Education and Experiences

• July 00 – Present: Professor of Statistics, Dept of Stat, Harvard University.
• Sep 01 – Present: Professor of Biostatistics (secondary), HSPH
• Nov 00 – Nov 02: Guest Professor, Peking University, (see photos here)
• July 03 – Sep 03: Professor (on leave), Dept of Stat, Stanford University
• Sep 00 – Jun 03: Associate Professor (on leave), Dept of Stat, Stanford University.
• Aug 94 – Aug 00: Assistant Professor, Dept of Stat, Stanford University.
• May 96 – Aug 02: Associate Editor, J Amer Statist Assoc
• July 99 – Present: Associate Editor, Statistica Sinica
• Dec 99 – Aug 02: Associate Editor, Biometrics
• Jan 98 – Dec 98: Visiting Faculty, Department of Statistics, UCLA.
• Mar 98 – May 98: Visiting Faculty, Dept. of Math, NUS.
• July 91 – Dec 94: Assistant Professor, Dept. of Stat., Harvard University.
• July 93 – Sep 93: Visiting Faculty, Nat'l Center. Biotech. Info., NIH.
• Sep 88 – Jun 91: Ph.D., Statistics, The University of Chicago.
• Sep 86 – Jun 88: Ph.D program in math,  Rutgers University
• Aug 81 – July 85: B.S. in Math., Peking University, Beijing, China.

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Awards and Honor

• Morningside Gold Metal for Applied Mathematics (晨兴数学奖), 2010. To outstanding mathematicians of Chinese decent under age 45, honored once every 3 years. ICCM 2010.
• Kuwait Lecturer, Cambridge University, 2008
• Fellow, American Statistical Association, 2005
• Bernoulli Lecturer, Bernoulli Society, 2004
• Fellow, Institute of Mathematical Statistics, 2004
• ISI most-cited mathematical scientists 2003
• The 2002 COPSS Presidents' Award. Given annually and jointly by five leading statistical societies in the north America to a young individual (under age 40) in recognition of outstanding contributions to the profession of statistics. See my award acceptance speech and the list of past COPSS Award recipients.
• The 2002 IMS Medallion Lecturer. Each year IMS nominates 8 Medallion lectures (also known as Special Invited Lectures) in fields across the IMS's subject range for presentations in different statistical meetings.
• The 2000 Mitchell Prize for the Best Bayesian Application Paper, 2000.
• Terman Fellow, Stanford University, 1995-1998.
• CAREER AWARD, National Science Foundation, 1995-1998.
• AMS-SIAM selection program winner, Beijing, 1985.

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Research Interests

• Statistical missing data problems, imputation methodology.
• Gibbs sampling and other MCMC methods, rate of convergence.
• Markov structure, graphical models (software BUGS), and genetics.
• Image reconstructions: PET, SPECT, etc.
• Bayesian methodology; Even Bill Gates talks about Bayesian ideas!!
• Nonparametric hierarchical models, model selections and testings.
• Large-scale computation and optimization, e.g., VLSI design; Dynamic systems; Computer vision.
• Monte Carlo filters, Sequential importance sampling and resampling.

Click the button to see an illustration of the SIS filter.

Click on the cover of my new book on Monte Carlo to get a copy from Amazon.com

• Computational Biology. See my collaborator Chip Lawrence's website for a tutorial.     Click the buttons for cartoon pictures of protein structures.

(JASA 1999, 94, 1-15)                      (Protein Sci. 1995, 4, 1618-32)

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Main Collaborators' Websites

• Dr. Rong Chen, Dept. of Info. and Decision Sciences, UIC.
• Dr. Charles E. Lawrence, Wadsworth Center, New York Dept of Health.
• Dr. Andrew Neuwald, Cold Spring Harbor Laboratory.
• Dr. Wing Hung Wong, Depts of Stat. and Biostat., Harvard University

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Computational Biology Softwares

The following downloadable softwares for analyzing biopolymer sequence data, microarray data, gene expression data, literature text data, etc. have been developed in my lab in collaboration with various collaborators. Please cite the related articles if you use them in your research. They are listed chronologically:

