Beifang Niu
Software Engineer at St. Jude Center for Applied Bioinformatics (CAB)
United States, China
Summary
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SeniorBeifang Niu is a senior bioinformatics research scientist with over 20 years of expertise in bioinformatics and high-performance computing, now focused on pediatric cancer at St. Jude Children’s Research Hospital. He has an extensive publication impact (>80 papers, ~40,000 citations) and is the principal developer of widely used tools such as MSIsensor and HotSpot3D, reflecting a rare blend of algorithmic rigor and production-grade software. His work spans cancer genomics, omics-driven neoepitope discovery, and ML/DL models applied to pathology and whole-slide imaging, built on a PhD in high-performance and parallel computing. Previously he led a research group at CNIC, mentored students, and created scalable pipelines from his time at Washington University and UC San Diego, where he contributed to CD-HIT and metagenomics tools. Known among peers for translating HPC techniques into practical bioinformatics software, he combines deep systems-level skill with hands-on programming and pipeline engineering.
13 years of coding experience
Github Skills (23)
pymol10
cancer-genomics10
perl10
uniprot10
genomes10
normal10
hotspot10
protein-structure10
genomics10
clustering10
blat10
3d9
bioinformatics9
conda6
bioconda5
Programming languages (7)
Github contributions (5)
ding-lab/MuSiC2
Sep 2013 - Dec 2018
identifying mutational significance in cancer genomes
Contributions:51 commits, 6 PRs, 31 pushes in 5 years 3 months
bioinformaticsgenomesgenomicscancersmg
niu-lab/msisensor2
Aug 2019 - Nov 2019
Microsatellite instability (MSI) detection for tumor only data.
Contributions:19 commits, 10 PRs, 29 pushes in 2 months
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