Shuai Wang, Ph.D.

Profile

I am a postdoc in Innovative Genomics Institute, UC berkeley. I focus on developing new computational methods to decifer the microbiome and human genome.

Education

• Ph.D. in Computer Science, City University of Hong Kong (2018 - 2022)
• Bachelor of Biotechnology, Northwestern Polytechnical University (2013 - 2017)
• Exchange Student, National Chung Hsing University (2015)

Work Experience

• Postdoctoral Scholar, UC Berkeley (Nov 2024 - Present)
• Research Scientist, OmicLab Limited / City University of Hong Kong (2022 - 2024)
• Bioinformatics Analyst, Beijing Genomics Institute (BGI) (2017 - 2018)
• Bioinformatics Intern, Beijing Genomics Institute (BGI) (2016 - 2017)

Research Interests

Investigating the interplay between the gut microbiome and human health, with a focus on microbiome and human genome characterization.

Research Projects

• PStrain: Strain profiling method for metagenomic data.
• LocalHGT: Accurate detection of horizontal gene transfer events.
• SpecHLA: Full-resolution HLA typing and LOH event detection.
• PStrain-tracer: Microbial engraftment tracking for FMT.

Selected Publications

• Wang, S. et al., PStrain: an iterative microbial strains profiling algorithm for shotgun metagenomic sequencing data. - Bioinformatics, 2021
• Wang, S. et al., SpecHLA: full-resolution HLA typing from sequencing data. - Cell Reports Methods, 2023
• Wang, S. et al., Enhancing insights into diseases through horizontal gene transfer event detection from gut microbiome. - Nucleic Acids Research, 2024
• Wang, S. et al., SpecImmune accurately genotypes diverse immune-related gene families using long-read data. - Biorxiv, 2025
• Li, Y. et al., Comprehensive human respiratory genome catalogue underlies the high resolution and precision of the respiratory microbiome. - Briefings in Bioinformatics, 2025, (co-first author)
• Wang, C. et al., Donkey genomes provide new insights into domestication and selection for coat color. - Nature communications, 2020

Honors and Awards

• Best Paper Award, ICIBM (2021)
• BGI Outstanding Talent Scholarship (2017)

Developed Software

• LocalHGT - HGT event detection
• PStrain - Strain profiling
• SpecHLA - HLA typing
• SpecImmune - Immune gene typing from long reads
• PStrain-tracer - Microbial tracking

Patents

• Method for determining SNP loci in microbial communities (Patent No. CN108504750B, 2018)
• Set of STR loci for Pandas (Patent No. CN110643713A, 2018)

Programming Languages

Python, C++, Perl, R, Linux, Shell, LaTeX

Hobbies

Enjoy movies, historical books, fictions, hiking, and nature.