About Me

I am a computational biologist interested in genetics, transcriptomics, and development. I have led projects studying the functional landscape of neurons (Harris et al 2021) and the developmental trajectory of hematopoiesis (in preparation). I made significant contributions to a collaboration studying maize meristem development (Xu et al 2021) and published software central to all of the above projects (Fisher et al 2021). I specialize in applying traditional statistical and machine learning methods in a robust meta-analytic framework. I use parallel, distributed, and GPU computing to process and analyze large scale genomics data.

I started my research career at the National Institutes of Health in the lab of Dr. William F. Simonds, studying neuroendocrine signal transduction using molecular biology and behavior. I then transitioned into computational biology with an internship at the Icahn School of Medicine in the lab of Dr. Eric Sobie. There I modeled cardiac action potentials using CUDA GPU computing in order to understand the paramters that are sensitive to an arythmia. I then went ot Cold Spring Harbor laboratory for a summer internship with Dr. Mickey Atwal. I searched for novel antigens expressed exclusively in cancer and immune priveleged tissues that could be used for new cancer therapeutics.

Work Experience

Stealth AI x Immunology Company
Consultant Oct 2024 - Present
Conduct strategy, scientific, and competitive intelligence research to advance a pre-seed stealth immunology company

Lyell Immunopharma
Senior Computational Biologist November 2021 - Present

Integrated clinical, translational, and sequencing data to support development of LYL314 (CD19/CD20 CAR-T) into 2 pivotal trials
Collaborated with research, process sciences, and MSAT teams on design, execution, analysis, and presentation of experiments that impact the direction of Tumor Infiltrating Lymphocytes (TIL) program
Built pipelines for bulkTCRseq and scRNA/TCR/CITEseq to standardize data analysis across the computational team
Co-authored regulatory documents (IND, RMAT, EOP1) and 7 clinical/research conference presentations across 3 clinical programs (presenter for 1)

Publications

Large-scale single-cell profiling of stem cells identifies redundant regulators of shoot development and yield trait variation
Xiaosa Xu and Michael Passalacqua and Brian Rice and Edgar Demesa-Arevalo and Mikiko Kojima and Yumiko Takebayashi and Xingyao Yu and Benjamin Harris and Yuchen Liu and Andrea Gallavotti and Hitoshi Sakakibara and Jesse Gillis and David Jackson
Developmental Cell, 2025 [Google Scholar]

Optimizing Stim-RTM, a synthetic stimulatory agent, for feeder-free tumor-infiltrating lymphocyte manufacturing
Riley P Allen and Jason Duecker and Mikayla Min and Samantha Chan and Christina Ta and Benjamin Harris and Emily Fu-Sum and Stefan Siebert and Purnima Sundar and Yogin Patel and Shobha Potluri and Suman Vodnala and Gary Lee and Alexander Cheung and Aileen Li
Cancer Research, 2025 [Google Scholar]

Large-scale single-cell profiling of stem cells uncovers redundant regulators of shoot development and yield trait variation
Xiaosa Xu and Michael Passalacqua and Brian Rice and Edgar Demesa-Arevalo and Mikiko Kojima and Yumiko Takebayashi and Benjamin Harris and Hitoshi Sakakibara and Andrea Gallavotti and Jesse Gillis and David Jackson
BioRxiv, 2024 [Google Scholar]

440 Utilizing Stim-RTM technology to reduce live feeder cells in the tumor infiltrating lymphocyte culture process
Riley P Allen and Jason Duecker and Mikayla Min and Samantha Chan and Christina Ta and Emily Fu-Sum and Benjamin Harris and Purnima Sundar and Yogin Patel and Aileen Li and Shobha Potluri and Suman Vodnala and Gary Lee and Alexander Cheung
Journal for ImmunoTherapy of Cancer 12 (Suppl 2), 2024, 2024 [Google Scholar]

Identification of pan-cancer/testis genes and validation of therapeutic targeting in triple-negative breast cancer: Lin28a-based and Siglece-based vaccination induces antitumor immunity and inhibits metastasis
Jason A Carter and Bharati Matta and Jenna Battaglia and Carter Somerville and Benjamin D. Harris and Margaret LaPan and Gurinder S Atwal and Betsy J Barnes
Journal for immunotherapy of cancer, 2023 [Google Scholar]

379 Epi-RTM P2 protocol produces a scalable polyclonal TIL product with a greater expansion success rate across hot and cold tumors in shorter culture time
Yogin Patel and Jaewon Yun and Melissa Bedard and Melissa DeFrancesco and Carson Harms and Benjamin Harris and Saeed Azimi and Ngoc-Han Ha and Audrey Garces and Shobha Potluri and Gary Lee and Suman Vodnala
Journal for ImmunoTherapy of Cancer 11 (Suppl 1), 2023, 2023 [Google Scholar]

