Dr Zhaohui S. Qin

20th International Workshop on Data Mining in Bioinformatics (BIOKDD 2021)

• August 2021

Glucocorticoid receptor wields chromatin interactions to tune transcription for cytoske...

• Communications Biology
• June 2021

Author Correction: Truncation of mutant huntingtin in knock-in mice demonstrates exon1 ...

• Nature Communications
• November 2020

Truncation of mutant huntingtin in knock-in mice demonstrates exon1 huntingtin is a key...

• Nature Communications
• May 2020

Lack of RAN-mediated toxicity in Huntington’s disease knock-in mice

• Proceedings of the National Academy of Sciences
• February 2020

Integrative characterization of G-Quadruplexes in the three-dimensional chromatin struc...

• Epigenetics
• June 2019

Inferring Spatial Organization of Individual Topologically Associated Domains via Piece...

• IEEE/ACM Transactions on Computational Biology and Bioinformatics
• January 2019

A comprehensive review of computational prediction of genome-wide features

• Briefings in Bioinformatics
• November 2018

Use replication timing data from multiple cell types to annotate human genome

• August 2018

EWS/ETS-Driven Ewing Sarcoma Requires BET Bromodomain Proteins

• Cancer Research
• June 2018

Special collection of bioinformatics in the era of precision medicine

• Quantitative Biology
• November 2017

Using DIVAN to assess disease/trait-associated single nucleotide variants in genome-wid...

• BMC Research Notes
• October 2017

CRISPR/Cas9-mediated gene editing ameliorates neurotoxicity in mouse model of Huntingto...

• Journal of Clinical Investigation
• June 2017

Identifying tagging SNPs for African specific genetic variation from the African Diaspo...

• Scientific Reports
• April 2017

10.1038/srep46398

• February 2017

An approach of identifying differential nucleosome regions in multiple samples

• BMC Genomics
• February 2017

Computationally Tractable Multivariate HMM in Genome-Wide Mapping Studies

• January 2017

Genome-Wide STAT3 Binding Analysis after Histone Deacetylase Inhibition Reveals Novel T...

• Journal of Innate Immunity
• November 2016

The single-species metagenome: subtyping Staphylococcus aureus core genome sequences fr...

• PeerJ
• October 2016

A continuum of admixture in the Western Hemisphere revealed by the African Diaspora genome

• Nature Communications
• October 2016

Use historical data to improve detection of differential expressed genes.

• Statistics in Biosciences
• July 2016

MLL1 and MLL1 fusion proteins have distinct functions in regulating leukemic transcript...

• Cell Discovery
• May 2016

Heat Shock Protein Beta-1 Modifies Anterior to Posterior Purkinje Cell Vulnerability in...

• PLoS Genetics
• May 2016

R package to test GWAS SNP enrichment in any genomic interval(s)

• Bioinformatics
• December 2015

Bayesian inference with historical data-based informative priors improves detection of ...

• Bioinformatics
• October 2015

One Size Doesn't Fit All - RefEditor: Building Personalized Diploid Reference Genome to...

• PLoS Computational Biology
• August 2015

Detection of differentially methylated regions from whole-genome bisulfite sequencing d...

• Nucleic Acids Research
• July 2015

Widespread Rearrangement of 3D Chromatin Organization Underlies Polycomb-Mediated Stres...

• Molecular Cell
• April 2015

Base-resolution methylation patterns accurately predict transcription factor bindings i...

• Nucleic Acids Research
• February 2015

A novel statistical method for quantitative comparison of multiple ChIP-seq datasets

• Bioinformatics
• February 2015

Systems biology and metagenomics: a showcase of Chinese bioinformatics researchers and ...

• Science in China Series C Life Sciences
• October 2014

Integrated Analysis of Whole-Genome Paired-End and Mate-Pair Sequencing Data for Identi...

• Cancer Informatics
• September 2014

Reciprocal occupancy of BCL6 and STAT5 on Growth Hormone target genes: contrasting tran...

• Molecular and Cellular Endocrinology
• September 2014

Direct Amplification, Sequencing and Profiling of Chlamydia trachomatis Strains in Sing...

