Shalmali S. Kulkarni
Bioinformatics | Data Science | Multi-Omics | Machine Learning
- Role
- Data Scientist, Center for Biometric Analysis at The Jackson Laboratory
- Location
- Kittery, ME, US
- LinkedIn followers
- 500 followers
About Shalmali S. Kulkarni
I’m a passionate and detail-oriented bioinformatics scientist with 4+ years of experience transforming complex biological data into actionable insights. With a strong foundation in multi-omics, genomics, and metagenomics, I specialize in building scalable pipelines, developing machine learning models, and bridging the gap between wet-lab biology and computational science.At The Jackson Laboratory and Seres Therapeutics, I’ve led initiatives that improved data quality, automated QC processes, and enhanced data accessibility for cross-functional teams. My toolkit includes Python, R, SQL, and tools like Galaxy, Nextflow, and OMERO, and I’ve deployed solutions that empower both scientists and non-programmers alike.I thrive in collaborative environments where I can contribute to impactful research, mentor others, and drive innovation in bioinformatics. Currently, I’m focused on advancing my expertise in statistical modeling and data integration to prepare for senior leadership roles in computational biology.Let’s connect if you’re working on cutting-edge problems in genomics, data science, or translational research — or if you’re looking for someone who can turn biological complexity into clarity.
Experience
Data Scientist, Center for Biometric Analysis
Mar 2024 — Present · Bar Harbor, ME, US
Spearheaded data integration and quality assurance for the NIH-funded Knockout Mouse Phenotyping Project (KOMP2), collaborating with 21 global centers and representing JAX in stakeholder meetings- Designed and deployed Python-based tools for automated QC, metadata validation, and experiment tracking, reducing manual errors and improving data submission efficiency- Led the development of a cross-platform data extraction tool integrating legacy SQL and OData LIMS systems, enabling weekly compliance tracking with breeding teams- Partnered with IT and data science teams to evaluate PowerBI and centralize KOMP2 data, enhancing accessibility and reporting- Optimized HTML for the new LIMS (PFS) database to improve performance and accessibility, contributing to web-based bioinformatics infrastructure- Automated image and metadata transfer using OMERO and Python, linking experimental images to mouse records and minimizing manual curation- Created R-based analysis workflows for biologists, enabling one-click execution and reproducibility, and maintained codebases on GitHub.
Education
University of Mumbai
Master of Science - MS, Biotechnology
2015 — 2017
University of Mumbai
Bachelor of Science - BS, Biotechnology
2012 — 2015
Northeastern University
Master of Science - MS, Bioinformatics
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