1.      Identification of transcription factor binding sites using local Markov models.

J. Computational Biology, to appear. Joint with H. Huang, M.J. Kao, X. Zhou, and W.H. Wong.

2.      Statistical resynchronization and Bayesian detection of periodically expressed genes.

Nucleic Acids Research, 32, 447-455. Joint with Xin Lu, Wen Zhang, Steve Qin, Kurt Kwast.

3.      Evaluation of the precision and accuracy of kinetic isotope effects estimated from different forms of the Rayleigh distillation equation.

Geochimica et Cosmochimica Acta, 68 433-442.  Joint with K Scott, X Lu, and CM Cavanaugh.

4.      Modeling within-motif dependence for transcription factor binding site predictions.

Bioinformatics, 6, 909-916. Joint with Qing Zhou

5.      Incorporating Genotyping Uncertainty in Haplotype Inference for Single-Nucleotide Polymorphisms

Am J Hum Genet, 74, 495-510. Joint with Hosung Kang, Steve Qin, and Tim Niu.

6.      BioOptimizer: the Bayesian Scoring Function Approach to Motif Discovery

Bioinformatics, to appar. Joint with Shane Jensen.

7.      Determining Differentially Expressed Genes of Bacillus subtilis from Replicated cDNA Microarray Experiments.

J. Mul. Analysis, to appear. Joint with E. Conlon and  P. Eichenberger.

8.      Haplotype Block Partitioning and Tag SNP Selection Using Genotype Data and Their Applications to Association Studies.

Genome Research, 14, 908-16. Joint with  Zhang,K., Qin, Z.S., Chen, T.,  Waterman, M.S., F. Sun.

9.      Computational Discovery of Gene Regulatory Binding Motifs: A Bayesian Perspective.

Statistical Science, 19, 188-204. Joint with S. Jensen et al.

10.      Statistical models for biological sequence motif discovery

Case Studies in Bayesian Statistics VI, 2002. Springer. With M. Gupta et al.

11.      Statistical inferences based on non-smooth estimating functions.

Biometrika, 91(4) 943-54. Joint with T. Lu, M. Zhao, and LJ Wei.

12.      Clustering Analysis of SAGE Data Using a Poisson Approach.

Genome Biology, 5:R51. Joint with Li Cai, H. Huang, Wing Wong et al.

13.      Decoding human regulatory circuits.

Genome Research, 14, 1967-74. Joint with W Thompson, W Wasserman, C Lawrence.

14.      Gapped alignment of protein sequence motifs through Monte Carlo optimization of a hidden Markov model

BMC Bioinformatcs, 5:157. Joint with Andrew F Neuwald.

15.      The program of gene transcription for a single differentiating cell type during sporulation in Bacillus subtilis.

PLOS Biology, 2 (10):e328. Joint with Rich Losick’s lab.