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ChromBPNet: bias factorized, base-resolution deep learning models of chromatin accessibility reveal cis-regulatory sequence syntax, transcription factor footprints and regulatory variants.
Pampari A, Shcherbina A, Kvon EZ, Kosicki M, Nair S, Kundu S, Kathiria AS, Risca VI, Kuningas K, Alasoo K, Greenleaf WJ, Pennacchio LA, Kundaje A. Pampari A, et al. Among authors: pennacchio la. bioRxiv [Preprint]. 2025 Jan 8:2024.12.25.630221. doi: 10.1101/2024.12.25.630221. bioRxiv. 2025. PMID: 39829783 Free PMC article. Preprint.
An Expanded Registry of Candidate cis-Regulatory Elements for Studying Transcriptional Regulation.
Moore JE, Pratt HE, Fan K, Phalke N, Fisher J, Elhajjajy SI, Andrews G, Gao M, Shedd N, Fu Y, Lacadie MC, Meza J, Ganna M, Choudhury E, Swofford R, Farrell NP, Pampari A, Ramalingam V, Reese F, Borsari B, Yu M, Wattenberg E, Ruiz-Romero M, Razavi-Mohseni M, Xu J, Galeev T, Beer MA, Guigó R, Gerstein M, Engreitz J, Ljungman M, Reddy TE, Snyder MP, Epstein CB, Gaskell E, Bernstein BE, Dickel DE, Visel A, Pennacchio LA, Mortazavi A, Kundaje A, Weng Z. Moore JE, et al. Among authors: pennacchio la. bioRxiv [Preprint]. 2024 Dec 26:2024.12.26.629296. doi: 10.1101/2024.12.26.629296. bioRxiv. 2024. PMID: 39763870 Free PMC article. Preprint.
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 OG, 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. Among authors: pennacchio la. J Clin Invest. 2024 Dec 17:e183353. doi: 10.1172/JCI183353. Online ahead of print. J Clin Invest. 2024. PMID: 39688912 Free article.
Integrative analysis of the 3D genome and epigenome in mouse embryonic tissues.
Yu M, Zemke NR, Chen Z, Juric I, Hu R, Raviram R, Abnousi A, Fang R, Zhang Y, Gorkin DU, Li YE, Zhao Y, Lee L, Mishra S, Schmitt AD, Qiu Y, Dickel DE, Visel A, Pennacchio LA, Hu M, Ren B. Yu M, et al. Among authors: pennacchio la. Nat Struct Mol Biol. 2024 Dec 16. doi: 10.1038/s41594-024-01431-2. Online ahead of print. Nat Struct Mol Biol. 2024. PMID: 39681766
Combinatorial transcription factor binding encodes cis-regulatory wiring of mouse forebrain GABAergic neurogenesis.
Catta-Preta R, Lindtner S, Ypsilanti A, Seban N, Price JD, Abnousi A, Su-Feher L, Wang Y, Cichewicz K, Boerma SA, Juric I, Jones IR, Akiyama JA, Hu M, Shen Y, Visel A, Pennacchio LA, Dickel DE, Rubenstein JLR, Nord AS. Catta-Preta R, et al. Among authors: pennacchio la. Dev Cell. 2025 Jan 20;60(2):288-304.e6. doi: 10.1016/j.devcel.2024.10.004. Epub 2024 Oct 30. Dev Cell. 2025. PMID: 39481376 Free article.
A gene desert required for regulatory control of pleiotropic Shox2 expression and embryonic survival.
Abassah-Oppong S, Zoia M, Mannion BJ, Rouco R, Tissières V, Spurrell CH, Roland V, Darbellay F, Itum A, Gamart J, Festa-Daroux TA, Sullivan CS, Kosicki M, Rodríguez-Carballo E, Fukuda-Yuzawa Y, Hunter RD, Novak CS, Plajzer-Frick I, Tran S, Akiyama JA, Dickel DE, Lopez-Rios J, Barozzi I, Andrey G, Visel A, Pennacchio LA, Cobb J, Osterwalder M. Abassah-Oppong S, et al. Among authors: pennacchio la. Nat Commun. 2024 Oct 10;15(1):8793. doi: 10.1038/s41467-024-53009-7. Nat Commun. 2024. PMID: 39389973 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. Among authors: pennacchio la. Nat Commun. 2024 Sep 27;15(1):8268. doi: 10.1038/s41467-024-52463-7. Nat Commun. 2024. PMID: 39333082 Free PMC article.
Mutagenesis Sensitivity Mapping of Human Enhancers In Vivo.
Kosicki M, Zhang B, Pampari A, Akiyama JA, Plajzer-Frick I, Novak CS, Tran S, Zhu Y, Kato M, Hunter RD, von Maydell K, Barton S, Beckman E, Kundaje A, Dickel DE, Visel A, Pennacchio LA. Kosicki M, et al. Among authors: pennacchio la. bioRxiv [Preprint]. 2024 Sep 8:2024.09.06.611737. doi: 10.1101/2024.09.06.611737. bioRxiv. 2024. PMID: 39282388 Free PMC article. Preprint.
198 results