Kelly V. Ruggles

Kelly V. Ruggles, PhD

Associate Professor, Department of Medicine

Keywords
Computational Biology, Bioinformatics, Proteomics, Genomics, Data Integration, Single Cell Sequencing, Spatial Transcriptomics, Machine Learning, Data Visualization, Autoimmune Disease, Cardiovascular Risk, Biomarker Discovery, Precision Medicine
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, spatial transcriptomics, metabolomics, 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.

Our research spans multiple diseases, with current focus areas in autoimmunity, cardiovascular disease, and cancer. In autoimmunity, we use single cell omics to molecularly and spatially characterize lupus nephritis, rheumatoid arthritis, and psoriatic arthritis disease progression. Our cardiovascular research leverages collaborations with NYU's ISCHEMIA biorepository and other large clinical cohorts to identify molecular predictors of cardiovascular events and disease vulnerability. In cancer, building on our work with the Clinical Proteomic Tumor Analysis Consortium (CPTAC), we have developed computational tools that identify clinically relevant targets in proteogenomic studies of breast, endometrial, and other cancers. This work has expanded through the NIH Metastasis Research Network, where we apply spatial and single cell technologies to understand early mechanisms of metastasis.

Phone

212-263-3642

Academic office

227 East 30th Street

Room 823

New York, NY 10016

Lab Website
Ruggles Lab
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Positions

Associate Professor, Department of Medicine at NYU Grossman School of Medicine

Assistant Director, Biomedical Informatics, Institute for Innovations in Medical Education

Director, Integrated Sciences, Office of Medical Education

Director, Masters Education, Vilcek Institute of Graduate Biomedical Sciences

Graduate Education

PhD from Columbia University

Rheumatology SAMPLE (Specimen And Matched Phenotype Linked Evaluation) Registry and Biorepository

Psoriatic Response and Onset: Genes Radiology Environment Skin and Synovium)

See All Studies (2)

BlackSheep: A Bioconductor and Bioconda Package for Differential Extreme Value Analysis

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

Discrete immune response signature to SARS-CoV-2 mRNA vaccination versus infection

Ivanova, Ellie N; Devlin, Joseph C; Buus, Terkild B; Koide, Akiko; Cornelius, Amber; Samanovic, Marie I; Herrera, Alberto; Zhang, Chenzhen; Desvignes, Ludovic; Odum, Niels; Ulrich, Robert; Mulligan, Mark J; Koide, Shohei; Ruggles, Kelly V; Herati, Ramin S; Koralov, Sergei B

medRxiv : the preprint server for health sciences. 2023 Aug 23;

Proteogenomics connects somatic mutations to signalling in breast cancer

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

Staphylococcus aureus induces a muted host response in human blood that blunts the recruitment of neutrophils

Zwack, Erin E; Chen, Ze; Devlin, Joseph C; Li, Zhi; Zheng, Xuhui; Weinstock, Ada; Lacey, Keenan A; Fisher, Edward A; Fenyö, David; Ruggles, Kelly V; Loke, P'ng; Torres, Victor J

Proceedings of the National Academy of Sciences of the United States of America (PNAS). 2022 Aug 02; 119(31):e2123017119

Gene Expression Signature in Patients With Symptomatic Peripheral Artery Disease

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

Distinct Features of Human Myeloid Cell Cytokine Response Profiles Identify Neutrophil Activation by Cytokines as a Prognostic Feature during Tuberculosis and Cancer

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

Integrative analysis of lung adenocarcinoma across diverse ethnicities and exposures

Satpathy, Shankha; Clark, Natalie M; Chen, Yi-Ju; Hosseini, Noshad; Chang, Ya-Hsuan; Hsiao, Yi; Lei, Jonathan T; Petralia, Francesca; Chen, Jin-Shing; Geffen, Yifat; Heiman, David I; Paul, Indranil; Cho, Hanbyul; Hollenberg, Michelle; Marino, Giacomo B; Lin, Kuen-Tyng; Mannan, Rahul; White, C Jackson; Allen, Joe; Avanessian, Shayan C; Kane, M Harry; Wolfe, Ashley; Kinarivala, Miloni; Liu, Wenke; Anand, Shankara; Lin, Mong-Wei; Haines, Moe; Bergstrom, Erik J; Hussey, Grant; Li, Ginny Xiaohe; Mani, Deepak C; Fang, Hao; Jaehnig, Eric J; Keshishian, Hasmik; Miller, Brecca; Su, Kang-Yi; Hsiao, Yi-Jing; Hsu, Hsao-Hsun; Hsieh, Min-Shu; Hsu, Kuo-Hsuan; Monovoukas, Alexi; Gohsman, Simone; Thorup, John R; Deng, Yamei; Akiyama, Yo; Deng, Eden; Sheng-Wen Chen, Eric; Krek, Azra; Espinoza, Rodrigo; Ma, Weiping; Charytonowicz, Daniel; Sebra, Robert; Lin, Jyun-Hong; Chen, Yan-Si; Hsu, Yin-Chen; Lin, Ze-Shiang; Chen, Kun-Chieh; Yeh, Chang-Wei; Wang, Yu-Tai; Lazar, Alexander J; Mesri, Mehdi; An, Eunkyung; Zhang, Xu; Clauser, Karl R; Fenyö, David; Chinnaiyan, Arul M; Zhang, Bing; Ding, Li; Ruggles, Kelly; Newton, Chelsea; Zhang, Hui; Wang, Pei; Hostetter, Galen; Omenn, Gilbert S; Kumar-Sinha, Chandan; Thiagarajan, Mathangi; Govindan, Ramaswamy; Paik, Paul; Parolia, Abhijit; Li, Qing K; Ma'ayan, Avi; Getz, Gad A; Dhanasekaran, Saravana M; Robles, Ana I; Chang, Gee-Chen; Yang, Pan-Chyr; Yu, Sung-Liang; Chen, Hsuan-Yu; Nesvizhskii, Alexey I; Carr, Steven A; Mani, D R; Cieslik, Marcin P; Chen, Yu-Ju; Gillette, Michael A; ,; ,

Cancer cell. 2025 Jul 30;

Tetraspanin CD37 regulates platelet hyperreactivity and thrombosis

Sowa, Marcin A; Hannemann, Carmen; Pinos Cabezas, Ivan; Ferreira, Elissa; Biwas, Bharti; Dai, Min; Corr, Emma M; Cornwell, Macintosh G; Drenkova, Kamelia; Lee, Angela H; Spruill, Tanya; Reynolds, Harmony R; Hochman, Judith; Ruggles, Kelly V; Campbell, Robert A; van Solingen, Coen; Wright, Mark D; Moore, Kathryn J; Berger, Jeffrey S; Barrett, Tessa J

Cardiovascular research. 2025 Jun 12; 121(6):943-956

See All Publications (127)

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