Dongze He
Computational Scientist
San Diego, California, United States
Summary
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Rockstar🎓
Top SchoolDongze He is a computational scientist with 8 years of experience at the intersection of wet-lab biology and production-grade computational engineering, currently building end-to-end AWS+Nextflow multi-omics platforms at Altos Labs. He designs efficient algorithms and user-friendly tools in Rust, R, and Python, and has driven impactful open-source work such as the alevin-fry/simpleaf ecosystem for single-cell and multi-omics processing. His research contributions include the first statistical model to resolve splicing-status ambiguity in scRNA-seq and novel causal inference frameworks that revealed aging-related biomarkers across genomic and proteomic layers. Dongze pairs deep domain knowledge in biology and statistics with practical ML and software engineering—evidenced by deployable Nextflow pipelines, RShiny AI-assisted dashboards, and collaborations with global research teams. He brings a track record of turning complex sequencing artifacts into interpretable insights and production tools that accelerate biological discovery.
8 years of coding experience
7 years of employment as a software developer
Bachelor's degree, Biotechnology, Bachelor's degree, Biotechnology at Huaqiao UniversityMaster's degree, Systems biology and Bioinformatics, Master's degree, Systems biology and Bioinformatics at Case Western Reserve University School of MedicineDoctor of Philosophy - PhD, Computational Biology, Doctor of Philosophy - PhD, Computational Biology at University of Maryland
Stackoverflow
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Github Skills (88)
seq10
gene-expression10
transcript10
bioconductor10
genomics10
nf-core10
kallisto10
in-progress10
nextflow10
pipeline10
rna-seq10
bioinformatics10
singularity9
reproducible-science9
slurm9
Programming languages (11)
Github contributions (5)
COMBINE-lab/usefulaf
May 2021 - Oct 2022
Useful scripts and tools related to alevin-fry
Contributions:59 commits, 4 PRs, 48 pushes in 1 year 5 months
tuplescriptscriptingperl5alevin-fry
COMBINE-lab/pyroe
Mar 2022 - Feb 2023
Contributions:97 commits, 29 PRs, 55 pushes in 11 months
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