Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation

Search Page

Filters

My Custom Filters

Edit custom filters

Publication date

Text availability

Article attribute

Article type

Additional filters

Article Language

Species

Sex

Age

Other

Search Results

35 results

Filters applied: . Clear all
Results are displayed in a computed author sort order. The Publication Date timeline is not available.
Page 1
Pertpy: an end-to-end framework for perturbation analysis.
Heumos L, Ji Y, May L, Green TD, Peidli S, Zhang X, Wu X, Ostner J, Schumacher A, Hrovatin K, Müller M, Chong F, Sturm G, Tejada A, Dann E, Dong M, Pinto G, Bahrami M, Gold I, Rybakov S, Namsaraeva A, Moinfar AA, Zheng Z, Roellin E, Mekki I, Sander C, Lotfollahi M, Schiller HB, Theis FJ. Heumos L, et al. Among authors: lotfollahi m. Nat Methods. 2026 Feb;23(2):350-359. doi: 10.1038/s41592-025-02909-7. Epub 2025 Dec 31. Nat Methods. 2026. PMID: 41476114 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.
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
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.
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.
Author Correction: Opportunities and challenges of single-cell and spatially resolved genomics methods for neuroscience discovery.
Bonev B, Castelo-Branco G, Chen F, Codeluppi S, Corces MR, Fan J, Heiman M, Harris K, Inoue F, Kellis M, Levine A, Lotfollahi M, Luo C, Maynard KR, Nitzan M, Ramani V, Satijia R, Schirmer L, Shen Y, Sun N, Green GS, Theis F, Wang X, Welch JD, Gokce O, Konopka G, Liddelow S, Macosko E, Ali Bayraktar O, Habib N, Nowakowski TJ. Bonev B, et al. Among authors: lotfollahi m. Nat Neurosci. 2025 Jan;28(1):216. doi: 10.1038/s41593-024-01858-2. Nat Neurosci. 2025. PMID: 39681663 Free PMC article. No abstract available.
Opportunities and challenges of single-cell and spatially resolved genomics methods for neuroscience discovery.
Bonev B, Castelo-Branco G, Chen F, Codeluppi S, Corces MR, Fan J, Heiman M, Harris K, Inoue F, Kellis M, Levine A, Lotfollahi M, Luo C, Maynard KR, Nitzan M, Ramani V, Satijia R, Schirmer L, Shen Y, Sun N, Green GS, Theis F, Wang X, Welch JD, Gokce O, Konopka G, Liddelow S, Macosko E, Ali Bayraktar O, Habib N, Nowakowski TJ. Bonev B, et al. Among authors: lotfollahi m. Nat Neurosci. 2024 Dec;27(12):2292-2309. doi: 10.1038/s41593-024-01806-0. Epub 2024 Dec 3. Nat Neurosci. 2024. PMID: 39627587 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.
35 results