Chen Li
Bioinformatics Scientist
Palo Alto, California, United States
Summary
👤
Senior🎓
Top SchoolChen Li is a bioinformatics scientist with 8 years of experience translating single-cell multi-omic data into mechanistic insights about gene regulation. With a Ph.D. in Computational Medicine & Bioinformatics from the University of Michigan, Chen developed ODE- and deep learning–based dynamical models and a cVAE RNA velocity framework that improve cell fate prediction and enable in silico perturbation analysis across many tissues. He pairs method development with practical engineering, building scalable Nextflow and Snakemake pipelines and applying them to real-world problems such as discovering HIV integration events from mixed human/HIV read mapping. Skilled in Python, R, PyTorch, and modern ML tooling, he bridges computational and experimental teams to turn complex datasets into testable biological stories. Notably, his work quantifies time lags between chromatin accessibility and transcription and produces Bayesian tests for dynamic gene properties, revealing temporal regulatory patterns where transcription factor expression often precedes motif accessibility. Now based in Palo Alto and working at Boston Children’s Hospital, he focuses on reproducible, impactful bioinformatics that drives biological discovery.
8 years of coding experience
6 years of employment as a software developer
Doctor of Philosophy - PhD, Doctor of Philosophy - PhD at University of MichiganUniversity of California, San DiegoAssociate of Arts, Natural Sciences, Associate of Arts, Natural Sciences at Pasadena City CollegeDoctor of Philosophy, Medicine, Doctor of Philosophy, Medicine at University of Michigan - Ann Arbor
Github Skills (61)
package-management10
conda10
bioinformatics10
bioconda10
rna-velocity9
fan-control9
rna-seq8
cran8
transcriptomics8
infer8
meta-analysis8
gene-expression8
seq8
issue-tracking8
r-package7
Programming languages (10)
Github contributions (5)
welch-lab/MultiVelo
Dec 2021 - Oct 2022
Contributions:58 commits, 38 pushes, 54 comments in 10 months
danielee0707/VeloVAE
Jul 2022 - Apr 2023
Deep Generative Modeling of RNA Velocity
Contributions:6 pushes in 8 months
rna-velocitygenerative-modelinggenerativemodelingvelocity
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