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Predicting regulatory variants with composite statistic.
Li MJ, Pan Z, Liu Z, Wu J, Wang P, Zhu Y, Xu F, Xia Z, Sham PC, Kocher JP, Li M, Liu JS, Wang J. Li MJ, et al. Among authors: zhu y. Bioinformatics. 2016 Sep 15;32(18):2729-36. doi: 10.1093/bioinformatics/btw288. Epub 2016 Jun 6. Bioinformatics. 2016. PMID: 27273672 Free PMC article.
Exploring genetic associations with ceRNA regulation in the human genome.
Li MJ, Zhang J, Liang Q, Xuan C, Wu J, Jiang P, Li W, Zhu Y, Wang P, Fernandez D, Shen Y, Chen Y, Kocher JA, Yu Y, Sham PC, Wang J, Liu JS, Liu XS. Li MJ, et al. Among authors: zhu y. Nucleic Acids Res. 2017 Jun 2;45(10):5653-5665. doi: 10.1093/nar/gkx331. Nucleic Acids Res. 2017. PMID: 28472449 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: zhu y. Bioinformatics. 2013 Dec 15;29(24):3204-10. doi: 10.1093/bioinformatics/btt558. Epub 2013 Sep 27. Bioinformatics. 2013. PMID: 24078702 Free PMC article.
Normalization and noise reduction for single cell RNA-seq experiments.
Ding B, Zheng L, Zhu Y, Li N, Jia H, Ai R, Wildberg A, Wang W. Ding B, et al. Among authors: zhu y. Bioinformatics. 2015 Jul 1;31(13):2225-7. doi: 10.1093/bioinformatics/btv122. Epub 2015 Feb 24. Bioinformatics. 2015. PMID: 25717193 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.
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