Jun S. Liu

According to our database, Jun S. Liu authored at least 87 papers between 1994 and 2024.

Collaborative distances:

• Dijkstra number of four.
• Erdős number of three.

2024

A phylogenetic method linking nucleotide substitution rates to rates of continuous trait evolution.

Patrick Gemmell, Timothy B. Sackton, Scott V. Edwards, Jun S. Liu

PLoS Comput. Biol., 2024

Power of knockoff: The impact of ranking algorithm, augmented design, and symmetric statistic.

Zheng Tracy Ke, Jun S. Liu, Yucong Ma

J. Mach. Learn. Res., 2024

Varying Coefficient Model via Adaptive Spline Fitting.

Xufei Wang, Bo Jiang, Jun S. Liu

J. Comput. Graph. Stat., 2024

2023

Convergence rate of multiple-try Metropolis independent sampler.

Xiaodong Yang, Jun S. Liu

Stat. Comput., August, 2023

Multi-Response Heteroscedastic Gaussian Process Models and Their Inference.

Taehee Lee, Jun S. Liu

CoRR, 2023

2022

Erratum to: A data-adaptive Bayesian regression approach for polygenic risk prediction.

Shuang Song, Lin Hou, Jun S. Liu

Bioinform., 2022

A data-adaptive Bayesian regression approach for polygenic risk prediction.

Shuang Song, Lin Hou, Jun S. Liu

Bioinform., 2022

2021

Bayesian Text Classification and Summarization via A Class-Specified Topic Model.

Feifei Wang, Junni L. Zhang, Yichao Li, Ke Deng, Jun S. Liu

J. Mach. Learn. Res., 2021

Openness weighted association studies: leveraging personal genome information to prioritize non-coding variants.

Shuang Song, Nayang Shan, Geng Wang, Xiting Yan, Jun S. Liu, Lin Hou

Bioinform., 2021

MiRACLe: an individual-specific approach to improve microRNA-target prediction based on a random contact model.

Pan Wang, Qi Li, Nan Sun, Yibo Gao, Jun S. Liu, Ke Deng, Jie He

Briefings Bioinform., 2021

2020

Inferring Spatial Organization of Individual Topologically Associated Domains via Piecewise Helical Model.

Rongrong Zhang, Ming Hu, Yu Zhu, Zhaohui S. Qin, Ke Deng, Jun S. Liu

IEEE ACM Trans. Comput. Biol. Bioinform., 2020

New Algorithms in RNA Structure Prediction Based on BHG.

Zhendong Liu, Gang Li, Jun S. Liu

Int. J. Pattern Recognit. Artif. Intell., 2020

IMMIGRATE: A Margin-Based Feature Selection Method with Interaction Terms.

Ruzhang Zhao, Pengyu Hong, Jun S. Liu

Entropy, 2020

Neural Gaussian Mirror for Controlled Feature Selection in Neural Networks.

Xin Xing, Yu Gui, Chenguang Dai, Jun S. Liu

CoRR, 2020

Measurement error models: from nonparametric methods to deep neural networks.

Zhirui Hu, Zheng Tracy Ke, Jun S. Liu

CoRR, 2020

NGM: Neural Gaussian Mirror for Controlled Feature Selection in Neural Networks.

Xin Xing, Yu Gui, Chenguang Dai, Jun S. Liu

Proceedings of the 19th IEEE International Conference on Machine Learning and Applications, 2020

Probabilistic Connection Importance Inference and Lossless Compression of Deep Neural Networks.

Xin Xing, Long Sha, Pengyu Hong, Zuofeng Shang, Jun S. Liu

Proceedings of the 8th International Conference on Learning Representations, 2020

2019

The Wang-Landau Algorithm as Stochastic Optimization and its Acceleration.

Chenguang Dai, Jun S. Liu

CoRR, 2019

Generative Parameter Sampler For Scalable Uncertainty Quantification.

