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Praveen Sethupathy, PhD

Praveen Sethupathy

Department of Biomedical Sciences

Professor of Physiological Genomics
Director, Center for Vertebrate Genomics

Sethupathy Lab

Department of Biomedical Sciences
Cornell University College of Veterinary Medicine
T7 006D Veterinary Research Tower, Box 17

Ithaca, NY 14853-6401

Office: 607-253-4375
Fax: 607-253-4447

Research & Teaching Interests

Research Interests

In my lab we use molecular and genome-scale approaches to gain insight into normal physiology and disease etiology, primarily in the digestive system (gastrointestinal tract, liver, and pancreas).  We are particularly interested in defining gene regulatory mechanisms that control liver and gut biology and disease.  Active projects in the lab span both basic science (e.g., microRNA control of lineage allocation in the gut epithelium) and translational science (with a focus on diseases of the digestive system such as diabetes, Crohn’s, and fibrolamellar carcinoma).  Our lab members have training and expertise in a diverse array of disciplines, including physiology, functional genomics, gene regulation, non-coding RNAs, bioinformatics, gut mucosal biology, molecular biology, and cancer biology.  Another important aspect of our research program is systems genetics, linking genetic variants to molecular pathways to phenotypes.

We are always on the lookout for motivated trainees and staff scientists with interests in one or more of several diverse areas of study, including gene regulation; regulatory RNAs; bioinformatics; molecular genetics; transgenic mouse models; metabolic disease; and liver & GI biology/physiology, stem cell behavior, and cancer.

We are indebted to our collaborators, colleagues, and funding sources, without whom we could not efficiently tackle what we believe are incredibly interesting and important problems in biomedicine.

Active research areas in the lab include:

  • Contribution of microRNAs to lineage allocation and function in the gut epithelium using mouse models and organoids
  • Genome-scale approaches to discover novel regulators of survival, growth, and metastasis in fibrolamellar carcinoma
  • Identification of mutation-specific gene regulatory programs in cancers of the digestive system using patient samples and organoids
  • Discovery of microRNAs as molecular markers and drivers of Crohn’s disease using patient samples and organoids
  • The role of microRNAs in shaping physiological response to diabetogens (e.g., diet, arsenic) using mouse models and cell lines

Our research has been supported by grants from a diverse set of funding sources, including the National Institutes of Health, the Fibrolamellar Cancer Foundation, the American Diabetes Association, the American Heart Association, the Crohn’s & Colitis Foundation of America, and Alnylam Pharmaceuticals Inc.  Our goal is to discover novel mechanisms in physiology and disease, primarily GI-related, advancing basic science and opening up new avenues for the development of effective therapeutics.

Teaching and Mentoring

Teaching and mentoring are my first passions. I am deeply committed to developing a strong, robust didactic and practical learning atmosphere for students in the classroom and trainees in the laboratory. My love for teaching took hold when I was an undergraduate at Cornell University, during which time I served for several years as either a teaching assistant or a course consultant, and it has intensified over the years because I believe that: (1) the ability to teach/articulate a concept effectively is the sign of when one has truly learned it well; (2) enthusiastic students at the best universities like Cornell should have direct access to their professors in order to nurture their creative spirit and sharpen their intellect at an early stage of their career; and (3) the overall scientific enterprise is strengthened when we take the time to invest in the next generation of scholars.

I am firmly committed to serving as a research mentor for undergraduate and graduate students, and I am particularly passionate about helping students grow not only as scientists, but also as artful and articulate communicators of their scientific work. Exchange of research ideas and goals, both with scientific and lay audiences, is extremely important and I have deeply enjoyed the opportunity to help train students improve their skills in this area. The most rewarding moments of my career so far have come in those times when I realize how much my students have grown not only as critical thinkers but also as effective communicators.

