NIMBus: a Negative Binomial Regression based Integrative Method for Mutation Burden Analysis
J Zhang, J Liu, P McGillivray, C Yi, L Lochovsky, D Lee, M Gerstein (2020). bioRxiv.

Storing and analyzing a genome on a blockchain
G Gursoy, C Brannon, S Wagner, M Gerstein (2020). bioRxiv.

To mock or not: a comprehensive comparison of mock IP and DNA input for ChIP-seq
J Xu, MM Kudron, A Victorsen, J Gao, HN Ammouri, FCP Navarro, L Gevirtzman, RH Waterston, KP White, V Reinke, M Gerstein (2019). bioRxiv.

Data Sanitization to Reduce Private Information Leakage from Functional Genomics.
G Gursoy, P Emani, CM Brannon, OA Jolanki, A Harmanci, JS Strattan, JM Cherry, AD Miranker, M Gerstein (2020). Cell 183: 905-917e16.

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.

Origins and characterization of variants shared between databases of somatic and germline human mutations.
W Meyerson, J Leisman, FCP Navarro, M Gerstein (2020). BMC Bioinformatics 21: 227.

Pan-cancer analysis of whole genomes.
ICGC/TCGA Pan-Cancer Analysis of Whole Genomes Consortium (2020). Nature 578: 82-93.

Analyses of non-coding somatic drivers in 2,658 cancer whole genomes.
E Rheinbay, MM Nielsen, F Abascal, JA Wala, O Shapira, G Tiao, H Hornshj, JM Hess, RI Juul, Z Lin, L Feuerbach, R Sabarinathan, T Madsen, J Kim, L Mularoni, S Shuai, A Lanzos, C Herrmann, YE Maruvka, C Shen, SB Amin, P Bandopadhayay, J Bertl, KA Boroevich, J Busanovich, J Carlevaro-Fita, D Chakravarty, CWY Chan, D Craft, P Dhingra, K Diamanti, NA Fonseca, A Gonzalez-Perez, Q Guo, MP Hamilton, NJ Haradhvala, C Hong, K Isaev, TA Johnson, M Juul, A Kahles, A Kahraman, Y Kim, J Komorowski, K Kumar, S Kumar, D Lee, KV Lehmann, Y Li, EM Liu, L Lochovsky, K Park, O Pich, ND Roberts, G Saksena, SE Schumacher, N Sidiropoulos, L Sieverling, N Sinnott-Armstrong, C Stewart, D Tamborero, JMC Tubio, HM Umer, L Uuskula-Reimand, C Wadelius, L Wadi, X Yao, CZ Zhang, J Zhang, JE Haber, A Hobolth, M Imielinski, M Kellis, MS Lawrence, C von Mering, H Nakagawa, BJ Raphael, MA Rubin, C Sander, LD Stein, JM Stuart, T Tsunoda, DA Wheeler, R Johnson, J Reimand, M Gerstein, E Khurana, PJ Campbell, N Lopez-Bigas, PCAWG Drivers and Functional Interpretation Working Group, PCAWG Structural Variation Working Group, J Weischenfeldt, R Beroukhim, I Martincorena, JS Pedersen, G Getz, PCAWG Consortium (2020). Nature 578: 102-111.

Pan-cancer analysis of whole genomes identifies driver rearrangements promoted by LINE-1 retrotransposition.
B Rodriguez-Martin, EG Alvarez, A Baez-Ortega, J Zamora, F Supek, J Demeulemeester, M Santamarina, YS Ju, J Temes, D Garcia-Souto, H Detering, Y Li, J Rodriguez-Castro, A Dueso-Barroso, AL Bruzos, SC Dentro, MG Blanco, G Contino, D Ardeljan, M Tojo, ND Roberts, S Zumalave, PAW Edwards, J Weischenfeldt, M Puiggros, Z Chong, K Chen, EA Lee, JA Wala, K Raine, A Butler, SM Waszak, FCP Navarro, SE Schumacher, J Monlong, F Maura, N Bolli, G Bourque, M Gerstein, PJ Park, DC Wedge, R Beroukhim, D Torrents, JO Korbel, I Martincorena, RC Fitzgerald, P Van Loo, HH Kazazian, KH Burns, PCAWG Structural Variation Working Group, PJ Campbell, JMC Tubio, PCAWG Consortium (2020). Nat Genet 52: 306-319.

Estimating growth patterns and driver effects in tumor evolution from individual samples.
L Salichos, W Meyerson, J Warrell, M Gerstein (2020). Nat Commun 11: 732.

Genomics and data science: an application within an umbrella.
FCP Navarro, H Mohsen, C Yan, S Li, M Gu, W Meyerson, M Gerstein (2019). Genome Biol 20: 109.

Analysis of sensitive information leakage in functional genomics signal profiles through genomic deletions.
A Harmanci, M Gerstein (2018). Nat Commun 9: 2453.


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