Jun S. Liu

发表

Adaptive Bayesian signal processing - a sequential Monte Carlo paradigm

Xiaodong Wang, Rong Chen, Jun S. Liu, 2000, Proceedings of the Tenth IEEE Workshop on Statistical Signal and Array Processing (Cat. No.00TH8496).

Information Flow Analysis of Interactome Networks

Kesheng Liu, Jun S. Liu, Patrycja Vasilyev Missiuro, 2009, PLoS Comput. Biol..

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

Yu Gui, Jun S. Liu, Xin Xing, 2020, 2020 19th IEEE International Conference on Machine Learning and Applications (ICMLA).

Bayesian adaptive sequence alignment algorithms

Jun Zhu, Jun S. Liu, Charles E. Lawrence, 1998, Bioinform..

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

Rong Chen, Xiaodong Wang, Jun S. Liu, 2000, IEEE Trans. Inf. Theory.

Statistical resynchronization and detection of periodic transcripts

Wen Zhang, Xin Lu, Zhaohui S. Qin, 2003, Computational Systems Bioinformatics. CSB2003. Proceedings of the 2003 IEEE Bioinformatics Conference. CSB2003.

Selected Theoretical Topics

Jun S. Liu, 2004 .

An Extended Mallows Model for Ranked Data Aggregation

Han Li, Jun S. Liu, Minxuan Xu, 2020, Journal of the American Statistical Association.

Lookahead Strategies for Sequential Monte Carlo

Rong Chen, Jun S. Liu, Ming Lin, 2013, 1302.5206.

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

Jun S. Liu, Andrew F. Neuwald, A. F. Neuwald, 2004, BMC Bioinformatics.

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

Ming Hu, Bing Ren, Zhaohui S. Qin, 2012, Bioinform..

A Bayesian Partition Method for Detecting Pleiotropic and Epistatic eQTL Modules

Wei Zhang, Jun Zhu, Jun S. Liu, 2010, PLoS Comput. Biol..

Probabilistic Connection Importance Inference and Lossless Compression of Deep Neural Networks

Pengyu Hong, Jun S. Liu, Xin Xing, 2020, ICLR.

Fast Bayesian Implementation of Hierarchical Mixtures of Experts and Stochastic Neural Networks

Jun S. Liu, Samuel P. Wong, Tze-Leung Lai, 2003 .

Bayesian Inference of Spatial Organizations of Chromosomes

Ming Hu, Bing Ren, Zhaohui S. Qin, 2013, PLoS Comput. Biol..

Exploring Hybrid Monte Carlo in Bayesian Computation

Lingyu Chen, Jun S. Liu, Zhaohui S. Qin, 2000 .

False Discovery Rate Control via Data Splitting

Xin Xing, Jun S. Liu, Chenguang Dai, 2020 .

Metropolized independent sampling with comparisons to rejection sampling and importance sampling

Jun S. Liu, Jun S. Liu, 1996, Stat. Comput..

Bayesian Functional Data Clustering for Temporal Microarray Data

Yang Feng, Ping Ma, Jun S. Liu, 2008, International journal of plant genomics.

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

Yang Li, Jun S. Liu, Alexis A. Jourdain, 2017, PLoS Comput. Biol..

Predicting Gene Expression from Sequence: A Reexamination

Lei Guo, Lei Shen, Yuan Yuan, 2007, PLoS Comput. Biol..

Bayesian Inference for Assessing Effects of Email Marketing Campaigns

Jun S. Liu, Kate J. Li, Jiexing Wu, 2018 .

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

Lei Shen, Shane T. Jensen, Jun S. Liu, 2005, Bioinform..

Bayesian models for pooling microarray studies with multiple sources of replications

Jun S. Liu, Erin M. Conlon, Joon J. Song, 2006, BMC Bioinformatics.

Markov Chains and Their Convergence

Jun S. Liu, 2004 .

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

Tianxi Cai, Jun S. Liu, Matey Neykov, 2016, J. Mach. Learn. Res..

Stopping‐time resampling for sequential Monte Carlo methods

Yuguo Chen, Jun S. Liu, Junyi Xie, 2005 .

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

Douglas L. Brutlag, X. Liu, Jun S. Liu, 2000, Pacific Symposium on Biocomputing.

Bayesian Protein Structure Prediction

Douglas L. Brutlag, Jun S. Liu, Scott C. Schmidler, 2002 .

A boosting approach for motif modeling using ChIP-chip data

Qing Zhou, Xin Lu, Pengyu Hong, 2005, Bioinform..

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

Martha L. Bulyk, Bo Jiang, Jun S. Liu, 2013, Bioinform..

Bayesian Segmentation of Protein Secondary Structure

Douglas L. Brutlag, Jun S. Liu, Scott C. Schmidler, 2000, J. Comput. Biol..

Lookahead Strategies for Sequential

Rong Chen, Jun S. Liu, 2013 .

PFP: A Computational Framework for Phylogenetic Footprinting in Prokaryotic Genomes

Ying Xu, Dongsheng Che, Shane T. Jensen, 2008, ISBRA.

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

Wing Hung Wong, Haiyan Huang, Jun S. Liu, 2004, J. Comput. Biol..

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

Faming Liang, Jason Cong, Wing Hung Wong, 2000, ASP-DAC '00.

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

Faming Liang, Jason Cong, Wing Hung Wong, 2000, Proceedings 2000. Design Automation Conference. (IEEE Cat. No.00CH37106).

