00 - Present: Professor of Statistics, Dept of Stat, Harvard University.
01 - Present: Professor of Biostatistics (secondary), HSPH
00 - Nov 02: Guest Professor, Peking
University, (see photos
03 - Sep 03: Professor (on leave), Dept of Stat, Stanford University
00 - Jun 03: Associate Professor (on leave), Dept of Stat, Stanford University.
94 - Aug 00: Assistant Professor, Dept
of Stat, Stanford University.
96 - Aug 02: Associate Editor, J Amer Statist Assoc
99 - Present: Associate Editor, Statistica Sinica
99 - Aug 02: Associate Editor, Biometrics
98 - Dec 98: Visiting Faculty, Department
of Statistics, UCLA.
98 - May 98: Visiting Faculty, Dept.
of Math, NUS.
91 - Dec 94: Assistant Professor, Dept. of Stat., Harvard
93 - Sep 93: Visiting Faculty, Nat'l
Center. Biotech. Info., NIH.
88 - Jun 91: Ph.D., Statistics,
86 - Jun 88: Ph.D program in math, Rutgers University
81 - July 85: B.S. in Math., Peking
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.
Lecturer, Cambridge University, 2008
American Statistical Association, 2005
Lecturer, Bernoulli Society,
Institute of Mathematical Statistics,
most-cited mathematical scientists 2003
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.
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.
2000 Mitchell Prize
for the Best Bayesian Application Paper, 2000.
Fellow, Stanford University,
AWARD, National Science Foundation,
selection program winner, Beijing, 1985.
missing data problems, imputation methodology.
sampling and other MCMC
structure, graphical models (software BUGS),
- Image reconstructions: PET,
methodology; Even Bill Gates talks about
hierarchical models, model selections and testings.
computation and optimization, e.g., VLSI design; Dynamic systems; Computer
Carlo filters, Sequential importance sampling and resampling.
Click the button to see an illustration of the
(JASA 1999, 94, 1-15)
(Protein Sci. 1995, 4,
Main Collaborators' Websites
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
- 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
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.
(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
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
- HAPLOTYPER 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. Natíl
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
- 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.
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.
Some Talks in
Courses I have taught
and am Teaching
- STAT 315b (Bioinformatics) ;
- STAT 171
STAT 115 (Bioinformatics) ;
STAT 220 (Stochastic Processes);
STAT 311 (Monte
STAT 311 (Monte
(Stochastic Processes). Meetings: SC 309, TTh 11:30-1.
STAT 315 (Comp
Biology and Related Topics). Meetings: SC 706, Th 2:30-4.
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
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),
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
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
(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
Yu Zhang (2004-2006). Current: Dept
of Statistics, Penn State U
Castillo-Davis (2004-2006). Current: Dept of Biology, U of Maryland, College Park.
Lihua Zou (2004-2006). Current: Research Scientist, Danna-Farber
Guocheng Yuan (2005-2006).
Current: Dept of Biostat, Harvard School of Public
Wenxuan Zhong (2005-2007). Current: Dept of Statistics, UIUC
(2004-2007). Current: Florida State University
(2006-2008). Current: Marshfield Clinic Research Foundation
Liu, Xuxin (2007-2010).
Ke Deng (2008-Present).
Feng Hong (2009-Present).
Junni Zhang (2000-2002)
Epaminondas Sourlas (2002)
Su Ying Quek
Calvin Chiu (2001)
Lihua Zou (2003)
Qing Zhou (2003)
James Signorovitch (HSPH, 2005-2006)
Jiong Du (PKU,
(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,
Jianhua Xu (2008-2009): Professor, Nanjing Normal University
Jack Y. Yang
(2007-present): Research Assoc, UCSD
My Top Ten Interesting Papers (till 2007)
My Book on Monte Carlo (2001)
from the book: Preface, Table of Content, and Chapter 1,
Chapter 4, and Chapter 5.