Minsuk Shin, Young Lee, Jun S. Liu

CoRR, 2019

Characterizing Mutually Exclusive Driver Mutations in Pan-Cancer.

Yifan Zhang, William Yang, Jun S. Liu, Mary Qu Yang

Proceedings of the 2019 IEEE International Conference on Bioinformatics and Biomedicine, 2019

2018

On parallelizable Markov chain Monte Carlo algorithms with waste-recycling.

Shihao Yang, Yang Chen, Espen Bernton, Jun S. Liu

Stat. Comput., 2018

Sentence Segmentation for Classical Chinese Based on LSTM with Radical Embedding.

Xu Han, Hongsu Wang, Sanqian Zhang, Qunchao Fu, Jun S. Liu

CoRR, 2018

Systems biology analysis reveals new insights into invasive lung cancer.

Dan Li, William Yang, Carolyn Arthur, Jun S. Liu, Carolina Cruz-Niera, Mary Qu Yang

BMC Syst. Biol., 2018

A hotspots analysis-relation discovery representation model for revealing diabetes mellitus and obesity.

Guannan He, Yanchun Liang, Yan Chen, William Yang, Jun S. Liu, Mary Qu Yang, Renchu Guan

BMC Syst. Biol., 2018

2017

CLIC, a tool for expanding biological pathways based on co-expression across thousands of datasets.

Yang Li, Alexis A. Jourdain, Sarah E. Calvo, Jun S. Liu, Vamsi K. Mootha

PLoS Comput. Biol., 2017

Relation discovery and hotspots analysis on diabetes mellitus and obesity with representation model.

Guannan He, Yanchun Liang, Yan Chen, William Yang, Jun S. Liu, Mary Qu Yang, Renchu Guan

Proceedings of the 2017 IEEE International Conference on Bioinformatics and Biomedicine, 2017

2016

L1-Regularized Least Squares for Support Recovery of High Dimensional Single Index Models with Gaussian Designs.

Matey Neykov, Jun S. Liu, Tianxi Cai

J. Mach. Learn. Res., 2016

On the Characterization of a Class of Fisher-Consistent Loss Functions and its Application to Boosting.

Matey Neykov, Jun S. Liu, Tianxi Cai

J. Mach. Learn. Res., 2016

Statistical inference for time course RNA-Seq data using a negative binomial mixed-effect model.

Xiaoxiao Sun, David Dalpiaz, Di Wu, Jun S. Liu, Wenxuan Zhong, Ping Ma

BMC Bioinform., 2016

Predicting regulatory variants with composite statistic.

Mulin Jun Li, Zhicheng Pan, Zipeng Liu, Jiexing Wu, Panwen Wang, Yun Zhu, Feng Xu, Zhengyuan Xia, Pak Chung Sham, Jean-Pierre A. Kocher, Miao-Xin Li, Jun S. Liu, Junwen Wang

Bioinform., 2016

2015

dslice: an R package for nonparametric testing of associations with application in QTL and gene set analysis.

Chao Ye, Bo Jiang, Xuegong Zhang, Jun S. Liu

Bioinform., 2015

Conformational sampling and structure prediction of multiple interacting loops in soluble and <i>β</i>-barrel membrane proteins using multi-loop distance-guided chain-growth Monte Carlo method.

Ke Tang, Samuel W. K. Wong, Jun S. Liu, Jinfeng Zhang, Jie Liang

Bioinform., 2015

2014

Identification of genes and pathways involved in kidney renal clear cell carcinoma.

William Yang, Kenji Yoshigoe, Xiang Qin, Jun S. Liu, Jack Y. Yang, Andrzej Niemierko, Youping Deng, Yunlong Liu, A. Keith Dunker, Zhongxue Chen, Liangjiang Wang, Dong Xu, Hamid R. Arabnia, Weida Tong, Mary Qu Yang

BMC Bioinform., 2014

Advances in translational bioinformatics facilitate revealing the landscape of complex disease mechanisms.

