Jun S. Liu

Ming Hu, Yu Zhu, Jeremy M. G. Taylor, Jun S. Liu, Zhaohui S. Qin: Using Poisson mixed-effects model to quantify transcript-level gene expression in RNA-Seq. Bioinformatics 28(1): 63-68 (2012)

Sentil Balaji, Charles Mcclendon, Rajesh Chowdhary, Jun S. Liu, Jinfeng Zhang: IMID: integrated molecular interaction database. Bioinformatics 28(5): 747-749 (2012)

Jianxing Feng, Clifford A. Meyer, Qian Wang, Jun S. Liu, X. Shirley Liu, Yong Zhang: GFOLD: a generalized fold change for ranking differentially expressed genes from RNA-seq data. Bioinformatics 28(21): 2782-2788 (2012)

Ming Hu, Ke Deng, Siddarth Selvaraj, Zhaohui S. Qin, Bing Ren, Jun S. Liu: HiCNorm: removing biases in Hi-C data via Poisson regression. Bioinformatics 28(23): 3131-3133 (2012)

Ke Deng, Yang Li, Weiping Zhu, Zhi Geng, Jun S. Liu: On Delay Tomography: Fast Algorithms and Spatially Dependent Models. IEEE Transactions on Signal Processing 60(11): 5685-5697 (2012)

Bo Jiang, Jun S. Liu: Statistical Learning and Modeling of TF-DNA Binding. Handbook of Statistical Bioinformatics 2011: 55-72

Hanchang Sun, Yuan Yuan, Yibo Wu, Hui Liu, Jun S. Liu, Hongwei Xie: Tmod: toolbox of motif discovery. Bioinformatics 26(3): 405-407 (2010)

Wei Zhang, Jun Zhu, Eric E. Schadt, Jun S. Liu: A Bayesian Partition Method for Detecting Pleiotropic and Epistatic eQTL Modules. PLoS Computational Biology 6(1) (2010)

Rajesh Chowdhary, Jinfeng Zhang, Jun S. Liu: Bayesian inference of protein-protein interactions from biological literature. Bioinformatics 25(12): 1536-1542 (2009)

Patrycja Vasilyev Missiuro, Kesheng Liu, Lihua Zou, Brian C. Ross, Guoyan Zhao, Jun S. Liu, Hui Ge: Information Flow Analysis of Interactome Networks. PLoS Computational Biology 5(4) (2009)

Guo-Cheng Yuan, Jun S. Liu: Genomic Sequence Is Highly Predictive of Local Nucleosome Depletion. PLoS Computational Biology 4(1) (2008)

Lihua Zou, Sira Sriswasdi, Brian C. Ross, Patrycja Vasilyev Missiuro, Jun S. Liu, Hui Ge: Systematic Analysis of Pleiotropy in C. elegans Early Embryogenesis. PLoS Computational Biology 4(2) (2008)

Dongsheng Che, Guojun Li, Shane T. Jensen, Jun S. Liu, Ying Xu: PFP: A Computational Framework for Phylogenetic Footprinting in Prokaryotic Genomes. ISBRA 2008: 110-121

Xiaodan Fan, Jun Zhu, Eric E. Schadt, Jun S. Liu: Statistical power of phylo-HMM for evolutionarily conserved element detection. BMC Bioinformatics 8 (2007)

Yuan Yuan, Lei Guo, Lei Shen, Jun S. Liu: Predicting Gene Expression from Sequence: A Reexamination. PLoS Computational Biology 3(11) (2007)

Gopi Goswami, Jun S. Liu: On learning strategies for evolutionary Monte Carlo. Statistics and Computing 17(1): 23-38 (2007)

Guo-Cheng Yuan, Jun S. Liu: Statistial Analysis of nucleosome occupancy and histone modification data. BIBE 2007: 8

Jiajun Gu, Jun S. Liu: Bayesian Biclustering of Microarray Data. BIOCOMP 2007: 113-120

Xuegong Zhang, Xin Lu, Qian Shi, Xiu-qin Xu, Hon-chiu E. Leung, Lyndsay N. Harris, James D. Iglehart, Alexander Miron, Jun S. Liu, Wing Hung Wong: Recursive SVM feature selection and sample classification for mass-spectrometry and microarray data. BMC Bioinformatics 7: 197 (2006)

Erin M. Conlon, Joon J. Song, Jun S. Liu: Bayesian models for pooling microarray studies with multiple sources of replications. BMC Bioinformatics 7: 247 (2006)

Jinfeng Zhang, Jun S. Liu: On Side-Chain Conformational Entropy of Proteins. PLoS Computational Biology 2(12) (2006)

Kui Zhang, Zhaohui S. Qin, Ting Chen, Jun S. Liu, Michael S. Waterman, Fengzhu Sun: HapBlock: haplotype block partitioning and tag SNP selection software using a set of dynamic programming algorithms. Bioinformatics 21(1): 131-134 (2005)

