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Page 1
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. Among authors: ibarra il. 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.
Squidpy: a scalable framework for spatial omics analysis.
Palla G, Spitzer H, Klein M, Fischer D, Schaar AC, Kuemmerle LB, Rybakov S, Ibarra IL, Holmberg O, Virshup I, Lotfollahi M, Richter S, Theis FJ. Palla G, et al. Among authors: ibarra il. Nat Methods. 2022 Feb;19(2):171-178. doi: 10.1038/s41592-021-01358-2. Epub 2022 Jan 31. Nat Methods. 2022. PMID: 35102346 Free PMC article.
Parkinson's disease motor symptoms rescue by CRISPRa-reprogramming astrocytes into GABAergic neurons.
Giehrl-Schwab J, Giesert F, Rauser B, Lao CL, Hembach S, Lefort S, Ibarra IL, Koupourtidou C, Luecken MD, Truong DJ, Fischer-Sternjak J, Masserdotti G, Prakash N, Ninkovic J, Hölter SM, Vogt Weisenhorn DM, Theis FJ, Götz M, Wurst W. Giehrl-Schwab J, et al. Among authors: ibarra il. EMBO Mol Med. 2022 May 9;14(5):e14797. doi: 10.15252/emmm.202114797. Epub 2022 Apr 4. EMBO Mol Med. 2022. PMID: 35373464 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: ibarra il. 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.
SARS-CoV-2 infection triggers profibrotic macrophage responses and lung fibrosis.
Wendisch D, Dietrich O, Mari T, von Stillfried S, Ibarra IL, Mittermaier M, Mache C, Chua RL, Knoll R, Timm S, Brumhard S, Krammer T, Zauber H, Hiller AL, Pascual-Reguant A, Mothes R, Bülow RD, Schulze J, Leipold AM, Djudjaj S, Erhard F, Geffers R, Pott F, Kazmierski J, Radke J, Pergantis P, Baßler K, Conrad C, Aschenbrenner AC, Sawitzki B, Landthaler M, Wyler E, Horst D; Deutsche COVID-19 OMICS Initiative (DeCOI); Hippenstiel S, Hocke A, Heppner FL, Uhrig A, Garcia C, Machleidt F, Herold S, Elezkurtaj S, Thibeault C, Witzenrath M, Cochain C, Suttorp N, Drosten C, Goffinet C, Kurth F, Schultze JL, Radbruch H, Ochs M, Eils R, Müller-Redetzky H, Hauser AE, Luecken MD, Theis FJ, Conrad C, Wolff T, Boor P, Selbach M, Saliba AE, Sander LE. Wendisch D, et al. Among authors: ibarra il. Cell. 2021 Dec 22;184(26):6243-6261.e27. doi: 10.1016/j.cell.2021.11.033. Epub 2021 Nov 27. Cell. 2021. PMID: 34914922 Free PMC article.
APOBEC2 safeguards skeletal muscle cell fate through binding chromatin and regulating transcription of non-muscle genes during myoblast differentiation.
Lorenzo JP, Molla L, Amro EM, Ibarra IL, Ruf S, Neber C, Gkougkousis C, Ridani J, Subramani PG, Boulais J, Harjanto D, Vonica A, Di Noia JM, Dieterich C, Zaugg JB, Papavasiliou FN. Lorenzo JP, et al. Among authors: ibarra il. Proc Natl Acad Sci U S A. 2024 Apr 23;121(17):e2312330121. doi: 10.1073/pnas.2312330121. Epub 2024 Apr 16. Proc Natl Acad Sci U S A. 2024. PMID: 38625936 Free PMC article.
Integrated multi-omics single cell atlas of the human retina.
Li J, Wang J, Ibarra IL, Cheng X, Luecken MD, Lu J, Monavarfeshani A, Yan W, Zheng Y, Zuo Z, Colborn SLZ, Cortez BS, Owen LA, Tran NM, Shekhar K, Sanes JR, Stout JT, Chen S, Li Y, DeAngelis MM, Theis FJ, Chen R. Li J, et al. Among authors: ibarra il. Res Sq [Preprint]. 2023 Nov 17:rs.3.rs-3471275. doi: 10.21203/rs.3.rs-3471275/v1. Res Sq. 2023. PMID: 38014002 Free PMC article. Preprint.
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.
MYT1L haploinsufficiency in human neurons and mice causes autism-associated phenotypes that can be reversed by genetic and pharmacologic intervention.
Weigel B, Tegethoff JF, Grieder SD, Lim B, Nagarajan B, Liu YC, Truberg J, Papageorgiou D, Adrian-Segarra JM, Schmidt LK, Kaspar J, Poisel E, Heinzelmann E, Saraswat M, Christ M, Arnold C, Ibarra IL, Campos J, Krijgsveld J, Monyer H, Zaugg JB, Acuna C, Mall M. Weigel B, et al. Among authors: ibarra il. Mol Psychiatry. 2023 May;28(5):2122-2135. doi: 10.1038/s41380-023-01959-7. Epub 2023 Feb 14. Mol Psychiatry. 2023. PMID: 36782060 Free PMC article.
13 results