Haiyan Huang, PhD

 

 

 

 

 

Assistant Professor
Department of Statistics

Interdepartmental Group in Biostatistics

Graduate Group in Computational and Genomic Biology.

University of California, Berkeley

CA, 94720, USA

 

Tel: (510)642-6433

Fax: (510)642-7892

Email: hhuang

AT stat DOT berkeley DOT edu

 

 

Research

[Web version]

 

CV

 [download]

 

 

 

Job Openings:

Applicants are invited for a two-year postdoctoral position to work on computational biology / bioinformatics, particularly on large-scale integrative analysis of genomic data and metadata.  Interested candidates possessing a Ph.D. in related field (physical sciences or biology), with a strong computer programming and quantitative background or computational genomics experiences should forward their CV, selected reprints, a statement of research interests and goals (2-3 pages), and the contact information (phone, email, address) for three references to:  hhuang ((AT)) stat ((DOT)) berkeley ((DOT)) edu

 

 

 

Group Meetings

 

 

Time and Location are subject to change

 

l       ENCODE project (with P. Bickel group)

Time: Friday, 10am-12pm

Location: 443 Evans Hall

Please contact Qunhua Li (qli) for time and location changes

l       Gene functional relationships, pathways, networks; Translational Bioinformatics

Time: Friday, 2pm-4pm

Location: 1011 Evans Hall

Please contact Daisy Huang (yanhuang) for time and location changes

 

 

People

 

Graduate Students:

l       Daisy Yan Huang (Mar 2008 – present)

l       Kyungpil Kim (Aug 2008 – present)

l       Ling Meng (Master, Dec 2008 – present)

l       Qinghui Gao (Visiting student, Nov 2008 – Oct 2009)

 

Post-docs

l       Qunhua Li (joint with Professor Peter Bickel, Sept 2008 – present)

l       Ci-Ren Jiang (Sept 2009 – present)

 

Former Graduate Students:

l       Siew-leng Melinda Teng, PhD, 2007 Summer

Thesis Title: Statistical methods in integrative analysis of gene expression data with applications to biological pathways

Current Position: Statistician, Genentech, Inc.

l       Na Xu, PhD, 2008 summer (co-advised with Prof. Peter Bickel)

Thesis Title: Transcriptome Detection by Multiple RNA Tiling Array Analysis and Identifying Functional Conserved Non-coding Elements by Statistical Testing

Current position: statistician, Genentech, Inc.

l       Hua Chen, Master 2008

Thesis Title: Bayesian Method for Multi-Loci Association Study of Human Disease

Current Position: Research fellow, Harvard University

 

Major Collaborators:

l       Peter Bickel, Statistics Department, UC Berkeley

l       Xianghong Zhou, Computational and Molecular Biology, USC

l       Lewis Feldman, Plant & Microbial Biology, UC Berkeley

l       Li Cai, Biomedical Engineering, Rutgers University

l       Lydia Sohn, Mechanical Engineering, UC Berkeley

 

 

 

Teaching

 

Undergraduate courses:

STAT 152: Survey Sampling (Fall 2003, Fall 2004, Fall 2005, Fall 2006)

BIOE/STAT C141: Statistics for Bioinformatics (Spring 2004, Spring 2005, Spring 2006, Spring 2007, Spring 2008)

STAT 131A: Statistical Inferences for Social and Life Scientists (Spring 2009)

STAT 157: Seminar on Topics in Probability and Statistics (Fall 2009: class materials can be found at bspace)

 

Master courses:

    STAT 200B: Introduction to Probability and Statistics at an Advanced Level (Spring 2006, Spring 2007)

 

PhD courses:

    STAT 210A: Theoretical Statistics (Fall 2008, Fall 2009: class materials can be found at bspace)

    STAT 246: Statistical Genetics (co-teaching with Prof. Sandrine Dudoit in Biostatistics)

 

Seminars: Tuesday Statistics Colloquium

 

 

Publications

 

  1. Bickel PJ, Boley N, Brown JB, Huang H, Zhang NR (2009). Non Parametric Methods for Genomic Inference. Annals of Applied Statistics.  Accepted with minor revision.

*authors ordered alphabetically

  1. Jiang K, Zhu T, Huang H, Feldman L (2009). The Maize Root Stem Cell Niche: A partnership between two transcriptionally distinct stem cell Populations. Planta. In press.
  2. Bickel P, Brown B, Huang H, Li Q (2009). An overview of recent developments in genomics and associated statistical methods. Philosophical Transactions of the Royal Society A. In press.

