Genome-wide functional element detection using pairwise statistical alignment outperforms multiple genome footprinting techniques. by Satija, R, Hein, J, Lunter, G

Combining statistical alignment and phylogenetic footprinting to detect regulatory elements. by Satija, R, Pachter, L, Hein, J

BigFoot: Bayesian alignment and phylogenetic footprinting with MCMC by Satija, R, Novák, A, Miklós, I, Lyngsø, R, Hein, J

Stochastic models of sequence evolution including insertion-deletion events. by Miklós, I, Novák, A, Satija, R, Lyngsø, R, Hein, J

Dynamic profiling of the protein life cycle in response to pathogens by Jovanovic, M., Mertins, P., Przybylski, D., Chevrier, N., Satija, R., Rodriguez, E. H., Fields, A. P., Schwartz, S., Raychowdhury, R., Mumbach, M. R., Eisenhaure, T., Rabani, M., Gennert, D., Lu, D., Delorey, T., Weissman, J. S., Carr, S. A., Hacohen, N., Regev, Aviv, Rooney, Michael Steven

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The regulatory factor ZFHX3 modifies circadian function in SCN via an AT motif-driven axis by Parsons, M, Brancaccio, M, Sethi, S, Maywood, E, Satija, R, Edwards, J, Jagannath, A, Couch, Y, Finelli, M, Smyllie, N, Esapa, C, Butler, R, Barnard, A, Chesham, J, Saito, S, Joynson, G, Wells, S, Foster, R, Oliver, P, Simon, M, Mallon, A, Hastings, M, Nolan, P

Landscape of X chromosome inactivation across human tissues by Tukiainen, T, Villani, A-C, Yen, A, Rivas, MA, Marshall, JL, Satija, R, Aguirre, M, Gauthier, L, Fleharty, M, Kirby, A, Cummings, BB, Castel, SE, Karczewski, KJ, Aguet, F, Byrnes, A, GTEx Consortium, Lappalainen, T, Regev, A, Ardlie, KG, Hacohen, N, MacArthur, DG

Dynamic regulatory network controlling TH 17 cell differentiation by Yosef, N, Shalek, A, Gaublomme, J, Jin, H, Lee, Y, Awasthi, A, Wu, C, Karwacz, K, Xiao, S, Jorgolli, M, Gennert, D, Satija, R, Shakya, A, Lu, D, Trombetta, J, Pillai, MR, Ratcliffe, P, Coleman, M, Bix, M, Tantin, D, Park, H, Kuchroo, V, Regev, A

Dynamic regulatory network controlling TH17 cell differentiation. by Yosef, N, Shalek, A, Gaublomme, J, Jin, H, Lee, Y, Awasthi, A, Wu, C, Karwacz, K, Xiao, S, Jorgolli, M, Gennert, D, Satija, R, Shakya, A, Lu, D, Trombetta, J, Pillai, MR, Ratcliffe, P, Coleman, M, Bix, M, Tantin, D, Park, H, Kuchroo, V, Regev, A

Science Forum: The Human Cell Atlas. by Regev, A, Teichmann, SA, Lander, ES, Amit, I, Benoist, C, Birney, E, Bodenmiller, B, Campbell, PJ, Carninci, P, Clatworthy, M, Clevers, H, Deplancke, B, Dunham, I, Eberwine, J, Eils, R, Enard, W, Farmer, A, Fugger, L, Göttgens, B, Hacohen, N, Haniffa, M, Hemberg, M, Kim, SK, Klenerman, P, Kriegstein, A, Lein, E, Linnarsson, S, Lundberg, E, Lundeberg, J, Majumder, P, Marioni, JC, Merad, M, Mhlanga, M, Nawijn, M, Netea, M, Nolan, G, Pe'er, D, Phillipakis, A, Ponting, CP, Quake, SR, Reik, W, Rozenblatt-Rosen, O, Sanes, JR, Satija, R, Schumacher, TN, Shalek, AK, Shapiro, E, Sharma, P, Shin, JW, Stegle, O, Stratton, MR, Stubbington, MJT, Theis, FJ, Uhlen, M, van Oudenaarden, A, Wagner, A, Watt, FM, Weissman, JS, Wold, BJ, Xavier, RJ, Yosef, N