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.
Awards
and Honor
- Bernoulli Lecturer, Bernoulli Society, 2004
- Fellow, Institute
of Mathematical Statistics, 2004
- 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.
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


(JASA 1999,
94, 1-15)
(Protein Sci. 1995, 4,
1618-32)
Main Collaborators' Websites
Computational Biology Softwares
The following downloadable
softwares for analyzing biopolymer sequence data have been developed by my
collaborators and myself. 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 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.
Some Talks in Slides
Courses I have taught and am Teaching
- Year 1995-1996:
- Year 1996-1997:
- Year 1997-1998:
- Year 1998-1999:
- Year 1999-2000:
- Year 2000-2001:
- Year 2001-2002:
1. STAT
115 (Bioinformatics) ;
2. STAT
220 (Stochastic Processes);
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)
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.
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);
Assistant Professor, Dept Statistics, Duke University
·
Mayetri
Gupta (2003); Assistant Professor, Dept Biostatistics, Boston University
·
Tanya
Logvinenko (2003); Assist Prof of Medicine, Institute
of CRHPS, Tufts University
·
Shane Jensen (2004); Assistant 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), Harvard Fellow
·
Yuan Yuan (2009), Researcher, Google
·
Wei Zhang (2009), Quantitative Analyst, UBS Investment Bank
·
Jing Maria Zhang (2009), Postdoctoral Fellow, Harvard University
Current Ph.D. Students:
·
Roee Gutman (joint with Don Rubin)
·
Lei Guo
·
Bo Jiang
·
Simeng Han
·
Daniel Fernendez
Associates
and Postdoctoral fellows:
·
Saunak Sen
(1998-1999). Current: UCSF
·
Tim Niu (2000-2001). Current: HSPH and Harvard Medical
School
·
Steve Qin (2000-2003).
Current: Dept of Biostat, U of Michigan
·
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 (20042006). 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 – Present).
·
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)
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): Assit Prof, Harvard Medical
School
·
Marry Q. Yang (2007-present): Scientist, NIH
Selected
Publications and Technical Reports:
· My Ten
Interesting Papers
· 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.