Yu S. Huang

Before joining SIMM as PI, I had >10 years of experience in genomic big-data algorithm development and analysis, database and web portal development. In 2010, I obtained my Ph.D. in Bioinformatics from the computational biology department founded by Prof. Michael Waterman at USC. My main expertise is in statistics, algorithms, machine learning, and population genetics.
At Illumina Inc., I was the main developer behind the BaseSpace App, MethylSeq, which is the bioinformatics solution to discover methylated cytosines in DNA from bisulfite treated next-gen sequencing data. I was also the bioinformatician in various projects involving cancer, forensics, exome, whole-genome sequencing. During my PostDoc for the 1000-vervet genomics project, I was the bioinformatics lead in creating the first non-human primate population genomics resource and subsequent trait mapping in a complex pedigree. The first non-human GWAS from my Ph.D. was published in Nature, 2010. Up until early 2015, I have published over 15 publications (4 first-author), accumulating over 1800 citations, h-index=13.
Email me at yuhuang at simm.ac.cn

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

Work Experience
2015.05 –  Professor, 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

  • Pharmacogenomics
  • Personalized medicine

Awards & Honors

  • 2016 国家青年千人计划
  • 2015 中国科学院百人计划
  • 2003-2008 USC Graduate School Merit Award
  • 1999-2003 People’s Scholarship, Fudan University
  • 2000 Computer Programming Contest, Fudan University,  3rd Award


  • 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

  1. YS Huang, V Ramensky, et al., Nelson Freimer (2015) Sequencing strategies and characterization of 721 vervet monkey genomes for future genetic analyses of medically relevant traits. BMC Biology (http://www.biomedcentral.com/1741-7007/13/41/abstract
  2. MW Horton, AM Hancock*, YS Huang*, C Toomajian*, S Atwell, A Auton, NW Muliyati, A Platt, FG Sperone, BJ Vilhjálmsson, M Nordborg, JO Borevitz, J Bergelson (2012): Genome-wide patterns of genetic variation in worldwide Arabidopsis thalianaaccessions from the RegMap panel. Nature Genetics 116 citations.
  3. YS Huang#, M Horton, BJ Vilhjálmsson, Ü Seren, D Meng, C Meyer, MA Amer, JO Borevitz, J Bergelson, M Nordborg (2011): Analysis and visualization of Arabidopsis thaliana GWAS using web 2.0 technologies. http://arabidopsis.usc.edu/ Database 2011; (#: corresponding author) 9 citations.
  4. S Atwell*, YS Huang*, BJ Vilhjálmsson*, G Willems*, M Horton, Y Li, D Meng, A Platt, A Tarone, TT. Hu, R Jiang, NW Muliyati, X Zhang, MAi Amer, I Baxter, B Brachi, J Chory, C Dean, M Debieu, J de Meaux, JR Ecker, N Faure, JM Kniskern, JD Jones, T Michael, A Nemri, F Roux, DE Salt, C Tang, M Todesco, MB Traw, D Weigel, P Marjoram, JO Borevitz, J Bergelson, M Nordborg (2010): Genome-wide association study of 107 phenotypes in a common set of Arabidopsis thaliana inbred lines. Nature (*: equal contribution.)  577 citations.
  5. A Platt, M Horton*, YS Huang*, Y Li*, A Anastasio, NW Mulyati, J Ågren, O Bossdorf, D Byers, K Donohue, M Dunning, E Holub, A Hudson, V Le Corre, O Loudet, F Roux, N Warthmann, D Weigel, L Rivero, R Scholl, M Nordborg, J Bergelson, JO. Borevitz (2010): The Scale of Population Structure in Arabidopsis thaliana. Plos Genetics (*: equal contribution.) 144 citations.
  6. Y Huang*, H Li*, H Hu, X Yan, MS. Waterman, H Huang and XJ Zhou (2007): Systematic discovery of functional modules and context-specific functional annotation of human genome. Bioinformatics (ISMB 2007) 23:i222-229. (*: equal contribution.) 62 citations