Tmod: toolbox of motif discovery

Hui Liu, Yuan Yuan, Hongwei Xie, 2010, Bioinform..

BioOptimizer: a Bayesian scoring function approach to motif discovery

Shane T. Jensen, Jun S. Liu, S. Jensen, 2004, Bioinform..

Bayesian Adaptive Alignment and Inference

Jun Zhu, Jun S. Liu, Charles E. Lawrence, 1997, ISMB.

RSIR: regularized sliced inverse regression for motif discovery

Peng Zeng, Wenxuan Zhong, Ping Ma, 2005, Bioinform..

IEEE 7th BIBE Invited Plenary Keynote: Statistial Analysis of nucleosome occupancy and histone modification data

Guo-Cheng Yuan, Jun S. Liu, 2007, 2007 IEEE 7th International Symposium on BioInformatics and BioEngineering.

BAYESIAN META-ANALYSIS FOR IDENTIFYING PERIODICALLY EXPRESSED GENES IN FISSION YEAST CELL CYCLE

Saumyadipta Pyne, Jun S. Liu, Xiaodan Fan, 2010, 1011.2104.

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

Limsoon Wong, Vladimir B. Bajic, Rajesh Chowdhary, 2010, BMC Systems Biology.

BEST: Binding-site Estimation Suite of Tools

Liming Cai, Dongsheng Che, Shane T. Jensen, 2005, Bioinform..

Interpretable Selection and Visualization of Features and Interactions Using Bayesian Forests

Jun S. Liu, Jiong Du, Jun S. Liu, 2015, 1506.02371.

Generative Parameter Sampler For Scalable Uncertainty Quantification pdf

Minsuk Shin, Young Lee, Jun S. Liu, 2019, ArXiv.

Monte Carlo Approximation of Bayes Factors via Mixing with Surrogate Distributions

Jun S. Liu, Chenguang Dai, 2019 .

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

Chao Ye, Xuegong Zhang, Bo Jiang, 2015, Bioinform..

Statistical Learning and Modeling of TF-DNA Binding

Bo Jiang, Jun S. Liu, Jun S. Liu, 2011, Handbook of Statistical Bioinformatics.

New Algorithms in RNA Structure Prediction Based on BHG

Gang Li, Zhendong Liu, Jun S. Liu, 2020, Int. J. Pattern Recognit. Artif. Intell..

A Gibbs sampler for the detection of subtle motifs in multiple sequences

John C. Wootton, Mark S. Boguski, Jun S. Liu, 1994, 1994 Proceedings of the Twenty-Seventh Hawaii International Conference on System Sciences.

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

Di Wu, Wenxuan Zhong, Ping Ma, 2016, BMC Bioinformatics.

Haplotype Inference and Its Application in Linkage Disequilibrium Mapping

Xin Lu, Tianhua Niu, Zhaohui S. Qin, 2002, Computational Methods for SNPs and Haplotype Inference.

Discussions on “A Bayesian Approach to DNA Sequence Segmentation”

Mayetri Gupta, Jun S. Liu, Mayetri Gupta, 2004 .

SIMPLEs: a single-cell RNA sequencing imputation strategy preserving gene modules and cell clusters variation

Songpeng Zu, Jun S. Liu, Zhirui Hu, 2020, bioRxiv.

Relaxed simulated tempering for VLSI floorplan designs

Faming Liang, Jason Cong, Wing Hung Wong, 1999, Proceedings of the ASP-DAC '99 Asia and South Pacific Design Automation Conference 1999 (Cat. No.99EX198).

On Delay Tomography: Fast Algorithms and Spatially Dependent Models

Yang Li, Zhi Geng, Ke Deng, 2012, IEEE Transactions on Signal Processing.

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

Yan Chen, Yanchun Liang, Renchu Guan, 2018, BMC Systems Biology.

Bayesian Biclustering of Microarray Data

Jun S. Liu, Jiajun Gu, 2007, BIOCOMP.

IMID: integrated molecular interaction database

Jinfeng Zhang, Rajesh Chowdhary, Jun S. Liu, 2012, Bioinform..

On Posterior Consistency of Bayesian Factor Models in High Dimensions

Jun S. Liu, Yucong Ma, Yucong Ma, 2020, Bayesian Analysis.

Dynamic Weighting In Markov Chain Monte Carlo

Faming Liang, Jun S. Liu, Jun S. Liu, 2007 .

On parallelizable Markov chain Monte Carlo algorithms with waste-recycling

Yang Chen, Jun S. Liu, Espen Bernton, 2018, Stat. Comput..

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

Yunlong Liu, Dong Xu, Hamid R. Arabnia, 2014, BMC Bioinformatics.

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

Ming Hu, Ke Deng, Zhaohui S. Qin, 2013, Quantitative Biology.

Hapblock: Haplotype Block Partitioning and Tag Snp Selection Software Using a Set of Dynamic Programming Algorithms

Kui Zhang, Ting Chen, Zhaohui S. Qin, 2022 .

The Wang-Landau Algorithm as Stochastic Optimization and its Acceleration

Jun S. Liu, Chenguang Dai, Jun S. Liu, 2019, Physical review. E.

Additional file 17

Limsoon Wong, Vladimir B. Bajic, Rajesh Chowdhary, 2010 .

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

Ke Tang, Jinfeng Zhang, Samuel W. K. Wong, 2015, Bioinform..