• MACAW. A self-extracting Window's software developed jointly with people at NCBI. Search and align a subtly conserved single block-motif among multiple sequences, assuming one occurrence in each sequence. See its companion articles published in Science (Lawrence et al. 1993) and J. Am. Statist. Assoc. (Liu 1994).
• Gibbs Motif Sampler. (Use command "tar -xvf gibbs9_95.tar" after the download.) A UNIX (Sun OS) software to search for multiple motifs with unknown number of repeats in multiple protein sequences. Its companion articles were published in J. Am. Statist. Assoc. (Liu et al. 1995) and Protein Sci. (Neuwald et al 1995). A server of the Motif Sampler for both discovering DNA regulatory binding sites and protein sequence motifs can be accessed from the Wadsworth Lab Bioinformatics Center directed by Dr. Chip Lawrence.
• PROBE. (Use command "tar -xvf probe.tar" after the download.) A UNIX (Sun OS) software tool for block-based multiple protein sequence alignment and for database search to detect remote protein homology. Its companion articles appeared in Nucl. Acid Res. (Neuwald
et al. 1997 ) and J. Am. Statist. Assoc. (Liu et al. 1999)
• Bayesian Aligner. A Bayesian pairwise alignment tool; also called 'Bayesian Phylogenetic Footprint.' Its companion article appeared in Bioinformatics
• BioProspector. An improved web-interactive algorithm for finding gene regulatory binding motifs. See the companion article published in the Proceedings of Pacific Symposium on Biocomputing.
• BLADE v2. Bayesian LinkAge DisEquilibrium mapping algorithm based on Liu et al. (2001) published in Genome Research. This executable program was produced by Dr. Xin Lu with a companion publication Lu, Niu and Liu (2003) in the same journal.
• HAPLOTYPER Users’ Documentation for SNP haplotype reconstruction based on the Partition-Ligation method (Niu et al. 2002) published in Am. J. Hum. Genet.
• PL-EM for SNP haplotype reconstruction based on the Partition-Ligation method and EM Algorithm (Qin et al. 2002) published in Am. J. Hum. Genet.
• EM-DeCODER for SNP haplotype reconstruction (with Z. Qin and T. Niu)
• MDScan. A new, fast, and accurate algorithm for finding protein-DNA interacting sites (gene regulatory binding motifs) from the 5' untranslated sequences selected by Chromatin-immunoprecipitation microarray (ChIP-array) and other microarray experiments. Its companion paper was published in Nature Biotechnology, 2002.
• BMC. A novel Bayesian algorithm for putative motif clustering, see the companion paper published in Nature Biotechnology, 2003.
• Motif Regressor. An efficient algorithm for integrating sequence motif discovery with measures from mRNA expression microarray or Chromatin-Immunoprecipitation microarray (ChIP-chip) experiments. Its companion paper was published in Proc. Nat’l Acad. Sci. USA, 2003. A more user-friendly download site is maintained by Erin Conlon at here.
• GMS-MP: Gibbs Motif Sampler for Paired Correlation Model. See the Zhou & Liu (2004) in Bioinformatics.
• BioOptimizer: A Bayesian scoring method for comparing and optimizing regulatory motif predictions from AlignACE, BioProspector, CONSENSUS, and MEME. Read details in Jensen & Liu (2004) in Bioinformatics.
• Smoothing Spline Clustering (SSC) algorithm (Ma et al. 2006): a data-driven statistical method for clustering time-series gene expression data. A newer version of the software is available here.
• BEAM (Bayesian Epistasis Association Mapping): A powerful Bayesian inference algorithm for detecting marker interactions in case-control population genetic studies. The companion paper, Zhang and Liu (2007) was published in Nature Genetics.
• Tmod (Toolbox for Motif Discovery): A windows-based software suite that incorporates 12 different popular sequence motif discovery algorithms such as MEME, BioProspector, AlignACE, GLAM, YMF, etc. It helps researchers to compare and combine motif finding results from different algorithms. Compatible with Windows 2000, XP, Vista, and 7! The companion paper, Sun et al. (2009), is accepted by Bioinformatics for publication.
• Mining Biological Literature for Protein-Protein Interactions: Webserver is available! The companion paper, Chowdhary, Zhang, and Liu (2009) was published in Bioinformatics. Programs and Scripts also available here.

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Some Talks in Slides

• Introduction Overview Lecture, JSM 2001 --- Biological Sequence Analysis
• Statistical Models for Multiple Sequence Alignment
• Markov chain Monte Carlo and Related Topics
• Haar Measure and Gibbs Sampler
• The Multiple-Try Metropolis Method
• Sequential Importance Sampling and Mixture Kalman Filtering

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Courses I have taught and am Teaching

• Year 1995-1996:
• Autumn: STAT 300A and STAT 110;
• Winter: STAT 300B and STAT 353 (Monte Carlo Methods) ;
• Spring Spring: STAT 319;
• Summer: Seminars.
• Year 1996-1997:
• Autumn: STAT 300A and STAT 371;
• Spring: STAT 190
• Year 1997-1998:
• Autumn: STAT 373 (Graphical Models & Bayes Network)
• Year 1998-1999:
• Winter: STAT 300B;
• Spring: STAT 200  and STAT 203.
• Year 1999-2000:
• Winter: STAT 217  and STAT 353
• Spring: STAT 190
• Year 2000-2001:
• Autumn: STAT 315a (Bioinformatics)
• Spring:
1. STAT 315b (Bioinformatics) ;
2. STAT 171 (Stochastic Processes);
• Year 2001-2002:
• Autumn: STAT 210 (Probability Theory)
• Spring:

1. STAT 115 (Bioinformatics) ;

2. STAT 220 (Stochastic Processes);

• Year 2002-2003:
• Spring:

1. STAT 171 (Stochastic Processes)

2. STAT 311 (Monte Carlo Computation)

• Year 2003-2004:
• Autumn: STAT 220 (Bayesian modeling and computation)
• Spring:

1. STAT 171 (Stochastic Processes)

2. STAT 311 (Monte Carlo Computation)

• Year 2004-2005:
• Spring:

1. STAT 171 (Stochastic Processes). Meetings: SC 309, TTh 11:30-1.

2. STAT 315 (Comp Biology and Related Topics). Meetings: SC 706, Th 2:30-4.

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Students and Visitors

Former Ph.D. Students:

· Chiara Sabatti (1998); Associate Professor, Dept Biostatistics, Stanford

· Yuguo Chen (2001); Associate Professor, Dept Statistics, UIUC

· Xiaole Liu (2002); Associate Professor, Dept Biostatistics and Dana-Farber Cancer Institute, HSPH.

