Yupeng He
Director, Bioinformatics
San Francisco, California, United States
Summary
👤
Senior🎓
Top SchoolYupeng He is a Director of Bioinformatics based in San Francisco with 11 years of experience applying machine learning to large-scale genomics and epigenomics datasets. He has advanced through technical and leadership roles at Guardant Health, driving teams that translate complex methylation and chromatin data into clinically relevant insights. His academic work at the Salk Institute includes co-developing a widely used end-to-end DNA methylation pipeline (methylpy) and contributing to high-impact consortium projects such as the Roadmap Epigenome effort. He combines strong computational skills (random forest, CRF, predictive modeling) with practical product-minded execution, moving methods from prototype to pipelines used across many publications. Notably, he has repeatedly improved enhancer and biomarker discovery accuracy and led cross-disciplinary projects that bridge single-cell epigenomics and clinical genomics.
11 years of coding experience
8 years of employment as a software developer
University of California, San DiegoB.S. Biotechnology with Minor in Applied Mathematics, B.S. Biotechnology with Minor in Applied Mathematics at Shanghai Jiao Tong University
English, Chinese
Github Skills (29)
seq10
structural-variation10
pairwise9
sequence-alignment9
data-processing9
bioinformatics9
genomics9
ncbi7
treeview7
pathogen6
probabilistic6
tree-structure6
phylogenetics5
sequencing5
python5
Programming languages (7)
Github contributions (5)
yupenghe/REPTILE
Jun 2016 - Jul 2018
Contributions:3 releases, 37 commits, 36 pushes in 2 years 1 month
yupenghe/methylpy
Jun 2016 - Jul 2021
WGBS/NOMe-seq Data Processing & Differential Methylation Analysis
Contributions:17 releases, 252 commits, 5 PRs in 5 years 1 month
wgbsnomedata-processingseqdifferential
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