• PLoS ONE
• June 2014

H2B Ubiquitylation Promotes RNA Pol II Processivity via PAF1 and pTEFb

• Molecular Cell
• June 2014

Therapeutic targeting of BET bromodomain proteins in castration-resistant prostate cancer

• Nature
• April 2014

The central role of EED in the orchestration of polycomb group complexes

• Nature Communications
• January 2014

Targeting MLL1 H3K4 Methyltransferase Activity in Mixed-Lineage Leukemia

• Molecular Cell
• January 2014

EgoNet: identification of human disease ego-network modules

• BMC Genomics
• January 2014

Insulator function and topological domain border strength scale with architectural prot...

• Genome Biology
• January 2014

Allogeneic T cell responses are regulated by a specific miRNA-mRNA network

• Journal of Clinical Investigation
• October 2013

Impaired replication elongation in Tetrahymena mutants deficient in histone H3 Lys 27 m...

• Genes & Development
• July 2013

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

• Quantitative Biology
• June 2013

Bayesian Inference of Spatial Organizations of Chromosomes

• PLoS Computational Biology
• January 2013

Sparsely correlated hidden Markov models with application to genome-wide location studies

• Bioinformatics
• January 2013

A genome-wide MeSH-based literature mining system predicts implicit gene-to-gene relati...

• BMC Systems Biology
• January 2013

Characterization of the EZH2-MMSET Histone Methyltransferase Regulatory Axis in Cancer

• Molecular Cell
• January 2013

Exploring the Cooccurrence Patterns of Multiple Sets of Genomic Intervals

• BioMed Research International
• January 2013

MotifOrganizer a scalable model-based motif clustering tool for mammalian genomes

• Frontiers in Bioscience
• January 2013

Gene Density, Transcription, and Insulators Contribute to the Partition of the Drosophi...

• Molecular Cell
• November 2012

Read-mapping using personalized diploid reference genome for RNA sequencing data reduce...

• October 2012

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

• Bioinformatics
• September 2012

The Histone Acetyltransferase MOF Is a Key Regulator of the Embryonic Stem Cell Core Tr...

• Cell Stem Cell
• August 2012

PM-Seq: Using Finite Poisson Mixture Models for RNA-Seq Data Analysis and Transcript Ex...

• Statistics in Biosciences
• June 2012

GPUmotif: An Ultra-Fast and Energy-Efficient Motif Analysis Program Using Graphics Proc...

• PLoS ONE
• May 2012

Cooperation between Polycomb and androgen receptor during oncogenic transformation

• Genome Research
• December 2011

FOXP3 Orchestrates H4K16 Acetylation and H3K4 Trimethylation for Activation of Multiple...

• Molecular Cell
• December 2011

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

• Bioinformatics
• November 2011

Coordinated Regulation of Polycomb Group Complexes through microRNAs in Cancer

• Cancer Cell
• August 2011

Deep sequencing reveals distinct patterns of DNA methylation in prostate cancer

• Genome Research
• July 2011

C/EBPβ Mediates Growth Hormone-Regulated Expression of Multiple Target Genes

• Molecular Endocrinology
• April 2011

SAINT: probabilistic scoring of affinity purification–mass spectrometry data

• Nature Methods
• December 2010

Statistical Issues in the Analysis of ChIP-Seq and RNA-Seq Data

• Genes
• September 2010

A Global Protein Kinase and Phosphatase Interaction Network in Yeast

• Science
• May 2010

An Integrated Network of Androgen Receptor, Polycomb, and TMPRSS2-ERG Gene Fusions in P...

• Cancer Cell
• May 2010

A Double-Layered Mixture Model for the Joint Analysis of DNA Copy Number and Gene Expre...

• Journal of Computational Biology
• February 2010

On the detection and refinement of transcription factor binding sites using ChIP-Seq data

• Nucleic Acids Research
• January 2010

HPeak: an HMM-based algorithm for defining read-enriched regions in ChIP-Seq data

• BMC Bioinformatics
• January 2010

Global Gene Expression Analysis Reveals Evidence for Decreased Lipid Biosynthesis and I...

• Journal of Investigative Dermatology
• December 2009

Computational and Functional Analysis of Growth Hormone (GH)-Regulated Genes Identifies...

• Endocrinology
• August 2009

Drug–Drug Interaction Prediction Assessment

• Journal of Biopharmaceutical Statistics
• June 2009

Hierarchical hidden Markov model with application to joint analysis of ChIP-chip and Ch...

