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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.
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: dony l. 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.
Human cortical neurogenesis is altered via glucocorticoid-mediated regulation of ZBTB16 expression.
Krontira AC, Cruceanu C, Dony L, Kyrousi C, Link MH, Rek N, Pöhlchen D, Raimundo C, Penner-Goeke S, Schowe A, Czamara D, Lahti-Pulkkinen M, Sammallahti S, Wolford E, Heinonen K, Roeh S, Sportelli V, Wölfel B, Ködel M, Sauer S, Rex-Haffner M, Räikkönen K, Labeur M, Cappello S, Binder EB. Krontira AC, et al. Among authors: dony l. Neuron. 2024 May 1;112(9):1426-1443.e11. doi: 10.1016/j.neuron.2024.02.005. Epub 2024 Mar 4. Neuron. 2024. PMID: 38442714 Free article.
Cell-Type-Specific Impact of Glucocorticoid Receptor Activation on the Developing Brain: A Cerebral Organoid Study.
Cruceanu C, Dony L, Krontira AC, Fischer DS, Roeh S, Di Giaimo R, Kyrousi C, Kaspar L, Arloth J, Czamara D, Gerstner N, Martinelli S, Wehner S, Breen MS, Koedel M, Sauer S, Sportelli V, Rex-Haffner M, Cappello S, Theis FJ, Binder EB. Cruceanu C, et al. Among authors: dony l. Am J Psychiatry. 2022 May;179(5):375-387. doi: 10.1176/appi.ajp.2021.21010095. Epub 2021 Oct 26. Am J Psychiatry. 2022. PMID: 34698522
Sfaira accelerates data and model reuse in single cell genomics.
Fischer DS, Dony L, König M, Moeed A, Zappia L, Heumos L, Tritschler S, Holmberg O, Aliee H, Theis FJ. Fischer DS, et al. Among authors: dony l. Genome Biol. 2021 Aug 25;22(1):248. doi: 10.1186/s13059-021-02452-6. Genome Biol. 2021. PMID: 34433466 Free PMC article.