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Kelly V. Ruggles

Kelly V. Ruggles, PhD

Associate Professor, Department of Medicine

Keywords
Computational Biology, Bioinformatics, Proteomics, Genomics, Immunology, Cancer
Summary

My laboratory focuses on understanding human health and biology using data science, data visualization and predictive modeling. A primary goal of this research is in analyzing and integrating diverse data modalities including bulk and single cell sequencing, phospho- and global- proteomics, metagenomics, flow cytometry, imaging, and clinical data. In addition to collaborating extensively with clinicians and wet-lab biologists on the analysis of large, translationally focused datasets, our goal is to continually develop novel statistical and data integrative approaches to uncover important biological insights. As part of the Clinical Proteomic Tumor Analysis Consortium (CPTAC) much of our work has focused on the development of such methods to analyze phospho- and global-proteomics, transcriptomics, and genomics data with a goal of obtaining a comprehensive understanding of cancer biology. Within this project, we have developed computational tools that have been used extensively to identify new potentially clinically relevant targets in proteogenomic studies of breast (Mertins et al., Nature, 2016) and endometrial (Duo et al., Cell 2020) cancers.  In addition to our work in cancer, a portion of the lab now focuses on other areas of multi-omic integration, including studying genetic and environmental factors in immune variation (Lin et al., Cell Host Microbe 2020) and stable ischemic heart disease.

Phone

212-263-3642

Academic office

227 East 30th Street

Room 841

New York, NY 10016

Lab Website
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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

Blumenberg, Lili; Kawaler, Emily A; Cornwell, MacIntosh; Smith, Shaleigh; Ruggles, Kelly V; Fenyö, David

Journal of proteome research. 2021 Jul 02; 20(7):3767-3773

Devlin, Joseph C; Zwack, Erin E; Tang, Mei San; Li, Zhi; Fenyo, David; Torres, Victor J; Ruggles, Kelly V; Loke, P'ng

Journal of immunology (1950). 2020 Jun 15; 204(12):3389-3399

Newman, Jonathan D; Cornwell, MacIntosh G; Zhou, Hua; Rockman, Caron; Heguy, Adriana; Suarez, Yajaira; Cheng, Henry S; Feinberg, Mark W; Hochman, Judith S; Ruggles, Kelly V; Berger, Jeffrey S

Arteriosclerosis, thrombosis, & vascular biology. 2021 Mar 04; ATVBAHA120315857

Barrett, Tessa J; Cornwell, MacIntosh; Myndzar, Khrystyna; Rolling, Christina C; Xia, Yuhe; Drenkova, Kamelia; Biebuyck, Antoine; Fields, Alexander T; Tawil, Michael; Luttrell-Williams, Elliot; Yuriditsky, Eugene; Smith, Grace; Cotzia, Paolo; Neal, Matthew D; Kornblith, Lucy Z; Pittaluga, Stefania; Rapkiewicz, Amy V; Burgess, Hannah M; Mohr, Ian; Stapleford, Kenneth A; Voora, Deepak; Ruggles, Kelly; Hochman, Judith; Berger, Jeffrey S

Science advances. 2021 Sep 10; 7(37):eabh2434

Dou, Yongchao; Kawaler, Emily A; Cui Zhou, Daniel; Gritsenko, Marina A; Huang, Chen; Blumenberg, Lili; Karpova, Alla; Petyuk, Vladislav A; Savage, Sara R; Satpathy, Shankha; Liu, Wenke; Wu, Yige; Tsai, Chia-Feng; Wen, Bo; Li, Zhi; Cao, Song; Moon, Jamie; Shi, Zhiao; Cornwell, MacIntosh; Wyczalkowski, Matthew A; Chu, Rosalie K; Vasaikar, Suhas; Zhou, Hua; Gao, Qingsong; Moore, Ronald J; Li, Kai; Sethuraman, Sunantha; Monroe, Matthew E; Zhao, Rui; Heiman, David; Krug, Karsten; Clauser, Karl; Kothadia, Ramani; Maruvka, Yosef; Pico, Alexander R; Oliphant, Amanda E; Hoskins, Emily L; Pugh, Samuel L; Beecroft, Sean J I; Adams, David W; Jarman, Jonathan C; Kong, Andy; Chang, Hui-Yin; Reva, Boris; Liao, Yuxing; Rykunov, Dmitry; Colaprico, Antonio; Chen, Xi Steven; CzekaÅ„ski, Andrzej; JÄ™dryka, Marcin; Matkowski, RafaÅ‚; Wiznerowicz, Maciej; Hiltke, Tara; Boja, Emily; Kinsinger, Christopher R; Mesri, Mehdi; Robles, Ana I; Rodriguez, Henry; Mutch, David; Fuh, Katherine; Ellis, Matthew J; DeLair, Deborah; Thiagarajan, Mathangi; Mani, D R; Getz, Gad; Noble, Michael; Nesvizhskii, Alexey I; Wang, Pei; Anderson, Matthew L; Levine, Douglas A; Smith, Richard D; Payne, Samuel H; Ruggles, Kelly V; Rodland, Karin D; Ding, Li; Zhang, Bing; Liu, Tao; Fenyö, David

Cell. 2020 Feb 20; 180(4):729-748.e26

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

Satpathy, Shankha; Krug, Karsten; Jean Beltran, Pierre M; Savage, Sara R; Petralia, Francesca; Kumar-Sinha, Chandan; Dou, Yongchao; Reva, Boris; Kane, M Harry; Avanessian, Shayan C; Vasaikar, Suhas V; Krek, Azra; Lei, Jonathan T; Jaehnig, Eric J; Omelchenko, Tatiana; Geffen, Yifat; Bergstrom, Erik J; Stathias, Vasileios; Christianson, Karen E; Heiman, David I; Cieslik, Marcin P; Cao, Song; Song, Xiaoyu; Ji, Jiayi; Liu, Wenke; Li, Kai; Wen, Bo; Li, Yize; Gümüş, Zeynep H; Selvan, Myvizhi Esai; Soundararajan, Rama; Visal, Tanvi H; Raso, Maria G; Parra, Edwin Roger; Babur, Özgün; Vats, Pankaj; Anand, Shankara; Schraink, Tobias; Cornwell, MacIntosh; Rodrigues, Fernanda Martins; Zhu, Houxiang; Mo, Chia-Kuei; Zhang, Yuping; da Veiga Leprevost, Felipe; Huang, Chen; Chinnaiyan, Arul M; Wyczalkowski, Matthew A; Omenn, Gilbert S; Newton, Chelsea J; Schurer, Stephan; Ruggles, Kelly V; Fenyö, David; Jewell, Scott D; Thiagarajan, Mathangi; Mesri, Mehdi; Rodriguez, Henry; Mani, Sendurai A; Udeshi, Namrata D; Getz, Gad; Suh, James; Li, Qing Kay; Hostetter, Galen; Paik, Paul K; Dhanasekaran, Saravana M; Govindan, Ramaswamy; Ding, Li; Robles, Ana I; Clauser, Karl R; Nesvizhskii, Alexey I; Wang, Pei; Carr, Steven A; Zhang, Bing; Mani, D R; Gillette, Michael A

Cell. 2021 Aug 05; 184(16):4348-4371.e40