al. Among authors: valdeolivas a. NPJ Syst Biol Appl. 2022 May 2;8(1):15. doi: 10.1038/s41540-022-00224-x. NPJ Syst Biol Appl. 2022. PMID: 35501398 Free PMC article.
20 results