Shuai Wang, Ph.D.

Profile

I am a postdoctoral scholar at the Innovative Genomics Institute, University of California, Berkeley. I received my Ph.D. in Computer Science from the City University of Hong Kong, where I developed computational methods for strain-level microbiota characterization, and my B.Sc. in Biotechnology from Northwestern Polytechnical University. My research integrates computer science and microbiology to study epigenomic signaling in microbial communities and to advance microbiome engineering—by establishing MGE–host linkages and mitigating host immune barriers in phage delivery.

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.