*authors ordered alphabetically

  1. Teng S, Huang H* (2009). A statistical framework to infer functional gene associations from multiple biologically interrelated microarray experiments. Journal of the American Statistical Association, June 2009, Vol. 104, No. 486. [Paper Link]

*work with PhD student

  1. Wang F, Jiang T, Sun Z, Teng SL, Luo X, Zhu Z, Zang Y, Zhang H, Yue W, Hong N, Huang H, Blumberg H, Zhang, D (2009). Neuregulin 1 genetic variation and anterior cingulum integrity in patients with schizophrenia and healthy controls. Journal of Psychiatry & Neuroscience, 2009 May;34(3):181-6. [Paper Link]
  2. Liu C, Hu J, Kalakrishnan M, Huang H*, Zhou XJ* (2009) Integrative disease classification based on cross-platform microarray Data. BMC Bioinformatics, 2009 Jan;10 Suppl 1:S25. [Paper Link]

*co-corresponding authors

  1. Carbonaro A, Mohanty SK, Huang H, Godley LA and Sohn LL (2008) Cell characterization using a protein-functionalized Pore. Lab Chip, 8(9):1478-85. [Paper Link]
  2. Huang H, Cai L, Wong WH. (2008) Clustering analysis of SAGE transcription profiles using a Poisson approach. Methods Mol Biol. 2008; 387:185-98. (Book Chapter) [Paper Link]
  3. Huang Y, Li H, Hu H, Yan X, Waterman MS, Huang H, Zhou XJ (2007). Systematic discovery of functional modules and context-specific functional annotation of human genome. Bioinformatics, 23(13):i222-i229. [Paper Link]
  4. ENCODE Consortium (2007).  Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature. 447, 799-816. [Paper Link]
  5. Kim K, Zhang S, Jiang K, Cai L, Lee IB, Feldman LJ, Huang H* (2007). Measuring similarities between gene expression profiles through data transformations. BMC Bioinformatics, 8:29 (highly accessed paper). [Paper Link]

*corresponding author; work with graduate student

  1. Jiang K, Zhang S, Lee S, Tsai G, Kim K, Huang H, Zhu T, Feldman LJ (2006). Transcription profile analyses identify genes and pathways central to root cap functions in Maize. Plant Molecular Biology, 60(3):343-63. [Paper Link]
  2. Huang H, Kim K (2006). Unsupervised clustering analysis of gene expression, Chance, vol. 19, No.3. [Paper Link]
  3. Zhou XJ, Kao MJ, Huang H, Wong A, Nunez-Iglesias J, Aparicio OM, Morgan TE, Wong WH (2005). Functional annotation and network reconstruction through cross-platform integration of microarray data. Nature Biotechnology, 23(2):238-43. [Paper Link]
  4. Zhao X, Huang H, Speed T (2005). Finding short DNA motifs using permuted Markov models. Journal of Computational Biology, 12(6): 894-906 (journal version of the 2004 RECOMB paper; numbered as 16 below) [Paper Link]
  5. Huang H, Kao MJ, Zhou X, Liu JS, Wong WH (2004). Determination of local statistical significance of patterns in Markov sequences with application to promoter element identification.” Journal of Computational Biology, 11(1):1-14. [Paper Link]
  6. Cai L*, Huang H*, Blackshaw S, Liu JS, Cepko CL, Wong WH (2004). Clustering analysis of SAGE data using a Poisson approach. Genome Biology, 5(7):R51. [Paper Link]

*Joint first authors

  1. Zhao X, Huang H, Speed T (2004). Finding short DNA motifs using permuted Markov models. Proceedings of RECOMB 2004. [Paper Link]
  2. Blackshaw S, Harpavat S, Trimarchi J, Cai L, Huang H, Kuo W, Fraioli R, Cho S, Yung R, Asch E, Wong WH, Cepko CL (2004). Genomic analysis of mouse retinal development. PLoS Biol, 2(9):E247. [Paper Link]
  3. Allinen M, Beroukhim R, Cai L, Brennan C, Domenici CJ, Huang H, Porter D, Hu M, Chin L, Richardson A, Schnitt S, Sellers W, Polyak K (2004). Molecular characterization of the tumor microenvironment in breast cancer. Cancer Cell, 6(1):17-32. [Paper Link]
  4. Lippert RA, Huang H, Waterman MS (2002). Distributional regimes for the number of k-word matches between two random sequences. Proc Natl Acad Sci. USA, 99(22):13980-9. [Paper Link]
  5. Huang H (2002). Error bounds on multivariate normal approximations for word count statistics. Advances in Applied Probability, 34(3): 559-586.  [Paper Link]

 

 

Books Edited

 

  1.  “Research in Computational Molecular Biology” (11th Annual International Conference, RECOMB 2007), edited by Terry Speed and Haiyan Huang, Published by Springer. [Book Link]

 

 

Articles Submitted

 

  1. Huang H, Liu C, Zhou XJ (2009). A bayesian probabilistic approach toward transforming public microarray repositories into disease diagnosis databases, submitted. 
  2. Na Xu, Bickel PJ, Huang H (2009). Semi-parametric methods for multiple RNA tiling array analysis, submitted.

 

Manuscripts in Preparation

 

  1. Brown JB, Kechris KJ, Poulin F, Xu N, Bickel PJ, Huang H. Classification of  Transcriptional Function in Human Conserved Non-Coding Elements.

 

 

 

News & Events

 

I am the Local Activity Committee Chair for the ICSA 2009 Applied Statistics Symposium to be held on June 21-24 in San Francisco, California, USA. Here is the link for the symposium:  http://icsa2.org/2009/

 

I am the IMS Program Chair for the 2009 WNAR/IMS annual meeting to be held on June 14-17 at Portland State University.  Here is the link for the meeting:  http://www.mth.pdx.edu/wnar