Sudheshna Bodapati
Mount Laurel,NJ
Summary
Dedicated life sciences graduate with a strong focus in computational biology and machine learning, driven by advancing human health through biological research, disease prevention, and data-powered diagnostic innovation
Overview
8
8
years of professional experience
Work History
Computational Biologist
Hale Pancreatic Cancer Center
11.2023 - Current
- Perform large-scale analysis of CosMx/Nanostring spatial transcriptomics to model cellular ecosystems in pancreatic tumors and quantify cell–cell signaling networks.
- Build ML and deep-learning models for spatial representation learning, cell-state prediction, and discovery of prognostic molecular signatures within the tumor microenvironment.
Computational Biologist
Dana Farber Cancer Institute
05.2022 - Current
- Tested, debugged, and deployed the RIMA bulk RNA-seq computational pipeline for tumor immunity profiling of multi-cohort clinical trial datasets, optimizing reproducibility and statistical rigor.
- First-author PNAS study leveraging high-dimensional immune profiling of 485 breast cancer patients to model TCR clonotype diversity, identify age-dependent immune correlates, and link systemic clonality to intratumoral CD8+ T-cell infiltration.
- Engineered Seurat-based single-cell RNA-seq workflows to discover markers and differential programs defining secretory basal cell populations in early tumorigenesis for a breast cancer prevention initiative.
- Conduct multi-omic integrative analysis of single-cell RNA, ATAC, and motif-regulatory networks to map transcription factor hierarchies in mouse embryonic neural development.
Data Quality Analyst
Dartmouth Medical Center
09.2019 - 09.2020
Director of Quality and Risk Analysis
Samuel Simmonds Memorial Hospital
12.2017 - 09.2019
Education
Ph.D. - Bioinformatics
Temple University
05-2027
Master of Science - Bioinformatics
Worcester Polytechnic Institute
Worcester, MA05.2023
Master of Science - Healthcare Management
George Mason University
Fairfax, VA2017
Bachelor of Science - Pharmacy
Osmania University
Hyderabad, India2014
Skills
Machine and deep learning for biomarker discovery, survival prediction, tissue-of-origin classification, and epigenomic modeling , with expertise in multi-omic analytics across DNA methylation, RNA-seq, single-cell, and spatial transcriptomics
Strong engineering foundation in Python, R, SQL, SAS, Nextflow, Docker, SLURM, PyTorch, scikit-learn, Seurat, Rosetta, and statistical modeling, dimensionality reduction, clustering, and advanced multi-omic visualization
Accomplishments
- 'In works of developing EHR and application for rural India'
Co-founder of 'DataDoc'
Timeline
Computational Biologist
Hale Pancreatic Cancer Center
11.2023 - Current
Computational Biologist
Dana Farber Cancer Institute
05.2022 - Current
Data Quality Analyst
Dartmouth Medical Center
09.2019 - 09.2020
Director of Quality and Risk Analysis
Samuel Simmonds Memorial Hospital
12.2017 - 09.2019
Master of Science - Healthcare Management
George Mason University
Bachelor of Science - Pharmacy
Osmania University
Ph.D. - Bioinformatics
Temple University
Master of Science - Bioinformatics
Worcester Polytechnic Institute
Publications
- Nishida, Cristea, Bodapati et al. (2023), “ Peripheral blood TCR clonotype diversity as an age-associated marker of breast cancer progression ,” PNAS
- Yang, L., Wang, J., Altreuter, J. et al. Tutorial: integrative computational analysis of bulk RNA-sequencing data to characterize tumor immunity using RIMA. Nat Protoc 18, 2404–2414 (2023).
- Liu Y, Altreuter J, Bodapati S et al. ‘Predicting patient outcomes after treatment with immune checkpoint blockade: A review of biomarkers derived from diverse data modalities’, CELL-GENOMICS [Accepted].
- Rosenkrantz, MD, A., Bodapati, S., Hughes, PhD, D., Wang, W., & Duszak Jr, MD, R. (2017)." Private Practice Radiologist Subspecialty Classification Using Medicare Claims". Journal Of The American College Of Radiology.