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Page 1
Single-cell, whole-embryo phenotyping of mammalian developmental disorders.
Huang X, Henck J, Qiu C, Sreenivasan VKA, Balachandran S, Amarie OV, Hrabě de Angelis M, Behncke RY, Chan WL, Despang A, Dickel DE, Duran M, Feuchtinger A, Fuchs H, Gailus-Durner V, Haag N, Hägerling R, Hansmeier N, Hennig F, Marshall C, Rajderkar S, Ringel A, Robson M, Saunders LM, da Silva-Buttkus P, Spielmann N, Srivatsan SR, Ulferts S, Wittler L, Zhu Y, Kalscheuer VM, Ibrahim DM, Kurth I, Kornak U, Visel A, Pennacchio LA, Beier DR, Trapnell C, Cao J, Shendure J, Spielmann M. Huang X, et al. Nature. 2023 Nov;623(7988):772-781. doi: 10.1038/s41586-023-06548-w. Epub 2023 Nov 15. Nature. 2023. PMID: 37968388 Free PMC article.
A cell type-aware framework for nominating non-coding variants in Mendelian regulatory disorders.
Lee AS, Ayers LJ, Kosicki M, Chan WM, Fozo LN, Pratt BM, Collins TE, Zhao B, Rose MF, Sanchis-Juan A, Fu JM, Wong I, Zhao X, Tenney AP, Lee C, Laricchia KM, Barry BJ, Bradford VR, Jurgens JA, England EM, Lek M, MacArthur DG, Lee EA, Talkowski ME, Brand H, Pennacchio LA, Engle EC. Lee AS, et al. Nat Commun. 2024 Sep 27;15(1):8268. doi: 10.1038/s41467-024-52463-7. Nat Commun. 2024. PMID: 39333082 Free PMC article.
Regulation of sarcomere formation and function in the healthy heart requires a titin intronic enhancer.
Kim Y, Kim SW, Saul D, Neyazi M, Schmid M, Wakimoto H, Slaven N, Lee JH, Layton O, Wasson LK, Letendre JH, Xiao F, Ewoldt JK, Gkatzis K, Sommer P, Gobert B, Wiest-Daesslé N, McAfee Q, Singhal N, Lun M, Gorham JM, Arany Z, Sharma A, Toepfer CN, Oudit GY, Pu WT, Dickel DE, Pennacchio LA, Visel A, Chen CS, Seidman JG, Seidman CE. Kim Y, et al. J Clin Invest. 2024 Dec 17;135(4):e183353. doi: 10.1172/JCI183353. J Clin Invest. 2024. PMID: 39688912 Free PMC article.
Molecular convergence of risk variants for congenital heart defects leveraging a regulatory map of the human fetal heart.
Ma XR, Conley SD, Kosicki M, Bredikhin D, Cui R, Tran S, Sheth MU, Qiu WL, Chen S, Kundu S, Kang HY, Amgalan D, Munger CJ, Duan L, Dang K, Rubio OM, Kany S, Zamirpour S, DePaolo J, Padmanabhan A; Birth Defects Research Laboratory; Olgin J, Damrauer S, Andersson R, Gu M, Priest JR, Quertermous T, Qiu X, Rabinovitch M, Visel A, Pennacchio L, Kundaje A, Glass IA, Gifford CA, Pirruccello JP, Goodyer WR, Engreitz JM. Ma XR, et al. medRxiv [Preprint]. 2024 Nov 22:2024.11.20.24317557. doi: 10.1101/2024.11.20.24317557. medRxiv. 2024. PMID: 39606363 Free PMC article. Preprint.
A cell type-aware framework for nominating non-coding variants in Mendelian regulatory disorders.
Lee AS, Ayers LJ, Kosicki M, Chan WM, Fozo LN, Pratt BM, Collins TE, Zhao B, Rose MF, Sanchis-Juan A, Fu JM, Wong I, Zhao X, Tenney AP, Lee C, Laricchia KM, Barry BJ, Bradford VR, Lek M, MacArthur DG, Lee EA, Talkowski ME, Brand H, Pennacchio LA, Engle EC. Lee AS, et al. medRxiv [Preprint]. 2023 Dec 27:2023.12.22.23300468. doi: 10.1101/2023.12.22.23300468. medRxiv. 2023. Update in: Nat Commun. 2024 Sep 27;15(1):8268. doi: 10.1038/s41467-024-52463-7. PMID: 38234731 Free PMC article. Updated. Preprint.
Massively parallel reporter assays and mouse transgenic assays provide complementary information about neuronal enhancer activity.
Kosicki M, Cintrón DL, Page NF, Georgakopoulos-Soares I, Akiyama JA, Plajzer-Frick I, Novak CS, Kato M, Hunter RD, von Maydell K, Barton S, Godfrey P, Beckman E, Sanders SJ, Pennacchio LA, Ahituv N. Kosicki M, et al. bioRxiv [Preprint]. 2024 Apr 23:2024.04.22.590634. doi: 10.1101/2024.04.22.590634. bioRxiv. 2024. Update in: Nat Commun. 2025 May 23;16(1):4786. doi: 10.1038/s41467-025-60064-1. PMID: 38712228 Free PMC article. Updated. Preprint.
Massively parallel reporter assays and mouse transgenic assays provide correlated and complementary information about neuronal enhancer activity.
Kosicki M, Laboy Cintrón D, Keukeleire P, Schubach M, Page NF, Georgakopoulos-Soares I, Akiyama JA, Plajzer-Frick I, Novak CS, Kato M, Hunter RD, von Maydell K, Barton S, Godfrey P, Beckman E, Sanders SJ, Kircher M, Pennacchio LA, Ahituv N. Kosicki M, et al. Nat Commun. 2025 May 23;16(1):4786. doi: 10.1038/s41467-025-60064-1. Nat Commun. 2025. PMID: 40404660 Free PMC article.