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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
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.

Phone

917-754-6066

Academic office

435 E 30th St

9th Floor, Room 907

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.
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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

Postdoctoral Training

Rockefeller University, Chait Lab

Phylogenetic debugging of a complete human biosynthetic pathway transplanted into yeast

Agmon, Neta; Temple, Jasmine; Tang, Zuojian; Schraink, Tobias; Baron, Maayan; Chen, Jun; Mita, Paolo; Martin, James A; Tu, Benjamin P; Yanai, Itai; Fenyö, David; Boeke, Jef D

Nucleic acids research. 2020 Jan 10; 48(1):486-499

The Hidden Story of Heterogeneous B-raf V600E Mutation Quantitative Protein Expression in Metastatic Melanoma-Association with Clinical Outcome and Tumor Phenotypes

Betancourt, Lazaro Hiram; Szasz, A Marcell; Kuras, Magdalena; Rodriguez Murillo, Jimmy; Sugihara, Yutaka; Pla, Indira; Horvath, Zsolt; Pawłowski, Krzysztof; Rezeli, Melinda; Miharada, Kenichi; Gil, Jeovanis; Eriksson, Jonatan; Appelqvist, Roger; Miliotis, Tasso; Baldetorp, Bo; Ingvar, Christian; Olsson, Håkan; Lundgren, Lotta; Horvatovich, Peter; Welinder, Charlotte; Wieslander, Elisabet; Kwon, Ho Jeong; Malm, Johan; Nemeth, Istvan Balazs; Jönsson, Göran; Fenyö, David; Sanchez, Aniel; Marko-Varga, György

Cancers. 2019 Dec 09; 11(12):

Comprehensive Scanning Mutagenesis of Human Retrotransposon LINE-1 Identifies Motifs Essential for Function

Adney, Emily M; Ochmann, Matthias T; Sil, Srinjoy; Truong, David M; Mita, Paolo; Wang, Xuya; Kahler, David J; Fenyö, David; Holt, Liam J; Boeke, Jef D

Genetics. 2019 Dec; 213(4):1401-1414

Integrated Proteogenomic Characterization of Clear Cell Renal Cell Carcinoma

Clark, David J; Dhanasekaran, Saravana M; Petralia, Francesca; Pan, Jianbo; Song, Xiaoyu; Hu, Yingwei; da Veiga Leprevost, Felipe; Reva, Boris; Lih, Tung-Shing M; Chang, Hui-Yin; Ma, Weiping; Huang, Chen; Ricketts, Christopher J; Chen, Lijun; Krek, Azra; Li, Yize; Rykunov, Dmitry; Li, Qing Kay; Chen, Lin S; Ozbek, Umut; Vasaikar, Suhas; Wu, Yige; Yoo, Seungyeul; Chowdhury, Shrabanti; Wyczalkowski, Matthew A; Ji, Jiayi; Schnaubelt, Michael; Kong, Andy; Sethuraman, Sunantha; Avtonomov, Dmitry M; Ao, Minghui; Colaprico, Antonio; Cao, Song; Cho, Kyung-Cho; Kalayci, Selim; Ma, Shiyong; Liu, Wenke; Ruggles, Kelly; Calinawan, Anna; Gümüş, Zeynep H; Geizler, Daniel; Kawaler, Emily; Teo, Guo Ci; Wen, Bo; Zhang, Yuping; Keegan, Sarah; Li, Kai; Chen, Feng; Edwards, Nathan; Pierorazio, Phillip M; Chen, Xi Steven; Pavlovich, Christian P; Hakimi, A Ari; Brominski, Gabriel; Hsieh, James J; Antczak, Andrzej; Omelchenko, Tatiana; Lubinski, Jan; Wiznerowicz, Maciej; Linehan, W Marston; Kinsinger, Christopher R; Thiagarajan, Mathangi; Boja, Emily S; Mesri, Mehdi; Hiltke, Tara; Robles, Ana I; Rodriguez, Henry; Qian, Jiang; Fenyö, David; Zhang, Bing; Ding, Li; Schadt, Eric; Chinnaiyan, Arul M; Zhang, Zhen; Omenn, Gilbert S; Cieslik, Marcin; Chan, Daniel W; Nesvizhskii, Alexey I; Wang, Pei; Zhang, Hui

Cell. 2019 Oct 31; 179(4):964-983.e31

L1EM: A tool for accurate locus specific LINE-1 RNA quantification

McKerrow, Wilson; Fenyö, David

Bioinformatics. 2019 Oct 04;

Integration and analysis of CPTAC proteomics data in the context of cancer genomics in the cBioPortal

Wu, Pamela; Heins, Zachary J; Muller, James; Katsnelson, Lizabeth; de Bruijn, Ino; Abeshouse, Adam A; Schultz, Nikolaus; Fenyö, David; Gao, Jianjiong

Molecular & cellular proteomics. 2019 Sep; 18(9):1893-1898

Extracting Pathway-Level Signatures from Proteogenomic data in Breast Cancer Using Independent Component Analysis

Liu, Wenke; Payne, Samuel H; Ma, Sisi; Fenyö, David

Molecular & cellular proteomics. 2019 Aug 09; 18(8 suppl 1):S169-S182

Regulated Phosphosignaling Associated with Breast Cancer Subtypes and Druggability

Huang, Kuan-Lin; Wu, Yige; Primeau, Tina; Wang, Yi-Ting; Gao, Yuqian; McMichael, Joshua F; Scott, Adam D; Cao, Song; Wendl, Michael C; Johnson, Kimberly J; Ruggles, Kelly; Held, Jason; Payne, Samuel H; Davies, Sherri R; Dar, Arvin; Kinsinger, Christopher R; Mesri, Mehdi; Rodriguez, Henry; Ellis, Matthew J; Townsend, R Reid; Chen, Feng; Fenyo, David; Li, Shunqiang; Liu, Tao; Carr, Steven A; Ding, Li

Molecular & cellular proteomics. 2019 Aug; 18(8):1630-1650

See All Publications (166)