On learning strategies for evolutionary Monte Carlo

Jun S. Liu, Jun S. Liu, Gopi Goswami, 2007, Stat. Comput..

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

Yan Chen, Yanchun Liang, Renchu Guan, 2017, 2017 IEEE International Conference on Bioinformatics and Biomedicine (BIBM).

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

Rong Chen, Xiaodong Wang, Jun S. Liu, 2002, IEEE Trans. Signal Process..

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

Kui Zhang, Ting Chen, Zhaohui S. Qin, 2002, Computational Methods for SNPs and Haplotype Inference.

Multilevel Sampling and Optimization Methods

Jun S. Liu, 2004 .

BPPS: an algorithm for analyzing protein sequence alignments

Jun S. Liu, 2003, Computational Systems Bioinformatics. CSB2003. Proceedings of the 2003 IEEE Bioinformatics Conference. CSB2003.

Model selection principles in misspecified models

Jun S. Liu, Jinchi Lv, Jun S. Liu, 2010, 1005.5483.

Statistical power of phylo-HMM for evolutionarily conserved element detection

Jun Zhu, Jun S. Liu, Eric E. Schadt, 2007, BMC Bioinformatics.

Systems biology analysis reveals new insights into invasive lung cancer

William Yang, Mary Yang, Jun S. Liu, 2018, BMC Systems Biology.

Systematic Analysis of Pleiotropy in C. elegans Early Embryogenesis

Jun S. Liu, Patrycja Vasilyev Missiuro, Lihua Zou, 2008, PLoS Comput. Biol..

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

Yu Zhu, Ming Hu, Zhaohui S. Qin, 2012, Bioinform..

Predicting regulatory variants with composite statistic

Feng Xu, Yun Zhu, Pak Chung Sham, 2016, Bioinform..

Metropolis Jumping Rules

Jun S. Liu, Chenguang Dai, Jun S. Liu, 2020 .

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

Vladimir B. Bajic, Sin Lam Tan, Rajesh Chowdhary, 2013, Int. J. Data Min. Bioinform..

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

Tianxi Cai, Jun S. Liu, Matey Neykov, 2015, J. Mach. Learn. Res..

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

Pengyu Hong, Jun S. Liu, Ruzhang Zhao, 2018, Entropy.

Bayesian inference on biopolymer models

Jun S. Liu, Charles E. Lawrence, C. Lawrence, 1999, Bioinform..

FRESS: an Efficient Monte Carlo Method for Biopolymer Structure Simulation

Gary S. Tyson, Samuel C. Kou, Yue Li, 2009 .

Monte Carlo Bayesian Signal Processing for Wireless Communications

Rong Chen, Xiaodong Wang, Jun S. Liu, 2002, J. VLSI Signal Process..

A Theoretical Framework for Sequential Importance Sampling with Resampling

Rong Chen, Jun S. Liu, Jun S. Liu, 2001, Sequential Monte Carlo Methods in Practice.

Sequential Monte Carlo Methods for Statistical Analysis of Tables

Yuguo Chen, Persi Diaconis, Jun S. Liu, 2005 .

A Unified Theory of Confidence Regions and Testing for High-Dimensional Estimating Equations

Han Liu, Yang Ning, Jun S. Liu, 2015, Statistical Science.

General Conditional Sampling

Jun S. Liu, 2004 .

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

Qian Wang, Jianxing Feng, Clifford A. Meyer, 2012, Bioinform..

Modeling within-motif dependence for transcription factor binding site predictions

Qing Zhou, Jun S. Liu, Qing Zhou, 2004, Bioinform..

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

Xu Han, Hongsu Wang, Jun S. Liu, 2018, ArXiv.

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

Serafim Batzoglou, Douglas L. Brutlag, Xiaole Shirley Liu, 2004, Nucleic Acids Res..

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

Yunlong Liu, Dong Xu, Hamid R. Arabnia, 2014, BMC Bioinformatics.

Bayesian Analysis of Rank Data with Covariates and Heterogeneous Rankers

Jun S. Liu, Jun S. Liu, Dingdong Yi, 2016 .

Genomic Sequence Is Highly Predictive of Local Nucleosome Depletion

Guo-Cheng Yuan, Jun S. Liu, Guo-cheng Yuan, 2007, PLoS Comput. Biol..

Bayesian inference of protein-protein interactions from biological literature

Jinfeng Zhang, Rajesh Chowdhary, Jun S. Liu, 2009, Bioinform..

Blind deconvolution of rever - berated speech signals

Henrique S. Malvar, Jun S. Liu, 2001 .

On Side-Chain Conformational Entropy of Proteins

Jinfeng Zhang, Jun S. Liu, Jinfeng Zhang, 2006, PLoS Comput. Biol..

Neuronized Priors for Bayesian Sparse Linear Regression

Jun S. Liu, Minsuk Shin, Minsuk Shin, 2018, Journal of the American Statistical Association.

On Posterior Consistency of Bayesian Factor Models in High Dimensions

Jun S. Liu, Yucong Ma, 2021, Bayesian Analysis.

Bayesian haplotype inference for multiple linked single-nucleotide polymorphisms.

Zhaohui S. Qin, Jun S. Liu, T. Niu, 2002, American journal of human genetics.

Bayesian Clustering with Variable and Transformation Selections

Jun S. Liu, C. Lawrence, Junni L. Zhang, 2003 .

