The rollout for the ENCODE consortium phase 3 papers occurred in 2020. The Gerstein lab is associated with 5 core papers. In addition to the core ENCODE papers, the Gerstein lab also contributed several papers utilized the ENCODE dataset.
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.

Transcriptional activity and strain-specific history of mouse pseudogenes.
C Sisu, P Muir, A Frankish, I Fiddes, M Diekhans, D Thybert, DT Odom, P Flicek, TM Keane, T Hubbard, J Harrow, M Gerstein (2020). Nat Commun 11: 3695.

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.

Supervised enhancer prediction with epigenetic pattern recognition and targeted validation.
A Sethi, M Gu, E Gumusgoz, L Chan, KK Yan, J Rozowsky, I Barozzi, V Afzal, JA Akiyama, I Plajzer-Frick, C Yan, CS Novak, M Kato, TH Garvin, Q Pham, A Harrington, BJ Mannion, EA Lee, Y Fukuda-Yuzawa, A Visel, DE Dickel, KY Yip, R Sutton, LA Pennacchio, M Gerstein (2020). Nat Methods 17: 807-814.

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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