Professional Summary
Computational biologist and ML engineer with 5+ years building production AI/ML systems for drug discovery and bioinformatics at the intersection of wet lab and HPC. Currently at Memorial Sloan Kettering, architecting end-to-end ML pipelines (LLMs, transformers, diffusion models) on SLURM clusters for de novo therapeutic generation against DNA repair targets (ATM, Ligase IV, DNA-PKcs, Rad51, Ku70/80). Dual CS + Biology background, published in JASN and AACR, with prior experience leading engineering teams of 3–8 across research institutions and international tech companies.
Work Experience
Research Technician, Computational Biology [Lead Computational Scientist]
Memorial Sloan Kettering Cancer Center | New York, New York | 2022 – Present
- Architect end-to-end ML pipelines on HPC (SLURM) integrating PyTorch, TensorFlow, Hugging Face transformers, and scikit-learn for production drug discovery workflows
- Build generative models (transformers, diffusion, RNNs) and chemistry-based LLMs for de novo therapeutic generation targeting DNA repair proteins (ATM, Ligase IV, DNA-PKcs, Rad51, Ku70/80)
- Lead computational programs: (1) Rad51 PROTAC program — fragment-based drug discovery (FBDD) combined with diffusion and RNN generative models for de novo payload design; linker design and optimization for novel peptide and small-molecule degraders; (2) DNA-PKcs PROTAC program — structure-based design and HPC-driven optimization of DNA-PKcs targeted degraders; (3) ATM-SMDC program — designed novel cleavable and uncleavable linker conjugates with SPR-validated binding kinetics (Kd <1 nM); (4) LIG4 AOC platform (t-NHEJ-P) — HER2-targeted antibody-oligonucleotide conjugate for tumor-restricted LIG4 degradation and radiosensitization; near-complete LIG4 degradation at ~10 nM in cancer cells (U2OS, H1299) while sparing normal cells, suppressing NHEJ without activating HR and enhancing radiosensitization (AACR 2026)
- Develop and maintain bioinformatics pipelines (Snakemake, Nextflow) for high-throughput sequencing (Illumina, Nanopore): automated QC, alignment, variant calling
- Design and deploy FastAPI/Flask services for molecular property prediction and generative model inference, containerized with Docker/Singularity and deployed on GCP
- Project lead coordinating dry-lab (generative chemistry, HPC pipelines, docking/MD, SPR kinetics) and wet-lab (synthesis, assay development, in-vitro validation) in parallel; design experiments and protocols, manage timelines, deliverables, and cross-functional scientists
- Manage CRO work for compound synthesis, SPR studies, and other assays across MSK drug discovery programs
- Perform and manage ADME and property optimization, including molecular property prediction (QSAR) and assay design/review across DMPK, solubility, permeability, metabolic stability, CYP, hERG, and toxicity; iterate on linker developability for PROTAC, ADC, and AOC programs
- Implement CI/CD, automated testing, and reproducibility practices across the group’s computational infrastructure
Research Scientist I
149 Bio, LLC | Miami, Florida | 2021 – 2022
- Developed integrins as therapeutic targets for IBD, Lupus, kidney disease, and cancer — combining homology modeling, high-throughput virtual screening, and cell-based validation (ELISA, adhesion, migration)
- Characterized protein-ligand interactions and drove hit optimization through iterative computational-experimental cycles
- Integrated third-party software packages into analytical workflows for structure-based drug design
Graduate Student Researcher
New Jersey Institute of Technology | Newark, New Jersey | January 2019 – May 2021
Thesis: The impact of IRAK-1 splice variants on inflammatory response in sepsis under Dr. Nan Gao, Dr. Patrick Morcillo & Dr. Dirk Bucher
- Analyzed large-scale genetic data to investigate the role of IRAK-1 in sepsis-induced inflammatory response using Python-based bioinformatics pipelines
- Demonstrated that pre-infection IRAK-1 levels dictate inflammatory response magnitude following endotoxin exposure
Publications
- Helmuth, R., et al. Integrin Activation as a Novel Therapeutic Strategy for Podocytopathies: FR-PO727. Journal of the American Society of Nephrology 33.11S (2022): 521.
- Pandey, M., Subramanian Sahasranamam, A., Higginson, D. Abstract 238: Targeted degradation of DNA ligase IV through a double-stranded DNA-based PROTAC for precision radiosensitization. AACR Annual Meeting 2026. Cancer Research 86(7_Supplement):238 (2026). Near-complete LIG4 degradation at ~10 nM in cancer cells (U2OS, H1299) while sparing normal cells; suppresses NHEJ repair without activating HR; enhances radiosensitization.
Education
Master of Science, Biology | New Jersey Institute of Technology | January 2019 – May 2021
Thesis: The Role of IRAK-1 in Sepsis
Bachelor of Science, Biology & Computer Science | Valparaiso University | August 2014 – May 2018
Minor: Chemistry
Certifications
Introduction to Molecular Modeling in Drug Discovery
Schrödinger, 2022
Advanced Image Analysis using MATLAB
Memorial Sloan Kettering Cancer Center, 2022