Education and Experiences

Awards and Honor

  • 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.
  • 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.

Recent Talks in Slides

Courses I have taught and am Teaching

1.     STAT 215 (Bioinformatics) ;

2.     STAT 171 (Stochastic Processes);


Former Ph.D. Students:

·        Chiara Sabatti; Assistant Professor, Departments of Statistics and Genetics, UCLA.

·        Scott Schmidler; Assistant Professor, Institute of Statistics and Decision Sciences, Duke University.

·        Yuguo Chen; Assistant Professor, Institute of Statistics and Decision Sciences, Duke University.

·        Xiaole Liu; Assistant Professor, Department of Biostatistics and Dana-Farber Cancer Institute, Harvard School of Public Health.

·        Mayetri Gupta; Assistant Professor, Dept Biostatistics, University of North Carolina

·        Tanya Logvinenko; Biostatistician, Mass General Hospital, Boston.

·        Shane Jensen; Assistant Professor, Dept Statistics, Wharton School, University of Pennsylvania

Current Ph.D. Students:

·        Hosung Kang

·        Gopika Goswami

·        Peng Zhang

·        Chenxin Li

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, U of California, Berkeley)

·        Xiaobin Dong (2003-2004, Visiting)

·        Xin Lu (2001-2004), Current: Dept of Biostat, Harvard School of Public Health

·        Lei Shen (2003-Present)

·        Ping Ma (2003-Present)

·        Cristian Castillo-Davis (2004-present)

·        Lihua Zou (2004-present)

·        Yu Zhang (2004-present)

Rotation Students:

·        Junni Zhang (2000-2002)

·        Epaminondas Sourlas (2002)

·        Su Ying Quek (2001)

·        Calvin Chiu (2001)

·        Lihua Zou (2003)

·        Qing Zhou (2003)

·        Wei Zhang (2004)

·        Tingting Zhang (2004)

·        Xiaodan Fan (2004)


Selected Publications and Technical Reports:

·  Ten Most Interesting Papers

·  2004

·  2003

·  2002

·  2001

·  2000

·  1999

·  1998

·  1997

·  1996

·  1995

·  1994

·  1993

·  1992

·  1991

 

My Book on Monte Carlo (2001)