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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: zhang m. Nature. 2014 Nov 20;515(7527):355-64. doi: 10.1038/nature13992. Nature. 2014. PMID: 25409824 Free PMC article.
An expansive human regulatory lexicon encoded in transcription factor footprints.
Neph S, Vierstra J, Stergachis AB, Reynolds AP, Haugen E, Vernot B, Thurman RE, John S, Sandstrom R, Johnson AK, Maurano MT, Humbert R, Rynes E, Wang H, Vong S, Lee K, Bates D, Diegel M, Roach V, Dunn D, Neri J, Schafer A, Hansen RS, Kutyavin T, Giste E, Weaver M, Canfield T, Sabo P, Zhang M, Balasundaram G, Byron R, MacCoss MJ, Akey JM, Bender MA, Groudine M, Kaul R, Stamatoyannopoulos JA. Neph S, et al. Among authors: zhang m. Nature. 2012 Sep 6;489(7414):83-90. doi: 10.1038/nature11212. Nature. 2012. PMID: 22955618 Free PMC article.
Conservation of trans-acting circuitry during mammalian regulatory evolution.
Stergachis AB, Neph S, Sandstrom R, Haugen E, Reynolds AP, Zhang M, Byron R, Canfield T, Stelhing-Sun S, Lee K, Thurman RE, Vong S, Bates D, Neri F, Diegel M, Giste E, Dunn D, Vierstra J, Hansen RS, Johnson AK, Sabo PJ, Wilken MS, Reh TA, Treuting PM, Kaul R, Groudine M, Bender MA, Borenstein E, Stamatoyannopoulos JA. Stergachis AB, et al. Among authors: zhang m. Nature. 2014 Nov 20;515(7527):365-70. doi: 10.1038/nature13972. Nature. 2014. PMID: 25409825 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. Nature. 2014 Nov 20;515(7527):371-375. doi: 10.1038/nature13985. Nature. 2014. PMID: 25409826 Free PMC article.
Mouse regulatory DNA landscapes reveal global principles of cis-regulatory evolution.
Vierstra J, Rynes E, Sandstrom R, Zhang M, Canfield T, Hansen RS, Stehling-Sun S, Sabo PJ, Byron R, Humbert R, Thurman RE, Johnson AK, Vong S, Lee K, Bates D, Neri F, Diegel M, Giste E, Haugen E, Dunn D, Wilken MS, Josefowicz S, Samstein R, Chang KH, Eichler EE, De Bruijn M, Reh TA, Skoultchi A, Rudensky A, Orkin SH, Papayannopoulou T, Treuting PM, Selleri L, Kaul R, Groudine M, Bender MA, Stamatoyannopoulos JA. Vierstra J, et al. Among authors: zhang m. Science. 2014 Nov 21;346(6212):1007-12. doi: 10.1126/science.1246426. Science. 2014. PMID: 25411453 Free PMC article.
Development of spirulina for the manufacture and oral delivery of protein therapeutics.
Jester BW, Zhao H, Gewe M, Adame T, Perruzza L, Bolick DT, Agosti J, Khuong N, Kuestner R, Gamble C, Cruickshank K, Ferrara J, Lim R, Paddock T, Brady C, Ertel S, Zhang M, Pollock A, Lee J, Xiong J, Tasch M, Saveria T, Doughty D, Marshall J, Carrieri D, Goetsch L, Dang J, Sanjaya N, Fletcher D, Martinez A, Kadis B, Sigmar K, Afreen E, Nguyen T, Randolph A, Taber A, Krzeszowski A, Robinett B, Volkin DB, Grassi F, Guerrant R, Takeuchi R, Finrow B, Behnke C, Roberts J. Jester BW, et al. Among authors: zhang m. Nat Biotechnol. 2022 Jun;40(6):956-964. doi: 10.1038/s41587-022-01249-7. Epub 2022 Mar 21. Nat Biotechnol. 2022. PMID: 35314813 Free PMC article.
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