Publications

Publications

Lu, X., Niu, T., and Liu, J.S. (2003). Haplotype information and linkage disequilibrium mapping for single nucleotide polymorphisms. Genome Research, 13: 2112-17

Conlon, E.M., Liu, X., Lieb, J.D., and Liu, J.S. (2003). Integrating regulatory motif discovery and genome-wide expression analysis. Proc Nat’l Acad Sci USA, 100: 3339-44.

Qin ZS, McCue LA, Thompson W, Mayerhofer L, Lawrence CE and Liu JS (2003). Identification of co-regulated genes through Bayesian clustering of predicted regulatory binding sites. Nature Biotech., 21: 435-39.

Neuwald AF, Kannan N, Poleksic A, Hata N & Liu JS (2003). Canonical Ras, Rab, Rho and Ran GTPase structural features and Ran?s C-terminal and basic patch mechanisms. Genome Res., 13: 673-92.

Gupta M & Liu JS (2003). Discovery of conserved sequence patterns using a stochastic dictionary model. J Am Statist Assoc, 98: 55-66.

Qin ZS, Niu T and Liu JS (2002). Partition-Ligation EM Algorithm for Haplotype Inference with Single Nucleotide Polymorphisms. Am. J. Hum. Genet. 71: 1242-47.

Niu T, Qin S, Xu X, and Liu JS (2002). Bayesian haplotype inference for multiple linked single nucleotide polymorphisms. Amer. J. Hum. Genet., 70, 157-169.

Liu XS, Brutlag DL and Liu JS (2002). An algorithm for finding protein-DNA binding sites with applications to chromatin immunoprecipitation microarry experiments. Nature Biotech., 20: 835-39.

Zhang JL and Liu JS (2002) A new sequential Importance sampling method and its application to the 2D HP model. J. Chem. Phys., 117, 3492-8.

Qin Z and Liu JS (2001). Multi-point Metropolis method with application to hybrid Monte Carlo. J. Comp. Phys., 172: 827-840.

Liu JS, Sabatti C, Teng J, Keats BJB, and Risch N (2001). Bayesian analysis of haplotypes for linkage disequilibrium mapping. Genome Research, 11:1716-24.

Liu JS (2001). Monte Carlo Strategies in Scientific Computing. Springer-Verlag: New York.

Liu JS and Sabatti C (2000). Generalized Gibbs sampler and multigrid Monte Carlo for Bayes computation. Biometrika, 87: 353-69.

Liu JS, Neuwald AF, and Lawrence CE (1999). Markovian structures in biological sequence alignments. J. Amer. Statist. Assoc., 94:1-15.

Liu JS and Chen R (1998). Sequential Monte Carlo methods for dynamic systems. J. Am. Statist. Assoc., 93:1032-44.

Neuwald AF, Liu JS, Lipman DJ, and Lawrence CE (1997). Extracting protein alignment models from the sequence database. Nucleic Acid Research, 25:1665-77.

Liu, J.S. (1996). Nonparametric hierarchical Bayes via sequential imputations. Ann. Statist., 24: 911-930.

Liu JS, Lawrence CE, Neuwald A. (1995). Bayesian models for multiple local sequence alignment and its Gibbs sampling strategies. J. Amer. Statist. Assoc., 90:1156-70.

Liu JS (1994). The collapsed Gibbs sampler with applications to a gene regulation problem. J. Amer. Statist. Assoc., 89: 958-66.

Lawrence CE, Altschul SF, Boguski MS, Liu JS, Neuwald AN and Wootton J (1993). Detecting subtle sequence signals: A Gibbs sampling strategy for multiple alignment. Science, 262:208-14.