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Page 1
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.
An integrated single-cell reference atlas of the human endometrium.
Marečková M, Garcia-Alonso L, Moullet M, Lorenzi V, Petryszak R, Sancho-Serra C, Oszlanczi A, Icoresi Mazzeo C, Wong FCK, Kelava I, Hoffman S, Krassowski M, Garbutt K, Gaitskell K, Yancheva S, Woon EV, Male V, Granne I, Hellner K, Mahbubani KT, Saeb-Parsy K, Lotfollahi M, Prigmore E, Southcombe J, Dragovic RA, Becker CM, Zondervan KT, Vento-Tormo R. Marečková M, et al. Among authors: lotfollahi m. Nat Genet. 2024 Sep;56(9):1925-1937. doi: 10.1038/s41588-024-01873-w. Epub 2024 Aug 28. Nat Genet. 2024. PMID: 39198675 Free PMC article.
Predicting cellular responses to complex perturbations in high-throughput screens.
Lotfollahi M, Klimovskaia Susmelj A, De Donno C, Hetzel L, Ji Y, Ibarra IL, Srivatsan SR, Naghipourfar M, Daza RM, Martin B, Shendure J, McFaline-Figueroa JL, Boyeau P, Wolf FA, Yakubova N, Günnemann S, Trapnell C, Lopez-Paz D, Theis FJ. Lotfollahi M, et al. Mol Syst Biol. 2023 Jun 12;19(6):e11517. doi: 10.15252/msb.202211517. Epub 2023 May 8. Mol Syst Biol. 2023. PMID: 37154091 Free PMC article.
An integrated cell atlas of the lung in health and disease.
Sikkema L, Ramírez-Suástegui C, Strobl DC, Gillett TE, Zappia L, Madissoon E, Markov NS, Zaragosi LE, Ji Y, Ansari M, Arguel MJ, Apperloo L, Banchero M, Bécavin C, Berg M, Chichelnitskiy E, Chung MI, Collin A, Gay ACA, Gote-Schniering J, Hooshiar Kashani B, Inecik K, Jain M, Kapellos TS, Kole TM, Leroy S, Mayr CH, Oliver AJ, von Papen M, Peter L, Taylor CJ, Walzthoeni T, Xu C, Bui LT, De Donno C, Dony L, Faiz A, Guo M, Gutierrez AJ, Heumos L, Huang N, Ibarra IL, Jackson ND, Kadur Lakshminarasimha Murthy P, Lotfollahi M, Tabib T, Talavera-López C, Travaglini KJ, Wilbrey-Clark A, Worlock KB, Yoshida M; Lung Biological Network Consortium; van den Berge M, Bossé Y, Desai TJ, Eickelberg O, Kaminski N, Krasnow MA, Lafyatis R, Nikolic MZ, Powell JE, Rajagopal J, Rojas M, Rozenblatt-Rosen O, Seibold MA, Sheppard D, Shepherd DP, Sin DD, Timens W, Tsankov AM, Whitsett J, Xu Y, Banovich NE, Barbry P, Duong TE, Falk CS, Meyer KB, Kropski JA, Pe'er D, Schiller HB, Tata PR, Schultze JL, Teichmann SA, Misharin AV, Nawijn MC, Luecken MD, Theis FJ. Sikkema L, et al. Among authors: lotfollahi m. Nat Med. 2023 Jun;29(6):1563-1577. doi: 10.1038/s41591-023-02327-2. Epub 2023 Jun 8. Nat Med. 2023. PMID: 37291214 Free PMC article.
Towards multimodal foundation models in molecular cell biology.
Cui H, Tejada-Lapuerta A, Brbić M, Saez-Rodriguez J, Cristea S, Goodarzi H, Lotfollahi M, Theis FJ, Wang B. Cui H, et al. Among authors: lotfollahi m. Nature. 2025 Apr;640(8059):623-633. doi: 10.1038/s41586-025-08710-y. Epub 2025 Apr 16. Nature. 2025. PMID: 40240854
Biomedical data and AI.
Xu H, Zhou S, Zhu Z, Vitelli V, Chen L, Dai Z, Yang N, Lai L, Yang S, Ovchinnikov S, Qiao Z, Liu S, Song C, Pei J, Wen H, Feng J, Zhang Y, Xie Z, Liu YY, Li Z, Jin F, Li H, Lotfollahi M, Zhang X, Yang G, Zhang S, Gao G, Li P, Liu Q, Han JJ. Xu H, et al. Among authors: lotfollahi m. Sci China Life Sci. 2025 May;68(5):1536-1540. doi: 10.1007/s11427-024-2859-1. Epub 2025 Mar 14. Sci China Life Sci. 2025. PMID: 40100542 No abstract available.
Quantitative characterization of cell niches in spatially resolved omics data.
Birk S, Bonafonte-Pardàs I, Feriz AM, Boxall A, Agirre E, Memi F, Maguza A, Yadav A, Armingol E, Fan R, Castelo-Branco G, Theis FJ, Bayraktar OA, Talavera-López C, Lotfollahi M. Birk S, et al. Among authors: lotfollahi m. Nat Genet. 2025 Apr;57(4):897-909. doi: 10.1038/s41588-025-02120-6. Epub 2025 Mar 18. Nat Genet. 2025. PMID: 40102688 Free PMC article.
A single-cell and spatial genomics atlas of human skin fibroblasts reveals shared disease-related fibroblast subtypes across tissues.
Steele L, Olabi B, Roberts K, Mazin PV, Koplev S, Tudor C, Rumney B, Admane C, Jiang T, Correa-Gallegos D, Chakala KP, Binkevich A, Gopee NH, Predeus A, Prete M, Winheim E, Annusver K, Forsthuber A, Francis L, Frech S, Ganier C, Layton T, Liu Y, Yuan H, Gudjonsson JE, Lichtenberger BM, Mahil S, Nanchahal J, O'Toole EA, Plikus MV, Rinkevich Y, Rognoni E, Smith CH, Teichmann SA, Kasper M, Foster AR, Lotfollahi M, Haniffa M. Steele L, et al. Among authors: lotfollahi m. Nat Immunol. 2025 Oct;26(10):1807-1820. doi: 10.1038/s41590-025-02267-8. Epub 2025 Sep 24. Nat Immunol. 2025. PMID: 40993240 Free PMC article.
33 results