Weighted finite population sampling to maximize entropy

Jun S. Liu, A. Dempster, Xiang-Hui Chen, 1994 .

Bayesian Models for Multiple Local Sequence Alignment and Gibbs Sampling Strategies

Jun S. Liu, A. F. Neuwald, C. Lawrence, 1995 .

Siegel's formula via Stein's identities

Jun S. Liu, Jun S. Liu, 1994 .

Covariance Structure and Convergence Rate of the Gibbs Sampler with Various Scans

Jun S. Liu, W. Wong, A. Kong, 1995 .

Discovery of Conserved Sequence Patterns Using a Stochastic Dictionary Model

Jun S. Liu, Mayetri Gupta, Jun S. Liu, 2003 .

An algorithm for finding protein–DNA binding sites with applications to chromatin-immunoprecipitation microarray experiments

Jun S. Liu, X. Liu, D. Brutlag, 2002, Nature Biotechnology.

The Genotype-Tissue Expression (GTEx) pilot analysis: Multitissue gene regulation in humans

Jun S. Liu, Ellen T. Gelfand, Ayellet V. Segrè, 2015, Science.

Topological Domains in Mammalian Genomes Identified by Analysis of Chromatin Interactions

Jesse R. Dixon, Jun S. Liu, B. Ren, 2012, Nature.

Integrated Bio-Entity Network: A System for Biological Knowledge Discovery

Jun S. Liu, Lindsey Bell, R. Chowdhary, 2011, PloS one.

Identifying Differentially Expressed Genes in Time Course Microarray Data

Jun S. Liu, Wenxuan Zhong, P. Ma, 2009 .

Statistical resynchronization and Bayesian detection of periodically expressed genes.

Zhaohui S. Qin, Jun S. Liu, Z. Qin, 2004, Nucleic acids research.

Genetics of rheumatoid arthritis contributes to biology and drug discovery

Jun S. Liu, Michael H. Guo, P. Visscher, 2013 .

Gibbs motif sampling: Detection of bacterial outer membrane protein repeats

Jun S. Liu, A. F. Neuwald, C. Lawrence, 1995, Protein science : a publication of the Protein Society.

Comprehensive analyses of tumor immunity: implications for cancer immunotherapy

Jun S. Liu, J. Aster, X. Liu, 2016, Genome Biology.

Fast and Accurate Approximation to Significance Tests in Genome-Wide Association Studies

Jun S. Liu, Yu Zhang, 2011, Journal of the American Statistical Association.

Bayesian inference of epistatic interactions in case-control studies

Jun S. Liu, Yu Zhang, Jun S. Liu, 2007, Nature Genetics.

BALSA: Bayesian algorithm for local sequence alignment.

Jun S. Liu, C. Lawrence, Bobbie-Jo M Webb, 2002, Nucleic acids research.

Partition-ligation-expectation-maximization algorithm for haplotype inference with single-nucleotide polymorphisms.

Zhaohui S. Qin, Jun S. Liu, T. Niu, 2002, American journal of human genetics.

Sequence determinants of improved CRISPR sgRNA design

Clifford A. Meyer, Jun S. Liu, Le Cong, 2015, Genome research.

Clustering analysis of SAGE data using a Poisson approach

Jun S. Liu, Haiyan Huang, C. Cepko, 2004, Genome Biology.

Defining a centromere-like element in Bacillus subtilis by Identifying the binding sites for the chromosome-anchoring protein RacA.

Jie Yan, Jun S. Liu, Jun S Liu, 2005, Molecular cell.

Monte Carlo Maximum Likelihood for Exponential Random Graph Models: From Snowballs to Umbrella Densities

Jun S. Liu, Kevin Bartz, Joseph K. Blitzstein, 2009 .

Inference of transcriptional regulation in cancers

Jun S. Liu, M. Freedman, Xiaole Shirley Liu, 2015, Proceedings of the National Academy of Sciences.

Exploring genetic associations with ceRNA regulation in the human genome

Pak Chung Sham, Jean-Pierre A. Kocher, Mulin Jun Li, 2017, Nucleic acids research.

Exploring functional variation affecting ceRNA regulation in humans

Mulin Jun Li, Jun S. Liu, Xuanyao Liu, 2015, bioRxiv.

A data-driven clustering method for time course gene expression data

Wenxuan Zhong, Ping Ma, Jun S. Liu, 2006, Nucleic acids research.

Model-based analysis of two-color arrays (MA2C)

Wei Li, Runsheng Chen, Jun S. Liu, 2007, Genome Biology.

MAGeCK enables robust identification of essential genes from genome-scale CRISPR/Cas9 knockout screens

Jun S. Liu, Le Cong, R. Irizarry, 2014, Genome Biology.

Quality control, modeling, and visualization of CRISPR screens with MAGeCK-VISPR

Jun S. Liu, Myles A Brown, X. Liu, 2015, Genome Biology.

Extracting sequence features to predict protein–DNA interactions: a comparative study

Jun S. Liu, Qing Zhou, Jun S. Liu, 2008, Nucleic acids research.

Linear Combinations of Multiple Diagnostic Markers

Jun S. Liu, John Q. Su, Jun S. Liu, 1993 .

Bayesian analysis of single‐molecule experimental data

Jun S. Liu, S. Kou, X. Sunney Xie, 2005 .

Phylogenomics of nonavian reptiles and the structure of the ancestral amniote genome

Jun S. Liu, Shaying Zhao, J. Shetty, 2007, Proceedings of the National Academy of Sciences.

