List of works - Zhaohui Steve Qin

A comparison of phasing algorithms for trios and unrelated individuals

scientific article

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

scientific article published on 11 October 2016

A double-layered mixture model for the joint analysis of DNA copy number and gene expression data

scientific article

A genome-wide MeSH-based literature mining system predicts implicit gene-to-gene relationships and networks

scientific article

A global protein kinase and phosphatase interaction network in yeast.

scientific article

A new probabilistic rule for drug-dug interaction prediction

scientific article published on 21 January 2009

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

scientific article

A second generation human haplotype map of over 3.1 million SNPs

scientific article

ATAD3A mediates activation of RAS-independent mitochondrial ERK1/2 signaling, favoring head and neck cancer development ⬇️

scientific article published on 29 January 2022

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

scientific article

An approach of identifying differential nucleosome regions in multiple samples

scientific article

An efficient comprehensive search algorithm for tagSNP selection using linkage disequilibrium criteria

scientific article published on 3 November 2005

An empirical bayesian approach for testing gene expression fold change and its application in detecting global dosage effects

scientific article published on 18 September 2020

An integrated network of androgen receptor, polycomb, and TMPRSS2-ERG gene fusions in prostate cancer progression

scientific article

Association study in African-admixed populations across the Americas recapitulates asthma risk loci in non-African populations

scientific article published on 20 February 2019

Author Correction: Association study in African-admixed populations across the Americas recapitulates asthma risk loci in non-African populations

scientific article published on 04 September 2019

Author Correction: Truncation of mutant huntingtin in knock-in mice demonstrates exon1 huntingtin is a key pathogenic form

scientific article published on 19 November 2020

Base-resolution methylation patterns accurately predict transcription factor bindings in vivo

scientific article

Bayesian haplotype inference for multiple linked single-nucleotide polymorphisms

scientific article published on 26 November 2001

Bayesian inference of spatial organizations of chromosomes

scientific article

Bayesian inference with historical data-based informative priors improves detection of differentially expressed genes

scientific article

C/EBPβ mediates growth hormone-regulated expression of multiple target genes

scientific article

CRCView: a web server for analyzing and visualizing microarray gene expression data using model-based clustering

scientific article

CRISPR/Cas9-mediated gene editing ameliorates neurotoxicity in mouse model of Huntington's disease

scientific article published on 19 June 2017

Characterization of the EZH2-MMSET histone methyltransferase regulatory axis in cancer

scientific article

Clustering microarray gene expression data using weighted Chinese restaurant process

scientific article

Comparison of laboratory-based and phylogenetic methods to distinguish between Haemophilus influenzae and H. haemolyticus

scientific article

Computational and functional analysis of growth hormone (GH)-regulated genes identifies the transcriptional repressor B-cell lymphoma 6 (Bc16) as a participant in GH-regulated transcription

scientific article published on 30 April 2009

Computationally Tractable Multivariate HMM in Genome-Wide Mapping Studies

scientific article published on January 2017

Controllable Data Generation by Deep Learning: A Review

scientific article published in 2024

Cooperation between Polycomb and androgen receptor during oncogenic transformation

scientific article

Coordinated regulation of polycomb group complexes through microRNAs in cancer.

scientific article

DIVAN: accurate identification of non-coding disease-specific risk variants using multi-omics profiles

scientific article published on 06 December 2016

Deep sequencing reveals distinct patterns of DNA methylation in prostate cancer

scientific article

Different normalization strategies for microarray gene expression traits affect the heritability estimation

scientific article

Direct amplification, sequencing and profiling of Chlamydia trachomatis strains in single and mixed infection clinical samples

scientific article

Drug-drug interaction prediction assessment

scientific article published in July 2009

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

EWS/ETS-Driven Ewing Sarcoma Requires BET Bromodomain Proteins

scientific article published on 13 June 2018

EgoNet: identification of human disease ego-network modules

scientific article

Exploring the cooccurrence patterns of multiple sets of genomic intervals

scientific article published on 28 May 2013

FOXP3 orchestrates H4K16 acetylation and H3K4 trimethylation for activation of multiple genes by recruiting MOF and causing displacement of PLU-1.