Jack Y. Yang, A. Keith Dunker, Jun S. Liu, Xiang Qin, Hamid R. Arabnia, William Yang, Andrzej Niemierko, Zhongxue Chen, Zuojie Luo, Liangjiang Wang, Yunlong Liu, Dong Xu, Youping Deng, Weida Tong, Mary Qu Yang

BMC Bioinform., 2014

2013

Understanding spatial organizations of chromosomes via statistical analysis of Hi-C data.

Ming Hu, Ke Deng, Zhaohui S. Qin, Jun S. Liu

Quant. Biol., 2013

Bayesian Inference of Spatial Organizations of Chromosomes.

Ming Hu, Ke Deng, Zhaohui S. Qin, Jesse R. Dixon, Siddarth Selvaraj, Jennifer Fang, Bing Ren, Jun S. Liu

PLoS Comput. Biol., 2013

PIMiner: a web tool for extraction of protein interactions from biomedical literature.

Rajesh Chowdhary, Jinfeng Zhang, Sin Lam Tan, Daniel E. Osborne, Vladimir B. Bajic, Jun S. Liu

Int. J. Data Min. Bioinform., 2013

Bayesian hierarchical model of protein-binding microarray <i>k</i>-mer data reduces noise and identifies transcription factor subclasses and preferred <i>k</i>-mers.

Bo Jiang, Jun S. Liu, Martha L. Bulyk

Bioinform., 2013

2012

On Delay Tomography: Fast Algorithms and Spatially Dependent Models.

Ke Deng, Yang Li, Weiping Zhu, Zhi Geng, Jun S. Liu

IEEE Trans. Signal Process., 2012

Using Poisson mixed-effects model to quantify transcript-level gene expression in RNA-Seq.

Ming Hu, Yu Zhu, Jeremy M. G. Taylor, Jun S. Liu, Zhaohui S. Qin

Bioinform., 2012

HiCNorm: removing biases in Hi-C data via Poisson regression.

Ming Hu, Ke Deng, Siddarth Selvaraj, Zhaohui S. Qin, Bing Ren, Jun S. Liu

Bioinform., 2012

GFOLD: a generalized fold change for ranking differentially expressed genes from RNA-seq data.

Jianxing Feng, Clifford A. Meyer, Qian Wang, Jun S. Liu, Xiaole Shirley Liu, Yong Zhang

Bioinform., 2012

IMID: integrated molecular interaction database.

Sentil Balaji, Charles Mcclendon, Rajesh Chowdhary, Jun S. Liu, Jinfeng Zhang

Bioinform., 2012

2011

Statistical Learning and Modeling of TF-DNA Binding.

Bo Jiang, Jun S. Liu

Proceedings of the Handbook of Statistical Bioinformatics., 2011

2010

A Bayesian Partition Method for Detecting Pleiotropic and Epistatic eQTL Modules.

Wei Zhang, Jun Zhu, Eric E. Schadt, Jun S. Liu

PLoS Comput. Biol., 2010

Genome-wide analysis of regions similar to promoters of histone genes.

Rajesh Chowdhary, Vladimir B. Bajic, Difeng Dong, Limsoon Wong, Jun S. Liu

BMC Syst. Biol., 2010

Tmod: toolbox of motif discovery.

Hanchang Sun, Yuan Yuan, Yibo Wu, Hui Liu, Jun S. Liu, Hongwei Xie

Bioinform., 2010

2009

Information Flow Analysis of Interactome Networks.

Patrycja Vasilyev Missiuro, Kesheng Liu, Lihua Zou, Brian C. Ross, Guoyan Zhao, Jun S. Liu, Hui Ge

PLoS Comput. Biol., 2009

Bayesian inference of protein-protein interactions from biological literature.

Rajesh Chowdhary, Jinfeng Zhang, Jun S. Liu

Bioinform., 2009

2008

Systematic Analysis of Pleiotropy in <i>C. elegans</i> Early Embryogenesis.

