David Fenyo

David Fenyo, PhD

Institute for Systems Genetics

Professor, Department of Biochemistry and Molecular Pharmacology

Keywords
biostatistics, cancer, computational biology, genomics, imaging, pharmacology, proteomics, systems biology
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Summary

Our goal is detailed understanding of the dynamics of cellular processes, and we apply mathematical, statistical and computational methods to solve practical problems in experimental design optimization, quantitative data analysis, and in the modeling of biological systems for generating new hypotheses. The focus of our research is proteomic data analysis: we are developing computational methods and databases for protein identification, characterization and quantitation using mass spectrometry-based proteomics.

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Phone

212-263-2216

Academic office

430 East 29th Street, Alexandria Building East

5th Floor, Room 507

New York, NY 10016

Lab Website
Fenyo Lab
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These focus areas and their associated publications are derived from medical subject headings from PubMed.
represents one publication
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Positions

Professor, Department of Biochemistry and Molecular Pharmacology

Director, Biomedical Informatics Masters Training Program

Director, Systems and Computational Biomedicine PhD Training Program

Graduate Education

PhD from Uppsala University

Transcription factor profiling reveals molecular choreography and key regulators of human retrotransposon expression

Sun, Xiaoji; Wang, Xuya; Tang, Zuojian; Grivainis, Mark; Kahler, David; Yun, Chi; Mita, Paolo; Fenyö, David; Boeke, Jef D

Proceedings of the National Academy of Sciences of the United States of America (PNAS). 2018 Jun 12; 115(24):E5526-E5535

Mass spectrometry-based proteomics reveals potential roles of NEK9 and MAP2K4 in resistance to PI3K inhibitors in triple negative breast cancers

Mundt, Filip; Rajput, Sandeep; Li, Shunqiang; Ruggles, Kelly V; Mooradian, Arshag D; Mertins, Philipp; Gillette, Michael A; Krug, Karsten; Guo, Zhanfang; Hoog, Jeremy; Erdmann-Gilmore, Petra; Primeau, Tina; Huang, Shixia; Edwards, Dean P; Wang, Xiaowei; Wang, Xuya; Kawaler, Emily; Mani, D R; Clauser, Karl R; Gao, Feng; Luo, Jingqin; Davies, Sherri R; Johnson, Gary L; Huang, Kuan-Lin; Yoon, Christopher J; Ding, Li; Fenyö, David; Ellis, Matthew J; Townsend, R Reid; Held, Jason M; Carr, Steven A; Ma, Cynthia X

Cancer research. 2018 May 15; 78(10):2732-2746

A toolbox of immunoprecipitation-grade monoclonal antibodies to human transcription factors

Venkataraman, Anand; Yang, Kun; Irizarry, Jose; Mackiewicz, Mark; Mita, Paolo; Kuang, Zheng; Xue, Lin; Ghosh, Devlina; Liu, Shuang; Ramos, Pedro; Hu, Shaohui; Bayron Kain, Diane; Keegan, Sarah; Saul, Richard; Colantonio, Simona; Zhang, Hongyan; Behn, Florencia Pauli; Song, Guang; Albino, Edisa; Asencio, Lillyann; Ramos, Leonardo; Lugo, Luvir; Morell, Gloriner; Rivera, Javier; Ruiz, Kimberly; Almodovar, Ruth; Nazario, Luis; Murphy, Keven; Vargas, Ivan; Rivera-Pacheco, Zully Ann; Rosa, Christian; Vargas, Moises; McDade, Jessica; Clark, Brian S; Yoo, Sooyeon; Khambadkone, Seva G; de Melo, Jimmy; Stevanovic, Milanka; Jiang, Lizhi; Li, Yana; Yap, Wendy Y; Jones, Brittany; Tandon, Atul; Campbell, Elliot; Montelione, Gaetano T; Anderson, Stephen; Myers, Richard M; Boeke, Jef D; Fenyö, David; Whiteley, Gordon; Bader, Joel S; Pino, Ignacio; Eichinger, Daniel J; Zhu, Heng; Blackshaw, Seth

Nature methods. 2018 May 12; 15(5):330-338

UXT is required for spermatogenesis in mice

Schafler, Eric D; Thomas, Phillip A; Ha, Susan; Wang, Yu; Bermudez-Hernandez, Keria; Tang, Zuojian; Fenyö, David; Vigodner, Margarita; Logan, Susan K

PLoS one. 2018 Apr 12; 13(4):e0195747-e0195747

Systematic Analysis of Splice-Site-Creating Mutations in Cancer

Jayasinghe, Reyka G; Cao, Song; Gao, Qingsong; Wendl, Michael C; Vo, Nam Sy; Reynolds, Sheila M; Zhao, Yanyan; Climente-González, Héctor; Chai, Shengjie; Wang, Fang; Varghese, Rajees; Huang, Mo; Liang, Wen-Wei; Wyczalkowski, Matthew A; Sengupta, Sohini; Li, Zhi; Payne, Samuel H; Fenyö, David; Miner, Jeffrey H; Walter, Matthew J; Vincent, Benjamin; Eyras, Eduardo; Chen, Ken; Shmulevich, Ilya; Chen, Feng; Ding, Li

Cell reports. 2018 Apr 03; 23(1):270-281.e3

Human Memory B Cells Targeting<i>Staphylococcus aureus</i>Exotoxins Are Prevalent with Skin and Soft Tissue Infection

Pelzek, Adam J; Shopsin, Bo; Radke, Emily E; Tam, Kayan; Ueberheide, Beatrix M; Fenyö, David; Brown, Stuart M; Li, Qianhao; Rubin, Ada; Fulmer, Yi; Chiang, William K; Hernandez, David N; El Bannoudi, Hanane; Sause, William E; Sommerfield, Alexis; Thomsen, Isaac P; Miller, Andy O; Torres, Victor J; Silverman, Gregg J

MBio. 2018 Mar 13; 9(2):

Human memory B cells targeting Staphylococcus aureus exotoxins are prevalent with skin and soft tissue infection

Pelzek, A J; Shopsin, B; Radke, E E; Tam, K; Ueberheide, B M; Fenyo, D; Brown, S M; Li, Q; Rubin, A; Fulmer, Y; Chiang, W K; Hernandez, D N; El, Bannoudi H; Sause, W E; Sommerfield, A; Thomsen, I P; Miller, A O; Torres, V J; Silverman, G J

MBio. 2018 March-April; 9(2):

The proBAM and proBed standard formats: enabling a seamless integration of genomics and proteomics data [Letter]

Menschaert, Gerben; Wang, Xiaojing; Jones, Andrew R; Ghali, Fawaz; Fenyö, David; Olexiouk, Volodimir; Zhang, Bing; Deutsch, Eric W; Ternent, Tobias; Vizcaíno, Juan Antonio

Genome biology. 2018 Jan 31; 19(1):12-12

See All Publications (171)