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Yu Huang

   Yu (黄宇) has been a Principal Investigator at SIMM (中国科学院上海药物研究所) since 2015.

My team interest is developing fast and accurate AI models, algorithms, distributed computing platforms, and databases for bioinformatics in personalized medicine, drug design, and virtual screening, as well as developing big-data algorithms, analysis tools, databases, and web portals. In 2010, I obtained my Ph.D. in Bioinformatics from the computational biology department at USC, co-advised by Michael Waterman and Magnus Nordborg. My main expertise is in statistics, algorithms, machine learning, and population genetics.

   Previously at Illumina Inc., I was the main developer behind the BaseSpace App, MethylSeq, which is the bioinformatics cloud software to detect methylated cytosines in DNA from bisulfite treated next-gen sequencing data. I was also the lead bioinformatician in inter-disciplinary company projects involving cancer, forensics, exome, whole-genome sequencing. I did a three-and-a-half-year PostDoc with Prof. Nelson Freimer at Human Genetics, UCLA (Nov 2010-Mar 2014), working on population genetics and trait mapping (pedigree or population) in vervet monkeys, analyzing the whole-genome DNA sequences from >700 monkeys of a vervet pedigree and >100 wild population monkeys. In Oct 2010, I completed my PhD in Computational Biology and Bioinformatics at USC, working primarily on association mapping and population genetics of Arabidopsis thaliana, under the supervision of Magnus Nordborg. Before pursuing my PhD under Magnus, I had worked on the topic of gene function/network inference from gene expression data through graph theory. In July 2003, I received B.S. of Biology from Fudan University. During my undergraduate, with lots of free time on hand (as expected for a college student), I learnt C/C++, PostgreSQL DB, Python, and Linux network administrations on the side. I have been fascinated with computers ever since I played with an Intel-8088 PC in my 8th grade.

Email: polyactis at



2003.08 - 2010.10 University of Southern California, Los Angeles, Ph.D. in Bioinformatics

1999.09 - 2003.07 Fudan University, Shanghai, B.S. in Biological Sciences

1996.09 - 1999.07 Shanghai Chuansha Senior High School


2022.01 - Senior Director of Bioinformatics, Genecast Corp Ltd.

2015.05 - (on leave) Professor, PI, Director of Bioinformatics, Shanghai Institute of Material Medica

2014.04 - 2015.05 Bioinformatics Scientist, Illumina Inc. San Diego

2010.11 - 2014.04 PostDoc, University of California Los Angeles

Research Directions

  • AI models, algorithms, distributed computing
  • Statistical models and algorithms in personalized medicine
  • Big-data analytical platforms

Awards & Honours

  • 2016 国家高层次人才引进计划A
  • 2015 国家高层次人才引进计划B
  • 2003-2008 USC Graduate School Merit Award
  • 1999-2003 People’s Scholarship, Fudan University
  • 2000 Computer Programming Contest, Fudan University,  3rd Award
  • 1999 National High-School Mathematics Contest, 3rd Award

Notable works

  • The first non-human primate (vervet monkeys) population genomic resource and trait mapping in complex pedigrees (>700 members).
  • DNA-methylation BaseSpace App at Illumina Inc.
  • The first non-human Genome Wide Association Studies (GWAS), Nature, 2010
  • Selected Publications


  • Surf, Snowboard, Swim

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