Parul Kudtarkar

Transforming health through AI and genomics.

20 years turning biological data into medical breakthroughs. Harvard, Caltech, UCSD. Currently the lead developer on multi-million dollar metabolic research at UC San Diego.

Technical expertise. Human empathy. Research that changes lives.

When not in the lab, you'll find me running trails, painting landscapes, or cooking for friends.

Work Experience

Common Metabolic Diseases

June 2017 – Present

I have spearheaded the development of The Common Metabolic Diseases Genome Atlas, an extensive bioinformatic and software platform that links thousands of genomic datasets to uncover the origins of metabolic diseases and accelerate drug discovery.

PanKbase

February 2024 – Present

Architected PanKbase, a key component of a $12.5M NIH-funded project, building a comprehensive data library to support diabetes research.

Echinobase

January 2011 – June 2017

Created a software platform and performed bioinformatics analyses to explore gene regulation and environmental impacts on evolution.

Cloud Computing for Comparative Genomics

January 2008 – December 2010

Enhanced reciprocal smallest-distance algorithm for cloud platforms, cutting computational costs by 40%, pioneering the first cloud-based comparative genomics system.

Education

Master of Science, Bioinformatics

Northeastern University, USA

Courses: Biochemistry, Molecular Biology, Programming, Database Management, Proteomics, Imaging, Ethics

Internship: Intelligent Medical Devices, Cambridge, MA

Bachelor of Engineering, Biomedical Engineering

University of Mumbai, India

Courses: Medical Instrumentation, Anatomy, Embedded Systems, Hospital Management

Experience: Jaslok Hospital and Research Center

MBA Certification

Rady School of Management, UC San Diego

Courses: Business Strategy, Innovation, Venture Creation, Leadership

Reviewing Experience

Editorial Board

Database: The Journal of Biological Databases and Curation

Journals Reviewed For

American Journal of Human Genetics, Bioinformatics, Evolutionary Bioinformatics, BMC Bioinformatics, PLOS Computational Biology, Journal of Endocrinology, Faculty of 1000

Conference Jury

Intel International Science and Engineering Fair (Computational Biology and Bioinformatics category)

The Cell Metabolism cover image that accompanies the article illustrates how the T2DKP integrates multiple types of genetic and genomic data to provide insights that can be the building blocks for new therapeutics.

Peer-Reviewed Publications

An integrated map of cell type-specific gene expression in pancreatic islets

Elgamal, Ruth; Kudtarkar, Parul; Melton, Rebecca; Mummey, Hannah; Benaglio, Paola; Okino, Mei-Lin; Gaulton, Kyle J

Diabetes (2023)

Leveraging type 1 diabetes human genetic and genomic data in the T1D Knowledge Portal

Kudtarkar, Parul; Costanzo, Maria; Sun, Ying; Jang, Dongkeun; Koesterer, Ryan; Mychaleckyj, Josyf C; Nayak, Uma; Onengut-Gumuscu, Suna; Rich, Stephen S; Flannick, Jason A

PLoS Biology (2023)

Echinobase: an expanding resource for echinoderm genomic information

Kudtarkar, Parul; Cameron, R. Andrew;

Database: The Journal of Biological Databases and Curation (2017)

Do echinoderm genomes measure up?

Cameron, R Andrew; Kudtarkar, Parul; Gordon, Susan M; Worley, Kim C; Gibbs, Richard A

Marine genomics (2015)

Cost-effective cloud computing: a case study using the comparative genomics tool, roundup

Kudtarkar, Parul; DeLuca, Todd F; Fusaro, Vincent A; Tonellato, Peter J; Wall, Dennis P;

Evolutionary Bioinformatics (2010)

Cloud computing for comparative genomics

Wall, Dennis P; Kudtarkar, Parul; Fusaro, Vincent A; Pivovarov, Rimma; Patil, Prasad; Tonellato, Peter J

BMC bioinformatics (2010)

Genetic association and machine learning improves discovery and prediction of type 1 diabetes

McGrail, Carolyn; Kudtarkar, Parul; et al.

medRxiv (2024)

Single cell multiome profiling of pancreatic islets reveals physiological changes in cell type-specific regulation associated with diabetes risk

Mummey, Hannah M; Kudtarkar, Parul; et al.

bioRxiv (2024)

Sex-specific regulatory architecture of pancreatic islets from subjects with and without type 2 diabetes

Qadir, Mirza Muhammad Fahd; Kudtarkar, Parul; et al.

The EMBO Journal (2024)

The Type 2 Diabetes Knowledge Portal: An open access genetic resource dedicated to type 2 diabetes and related traits

Costanzo, Maria C; Kudtarkar, Parul; et al.

Cell metabolism (2023)

Cardiovascular disease knowledge portal: a community resource for cardiovascular disease research

Costanzo, Maria C; Kudtarkar, Parul; et al.

Circulation: Genomic and Precision Medicine (2023)

Single-cell chromatin accessibility identifies pancreatic islet cell type– and state-specific regulatory programs of diabetes risk.

Chiou, Joshua; Kudtarkar, Parul; et al.

Nature Genetics (2021)

Single-cell multiomic profiling of human lungs reveals cell-type-specific and age-dynamic control of SARS-CoV2 host genes

Wang, Allen; Kudtarkar, Parul; et al.

Elife (2020)

Developmental effector gene regulation: Multiplexed strategies for functional analysis

Wang, Lijun; Kudtarkar, Parul; et al.

Developmental biology (2019)

Invited Talks

AMP CMD Portals

Kudtarkar, Parul

AMP CMD Parliament Meeting (2025)

Single Cell Maps and Analysis Tools in CMDGA

Kudtarkar, Parul

AMP CMD Parliament Meeting (2024)

Gene Expression Integration and Representation in CMDGA/KP

Kudtarkar, Parul

AMP CMD Parliament Meeting (2023)

Representing Genomic Perturbation Studies in CMDGA

Kudtarkar, Parul

AMP CMD Leadership Conference (2022)

Introducing the Common Metabolic Diseases Genome Atlas

Kudtarkar, Parul

AMP T2DKP Webinar Series (2021)

Diabetes Epigenome Atlas and T2D Knowledge Portal: Connected and Complementary Resources

Kudtarkar, Parul

AMP T2DKP Webinar Series (2019)

Poster Presentations

The Type 1 Diabetes Knowledge Portal: An Open-Access Resource for Insights into the Genetic and Genomic Basis of Type 1 Diabetes

Costanzo MC; Kudtarkar, Parul; Sun Y; Jang D; Koesterer R; Mychaleckyj J; Nayak U; Onengut-Gumuscu S; Rich SS; Flannick J; Gaulton KJ; Burtt NP.

American Diabetes Association (2022)

Type 2 Diabetes Epigenome Data Repository and Resource

Y. Sun; Kudtarkar, Parul; S. Morabito; K Gaulton.

American Society of Human Genetics Annual Meeting (2017)

Proteomics Approach to Study Neuronal Regeneration Events of the Sequenced Sea Star Patiria miniata

C Franco; Kudtarkar, Parul; et al.

The FASEB Journal (2014)

Infusion Controller

Ahmed T.; Kudtarkar, Parul; et al.

International Conference on Biological and Medical Physics (2005)

Exhibitions

• Swiss Riviera – Armory Center for the Arts (2018)

• California Wine – Caltech Art Gallery (2019)

• Grecian Dreams – Caltech Art Gallery (2020)