Arpita Kulkarni
Boston
Summary
- Leader in genomics and bioinformatics with extensive experience at Harvard Medical School. Specializes in single-cell biology and AI-driven therapeutics, spearheading innovative research initiatives. Proven ability to enhance experimental design and data strategy, resulting in impactful discoveries and advancements in therapeutic programs.
Overview
10
10
years of professional experience
Work History
Director, Functional Genomics & Bioinformatics Core
Beth Israel Deaconess Medical Center / Harvard Medical School / Broad Institute
Boston
03.2025 - Current
- Lead a cross-disciplinary genomics and bioinformatics program supporting experimental and computational research across academia and industry.
- Advise investigators on experimental design and data strategy for single-cell and multi-omics studies, including AI-informed approaches to maximize biological insight.
- Translate emerging computational methods into robust, scalable laboratory workflows.
Associate Director, Single Cell Core
Harvard Medical School
Boston
02.2022 - 03.2025
- Spearheaded cross-disciplinary collaboration in dynamic research settings, assisting over 150 Harvard Labs and directing single-cell biology initiatives totaling 20 million in federal grant funding, including CZI and HHMI initiatives.
- Oversaw deployment of single-cell genomics technologies across various biological systems.
Translated biological constraints into machine learning objectives to enhance research outcomes. - Partnered with computational teams to formulate experiments facilitating downstream modeling, benchmarking, and biological validation for AI-accelerated biological discovery.
- Collaborate on multiple, high-impact single-cell atlas projects (including CZI)
Postdoctoral Researcher
Harvard University
Boston
10.2015 - 02.2022
- Co-developed brain organoid platform for neurodegenerative disease, commercialized by Cannex Scientific Inc. ($1.5M).
- Engineered first blood-brain barrier-crossing Hsp90 inhibitor for glioblastoma, securing $100K MGB Innovation Discovery Grant.
- Co-discovered novel mechanisms of immune evasion in cancer, featured on Nature Nanotechnology cover and Editor’s Choice.
- Co-developed nanomedicine platforms modulating cancer-associated fibroblasts to enhance immunotherapy, awarded $100K BRIght Futures Prize.
- Co-developed AT-1965, first-in-class immunomodulatory small molecule, resulting in IND approval 2023 and $26M funding.
Education
Ph.D. - Cell & Developmental Biology
Max Planck Institute For Biology
Tübingen, Germany09-2015
Master of Science - Biology
University of Pune
India05-2006
Skills
- Cell and developmental biology
- Genomics technologies
- Single-cell RNA sequencing
- Multi-omics integration
- Biological database utilization
- AI-driven therapeutics discovery
- Computational biology
- Single-cell analysis frameworks
- Model evaluation and benchmarking
Selected Leadership And Service
- Scientific advisor and collaborator across academic, biotech, and translational research programs.
- Mentor to trainees spanning experimental biology and computational analysis.
Google Scholar
https://scholar.google.com/citations?user=EXiUbcAAAAAJ&hl=en
Selected Scientific Contributions
- Foundation models for human cell differentiation (Science, 2025), Co-author on a Science publication describing an AI-enabled single-cell platform for modeling and predicting human cell differentiation trajectories. Contributed to the integration of large-scale experimental data generation with computational modeling, enabling systematic evaluation of AI-predicted cell fate outcomes against biological ground truth. Platform subsequently commercialized and now underpins DeltaStem, a foundation model for human stem cells (Somite; Series A led by Khosla Ventures).
- Human Lineage Atlas of Bone Marrow Hematopoiesis (CZI-funded), Lead co-author on an ongoing Chan Zuckerberg Initiative–funded study constructing the first human lineage atlas of bone marrow hematopoiesis. Developed experimentally grounded lineage maps to support evaluation of computational and AI models of long-horizon cell fate decisions. Integrated large-scale single-cell datasets to resolve complex differentiation trajectories and lineage relationships.
- Multi-Omics Playbook (2025), Contributing author to the Multi-Omics Playbook (2025), authoring sections (pp. 7–10) on AI-informed experimental design, model evaluation, and decision-making under biological uncertainty. Articulated practical frameworks for aligning biological questions with computational objectives, reducing trial-and-error in experimental workflows.
- Invited Thought Leadership & panelist, British Consulate General Boston, speaking on AI × Engineering in Biology, addressing opportunities, limitations, and responsible deployment of AI systems in biological research (January 2026)
Core Expertise
- AI-accelerated biological discovery
- Computational and experimental biology (wet-lab + in silico)
- Single-cell and multi-omics analysis
- Model evaluation and benchmarking using biological ground truth
- Translating biological constraints into ML objectives
- Biological databases (e.g., UniProt, GenBank, PDB)
- Experimental design informed by AI
- Cross-disciplinary collaboration in fast-paced research environments
Languages
English
Native/ Bilingual
German
Professional
Accomplishments
Creative Destruction Lab Therapeutics Accelerator (1 of 20 global inventors, 2025)
Timeline
Director, Functional Genomics & Bioinformatics Core
Beth Israel Deaconess Medical Center / Harvard Medical School / Broad Institute
03.2025 - Current
Associate Director, Single Cell Core
Harvard Medical School
02.2022 - 03.2025
Postdoctoral Researcher
Harvard University
10.2015 - 02.2022
Ph.D. - Cell & Developmental Biology
Max Planck Institute For Biology
Master of Science - Biology
University of Pune