Pengyu Hong, X. Shirley Liu, Qing Zhou, Xin Lu, Jun S. Liu, Wing Hung Wong: A boosting approach for motif modeling using ChIP-chip data. Bioinformatics 21(11): 2636-2643 (2005)

Dongsheng Che, Shane T. Jensen, Liming Cai, Jun S. Liu: BEST: Binding-site Estimation Suite of Tools. Bioinformatics 21(12): 2909-2911 (2005)

Shane T. Jensen, Lei Shen, Jun S. Liu: Combining phylogenetic motif discovery and motif clustering to predict co-regulated genes. Bioinformatics 21(20): 3832-3839 (2005)

Wenxuan Zhong, Peng Zeng, Ping Ma, Jun S. Liu, Michael Yu Zhu: RSIR: regularized sliced inverse regression for motif discovery. Bioinformatics 21(22): 4169-4175 (2005)

Qing Zhou, Jun S. Liu: Modeling within-motif dependence for transcription factor binding site predictions. Bioinformatics 20(6): 909-916 (2004)

Shane T. Jensen, Jun S. Liu: BioOptimizer: a Bayesian scoring function approach to motif discovery. Bioinformatics 20(10): 1557-1564 (2004)

Andrew F. Neuwald, Jun S. Liu: Gapped alignment of protein sequence motifs through Monte Carlo optimization of a hidden Markov model. BMC Bioinformatics 5: 157 (2004)

Haiyan Huang, Ming-Chih J. Kao, Xianghong Jasmine Zhou, Jun S. Liu, Wing Hung Wong: Determination of Local Statistical Significance of Patterns in Markov Sequences with Application to Promoter Element Identification. Journal of Computational Biology 11(1): 1-14 (2004)

Yueyi Liu, Liping Wei, Serafim Batzoglou, Douglas L. Brutlag, Jun S. Liu, X. Shirley Liu: A suite of web-based programs to search for transcriptional regulatory motifs. Nucleic Acids Research 32(Web-Server-Issue): 204-207 (2004)

Xin Lu, Wen Zhang, Zhaohui S. Qin, Jun S. Liu: Statistical Resynchronization and Detection of Periodic Transcripts. CSB 2003: 394-395

Rong Chen, Jun S. Liu, Xiaodong Wang: Convergence analyses and comparisons of Markov chain Monte Carlo algorithms in digital communications. IEEE Transactions on Signal Processing 50(2): 255-270 (2002)

Xiaodong Wang, Rong Chen, Jun S. Liu: Monte Carlo Bayesian Signal Processing for Wireless Communications. VLSI Signal Processing 30(1-3): 89-105 (2002)

Tianhua Niu, Xin Lu, Hosung Kang, Zhaohui S. Qin, Jun S. Liu: Haplotype Inference and Its Application in Linkage Disequilibrium Mapping. Computational Methods for SNPs and Haplotype Inference 2002: 48-61

Kui Zhang, Ting Chen, Michael S. Waterman, Zhaohui S. Qin, Jun S. Liu, Fengzhu Sun: Dynamic Programming Algorithms for Haplotype Block Partitioning and Tag SNP Selection Using Haplotype Data or Genotype Data. Computational Methods for SNPs and Haplotype Inference 2002: 96-112

X. Liu, Douglas L. Brutlag, Jun S. Liu: BioProspector: Discovering Conserved DNA Motifs in Upstream Regulatory Regions of Co-Expressed Genes. Pacific Symposium on Biocomputing 2001: 127-138

Scott C. Schmidler, Jun S. Liu, Douglas L. Brutlag: Bayesian Segmentation of Protein Secondary Structure. Journal of Computational Biology 7(1-2): 233-248 (2000)

Rong Chen, Xiaodong Wang, Jun S. Liu: Adaptive joint detection and decoding in flat-fading channels via mixture Kalman filtering. IEEE Transactions on Information Theory 46(6): 2079-2094 (2000)

Jason Cong, Tianming Kong, Faming Liang, Jun S. Liu, Wing Hung Wong, Dongmin Xu: Dynamic weighting Monte Carlo for constrained floorplan designs in mixed signal application. ASP-DAC 2000: 277-282

Jun S. Liu, Charles E. Lawrence: Bayesian inference on biopolymer models. Bioinformatics 15(1): 38-52 (1999)

Jason Cong, Tianming Kong, Dongmin Xu, Faming Liang, Jun S. Liu, Wing Hung Wong: Relaxed Simulated Tempering for VLSI Floorplan Designs. ASP-DAC 1999: 13-16

Jun Zhu, Jun S. Liu, Charles E. Lawrence: Bayesian adaptive sequence alignment algorithms. Bioinformatics 14(1): 25-39 (1998)

Jun Zhu, Jun S. Liu, Charles E. Lawrence: Bayesian Adaptive Alignment and Inference. ISMB 1997: 358-368

Charles E. Lawrence, Stephen F. Altschul, John C. Wootton, Mark S. Boguski, Andrew F. Neuwald, Jun S. Liu: A Gibbs Sampler for the Detection of Subtle Motifs in Multiple Sequences. HICSS (5) 1994: 245-254