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Distinct epigenomic landscapes of pluripotent and lineage-committed human cells.
Hawkins RD, Hon GC, Lee LK, Ngo Q, Lister R, Pelizzola M, Edsall LE, Kuan S, Luu Y, Klugman S, Antosiewicz-Bourget J, Ye Z, Espinoza C, Agarwahl S, Shen L, Ruotti V, Wang W, Stewart R, Thomson JA, Ecker JR, Ren B. Hawkins RD, et al. Among authors: shen l. Cell Stem Cell. 2010 May 7;6(5):479-91. doi: 10.1016/j.stem.2010.03.018. Cell Stem Cell. 2010. PMID: 20452322 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. Nature. 2015 Feb 19;518(7539):317-30. doi: 10.1038/nature14248. Nature. 2015. PMID: 25693563 Free PMC article.
STAR: an integrated solution to management and visualization of sequencing data.
Wang T, Liu J, Shen L, Tonti-Filippini J, Zhu Y, Jia H, Lister R, Whitaker JW, Ecker JR, Millar AH, Ren B, Wang W. Wang T, et al. Among authors: shen l. Bioinformatics. 2013 Dec 15;29(24):3204-10. doi: 10.1093/bioinformatics/btt558. Epub 2013 Sep 27. Bioinformatics. 2013. PMID: 24078702 Free PMC article.
Histone serotonylation is a permissive modification that enhances TFIID binding to H3K4me3.
Farrelly LA, Thompson RE, Zhao S, Lepack AE, Lyu Y, Bhanu NV, Zhang B, Loh YE, Ramakrishnan A, Vadodaria KC, Heard KJ, Erikson G, Nakadai T, Bastle RM, Lukasak BJ, Zebroski H 3rd, Alenina N, Bader M, Berton O, Roeder RG, Molina H, Gage FH, Shen L, Garcia BA, Li H, Muir TW, Maze I. Farrelly LA, et al. Among authors: shen l. Nature. 2019 Mar;567(7749):535-539. doi: 10.1038/s41586-019-1024-7. Epub 2019 Mar 13. Nature. 2019. PMID: 30867594 Free PMC article.
ENL links histone acetylation to oncogenic gene expression in acute myeloid leukaemia.
Wan L, Wen H, Li Y, Lyu J, Xi Y, Hoshii T, Joseph JK, Wang X, Loh YE, Erb MA, Souza AL, Bradner JE, Shen L, Li W, Li H, Allis CD, Armstrong SA, Shi X. Wan L, et al. Among authors: shen l. Nature. 2017 Mar 9;543(7644):265-269. doi: 10.1038/nature21687. Epub 2017 Mar 1. Nature. 2017. PMID: 28241141 Free PMC article.
Dynamic changes in cis-regulatory occupancy by Six1 and its cooperative interactions with distinct cofactors drive lineage-specific gene expression programs during progressive differentiation of the auditory sensory epithelium.
Li J, Zhang T, Ramakrishnan A, Fritzsch B, Xu J, Wong EYM, Loh YE, Ding J, Shen L, Xu PX. Li J, et al. Among authors: shen l. Nucleic Acids Res. 2020 Apr 6;48(6):2880-2896. doi: 10.1093/nar/gkaa012. Nucleic Acids Res. 2020. PMID: 31956913 Free PMC article.
Integration of evidence across human and model organism studies: A meeting report.
Palmer RHC, Johnson EC, Won H, Polimanti R, Kapoor M, Chitre A, Bogue MA, Benca-Bachman CE, Parker CC, Verma A, Reynolds T, Ernst J, Bray M, Kwon SB, Lai D, Quach BC, Gaddis NC, Saba L, Chen H, Hawrylycz M, Zhang S, Zhou Y, Mahaffey S, Fischer C, Sanchez-Roige S, Bandrowski A, Lu Q, Shen L, Philip V, Gelernter J, Bierut LJ, Hancock DB, Edenberg HJ, Johnson EO, Nestler EJ, Barr PB, Prins P, Smith DJ, Akbarian S, Thorgeirsson T, Walton D, Baker E, Jacobson D, Palmer AA, Miles M, Chesler EJ, Emerson J, Agrawal A, Martone M, Williams RW. Palmer RHC, et al. Among authors: shen l. Genes Brain Behav. 2021 Apr 23;20(6):e12738. doi: 10.1111/gbb.12738. Online ahead of print. Genes Brain Behav. 2021. PMID: 33893716 Free PMC article. Review.
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