De novo cis-regulatory module elicitation for eukaryotic genomes.

Jun S. Liu, Mayetri Gupta, Jun S. Liu, 2005, Proceedings of the National Academy of Sciences of the United States of America.

Integrating regulatory motif discovery and genome-wide expression analysis

Jun S. Liu, Erin M. Conlon, J. Lieb, 2003, Proceedings of the National Academy of Sciences of the United States of America.

A database of annotated promoters of genes associated with common respiratory and related diseases.

Sin Lam Tan, Jun S. Liu, G. Pavesi, 2012, American journal of respiratory cell and molecular biology.

Decoding human regulatory circuits.

Jun S. Liu, C. Lawrence, M. Palumbo, 2004, Genome research.

Landscape of tumor-infiltrating T cell repertoire of human cancers

Jun S. Liu, N. Hacohen, X. Liu, 2016, Nature Genetics.

Markovian structures in biological sequence alignments

Jun S. Liu, A. F. Neuwald, C. Lawrence, 1999 .

TIMER: A Web Server for Comprehensive Analysis of Tumor-Infiltrating Immune Cells.

Jun S. Liu, X. Liu, Bo Li, 2017, Cancer research.

Statistical assessment of the global regulatory role of histone acetylation in Saccharomyces cerevisiae

Wenxuan Zhong, Ping Ma, Guo-Cheng Yuan, 2006, Genome Biology.

Convergent regulatory evolution and loss of flight in paleognathous birds

Jun S. Liu, Timothy B Sackton, M. Clamp, 2019, Science.

Broadly heterogeneous activation of the master regulator for sporulation in Bacillus subtilis

Guo-Cheng Yuan, Jun S. Liu, Jun S Liu, 2010, Proceedings of the National Academy of Sciences.

Personalized chemotherapy selection for breast cancer using gene expression profiles

Pei-Yau Lung, Jun S. Liu, Kaixian Yu, 2017, Scientific Reports.

Stratification and Optimal Resampling for Sequential Monte Carlo

Jun S. Liu, Wenshuo Wang, Ke Deng, 2020, 2004.01975.

Ultrasensitive detection of TCR hypervariable-region sequences in solid-tissue RNA–seq data

Jun S. Liu, Jun S Liu, X Shirley Liu, 2017, Nature Genetics.

SEQUENTIAL MONTE CARLO METHODS FOR PERMUTATION TESTS ON TRUNCATED DATA

Jun S. Liu, Yuguo Chen, Yuguo Chen, 2007 .

Stochastic Segment Interaction Models for Biological Sequence Analysis

Jun S. Liu, D. Brutlag, S. Schmidler, 2004 .

The Program of Gene Transcription for a Single Differentiating Cell Type during Sporulation in Bacillus subtilis

Shane T. Jensen, Shane T Jensen, Jun S. Liu, 2004, PLoS biology.

Discussion of “Equi-energy sampler” by Kou, Zhou and Wong

Jun S. Liu, Yves F. Atchad'e, 2006 .

Network analysis of gene essentiality in functional genomics experiments

Jon C. Aster, X. Shirley Liu, Chongzhi Zang, 2015, Genome Biology.

Identification of co-regulated genes through Bayesian clustering of predicted regulatory binding sites

Lee Ann McCue, Zhaohui S. Qin, Jun S. Liu, 2003, Nature Biotechnology.

Assumptions behind Intercoder Reliability Indices

Jun S. Liu, Xinshu Zhao, Xinshu Zhao, 2013 .

Evolutionary Monte Carlo Methods for Clustering

Jun S. Liu, Jun S. Liu, Wing Hung Wong, 2007 .

The properties of the cross-match estimate and split sampling

Augustine Kong, Jun S. Liu, Jun S. Liu, 1997 .

Convergent regulatory evolution and the origin of flightlessness in palaeognathous birds

Paul P. Gardner, Jun S. Liu, Timothy B Sackton, 2018, bioRxiv.

USAF Academy Center for Space Situational Awareness

Jun S. Liu, Michael E. Dearborn, F. K. H. Chun, 2011 .

On consistency and sparsity for sliced inverse regression in high dimensions

Jun S. Liu, Zhigen Zhao, Jun S. Liu, 2015, 1507.03895.

Locally weighted Markov chain Monte Carlo

Jun S. Liu, Neil Shephard, Espen Bernton, 2015, 1506.08852.

Robust Variable and Interaction Selection for High-Dimensional Classification via Logistic Regression

Yang Li, Jun S. Liu, Y. Li, 2016 .

Sequential importance sampling for

Jun S. Liu, Steven N. MacEachern, Merlise A. Clyde, 1999 .

Bayesian Inference for Gene Expression and Proteomics: Bayesian Modeling and Inference for Sequence Motif Discovery

Jun S. Liu, Mayetri Gupta, 2006 .

Systematic Investigation on Interactions for HIV Drug Resistance and Cross-Resistance among Protease Inhibitors

Xiao Yang, Wei Wang, Jun S. Liu, 2012 .

Revisit linear regression-based deconvolution methods for tumor gene expression data

X. Shirley Liu, Jun S. Liu, Bo Li, 2017, Genome Biology.

cepip: context-dependent epigenomic weighting for prioritization of regulatory variants and disease-associated genes

Pak Chung Sham, Feng Xu, Zhicheng Pan, 2017, Genome Biology.

