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A haplotype-resolved view of human gene regulation.
Vollger MR, Swanson EG, Neph SJ, Ranchalis J, Munson KM, Ho CH, Cheng YHH, Sedeño-Cortés AE, Fondrie WE, Bohaczuk SC, Dippel MA, Mao Y, Parmalee NL, Mallory BJ, Harvey WT, Kwon Y, Garcia GH, Hoekzema K, Meyer JG, Cicek M, Eichler EE, Noble WS, Witten DM, Bennett JT, Ray JP, Stergachis AB. Vollger MR, et al. Among authors: neph sj. bioRxiv [Preprint]. 2025 Jun 2:2024.06.14.599122. doi: 10.1101/2024.06.14.599122. bioRxiv. 2025. PMID: 40501892 Free PMC article. Preprint.
Genetic diversity and regulatory features of human-specific NOTCH2NL duplications.
Real TD, Hebbar P, Yoo D, Antonacci F, Pačar I, Diekhans M, Mikol GJ, Popoola OG, Mallory BJ, Vollger MR, Dishuck PC, Guitart X, Rozanski AN, Munson KM, Hoekzema K, Ranchalis JE, Neph SJ, Sedeño-Cortes AE, Paten B, Salama SR, Stergachis AB, Eichler EE. Real TD, et al. Among authors: neph sj. bioRxiv [Preprint]. 2025 Mar 17:2025.03.14.643395. doi: 10.1101/2025.03.14.643395. bioRxiv. 2025. PMID: 40166283 Free PMC article. Preprint.
CUT&TIME captures the history of open chromatin in developing neurons.
Eldred KC, Wooten M, Janssens DH, Hahn J, Neph SJ, Edgerton SJ, Wyatt-Draher G, Sherman SM, Ranchalis JE, Stergachis AB, Reh TA, Henikoff S. Eldred KC, et al. Among authors: neph sj. bioRxiv [Preprint]. 2025 Sep 6:2025.08.29.673195. doi: 10.1101/2025.08.29.673195. bioRxiv. 2025. PMID: 40950047 Free PMC article. Preprint.
DNase I-hypersensitive exons colocalize with promoters and distal regulatory elements.
Mercer TR, Edwards SL, Clark MB, Neph SJ, Wang H, Stergachis AB, John S, Sandstrom R, Li G, Sandhu KS, Ruan Y, Nielsen LK, Mattick JS, Stamatoyannopoulos JA. Mercer TR, et al. Among authors: neph sj. Nat Genet. 2013 Aug;45(8):852-9. doi: 10.1038/ng.2677. Epub 2013 Jun 23. Nat Genet. 2013. PMID: 23793028 Free PMC article.
Integrative analysis of 111 reference human epigenomes.
Roadmap Epigenomics Consortium; Kundaje A, Meuleman W, Ernst J, Bilenky M, Yen A, Heravi-Moussavi A, Kheradpour P, Zhang Z, Wang J, Ziller MJ, Amin V, Whitaker JW, Schultz MD, Ward LD, Sarkar A, Quon G, Sandstrom RS, Eaton ML, Wu YC, Pfenning AR, Wang X, Claussnitzer M, Liu Y, Coarfa C, Harris RA, Shoresh N, Epstein CB, Gjoneska E, Leung D, Xie W, Hawkins RD, Lister R, Hong C, Gascard P, Mungall AJ, Moore R, Chuah E, Tam A, Canfield TK, Hansen RS, Kaul R, Sabo PJ, Bansal MS, Carles A, Dixon JR, Farh KH, Feizi S, Karlic R, Kim AR, Kulkarni A, Li D, Lowdon R, Elliott G, Mercer TR, Neph SJ, Onuchic V, Polak P, Rajagopal N, Ray P, Sallari RC, Siebenthall KT, Sinnott-Armstrong NA, Stevens M, Thurman RE, Wu J, Zhang B, Zhou X, Beaudet AE, Boyer LA, De Jager PL, Farnham PJ, Fisher SJ, Haussler D, Jones SJ, Li W, Marra MA, McManus MT, Sunyaev S, Thomson JA, Tlsty TD, Tsai LH, Wang W, Waterland RA, Zhang MQ, Chadwick LH, Bernstein BE, Costello JF, Ecker JR, Hirst M, Meissner A, Milosavljevic A, Ren B, Stamatoyannopoulos JA, Wang T, Kellis M. Roadmap Epigenomics Consortium, et al. Among authors: neph sj. Nature. 2015 Feb 19;518(7539):317-30. doi: 10.1038/nature14248. Nature. 2015. PMID: 25693563 Free PMC article.