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Kelly V. Ruggles

Kelly V. Ruggles, PhD

Assistant Professor, Department of Medicine

Computational Biology, Bioinformatics, Proteomics, Genomics, Microbiome, Metabolism, Cancer

My research focuses on understanding human health and biology using data science, data visualization, and mathematical modeling. A chief goal of this research is to integrate diverse data modalities and develop complementary statistical analysis methods to uncover important biological insights from highly complex datasets.

Although my research interests are broad—including proteomics, genomics, and lipidomics analysis—my primary interests lie in developing data type–agnostic analysis methods to bridge the gap between biology and data science.

Previously, I applied computational methods to inform cancer proteogenomics, proteomic quantitation, and biomarker identification in collaboration with the Clinical Proteomic Tumor Analysis Consortium (CPTAC). Our goal was to obtain a comprehensive understanding of cancer biology by integrating quantitative phospho- and global proteomics, transcriptomics, and genomics.

Since assuming my faculty position at NYU School of Medicine in 2015, my research has been heavily focused on developing analytical methods for cancer proteogenomics, as part of the next iteration of CPTAC (3.0) and as part of external, local, and nationwide collaborations.

In addition, a portion of my work involves using informatics methods to understand the human microbiome through metagenomics, metatranscriptomics, microbial proteomics, and 16S ribosomal RNA gene sequencing.



Academic office

227 East 30th Street

Room 740

New York, NY 10016

Lab Website
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These focus areas and their associated publications are derived from medical subject headings from PubMed.
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Assistant Professor, Department of Medicine

Director, Academic Programs

PhD from Columbia University

Mertins, Philipp; Mani, D R; Ruggles, Kelly V; Gillette, Michael A; Clauser, Karl R; Wang, Pei; Wang, Xianlong; Qiao, Jana W; Cao, Song; Petralia, Francesca; Kawaler, Emily; Mundt, Filip; Krug, Karsten; Tu, Zhidong; Lei, Jonathan T; Gatza, Michael L; Wilkerson, Matthew; Perou, Charles M; Yellapantula, Venkata; Huang, Kuan-lin; Lin, Chenwei; McLellan, Michael D; Yan, Ping; Davies, Sherri R; Townsend, R Reid; Skates, Steven J; Wang, Jing; Zhang, Bing; Kinsinger, Christopher R; Mesri, Mehdi; Rodriguez, Henry; Ding, Li; Paulovich, Amanda G; Fenyo, David; Ellis, Matthew J; Carr, Steven A

Nature. 2016 06 02; 534(7605):55-62

Ruggles, Kelly V; Tang, Zuojian; Wang, Xuya; Grover, Himanshu; Askenazi, Manor; Teubl, Jennifer; Cao, Song; McLellan, Michael D; Clauser, Karl R; Tabb, David L; Mertins, Philipp; Slebos, Robbert; Erdmann-Gilmore, Petra; Li, Shunqiang; Gunawardena, Harsha P; Xie, Ling; Liu, Tao; Zhou, Jian-Ying; Sun, Shisheng; Hoadley, Katherine A; Perou, Charles M; Chen, Xian; Davies, Sherri R; Maher, Christopher A; Kinsinger, Christopher R; Rodland, Karin D; Zhang, Hui; Zhang, Zhen; Ding, Li; Townsend, R Reid; Rodriguez, Henry; Chan, Daniel; Smith, Richard D; Liebler, Daniel C; Carr, Steven A; Payne, Samuel; Ellis, Matthew J; Fenyo, David

Molecular & cellular proteomics. 2016 Mar; 15(3):1060-71

Ruggles, Kelly V; Garbarino, Jeanne; Liu, Ying; Moon, James; Schneider, Kerry; Henneberry, Annette; Billheimer, Jeff; Millar, John S; Marchadier, Dawn; Valasek, Mark A; Joblin-Mills, Aidan; Gulati, Sonia; Munkacsi, Andrew B; Repa, Joyce J; Rader, Dan; Sturley, Stephen L

Journal of biological chemistry. 2014 Feb 14; 289(7):4417-31

Basch, Corey H; Basch, Charles E; Ruggles, Kelly V; Hammond, Rodney

Disaster medicine & public health preparedness. 2015 Oct; 9(5):531-5

Ruggles, Kelly V; Fenyo, David

Advances in experimental medicine & biology. 2016 Feb; 926:11-19

Ruggles, Kelly V; Fang, Yixin; Tate, Janet; Mentor, Sherry M; Bryant, Kendall J; Fiellin, David A; Justice, Amy C; Braithwaite, R Scott

AIDS & behavior. 2017 Jul; 21(7):2014-2022

Mertins, Philipp; Yang, Feng; Liu, Tao; Mani, D R; Petyuk, Vladislav A; Gillette, Michael A; Clauser, Karl R; Qiao, Jana W; Gritsenko, Marina A; Moore, Ronald J; Levine, Douglas A; Townsend, Reid; Erdmann-Gilmore, Petra; Snider, Jacqueline E; Davies, Sherri A; Ruggles, Kelly V; Fenyo, David; Kitchens, R Thomas; Li, Shunqiang; Olvera, Narcisco; Dao, Fanny; Rodriguez, Henry; Chan, Daniel W; Liebler, Daniel; White, Forest; Rodland, Karin D; Mills, Gordon B; Smith, Richard D; Paulovich, Amanda G; Ellis, Matthew; Carr, Steven A

Molecular & cellular proteomics. 2014 Jul; 13(7):1690-704