STARRPeaker: Uniform processing and accurate identification of STARR-seq active regions
D Lee, M Shi, J Moran, M Wall, J Zhang, J Liu, D Fitzgerald, Y Kyono, L Ma, K White, M Gerstein (2019). bioRxiv.

Expanded encyclopaedias of DNA elements in the human and mouse genomes.
ENCODE Project Consortium, JE Moore, MJ Purcaro, HE Pratt, CB Epstein, N Shoresh, J Adrian, T Kawli, CA Davis, A Dobin, R Kaul, J Halow, EL Van Nostrand, P Freese, DU Gorkin, Y Shen, Y He, M Mackiewicz, F Pauli-Behn, BA Williams, A Mortazavi, CA Keller, XO Zhang, SI Elhajjajy, J Huey, DE Dickel, V Snetkova, X Wei, X Wang, JC Rivera-Mulia, J Rozowsky, J Zhang, SB Chhetri, J Zhang, A Victorsen, KP White, A Visel, GW Yeo, CB Burge, E Lecuyer, DM Gilbert, J Dekker, J Rinn, EM Mendenhall, JR Ecker, M Kellis, RJ Klein, WS Noble, A Kundaje, R Guigo, PJ Farnham, JM Cherry, RM Myers, B Ren, BR Graveley, MB Gerstein, LA Pennacchio, MP Snyder, BE Bernstein, B Wold, RC Hardison, TR Gingeras, JA Stamatoyannopoulos, Z Weng (2020). Nature 583: 699-710.

Perspectives on ENCODE.
ENCODE Project Consortium, MP Snyder, TR Gingeras, JE Moore, Z Weng, MB Gerstein, B Ren, RC Hardison, JA Stamatoyannopoulos, BR Graveley, EA Feingold, MJ Pazin, M Pagan, DA Gilchrist, BC Hitz, JM Cherry, BE Bernstein, EM Mendenhall, DR Zerbino, A Frankish, P Flicek, RM Myers (2020). Nature 583: 693-698.

An integrative ENCODE resource for cancer genomics.
J Zhang, D Lee, V Dhiman, P Jiang, J Xu, P McGillivray, H Yang, J Liu, W Meyerson, D Clarke, M Gu, S Li, S Lou, J Xu, L Lochovsky, M Ung, L Ma, S Yu, Q Cao, A Harmanci, KK Yan, A Sethi, G Gursoy, MR Schoenberg, J Rozowsky, J Warrell, P Emani, YT Yang, T Galeev, X Kong, S Liu, X Li, J Krishnan, Y Feng, JC Rivera-Mulia, J Adrian, JR Broach, M Bolt, J Moran, D Fitzgerald, V Dileep, T Liu, S Mei, T Sasaki, C Trevilla-Garcia, S Wang, Y Wang, C Zang, D Wang, RJ Klein, M Snyder, DM Gilbert, K Yip, C Cheng, F Yue, XS Liu, KP White, M Gerstein (2020). Nat Commun 11: 3696.

RADAR: annotation and prioritization of variants in the post-transcriptional regulome of RNA-binding proteins.
J Zhang, J Liu, D Lee, JJ Feng, L Lochovsky, S Lou, M Rutenberg-Schoenberg, M Gerstein (2020). Genome Biol 21: 151.

DiNeR: a Differential graphical model for analysis of co-regulation Network Rewiring.
J Zhang, J Liu, D Lee, S Lou, Z Chen, G Gursoy, M Gerstein (2020). BMC Bioinformatics 21: 281.

TopicNet: a framework for measuring transcriptional regulatory network change.
S Lou, T Li, X Kong, J Zhang, J Liu, D Lee, M Gerstein (2020). Bioinformatics 36: i474-i481.

Epigenome-based splicing prediction using a recurrent neural network.
D Lee, J Zhang, J Liu, M Gerstein (2020). PLoS Comput Biol 16: e1008006.


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