Rasch Model and Its Extensions for Analysis of Aphasic Deficits in Syntactic Comprehension

David Caplan, Jun S. Liu, Roee Gutman, 2011 .

Context-Specific Protein Network Miner – An Online System for Exploring Context-Specific Protein Interaction Networks from the Literature

Vladimir B. Bajic, Shreyas Karnik, Sin Lam Tan, 2012, PloS one.

Covariance structure of the Gibbs sampler with applications to the comparisons of estimators and augmentation schemes

Jun S. Liu, W. Wong, A. Kong, 1994 .

Siegel ’ s formula via Stein ’ s identities

Jun S. Liu, Jun S. Liu, 2003 .

NONPARAMETRIC HIERARCHICAL BAYES VIA SEQUENTIAL IMPUTATIONS 1 By

Jun S. Liu, Jun S. Liu, 2022 .

Nonparametric hierarchical Bayes analysis of binomial data via Bernstein polynomial priors

Jun S. Liu, Tingting Zhang, Tingting Zhang, 2012 .

Bayesian Partition Models for Identifying Expression Quantitative Trait Loci

Bo Jiang, Jun S. Liu, Jun S. Liu, 2015, Journal of the American Statistical Association.

An Adaptive Exchange Algorithm for Sampling From Distributions With Intractable Normalizing Constants

Faming Liang, Jun S. Liu, Qifan Song, 2016 .

Additivity tests for nonlinear autoregression

Jun S. Liu, Ruey S. Tsay, Jun S. Liu, 1995 .

Sparse Sliced Inverse Regression for High Dimensional Data

Jun S. Liu, Zhigen Zhao, Jun S. Liu, 2016 .

SAGE-Seq Gene expression profiling of human breast tissue samples using Material

Clifford A. Meyer, Jun S. Liu, X. Liu, 2010 .

Gene expression profiling of human breast tissue samples using SAGE-Seq.

Clifford A. Meyer, Jun S. Liu, Armin Schwartzman, 2010, Genome research.

A new sequential importance sampling method and its application to the two-dimensional hydrophobic-hydrophilic model

Jun S. Liu, Jun S. Liu, Junni L. Zhang, 2002 .

Nonparametric K-Sample Tests via Dynamic Slicing

Bo Jiang, Jun S. Liu, Jun S. Liu, 2015 .

Signed Support Recovery for Single Index Models in High-Dimensions

Jun S. Liu, Matey Neykov, Jun S. Liu, 2015, 1511.02270.

Variable selection for general index models via sliced inverse regression

Bo Jiang, Jun S. Liu, Jun S. Liu, 2013, 1304.4056.

Methylation of histone H3 Lys 4 in coding regions of active genes

Stuart L. Schreiber, Bradley E. Bernstein, Jun S. Liu, 2002, Proceedings of the National Academy of Sciences of the United States of America.

A Theory for Dynamic Weighting in Monte Carlo Computation

Faming Liang, Jun S. Liu, Jun S. Liu, 2001 .

The clinical significance of snail protein expression in gastric cancer: a meta-analysis

Hamid R. Arabnia, Jun S. Liu, Youping Deng, 2016, Human Genomics.

Title Extracting Sequence Features to Predict Protein-DNA Interactions : A Comparative Study Permalink

Jun S. Liu, Qing Zhou, Jun S. Liu, 2008 .

Predictive Modeling Approaches for Studying Protein-DNA Binding

Jun S. Liu, Qing Zhou, Jun S. Liu, 2007 .

Multipoint metropolis method with application to hybrid Monte Carlo

Jun S. Liu, Z. Qin, 2001 .

Computational Deconvolution of Tumor-Infiltrating Immune Components with Bulk Tumor Gene Expression Data.

Jun S. Liu, X. Liu, Taiwen Li, 2020, Methods in molecular biology.

THE CONFORMATIONAL SPACE FOR PROTEIN FOLDING WITH SEQUENTIAL MONTE CARLO By

Jun S. Liu, Samuel W. K. Wong, S. Kou, 2017 .

Determinants of transcription factor regulatory range

Clifford A. Meyer, Jun S. Liu, Myles A Brown, 2020, Nature Communications.

Haplotype information and linkage disequilibrium mapping for single nucleotide polymorphisms.

Tianhua Niu, Jun S. Liu, Jun S Liu, 2003, Genome research.

Additional file 19

Limsoon Wong, Vladimir B. Bajic, Rajesh Chowdhary, 2010 .

Bioinformatics : Microarrays Analyses and Beyond

Jun S. Liu, 2002 .

Bayesian detection of convergent rate changes of conserved noncoding elements on phylogenetic trees

Jun S. Liu, Timothy B Sackton, S. Edwards, 2018, bioRxiv.

The Collapsed Gibbs Sampler in Bayesian Computations with Applications to a Gene Regulation Problem

Jun S. Liu, Jun S. Liu, 1994 .

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

Nan Sun, Qi Li, Jun S. Liu, 2020, Briefings Bioinform..

Exploring the conformational space for protein folding with sequential Monte Carlo

Jun S. Liu, Samuel W. K. Wong, S. Kou, 2018, The Annals of Applied Statistics.

Fast de novo discovery of low‐energy protein loop conformations

Jun S. Liu, Samuel W. K. Wong, S. Kou, 2017, Proteins.