Lihua Zou, Sira Sriswasdi, Brian C. Ross, Patrycja Vasilyev Missiuro, Jun S. Liu, Hui Ge

PLoS Comput. Biol., 2008

Genomic Sequence Is Highly Predictive of Local Nucleosome Depletion.

Guo-Cheng Yuan, Jun S. Liu

PLoS Comput. Biol., 2008

PFP: A Computational Framework for Phylogenetic Footprinting in Prokaryotic Genomes.

Dongsheng Che, Guojun Li, Shane T. Jensen, Jun S. Liu, Ying Xu

Proceedings of the Bioinformatics Research and Applications, 2008

2007

On learning strategies for evolutionary Monte Carlo.

Gopi Goswami, Jun S. Liu

Stat. Comput., 2007

Predicting Gene Expression from Sequence: A Reexamination.

Yuan Yuan, Lei Guo, Lei Shen, Jun S. Liu

PLoS Comput. Biol., 2007

Statistical power of phylo-HMM for evolutionarily conserved element detection.

Xiaodan Fan, Jun Zhu, Eric E. Schadt, Jun S. Liu

BMC Bioinform., 2007

Bayesian Biclustering of Microarray Data.

Jiajun Gu, Jun S. Liu

Proceedings of the International Conference on Bioinformatics & Computational Biology, 2007

Statistial Analysis of nucleosome occupancy and histone modification data.

Guo-Cheng Yuan, Jun S. Liu

Proceedings of the 7th IEEE International Conference on Bioinformatics and Bioengineering, 2007

2006

On Side-Chain Conformational Entropy of Proteins.

Jinfeng Zhang, Jun S. Liu

PLoS Comput. Biol., 2006

Recursive SVM feature selection and sample classification for mass-spectrometry and microarray data.

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

BMC Bioinform., 2006

Bayesian models for pooling microarray studies with multiple sources of replications.

Erin M. Conlon, Joon J. Song, Jun S. Liu

BMC Bioinform., 2006

2005

RSIR: regularized sliced inverse regression for motif discovery.

Wenxuan Zhong, Peng Zeng, Ping Ma, Jun S. Liu, Michael Yu Zhu

Bioinform., 2005

HapBlock: haplotype block partitioning and tag SNP selection software using a set of dynamic programming algorithms.

Kui Zhang, Zhaohui S. Qin, Ting Chen, Jun S. Liu, Michael S. Waterman, Fengzhu Sun

Bioinform., 2005

Combining phylogenetic motif discovery and motif clustering to predict co-regulated genes.

Shane T. Jensen, Lei Shen, Jun S. Liu

Bioinform., 2005

A boosting approach for motif modeling using ChIP-chip data.

Pengyu Hong, Xiaole Shirley Liu, Qing Zhou, Xin Lu, Jun S. Liu, Wing Hung Wong

Bioinform., 2005

BEST: Binding-site Estimation Suite of Tools.

Dongsheng Che, Shane T. Jensen, Liming Cai, Jun S. Liu

Bioinform., 2005

2004

A suite of web-based programs to search for transcriptional regulatory motifs.

Yueyi Liu, Liping Wei, Serafim Batzoglou, Douglas L. Brutlag, Jun S. Liu, Xiaole Shirley Liu

Nucleic Acids Res., 2004

Determination of Local Statistical Significance of Patterns in Markov Sequences with Application to Promoter Element Identification.

Haiyan Huang, Ming-Chih J. Kao, Xianghong Jasmine Zhou, Jun S. Liu, Wing Hung Wong

J. Comput. Biol., 2004

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

Andrew F. Neuwald, Jun S. Liu

BMC Bioinform., 2004

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

Qing Zhou, Jun S. Liu

Bioinform., 2004

BioOptimizer: a Bayesian scoring function approach to motif discovery.

