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Haiyan
Huang, PhD
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Assistant Professor Interdepartmental Group in Biostatistics Graduate Group in Computational
and Genomic Biology. CA, 94720, Tel:
(510)642-6433 Fax:
(510)642-7892 Email: hhuang AT stat DOT Berkeley DOT edu |
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Teaching
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Research interestsDevelopment and application of mathematical/statistical methods for problems associated with various biological systems and data 1. Biological sequence analysis 2. Identification of transcription factor binding sites 3. Microarray/SAGE data analysis 4. Sequence weighting Methods 5. Interaction/regulatory networks 6. Comparative Genomics PeopleGraduate Students: l Na Xu (PhD candidate, Statistics, co-advised by Professor Peter Bickel) Current Project: Affymetrix RNA tiling array data analysis l Peter Dimitrov (PhD candidate, Biostatistics Program) Current Project: Statistical Methods for Analyzing Array Comparative Genomic Hybridization Data (working with Dr. Jane Fridlyand, UCSF) l
Jing Zhou (visiting
student, l
Kyungpil Kim
(visiting student, Research Topic: Clustering and Classification Methods with Application to Biological Data Post-doc l Juli Atherton (joint with Professor Peter Bickel) 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.
Major Collaborators: l Peter Bickel, Statistics Department, UC Berkeley l Bin Yu, Statistics Department, UC Berkeley l Lewis Feldman, Plant Molecular Biology, UC Berkeley l
l Yishi Jin,
Molecular Biology, UC Santa Cruz l Xianghong Zhou, Department of Computational and Molecular Biology, USC |
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Publications1. Carbonaro A, Huang H, Godley LA and Sohn LL “Multiparametric
Approach to Cell-Based Assays Using Protein-Functionalized Pores,” submitted 2. Brown JB, Kechris KJ, Poulin F, Xu N, Bickel PJ, Huang H “Classification of Transcriptional Function in
Human Conserved Non-Coding Elements,” submitted 3. Jiang K, Zhu T, Huang H, Feldman L “Maize Root Stem Cell Niche: A Partnership Between Two Transcriptionally Distinct Stem Cell Populations,” submitted 4. Wang F, Jiang T, Pan B, Sun Z, Teng S, Zhu Z, Gong G, Zang Y, Zhang H, Yue W, Hong N, Huang H, Blumberg H, Zhang, D “Neuregulin 1 Genetic Variation and anterior cingulum integrity in schizophrenia and in health,” Submitted 5.
Teng S, Zhou XJ, Huang H “A statistical framework to infer functional gene associations across multiple biologically related microarray experiments,” JASA, accepted. 6. Huang H, Cai L, Wong WH Clustering Analysis of SAGE transcription profiles using a Poisson Approach, chapter 14 of “Methods in Molecular Biology”, Humana Press Inc. 7. 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 (ISMB 2007), 23(13):i222-i229. 8. ENCODE Consortium (2007). “Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project” Nature. 447, 799-816. 9. Kim K, Jiang K, Zhang S, Cai L, Lee IB, Feldman LJ, Huang H (2007) “Measuring Similarities between Gene Expression Profiles through New Data Transformations” BMC Bioinformatics, 2007, 8:29 (27Jan2007) [link] 10.Huang H, Kim K (2006) “Unsupervised clustering analysis of gene expression”, Chance, vol. 19, No.3 / summer 2006. 11.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, 2006 60(3):343-63. 12.Zhou XJ, Kao MJ, Huang H, Wong A, Nunez-Iglesias J, Primig M, Aparicio OM, Finch CE, Morgan TE, Wong WH (2005) “Integrating Cross-Platform Microarray
Data by Second-order Analysis: Functional Annotation and Network Reconstruction” Nature
Biotechnology. 2005 Feb;23(2):238-43. 13.Zhao X, Huang H, Speed TP (2005) “Finding Short DNA Motifs Using Permuted Markov Models” Journal of Computational Biology (RECOMB2005), Jul 2005, Vol. 12, No. 6: 894-906 14.Li Cai*, Haiyan Huang*, Seth Blackshaw, Jun S. Liu, Connie L Cepko, Wing H Wong (2004) “Clustering analysis of SAGE data using a Poisson approach” Genome Biology, 2004;5(7):R51. *Joint first authors 15.Allinen1 M, Beroukhim R, Cai L, Brennan C, Domenici JL, 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, 2004 Jul;6(1):17-32. 16.Haiyan
Huang, Ming-Chih J. Kao, Xianghong
Zhou, Jun “Determination
of local statistical significance of patterns in Markov sequences with
application to promoter element identification” Journal of
Computational Biology, 2004 Vol 11, No 1. 17.Blackshaw S, Harpavat S, Trimarchi J, Cai L, Huang H, Kuo WP, Weber G, Lee K, Fraioli RE, Cho SH, Yung R, Asch E, Ohno-Machado L, Wong WH, Cepko CL. (2004) “Genomic Analysis of Mouse Retinal Development” PLoS Biol. 2004 Jun 29;2(9):E247 [full
text] 18.Ross
A. Lippert, Haiyan Huang, and Michael S.
Waterman (2002) “Distributional regimes for the number of k-word
matches between two random sequences” PNAS
2002 99: 13980-13989 19.Haiyan Huang (2002) “Error Bounds on Multivariate Books Edited20.“Research in Computational Molecular Biology” (11th Annual International Conference, RECOMB 2007), edited by Terry Speed and Haiyan Huang, Published by Springer |
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