Summary of Gerstein Lab Research in 2016
During 2016 the lab had a number of research highlights. We have published three interlinked tools: Stress, Frustration, and Intensification, for assessing the impact of rare genomic variants using knowledge of molecular structure. The tools are of particular interest to the medical genetics community because as they can help explain various cancer mutations as well as variants associated with genetic diseases. Another highlight is our publishing a framework for quantifying privacy risks as a result of linking clinical and phenotype variables. This paper is a timely work given the ongoing debate on data sharing. Apart from these works, we have a few research papers on topics in genomics, such as analyzing allele-specific binding and gene expression analysis, and several review articles on the role of non-coding variants, network comparison, and the cost of sequencing.
Regarding service, I worked on further developing the computational biology program at Yale. In particular, I co-chaired a committee about moving toward a Center for Biomedical Data Science at the Medical School. My lab served the research community in participating in many consortiums, such as PCAWG (the Pan-Cancer Analysis Working Group), the ENCODE consortium, PsychENCODE, 1000 Genomes' structural variation group (and its follow-ons), and the Extracellular RNA Communication Consortium. In 2016, I gave talks and participated in many meetings, including an important data-science education forum at the Cold Spring Harbor Laboratory.
Regarding teaching, I further developed my course in Bioinformatics by including more practical hands-on materials. For example, we introduced a collaborative programming assignment utilizing the GitHub site.
J Chen, B Wang, L Regan, M Gerstein (2016). J Mol Biol 429: 435-445.
S Kumar, D Clarke, M Gerstein (2016). Nucleic Acids Res 44: 10062-10073.
D Wang, F He, S Maslov, M Gerstein (2016). PLoS Comput Biol 12: e1005146.
D Greenbaum, M Gerstein (2016). The Scientist (30 Aug).
CC Yang, EH Andrews, MH Chen, WY Wang, JJ Chen, M Gerstein, CC Liu, C Cheng (2016). BMC Genomics 17: 632.
SW Choo, M Rayko, TK Tan, R Hari, A Komissarov, WY Wee, AA Yurchenko, S Kliver, G Tamazian, A Antunes, RK Wilson, WC Warren, KP Koepfli, P Minx, K Krasheninnikova, A Kotze, DL Dalton, E Vermaak, IC Paterson, P Dobrynin, FT Sitam, JJ Rovie-Ryan, WE Johnson, AM Yusoff, SJ Luo, KV Karuppannan, G Fang, D Zheng, MB Gerstein, L Lipovich, SJ O'Brien, GJ Wong (2016). Genome Res 26: 1312-1322.
JE Freedman, M Gerstein, E Mick, J Rozowsky, D Levy, R Kitchen, S Das, R Shah, K Danielson, L Beaulieu, FC Navarro, Y Wang, TR Galeev, A Holman, RY Kwong, V Murthy, SE Tanriverdi, M Koupenova, E Mikhalev, K Tanriverdi (2016). Nat Commun 7: 11902.
P Muir, S Li, S Lou, D Wang, DJ Spakowicz, L Salichos, J Zhang, GM Weinstock, F Isaacs, J Rozowsky, M Gerstein (2016). Genome Biol 17: 78.
R Shah, K Tanriverdi, D Levy, M Larson, M Gerstein, E Mick, J Rozowsky, R Kitchen, V Murthy, E Mikalev, JE Freedman (2016). PLoS One 11: e0153691.
JE Freedman, M Gerstein, E Mick, J Rozowsky, D Levy, R Kitchen, S Das, R Shah, K Danielson, L Beaulieu, FC Navarro, Y Wang, TR Galeev, A Holman, RY Kwong, V Murthy, SE Tanriverdi, M Koupenova-Zamor, E Mikhalev, K Tanriverdi (2016). Nat Commun 7: 11106.
KH Cheung, S Keerthikumar, P Roncaglia, SL Subramanian, ME Roth, M Samuel, S Anand, L Gangoda, S Gould, R Alexander, D Galas, MB Gerstein, AF Hill, RR Kitchen, J Lotvall, T Patel, DC Procaccini, P Quesenberry, J Rozowsky, RL Raffai, A Shypitsyna, AI Su, C Thery, K Vickers, MH Wauben, S Mathivanan, A Milosavljevic, LC Laurent (2016). J Biomed Semantics 7: 19.
J Chen, J Rozowsky, TR Galeev, A Harmanci, R Kitchen, J Bedford, A Abyzov, Y Kong, L Regan, M Gerstein (2016). Nat Commun 7: 11101.
D Clarke, A Sethi, S Li, S Kumar, RWF Chang, J Chen, M Gerstein (2016). Structure 24: 826-837.
KK Yan, D Wang, A Sethi, P Muir, R Kitchen, C Cheng, M Gerstein (2016). Cell Syst 2: 147-157.
D Greenbaum, M Gerstein (2016). Cell 165:257-258.
F He, S Yoo, D Wang, S Kumari, M Gerstein, D Ware, S Maslov (2016). Plant J 86: 472-80.
P Muir, S Li, S Lou, D Wang, DJ Spakowicz, L Salichos, J Zhang, GM Weinstock, F Isaacs, J Rozowsky, M Gerstein (2016). Genome Biol 17: 53.
D Wang, KK Yan, J Rozowsky, E Pan, M Gerstein (2016). Trends Genet 32: 251-253.
A Harmanci, M Gerstein (2016). Nat Methods 13: 251-6.
E Khurana, Y Fu, D Chakravarty, F Demichelis, MA Rubin, M Gerstein (2016). Nat Rev Genet 17: 93-108.
A Abyzov, S Li, MB Gerstein (2016). Oncotarget 7: 7370-1.
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