· Scott Schmidler (2001, delayed 2002); Associate Professor, Dept Statistics, Duke University

· Mayetri Gupta (2003); Associate Professor, Dept Biostatistics, Boston University

· Tanya Logvinenko (2003); Assist Prof of Medicine, Institute of CRHPS, Tufts University

· Shane Jensen (2004); Associate Professor, Dept Statistics, Wharton School, University of Pennsylvania

· Hosung Kang (2005); Quantitative Analyst, Washington Mutual.

· Gopika Goswami (2005); Quantitative Analyst, Barclay Bank.

· Peng Zhang (HSPH, 2007), Postdoc, Harvard.

· W. Evan Johnson (HSPH, 2007), Assist Prof, Brigham-Young University, Utah.

· Jiajun Gu (DEAS, 2008), Analyst, Swiss Bank

· Xiaodan Fan (2008), Assist Prof, Chinese University of Hong Kong

· Tingting Zhang (2008, Joint with Sam Kou), Assist Prof, Univ of Virginia

· Paul Edelfsen (2009, Joint with Art Dempster), Assistant Member, Fred Hutchinson Cancer Research Center

· Yuan Yuan (2009), Researcher, Google

· Wei Zhang (2009), Quantitative Analyst, UBS Investment Bank

· Jing Maria Zhang (2009), Dept of Statistics, Yale University

· Roee Gutman (2011, joint with Don Rubin), Assistant Prof., Department of Biostatistics, Brown University

Current Ph.D.Students:

· Lei Guo

· Bo Jiang

· Simeng Han

· Daniel Fernendez

Associates and Postdoctoral fellows:

· Saunak Sen (1998-1999). Current: UCSF

· Tianhua Niu (2000-2001). Current: Brigham and Women's Hospital

· Steve Qin (2000-2003). Current: Dept of Biostatistics and Bioinformatics, Emory University

· Erin Conlon (2000-2003). Current: Dept of Math, U of Mass, Amherst

· Haiyan Huang (2001-2003). Current: Dept of Stat, UC Berkeley

· Xin Lu (2001-2004). Current: Dept of Biostat, UC San Diego

· Lei Shen (2003-2005). Current: Senior Bioinformatics Scientist, Agencourt Bioscience Co.

· Ping Ma (2003-2005). Current: Dept of Statistics, UIUC

· Yu Zhang (2004-2006). Current: Dept of Statistics, Penn State U

· Cristian Castillo-Davis (2004-2006). Current: Dept of Biology, U of Maryland, College Park.

· Lihua Zou (2004-2006). Current: Research Scientist, Danna-Farber Cancer Institute

· Guocheng Yuan (2005-2006). Current: Dept of Biostat, Harvard School of Public Health

· Wenxuan Zhong (2005-2007). Current: Dept of Statistics, UIUC

· Jinfeng Zhang (2004-2007). Current: Florida State University

· Chowdhary, Rajesh (2006-2008). Current: Marshfield Clinic Research Foundation

· Liu, Xuxin (2007 – 2010).

· Ke Deng (2008 – Present).

· Feng Hong (2009 – Present).

Rotation Students:

· Junni Zhang (2000-2002)

· Epaminondas Sourlas (2002)

· Su Ying Quek (2001)

· Calvin Chiu (2001)

· Lihua Zou (2003)

· Qing Zhou (2003)

· James Signorovitch (HSPH, 2005-2006)

· Jiong Du (PKU, 2009-present)

Visitors:

· Wen Zhang (2003-2004). Research Scientist.

· Xiaobin Dong (2003-2004).

· Hongwei Xie (2004-2005): Professor and Chair, Technical University of Defense, China

· Xuegong Zhang (2006): Professor and Director of Bioinformatics, Tsinghua U, China

· Jianhua Xu (2008-2009): Professor, Nanjing Normal University

· Jack Y. Yang (2007-present): Research Assoc, UCSD

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Selected Publications and Reports:

· My Top Ten Interesting  Papers  (till 2007)

· 2010

· 2009

· 2008

· 2007

· 2006

· 2005

· 2004

· 2003

· 2002

· 2001

· 2000

· 1999

· 1998

· 1997

· 1996

· 1995

· 1994

· 1993

· 1992

· 1991

My Book on Monte Carlo (2001)

Sample chapters from the book: Preface, Table of Content, and Chapter 1, Chapter 4, and Chapter 5.