Faculty
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Faculty and Staff
Academicians
Faculty and Staff
 
Name:
Huang Yu
Education:
Ph.D

Positions:
Principal Investigator
Academic title:
Professor
Phone:
021-50806600
Fax:
E-mail:
yuhuang@simm.ac.cn
Personal Website:
http://www.yfish.org/
Postal Code:
201203
Mailing Address:
501 Haike Road, Pudong, Shanghai, China
Resume:

Resume:
  Our research theme at SIMM is pharmacogenomics and personalized medicine. In close collaboration with our colleagues, we aim to improve the understanding of inter-individual variation of drug response and facilitate the development of personalized medicine. Equipped with a state of the art genomics laboratory and a high-performance computing cluster consisting of over 1000 CPUs and 500TBs of storage, we collect large-scale drug response and corresponding omics (genome/epignome/transcriptome/proteome) data from clinical trial patients, PDX (patient-derived xenograft), animals and cell lines. We develop or apply (if available) intelligent computational methods to extract information from these large-scale data that can better our understanding of drug response variation, drug resistance and tumor heterogeneity.
  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.
  Team website: http://www.yfish.org/.

EDUCATION:
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 - Shanghai Institute of Material Medica, Principal Investigator
2014.04 - 2015.05 Illumina Inc. San Diego, Bioinformatics Scientist
2010.11 - 2014.04 University of California Los Angeles, PostDoc


Research Directions

1. Pharmacogenomics 
2.
Personalized medicine


Social Titles

Awards & Honors

1.2016 National “1000 Young Talents” program (China)
2.2015 Hundred-talent program of Chinese Academy of Sciences
3.2003-2008 USC Graduate School Merit Award
4.1999-2003 People’s Scholarship, Fudan University
5.2000 Computer Programming Contest, Fudan University,  3rd Award

 


Achievements

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


Grants & Research Projects

Pubilcations

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 thaliana accessions 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 ?gren, 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.