An Integrative Approach Revealing the Landscape of Long Noncoding RNAs in Human Brain

Jun S. Liu, W. Tong, Mary Yang, 2016, 2016 International Conference on Computational Science and Computational Intelligence (CSCI).

Determinants of transcription factor regulatory range

Clifford A. Meyer, Jun S. Liu, Shirley X. Liu, 2019, bioRxiv.

Evaluation of immune repertoire inference methods from RNA-seq data

Jun S. Liu, Xiaole Shirley Liu, Xihao Hu, 2018, Nature Biotechnology.

BioOptimizer : Improving Models for Discovery of Transcription Factor Binding Motifs

Shane T. Jensen, Jun S. Liu, 2005 .

HapBlock – A Suite of Dynamic Programming Algorithms for Haplotype Block Partitioning and Tag SNP Selection Based on Haplotype and Genotype Data

Jun S. Liu, Ting Chen, Fengzhu Sun, 2007 .

A Gene Module-Based eQTL Analysis Prioritizing Disease Genes and Pathways in Kidney Cancer

Jun S. Liu, Jun Liu, William Yang, 2017, Computational and structural biotechnology journal.

An Integrating Analysis Reveals Key Regulatory Networks in Breast Cancer

Jun S. Liu, Mary Yang, William Yang, 2019, 2019 International Conference on Computational Science and Computational Intelligence (CSCI).

FKBP, thought to be identical to PKCI-2, does not inhibit protein kinase C

Jun S. Liu, S. Schreiber, M. Albers, 1991 .

Relationship of FKBP to PKCI-2

Jun S. Liu, S. Schreiber, M. Albers, 1991, Nature.

Ultrasensitive detection of TCR hypervariable region in solid-tissue RNA-seq data

Jun S. Liu, S. Signoretti, T. Choueiri, 2016, bioRxiv.

Measuring evolutionary constraints as protein properties reflecting underlying mechanisms

Jun S. Liu, A. F. Neuwald, 2005 .

Multi-Cell-Type Openness-Weighted Association Studies for Trait-Associated Genomic Segments Prioritization

Jun S. Liu, Jun S. Liu, Shuang Song, 2022, Genes.

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

Xiting Yan, Jun S. Liu, Nayang Shan, 2021, Bioinform..

Discussion of “Equi-energy sampler” by Kou, Zhou and Wong

Jun S. Liu, Yves F. Atchad'e, 2006, math/0611217.

Exploring big-data analysis using integrative systems biology approaches for kidney renal clear cell carcinoma studies

Jun S. Liu, Jack Y. Yang, A. Niemierko, 2014 .

The distribution of genomic variations in human iPSCs is related to replication-timing reorganization during reprogramming.

Jun S. Liu, J. Collins, Hu Li, 2014, Cell reports.

Calcineurin is a common target of cyclophilin-cyclosporin A and FKBP-FK506 complexes

Stuart L. Schreiber, Jun S. Liu, Jun Liu, 1991, Cell.

Cognitive Neuropsychology Volume 27, 2010, Contents

Jun S. Liu, E. Warrington, P. Garthwaite, 2010 .

Incorporating genotyping uncertainty in haplotype inference for single-nucleotide polymorphisms.

Tianhua Niu, Zhaohui S. Qin, Zhaohui S Qin, 2004, American journal of human genetics.

From QTL Mapping to eQTL Analysis

Jun S. Liu, Wei Zhang, Jun S. Liu, 2010 .

TIMER : AWeb Server for Comprehensive Analysis of Tumor-In fi ltrating Immune Cells

Jun S. Liu, X. Liu, Taiwen Li, 2017 .

MM-ChIP enables integrative analysis of cross-platform and between-laboratory ChIP-chip or ChIP-seq data

Tao Liu, Clifford A. Meyer, Jun S. Liu, 2011, Genome Biology.

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

Xuegong Zhang, Qian Shi, Wing H Wong, 2006, BMC Bioinformatics.

QB-13016-LJ 156..174

Jun S. Liu, Ming Hu, Zhaohui Qin, 2013 .

High-dimensional genomic data bias correction and data integration using MANCIE

Ke Deng, Yang Xie, Chongzhi Zang, 2016, Nature Communications.

oncogenic transformation Cooperation between Polycomb and androgen receptor during Material Supplemental

Zhaohui S. Qin, Jun S. Liu, Z. Qin, 2012 .

Landscape of B cell immunity and related immune evasion in human cancers

Jun S. Liu, N. Hacohen, Jun Liu, 2018, Nature Genetics.

Bayesian Detection of Convergent Rate Changes of Conserved Noncoding Elements on Phylogenetic Trees

Jun S. Liu, Timothy B Sackton, S. Edwards, 2018, bioRxiv.

Systems-level analysis and evolution of the phototransduction network in Drosophila

Jun S. Liu, Cristian I. Castillo-Davis, D. Hartl, 2007, Proceedings of the National Academy of Sciences of the United States of America.

Bayesian Clustering of Transcription Factor Binding Motifs

Shane T. Jensen, Shane T Jensen, Jun S. Liu, 2006, math/0610655.

Correlation pursuit: forward stepwise variable selection for index models

Wenxuan Zhong, Yu Zhu, Jun S. Liu, 2012, Journal of the Royal Statistical Society. Series B, Statistical methodology.

Reduction of mNAT1/hNAT2 Contributes to Cerebral Endothelial Necroptosis and Aβ Accumulation in Alzheimer's Disease.

Jun S. Liu, J. Levin, X. Adiconis, 2020, Cell reports.