  • BIOMG 7800 Stem Cells & Cancer (Spring 2018, Spring 2019)
  • BIOMS/BIOAP/VTBMS 3100 Principles of Animal Physiology (Fall 2018 – Present)


  • PhD, Genomics, University of Pennsylvania
  • BA, Cornell University

Biography/Professional Experience

Praveen is Professor of Physiological Genomics in the Department of Biomedical Sciences and Director of the Center for Vertebrate Genomics at Cornell University, where he leads a research lab focused on genomic approaches to understand physiology and human disease.  He received his BA degree from Cornell University and his PhD in Genomics from the University of Pennsylvania.  After completing a post-doctoral fellowship at the National Human Genome Research Institute under the mentorship of NIH Director Dr. Francis Collins, he moved in 2011 to the University of North Carolina at Chapel Hill as an Assistant Professor in the Department of Genetics.  The same year he was selected by Genome Technology as one of the nation’s top 25 rising young investigators in genomics.  In 2017, he returned to Cornell University as an Associate Professor. Praveen has authored over 115 peer-reviewed publications in scientific journals such as PNAS, Cell and Science and has served as a reviewer for over 45 different journals.  Recent honors include a faculty merit award for outstanding teaching and mentoring and the prestigious American Diabetes Association Pathway To Stop Diabetes Research Accelerator, which is awarded to only three people per year.  Praveen is also dedicated to improving science communication and has served on the advisory board for the AAAS Dialogue on Science, Ethics, and Religion. Praveen’s laboratory is located on the 7th floor of the Research Tower on Tower Road. He lives in Brooktondale, NY with his wife and three children.


  1. T.A. Dinh, A.F. Utria, K.C. Barry, R. Ma, G.K. Abou-Alfa, J. Gordan, E.M. Jaffee, J.D. Scott, J. Zucman-Rossi, A.F. O’Neill, M.E. Furth, and P. Sethupathy (2022). Roadmap for fibrolamellar carcinoma research and clinical trials. Nature Reviews Gastroenterology and Hepatologydoi:10.1038/s41575-022-00580-3.
  2. M. Kanke, M. M. Kennedy, S. Connelly, M.S. Schaner, M.T. Shanahan, E.A. Wolber, C. Beasley, G. Lian, A. Jain, M.D. Long, E.L. Barnes, H.H. Herfarth, K.L. Isaacs, J.J. Hansen, M. Kapadia, J. G. Guillem, T.S. Furey, S.Z. Sheikh, and P. Sethupathy (2022). Single-cell analysis reveals unexpected cellular changes and transposon expression signatures in the colonic epithelium of treatment-naïve adult Crohn’s disease patients. CMGH, doi:10.1016/j.jcmgh.2022.02.005.
  3. M.T. Shanahan, M. Kanke, O.O. Oyesola, Y.H. Hung, K. Koch-Laskowski, A.P. Singh, B.C.E. Peck, M. Biraud, B. Sheahan, J. Cortes, H. Gong, D.K. Sahoo, R. Cubitt, N.A. Kurpios, J.P. Mochel, K. Allenspach, S.J. McElroy, S. Ding, J. von Moltke, C.M. Dekaney, E.D. Tait-Wojno, and P. Sethupathy (2021). Multi-omic analysis defines the first microRNA atlas across all small intestinal epithelial lineages and identifies novel markers for almost all major cell types. AJP Gastrointestinal and Liver Physiology, 321:G668-G681.
  4. K. Hsiao, C. Noble, W.A. Pitman, N. Yadav, S. Kumar, A. Terceros, G.R. Keele, M. Kanke, T. Conniff, C. Cheleuitte, R. Tolwani, P. Sethupathy*, and P. Rajasethupathy* (2020). A thalamic orphan receptor drives variability in short term memory. Cell, 183:522-536.
  5. T.A. Dinh, R. Sritharan, F.D. Smith, A.B. Francisco, R.K. Ma, R.P. Bunaciu, M. Kanke, C.G. Danko, A.P. Massa, J.D. Scott, and P. Sethupathy (2020). Hotspots of aberrant enhancer activity in fibrolamellar carcinoma reveal candidate oncogenic pathways and therapeutic vulnerabilities. Cell Reports, 31:107509.

Browse PubMed Browse PubMed for a complete listing of Dr. Sethupathy's publications

Awards and Honors


Professional/Academic Affiliations