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.

Publications

A Meta-Analytic Single-Cell Atlas of Mouse Bone Marrow Hematopoietic Development
Benjamin D. Harris, John Lee, and Jesse Gillis.
BioRxiv, 2021 doi: 10.1101/2021.08.12.456098

Single-cell co-expression analysis reveals that transcriptional modules are shared across cell types in the brain.
Benjamin D. Harris, Megan Crow, Stephan Fischer, and Jesse Gillis.
Cell Systems, 2021 doi: 10.1016/j.cels.2021.04.010

Scaling up reproducible research for single cell transcriptomics using MetaNeighbor.
Stephan Fischer, Megan Crow, Benjamin D. Harris, and Jesse Gillis.
Nature Protocols, 2021 doi: 10.1038/s41596-021-00575-5

Single-cell RNA sequencing of developing maize ears facilitates functional analysis and trait candidate gene discovery.
Xiaosa Xu, Megan Crow, Brian R. Rice, Forrest Li, Benjamin D. Harris ..., Jesse Gillis, and David Jackson.
Developmental Cell, 2021 doi: 10.1016/j.devcel.2020.12.015

Ten simple rules for getting the most out of a summer laboratory internship
Toby P. Aicher, Dániel L. Barabási, Benjamin D. Harris, Ajay Nadig, Kaitlin L. Williams
Plos Computational Biology 2017, doi: 10.1371/journal.pcbi.1005606

A central role for R7bp in the regulation of itch sensation
Mritunjay Pandey, Jian-Hua Zhang, Santosh K. Mishra, Poorni R. Adikaram, Benjamin Harris...William F. Simonds
Pain, 2017 doi:doi: 10.1097/j.pain.0000000000000860

Improving the specificity and efficacy of CRISPR/CAS9 and gRNA through target specific DNA reporter
Jian-Hua Zhang, Mritunjay Pandey, John F. Kahler, Anna Loshakov, Benjamin D. Harris, ..., William F. Simonds
Journal of Biotechnology, 2014 doi: 10.1016/j.jbiotec.2014.08.033

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...