370 The Epi-RTM technology produces a polyclonal TIL product (LYL845) with a greater expansion success rate across hot and cold tumors, improved product phenotype, and maintenance of TCR diversity
Yogin Patel and Benjamin Harris and Melissa Bedard and Joanna Kritikou and Meritxell Galindo Casas and Carson Harms and Melissa DeFrancesco and Purnima Sundar and Nicholas Restifo and Gary Lee and Shobha Potluri and Suman Kumar Vodnala
Journal for ImmunoTherapy of Cancer 10 (Suppl 2), 2022, 2022 [Google Scholar]

340 The Epi-RTM technology produces a polyclonal TIL product (LYL845) with diverse tumor-reactive clones that have stem-like qualities and anti-tumor function
Benjamin Harris and Yogin Patel and Ngoc-Han Ha and Lora Zhao and Sheila Lou and Stefan Siebert and Emily Fu-Sum and Rigel Kishton and Purnima Sundar and Suman Kumar Vodnala and Shobha Potluri
Journal for ImmunoTherapy of Cancer 10 (Suppl 2), 2022, 2022 [Google Scholar]

Single-cell RNA sequencing of developing maize ears facilitates functional analysis and trait candidate gene discovery
Xiaosa Xu and Megan Crow and Brian R Rice and Forrest Li and Benjamin Harris and Lei Liu and Edgar Demesa-Arevalo and Zefu Lu and Liya Wang and Nathan Fox and Xiaofei Wang and Jorg Drenkow and Anding Luo and Si Nian Char and Bing Yang and Anne W Sylvester and Thomas R Gingeras and Robert J Schmitz and Doreen Ware and Alexander E Lipka and Jesse Gillis and David Jackson
Developmental Cell, 2021 [Google Scholar]

Single-cell co-expression analysis reveals that transcriptional modules are shared across cell types in the brain
Benjamin D. Harris and Megan Crow and Stephan Fischer and Jesse Gillis
Cell systems, 2021 [Google Scholar]

Scaling up reproducible research for single-cell transcriptomics using MetaNeighbor
Stephan Fischer and Megan Crow and Benjamin D. Harris and Jesse Gillis
Nature Protocols 16 (8), 4031-4067, 2021, 2021 [Google Scholar]

A meta-analytic single-cell atlas of mouse bone marrow hematopoietic development
Benjamin D. Harris and John Lee and Jesse Gillis
BioRxiv, 2021 [Google Scholar]

Atlas level scRNAseq analysis reveals the functional landscape of cell types
Benjamin D. Harris
Cold Spring Harbor Laboratory, 2021, 2021 [Google Scholar]

A central role for R7bp in the regulation of itch sensation
Mritunjay Pandey and Jian-Hua Zhang and Santosh K Mishra and Poorni R Adikaram and Benjamin Harris and John F Kahler and Anna Loshakov and Roxanne Sholevar and Allison Genis and Claire Kittock and Juraj Kabat and Sundar Ganesan and Richard R Neubig and Mark A Hoon and William F Simonds
Pain, 2017 [Google Scholar]

Ten simple rules for getting the most out of a summer laboratory internship
Toby P Aicher and Dániel L Barabási and Benjamin D. Harris and Ajay Nadig and Kaitlin L Williams
PLOS Computational Biology 13 (8), e1005606, 2017, 2017 [Google Scholar]

Improving the specificity and efficacy of CRISPR/CAS9 and gRNA through target specific DNA reporter
Jian-Hua Zhang and Mritunjay Pandey and John F Kahler and Anna Loshakov and Benjamin Harris and Pradeep K Dagur and Yin-Yuan Mo and William F Simonds
Journal of biotechnology, 2014 [Google Scholar]

Utilizing Stim-RTM Technology to Reduce Irradiated Feeder Cell Use in the Tumor Infiltrating Lymphocyte Culture Process
Riley Allen and Jason Duecker and Jessica Ojeda and Benjamin Harris and Mikayla Min and Samantha Chan and Christina Ta and Emily Fu-Sum and Purnima Sundar and Yogin Patel and Aileen Li and Shobha Potluri and Suman Vodnala and Gary Lee and Alexander Cheung
, [Google Scholar]

Software

Python MetaNeighbor : a method to rapidly assess cell type identity using both functional and random gene sets
Github : pyMN

Teaching

Summer 2021 CSHL Intern Python Programming Course

I contributed 3 lectures to the 10 lecture course, linked below
Lecture 3: Pandas
Lecture 5: Pandas 2 + Statistics
Lecture 6: Genomics

I co-organize a seminar series in the CSHL quantiative biology department called "Practical Programming"
The seminars have been on topics including
Multiprocessing multithreading and vectorization
Style and Organization in Python
Elzar Batch System Usage
Snakemake
Python packages
Optimizing for performance/speed (matlab, python)
Github workflow
Unit Testing
Personal Web dev

I taught the Multiprocessing multithreading and vectorization lecture.
The materials are in this repository

Misc

In my free time you can find me in nature...