Parul Kudtarkar
ML & Genomics Researcher
20 years turning biological data into medical breakthroughs. 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 Genome Atlas & PanKbase
Principal architect for cmdga.org ($57M FNIH AMP CMD initiative) and PanKbase (data.pankbase.org, $10M NIH-funded), partnering with Amgen, Eli Lilly, Novo Nordisk, and Pfizer. Executed single-cell ATAC-seq analyses identifying disease-associated chromatin patterns for T1D and T2D. Architected scalable cloud solutions reducing costs while improving performance. Developed PerseusAI platform integrating knowledge graphs, vector embeddings and LLMs.
Echinobase
Built Echinobase and end-to-end sequence analysis for 7 echinoderm species. Built a comparative genomics platform serving 150+ labs worldwide. Integrated RNA-seq and ATAC-seq to infer transcriptional networks across 7 echinoderm species.
Cloud Computing for Comparative Genomics
Deployed distributed RSD algorithm on cloud platforms (Yahoo MapReduce, AWS ECS). Applied machine learning-based runtime prediction achieving 40% cost reduction, pioneering the first cloud-based comparative genomics system.
Latest from the blog
View allTERT AlphaGenome Analysis: A Notebook Walkthrough
Methods companion to the TERT promoter post: notebook setup, gnomAD control selection, model choice, AlphaGenome API calls, score_variant caveats and evaluation against published biology.
How a Single DNA Letter Change Switches On Cancer's Immortality Engine
A deep-dive into TERT promoter mutations using AlphaGenome to reconstruct chromatin, TF binding and transcriptional effects from sequence alone.
AlphaGenome Coverage Explorer: Check Training Data Coverage Before You Run the Model
A practical tool to check whether your tissue or cell type is covered in AlphaGenome training tracks before you run variant effect analyses.
Education
Master of Science, Bioinformatics
Courses: Biochemistry, Molecular Biology, Programming, Database Management, Proteomics, Imaging, Ethics
Bachelor of Engineering, Biomedical Engineering
Courses: Medical Instrumentation, Anatomy, Embedded Systems, Hospital Management
MBA Certification
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, Diabetes
Conference Jury
Intel International Science and Engineering Fair (Computational Biology and Bioinformatics category), Chen Institute Symposium for AI Accelerated Science