Bioinformatics : Microarrays Analyses and Beyond

Jun S. Liu, 2002 .

Transposon identification using profile HMMs

Jun S. Liu, P. Edlefsen, 2010, BMC Genomics.

Bayesian Methods in Biological Sequence Analysis

Jun S. Liu, T. Logvinenko, Jun S. Liu, 2004 .

The emerging genomics and systems biology research lead to systems genomics studies

Jun S. Liu, Jack Y. Yang, A. Niemierko, 2014, BMC Genomics.

Quantitative and functional interrogation of parent-of-origin allelic expression biases in the brain

Jun S. Liu, Nimrod D. Rubinstein, John Y. J. Choi, 2015, eLife.

Quantitative and Functional Interrogation of ParentofOrigin ParentofOrigin ParentofOrigin ofOrigin ofOrigin 9 Allelic Expression Biases in the Brain

Jun S. Liu, Chen, Nimrod D. Rubinstein, 2015 .

Long-term drug costs per life-month gained associated with first-line treatments for unresectable or metastatic melanoma

Jun S. Liu, Sumati Rao, Jun S. Liu, 2016, Experimental Hematology & Oncology.

Characterizing Mutually Exclusive Driver Mutations in Pan-Cancer

Mary Qu Yang, Jun S. Liu, William Yang, 2019, 2019 IEEE International Conference on Bioinformatics and Biomedicine (BIBM).

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

Ming Hu, Ke Deng, Rongrong Zhang, 2020, IEEE/ACM Transactions on Computational Biology and Bioinformatics.

Haplotype block partitioning and tag SNP selection using genotype data and their applications to association studies.

Ting Chen, Zhaohui S. Qin, Fengzhu Sun, 2004, Genome research.

Additional file 18

Limsoon Wong, Vladimir B. Bajic, Rajesh Chowdhary, 2010 .

PhyloAcc-GT: A Bayesian method for inferring patterns of substitution rate shifts and associations with binary traits under gene tree discordance

Jun S. Liu, Timothy B Sackton, S. Edwards, 2022, bioRxiv.

Ran's C-terminal, basic patch, and nucleotide exchange mechanisms in light of a canonical structure for Rab, Rho, Ras, and Ran GTPases.

Jun S. Liu, Aleksandar Poleksic, Jun S Liu, 2003, Genome research.

Selective Promoter Recognition by Chlamydial σ28 Holoenzyme

Jun S. Liu, K. Hughes, T. Hatch, 2006 .

The sigmaE regulon and the identification of additional sporulation genes in Bacillus subtilis.

Shane T. Jensen, Shane T Jensen, Jun S. Liu, 2003, Journal of molecular biology.

Computational Discovery of Gene Regulatory Binding Motifs: A Bayesian Perspective

Shane T. Jensen, Jun S. Liu, X. Shirley Liu, 2004 .

Stratification and Optimal Resampling for Sequential Monte Carlo

Jun S. Liu, Wenshuo Wang, Ke Deng, 2020, 2004.01975.

Genome-Scale Signatures of Gene Interaction from Compound Screens Predict Clinical Efficacy of Targeted Cancer Therapies.

Jun S. Liu, J. Aster, X. Liu, 2018, Cell systems.

Selective promoter recognition by chlamydial sigma28 holoenzyme.

Jun S. Liu, K. Hughes, T. Hatch, 2006, Journal of bacteriology.

Biopolymer structure simulation and optimization via fragment regrowth Monte Carlo.

Jun S. Liu, Jun S Liu, S C Kou, 2007, The Journal of chemical physics.

Risk Classification With an Adaptive Naive Bayes Kernel Machine Model

Tianxi Cai, Ming Yuan, Jun S. Liu, 2015, Journal of the American Statistical Association.

A Bayesian method for classification of images from electron micrographs.

Jun S. Liu, Jun S Liu, Michael Radermacher, 2002, Journal of structural biology.

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

Jun S. Liu, Di Wu, Ping Ma, 2016, BMC Bioinformatics.

A data-adaptive Bayesian regression approach for polygenic risk prediction

Jun S. Liu, Shuang Song, Lin Hou, 2022, Bioinform..

Randomization Inference for Peer Effects

Jun S. Liu, Qian Lin, Jun S. Liu, 2018, Journal of the American Statistical Association.

Kernel-Based Partial Permutation Test for Detecting Heterogeneous Functional Relationship

Jun S. Liu, Xinran Li, Bo Jiang, 2021, Journal of the American Statistical Association.

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

Jun S. Liu, D. Brutlag, X. Liu, 2000, Pacific Symposium on Biocomputing.

Sequence analysis Tmod : toolbox of motif discovery

Jun S. Liu, Yibo Wu, Hui Liu, 2010 .

Sequence analysis BEST : Binding-site Estimation Suite of Tools

Jun S. Liu, Liming Cai, Dongsheng Che, 2005 .

Detecting subtle sequence signals: a Gibbs sampling strategy for multiple alignment.

Jun S. Liu, S. Altschul, M. Boguski, 1993, Science.

Determining and analyzing differentially expressed genes from cDNA microarray experiments with complementary designs

Jun S. Liu, Patrick Eichenberger, Erin M. Conlon, 2004 .

Doubly stochastic continuous-time hidden Markov approach for analyzing genome tiling arrays

Jun S. Liu, W. Johnson, X. Liu, 2009, 0910.2090.