• Bioinformatics
• May 2009

Progress toward personalized medicine for glaucoma

• Expert Review of Ophthalmology
• April 2009

Query Large Scale Microarray Compendium Datasets Using a Model-Based Bayesian Approach ...

• PLoS ONE
• February 2009

A new probabilistic rule for drug–dug interaction prediction

• Journal of Pharmacokinetics and Pharmacodynamics
• January 2009

Advances in Statistical Bioinformatics

• January 2009

Comparison of laboratory-based and phylogenetic methods to distinguish between Haemophi...

• Journal of Microbiological Methods
• October 2008

Family‐based SNP association study on 8q24 in bipolar disorder

• American Journal of Medical Genetics Part B Neuropsychiatric Genetics
• July 2008

Genome-wide detection and characterization of positive selection in human populations

• Nature
• October 2007

A second generation human haplotype map of over 3.1 million SNPs

• Nature
• October 2007

p53-Mediated Activation of miRNA34 Candidate Tumor-Suppressor Genes

• Current Biology
• August 2007

CRCView: a web server for analyzing and visualizing microarray gene expression data usi...

• Bioinformatics
• May 2007

Different normalization strategies for microarray gene expression traits affect the her...

• BMC Proceedings
• January 2007

Operon Prediction for Sequenced Bacterial Genomes without Experimental Information

• Applied and Environmental Microbiology
• November 2006

Clustering microarray gene expression data using weighted Chinese restaurant process

• Bioinformatics
• June 2006

A Comparison of Phasing Algorithms for Trios and Unrelated Individuals

• The American Journal of Human Genetics
• March 2006

Energy, quiescence and the cellular basis of animal life spans

• Comparative Biochemistry and Physiology Part A Molecular & Integrative Physiology
• January 2006

TAGSNP SELECTION BASED ON PAIRWISE LD CRITERIA AND POWER ANALYSIS IN ASSOCIATION STUDIES

• December 2005

An efficient comprehensive search algorithm for tagSNP selection using linkage disequil...

• Bioinformatics
• November 2005

Improved Classification of Mass Spectrometry Database Search Results Using Newer Machin...

• Molecular & Cellular Proteomics
• November 2005

A haplotype map of the human genome

• Nature
• October 2005

High Throughput Screening of Co-Expressed Gene Pairs with Controlled False Discovery Ra...

• Journal of Computational Biology
• September 2005

Protein Tyrosine Phosphatase Gene PTPN22 Polymorphism in Psoriasis: Lack of Evidence fo...

• Journal of Investigative Dermatology
• August 2005

Fine Mapping of the Psoriasis Susceptibility Gene PSORS1: A Reassessment of Risk Associ...

• Journal of Investigative Dermatology
• May 2005

• BMC Bioinformatics
• January 2005

HapBlock: haplotype block partitioning and tag SNP selection software using a set of dy...

• Bioinformatics
• August 2004

Haplotype Block Partitioning and Tag SNP Selection Using Genotype Data and Their Applic...

• Genome Research
• May 2004

Incorporating Genotyping Uncertainty in Haplotype Inference for Single-Nucleotide Polym...

• The American Journal of Human Genetics
• March 2004

Statistical resynchronization and Bayesian detection of periodically expressed genes

• Nucleic Acids Research
• January 2004

Dynamic Programming Algorithms for Haplotype Block Partitioning and Tag SNP Selection U...

• January 2004

Haplotype Inference and Its Application in Linkage Disequilibrium Mapping

• January 2004

Identification of co-regulated genes through Bayesian clustering of predicted regulator...

• Nature Biotechnology
• March 2003

Scale Mixture Models with Applications to Bayesian Inference

• January 2003

Partition-Ligation–Expectation-Maximization Algorithm for Haplotype Inference with Sing...

• The American Journal of Human Genetics
• November 2002

Bayesian Haplotype Inference for Multiple Linked Single-Nucleotide Polymorphisms

• The American Journal of Human Genetics
• January 2002

Multipoint Metropolis Method with Application to Hybrid Monte Carlo

• Journal of Computational Physics
• September 2001

Model-Based Methods for Transcript Expression-Level Quantification in RNA-Seq

Plate section

Preface

Statistical resynchronization and detection of periodic transcripts