Shanghai Institute of Material Medical Chinese Academy of Sciences

Biography

Our research theme is to develop bioinformatics algorithms and models and discover patterns from big-scale bioinformatics data. 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 Materia 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.Bioinformatics algorithms and statistical models

2.Large-scale bioinformatics data mining

Grants & Research Projects

1.Drug biomarker discovery in patients, PDX, and cell lines.

2.Computational method development for drug biomarker discovery, patient stratification, risk prediction.

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.

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Social Titles

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Awards & Honors

2003-2008 USC Graduate School Merit Award

1999-2003 People’s Scholarship, Fudan University
2000 Computer Programming Contest, Fudan University, 3^rd Award

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Pubilcations

Full Publication List

Selected Publications

1.Z Luo*, X Fan*, Y Su, YS Huang# (2018) Accurity: accurate tumor purity and ploidy inference from tumor-normal WGS data by jointly modelling somatic copy number alterations and heterozygous germline single-nucleotide-variants. Bioinformatics

2.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

3.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

4.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. Database

5.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

6.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

7.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)

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