Shane T. Jensen, Jun S. Liu

Bioinform., 2004

2003

Statistical Resynchronization and Detection of Periodic Transcripts.

Xin Lu, Wen Zhang, Zhaohui S. Qin, Jun S. Liu

Proceedings of the 2nd IEEE Computer Society Bioinformatics Conference, 2003

BPPS: An Algorithm for Analyzing Protein Sequence Alignments.

Jun S. Liu

Proceedings of the 2nd IEEE Computer Society Bioinformatics Conference, 2003

2002

Monte Carlo Bayesian Signal Processing for Wireless Communications.

Xiaodong Wang, Rong Chen, Jun S. Liu

J. VLSI Signal Process., 2002

Convergence analyses and comparisons of Markov chain Monte Carlo algorithms in digital communications.

Rong Chen, Jun S. Liu, Xiaodong Wang

IEEE Trans. Signal Process., 2002

Dynamic Programming Algorithms for Haplotype Block Partitioning and Tag SNP Selection Using Haplotype Data or Genotype Data.

Kui Zhang, Ting Chen, Michael S. Waterman, Zhaohui S. Qin, Jun S. Liu, Fengzhu Sun

Proceedings of the Computational Methods for SNPs and Haplotype Inference, 2002

Haplotype Inference and Its Application in Linkage Disequilibrium Mapping.

Tianhua Niu, Xin Lu, Hosung Kang, Zhaohui S. Qin, Jun S. Liu

Proceedings of the Computational Methods for SNPs and Haplotype Inference, 2002

2001

BioProspector: Discovering Conserved DNA Motifs in Upstream Regulatory Regions of Co-Expressed Genes.

X. Liu, Douglas L. Brutlag, Jun S. Liu

Proceedings of the 6th Pacific Symposium on Biocomputing, 2001

A Theoretical Framework for Sequential Importance Sampling with Resampling.

Jun S. Liu, Rong Chen, Tanya Logvinenko

Proceedings of the Sequential Monte Carlo Methods in Practice, 2001

2000

Adaptive joint detection and decoding in flat-fading channels via mixture Kalman filtering.

Rong Chen, Xiaodong Wang, Jun S. Liu

IEEE Trans. Inf. Theory, 2000

Bayesian Segmentation of Protein Secondary Structure.

Scott C. Schmidler, Jun S. Liu, Douglas L. Brutlag

J. Comput. Biol., 2000

Dynamic weighting Monte Carlo for constrained floorplan designs in mixed signal application.

Jason Cong, Tianming Kong, Faming Liang, Jun S. Liu, Wing Hung Wong, Dongmin Xu

Proceedings of ASP-DAC 2000, 2000

1999

Bayesian inference on biopolymer models.

Jun S. Liu, Charles E. Lawrence

Bioinform., 1999

Relaxed Simulated Tempering for VLSI Floorplan Designs.

Jason Cong, Tianming Kong, Dongmin Xu, Faming Liang, Jun S. Liu, Wing Hung Wong

Proceedings of the 1999 Conference on Asia South Pacific Design Automation, 1999

1998

Bayesian adaptive sequence alignment algorithms.

Jun Zhu, Jun S. Liu, Charles E. Lawrence

Bioinform., 1998

1997

Bayesian Adaptive Alignment and Inference.

Jun Zhu, Jun S. Liu, Charles E. Lawrence

Proceedings of the 5th International Conference on Intelligent Systems for Molecular Biology, 1997

1996

Metropolized independent sampling with comparisons to rejection sampling and importance sampling.

Jun S. Liu

Stat. Comput., 1996

1994

A Gibbs Sampler for the Detection of Subtle Motifs in Multiple Sequences.

Charles E. Lawrence, Stephen F. Altschul, John C. Wootton, Mark S. Boguski, Andrew F. Neuwald, Jun S. Liu

Proceedings of the 27th Annual Hawaii International Conference on System Sciences (HICSS-27), 1994