scientific article published on December 2011

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

scientific article published on July 2008

GPUmotif: an ultra-fast and energy-efficient motif analysis program using graphics processing units

scientific article

Gene density, transcription, and insulators contribute to the partition of the Drosophila genome into physical domains

scientific article

Genome-Wide STAT3 Binding Analysis after Histone Deacetylase Inhibition Reveals Novel Target Genes in Dendritic Cells

scientific article published on 19 November 2016

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

scientific article

Global gene expression analysis reveals evidence for decreased lipid biosynthesis and increased innate immunity in uninvolved psoriatic skin

scientific article published on 02 July 2009

Glucocorticoid receptor wields chromatin interactions to tune transcription for cytoskeleton stabilization in podocytes

scientific article published on 03 June 2021

H2B ubiquitylation promotes RNA Pol II processivity via PAF1 and pTEFb

scientific article

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

scientific article

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

scientific article published on 27 August 2004

Haplotype Inference and Its Application in Linkage Disequilibrium Mapping

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

scientific article

Heat Shock Protein Beta-1 Modifies Anterior to Posterior Purkinje Cell Vulnerability in a Mouse Model of Niemann-Pick Type C Disease

scientific article

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

scientific article

Hierarchical hidden Markov model with application to joint analysis of ChIP-chip and ChIP-seq data

scientific article

High throughput screening of co-expressed gene pairs with controlled false discovery rate (FDR) and minimum acceptable strength (MAS).

scientific article published in September 2005

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

scientific article

Identifying tagging SNPs for African specific genetic variation from the African Diaspora Genome

scientific article

Impaired replication elongation in Tetrahymena mutants deficient in histone H3 Lys 27 monomethylation

scientific article published on 24 July 2013

Improved classification of mass spectrometry database search results using newer machine learning approaches

scientific article published on 30 November 2005

Improving Hierarchical Models Using Historical Data with Applications in High-Throughput Genomics Data Analysis

scientific article published on 8 July 2016

Incorporating genotyping uncertainty in haplotype inference for single-nucleotide polymorphisms

scientific article

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

scientific article published on 15 August 2018

Insulator function and topological domain border strength scale with architectural protein occupancy

scientific article

Integrated analysis of whole-genome paired-end and mate-pair sequencing data for identifying genomic structural variations in multiple myeloma

scientific article

MLL1 and MLL1 fusion proteins have distinct functions in regulating leukemic transcription program

scientific article published on 17 May 2016

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

article

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

scientific article published in January 2013

Multipoint Metropolis Method with Application to Hybrid Monte Carlo

article

OUP accepted manuscript

scientific article published on 16 November 2018

Omicseq: a web-based search engine for exploring omics datasets.

scientific article published on 10 April 2017

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

scientific article

One Size Doesn't Fit All - RefEditor: Building Personalized Diploid Reference Genome to Improve Read Mapping and Genotype Calling in Next Generation Sequencing Studies

scientific article published on 12 August 2015

Operon prediction for sequenced bacterial genomes without experimental information

scientific article published on 22 November 2006

Optimized distributed systems achieve significant performance improvement on sorted merging of massive VCF files.

scientific article published in June 2018

PM-Seq: Using Finite Poisson Mixture Models for RNA-Seq Data Analysis and Transcript Expression Level Quantification

scholarly article by Han Wu et al published 21 June 2012 in Statistics in biosciences

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

scientific article published in November 2002

Progress toward personalized medicine for glaucoma

scientific article published on April 2009

Protein tyrosine phosphatase gene PTPN22 polymorphism in psoriasis: lack of evidence for association

scientific article published in August 2005

Query large scale microarray compendium datasets using a model-based bayesian approach with variable selection

scientific article

RT States: systematic annotation of the human genome using cell type-specific replication timing programs

Read-mapping using personalized diploid reference genome for RNA sequencing data reduced bias for detecting allele-specific expression

article

Reciprocal occupancy of BCL6 and STAT5 on Growth Hormone target genes: contrasting transcriptional outcomes and promoter-specific roles of p300 and HDAC3.

scientific article

SAINT: probabilistic scoring of affinity purification-mass spectrometry data

scientific article

Scale Mixture Models with Applications to Bayesian Inference

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

scientific article published on 16 January 2013

Special collection of bioinformatics in the era of precision medicine

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

scientific article

Statistical resynchronization and Bayesian detection of periodically expressed genes

scientific article published on 22 January 2004

Structural comparison of metabolic networks in selected single cell organisms

scientific article

Super-Enhancer-Associated Transcription Factors Maintain Transcriptional Regulation in Mature Podocytes

scientific article published on 26 March 2021

Systems biology and metagenomics: a showcase of Chinese bioinformatics researchers and their work

scientific article published on 17 October 2014

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

Targeting MLL1 H3K4 methyltransferase activity in mixed-lineage leukemia

scientific article published on 02 January 2014

Ten-eleven translocation 2 interacts with forkhead box O3 and regulates adult neurogenesis

scientific article

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

scientific article

The histone acetyltransferase MOF is a key regulator of the embryonic stem cell core transcriptional network

scientific article published on August 2012

The single-species metagenome: subtyping Staphylococcus aureus core genome sequences from shotgun metagenomic data

scientific article

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

scientific article

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

scientific article published on 22 May 2020

UALCAN: An update to the integrated cancer data analysis platform

scientific article published on 22 January 2022

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

scientific article

Using DIVAN to assess disease/trait-associated single nucleotide variants in genome-wide scale

scientific article

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

scientific article published on 8 November 2011

Widespread rearrangement of 3D chromatin organization underlies polycomb-mediated stress-induced silencing

scientific article

p53-mediated activation of miRNA34 candidate tumor-suppressor genes.

