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Page 1
Predicting gene expression in massively parallel reporter assays: A comparative study.
Kreimer A, Zeng H, Edwards MD, Guo Y, Tian K, Shin S, Welch R, Wainberg M, Mohan R, Sinnott-Armstrong NA, Li Y, Eraslan G, Amin TB, Tewhey R, Sabeti PC, Goke J, Mueller NS, Kellis M, Kundaje A, Beer MA, Keles S, Gifford DK, Yosef N. Kreimer A, et al. Among authors: kundaje a. Hum Mutat. 2017 Sep;38(9):1240-1250. doi: 10.1002/humu.23197. Epub 2017 Mar 9. Hum Mutat. 2017. PMID: 28220625 Free PMC article.
Extensive variation in chromatin states across humans.
Kasowski M, Kyriazopoulou-Panagiotopoulou S, Grubert F, Zaugg JB, Kundaje A, Liu Y, Boyle AP, Zhang QC, Zakharia F, Spacek DV, Li J, Xie D, Olarerin-George A, Steinmetz LM, Hogenesch JB, Kellis M, Batzoglou S, Snyder M. Kasowski M, et al. Among authors: kundaje a. Science. 2013 Nov 8;342(6159):750-2. doi: 10.1126/science.1242510. Epub 2013 Oct 17. Science. 2013. PMID: 24136358 Free PMC article.
Defining functional DNA elements in the human genome.
Kellis M, Wold B, Snyder MP, Bernstein BE, Kundaje A, Marinov GK, Ward LD, Birney E, Crawford GE, Dekker J, Dunham I, Elnitski LL, Farnham PJ, Feingold EA, Gerstein M, Giddings MC, Gilbert DM, Gingeras TR, Green ED, Guigo R, Hubbard T, Kent J, Lieb JD, Myers RM, Pazin MJ, Ren B, Stamatoyannopoulos JA, Weng Z, White KP, Hardison RC. Kellis M, et al. Among authors: kundaje a. Proc Natl Acad Sci U S A. 2014 Apr 29;111(17):6131-8. doi: 10.1073/pnas.1318948111. Epub 2014 Apr 21. Proc Natl Acad Sci U S A. 2014. PMID: 24753594 Free PMC article. Review.
Diverse patterns of genomic targeting by transcriptional regulators in Drosophila melanogaster.
Slattery M, Ma L, Spokony RF, Arthur RK, Kheradpour P, Kundaje A, Nègre N, Crofts A, Ptashkin R, Zieba J, Ostapenko A, Suchy S, Victorsen A, Jameel N, Grundstad AJ, Gao W, Moran JR, Rehm EJ, Grossman RL, Kellis M, White KP. Slattery M, et al. Among authors: kundaje a. Genome Res. 2014 Jul;24(7):1224-35. doi: 10.1101/gr.168807.113. Genome Res. 2014. PMID: 24985916 Free PMC article.
Comparative analysis of regulatory information and circuits across distant species.
Boyle AP, Araya CL, Brdlik C, Cayting P, Cheng C, Cheng Y, Gardner K, Hillier LW, Janette J, Jiang L, Kasper D, Kawli T, Kheradpour P, Kundaje A, Li JJ, Ma L, Niu W, Rehm EJ, Rozowsky J, Slattery M, Spokony R, Terrell R, Vafeados D, Wang D, Weisdepp P, Wu YC, Xie D, Yan KK, Feingold EA, Good PJ, Pazin MJ, Huang H, Bickel PJ, Brenner SE, Reinke V, Waterston RH, Gerstein M, White KP, Kellis M, Snyder M. Boyle AP, et al. Among authors: kundaje a. Nature. 2014 Aug 28;512(7515):453-6. doi: 10.1038/nature13668. Nature. 2014. PMID: 25164757 Free PMC article.
A comparative encyclopedia of DNA elements in the mouse genome.
Yue F, Cheng Y, Breschi A, Vierstra J, Wu W, Ryba T, Sandstrom R, Ma Z, Davis C, Pope BD, Shen Y, Pervouchine DD, Djebali S, Thurman RE, Kaul R, Rynes E, Kirilusha A, Marinov GK, Williams BA, Trout D, Amrhein H, Fisher-Aylor K, Antoshechkin I, DeSalvo G, See LH, Fastuca M, Drenkow J, Zaleski C, Dobin A, Prieto P, Lagarde J, Bussotti G, Tanzer A, Denas O, Li K, Bender MA, Zhang M, Byron R, Groudine MT, McCleary D, Pham L, Ye Z, Kuan S, Edsall L, Wu YC, Rasmussen MD, Bansal MS, Kellis M, Keller CA, Morrissey CS, Mishra T, Jain D, Dogan N, Harris RS, Cayting P, Kawli T, Boyle AP, Euskirchen G, Kundaje A, Lin S, Lin Y, Jansen C, Malladi VS, Cline MS, Erickson DT, Kirkup VM, Learned K, Sloan CA, Rosenbloom KR, Lacerda de Sousa B, Beal K, Pignatelli M, Flicek P, Lian J, Kahveci T, Lee D, Kent WJ, Ramalho Santos M, Herrero J, Notredame C, Johnson A, Vong S, Lee K, Bates D, Neri F, Diegel M, Canfield T, Sabo PJ, Wilken MS, Reh TA, Giste E, Shafer A, Kutyavin T, Haugen E, Dunn D, Reynolds AP, Neph S, Humbert R, Hansen RS, De Bruijn M, Selleri L, Rudensky A, Josefowicz S, Samstein R, Eichler EE, Orkin SH, Levasseur D, Papayannopoulou T, Chang KH, Skoultchi A, Gosh S, Disteche C, Treu… See abstract for full author list ➔ Yue F, et al. Among authors: kundaje a. Nature. 2014 Nov 20;515(7527):355-64. doi: 10.1038/nature13992. Nature. 2014. PMID: 25409824 Free PMC article.
Principles of regulatory information conservation between mouse and human.
Cheng Y, Ma Z, Kim BH, Wu W, Cayting P, Boyle AP, Sundaram V, Xing X, Dogan N, Li J, Euskirchen G, Lin S, Lin Y, Visel A, Kawli T, Yang X, Patacsil D, Keller CA, Giardine B; mouse ENCODE Consortium; Kundaje A, Wang T, Pennacchio LA, Weng Z, Hardison RC, Snyder MP. Cheng Y, et al. Among authors: kundaje a. Nature. 2014 Nov 20;515(7527):371-375. doi: 10.1038/nature13985. Nature. 2014. PMID: 25409826 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: kundaje a. Nature. 2015 Feb 19;518(7539):317-30. doi: 10.1038/nature14248. Nature. 2015. PMID: 25693563 Free PMC article.
180 results