scientific article

traseR: an R package for performing trait-associated SNP enrichment analysis in genomic intervals.

scientific article published on 18 December 2015

List of works by Zhaohui Steve Qin

A comparison of phasing algorithms for trios and unrelated individuals

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

A double-layered mixture model for the joint analysis of DNA copy number and gene expression data

A genome-wide MeSH-based literature mining system predicts implicit gene-to-gene relationships and networks

A global protein kinase and phosphatase interaction network in yeast.

A new probabilistic rule for drug-dug interaction prediction

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

A second generation human haplotype map of over 3.1 million SNPs

ATAD3A mediates activation of RAS-independent mitochondrial ERK1/2 signaling, favoring head and neck cancer development ⬇️

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

An approach of identifying differential nucleosome regions in multiple samples

An efficient comprehensive search algorithm for tagSNP selection using linkage disequilibrium criteria

An empirical bayesian approach for testing gene expression fold change and its application in detecting global dosage effects

An integrated network of androgen receptor, polycomb, and TMPRSS2-ERG gene fusions in prostate cancer progression

Association study in African-admixed populations across the Americas recapitulates asthma risk loci in non-African populations

Author Correction: Association study in African-admixed populations across the Americas recapitulates asthma risk loci in non-African populations

Author Correction: Truncation of mutant huntingtin in knock-in mice demonstrates exon1 huntingtin is a key pathogenic form

Base-resolution methylation patterns accurately predict transcription factor bindings in vivo

Bayesian haplotype inference for multiple linked single-nucleotide polymorphisms

Bayesian inference of spatial organizations of chromosomes

Bayesian inference with historical data-based informative priors improves detection of differentially expressed genes

C/EBPβ mediates growth hormone-regulated expression of multiple target genes

CRCView: a web server for analyzing and visualizing microarray gene expression data using model-based clustering

CRISPR/Cas9-mediated gene editing ameliorates neurotoxicity in mouse model of Huntington's disease

Characterization of the EZH2-MMSET histone methyltransferase regulatory axis in cancer

Clustering microarray gene expression data using weighted Chinese restaurant process

Comparison of laboratory-based and phylogenetic methods to distinguish between Haemophilus influenzae and H. haemolyticus

Computational and functional analysis of growth hormone (GH)-regulated genes identifies the transcriptional repressor B-cell lymphoma 6 (Bc16) as a participant in GH-regulated transcription

Computationally Tractable Multivariate HMM in Genome-Wide Mapping Studies

Controllable Data Generation by Deep Learning: A Review

Cooperation between Polycomb and androgen receptor during oncogenic transformation

Coordinated regulation of polycomb group complexes through microRNAs in cancer.

DIVAN: accurate identification of non-coding disease-specific risk variants using multi-omics profiles

Deep sequencing reveals distinct patterns of DNA methylation in prostate cancer

Different normalization strategies for microarray gene expression traits affect the heritability estimation

Direct amplification, sequencing and profiling of Chlamydia trachomatis strains in single and mixed infection clinical samples

Drug-drug interaction prediction assessment

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

EWS/ETS-Driven Ewing Sarcoma Requires BET Bromodomain Proteins

EgoNet: identification of human disease ego-network modules

Exploring the cooccurrence patterns of multiple sets of genomic intervals

FOXP3 orchestrates H4K16 acetylation and H3K4 trimethylation for activation of multiple genes by recruiting MOF and causing displacement of PLU-1.

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

GPUmotif: an ultra-fast and energy-efficient motif analysis program using graphics processing units

Gene density, transcription, and insulators contribute to the partition of the Drosophila genome into physical domains

Genome-Wide STAT3 Binding Analysis after Histone Deacetylase Inhibition Reveals Novel Target Genes in Dendritic Cells

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

Global gene expression analysis reveals evidence for decreased lipid biosynthesis and increased innate immunity in uninvolved psoriatic skin

Glucocorticoid receptor wields chromatin interactions to tune transcription for cytoskeleton stabilization in podocytes

H2B ubiquitylation promotes RNA Pol II processivity via PAF1 and pTEFb

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

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

Haplotype Inference and Its Application in Linkage Disequilibrium Mapping

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

Heat Shock Protein Beta-1 Modifies Anterior to Posterior Purkinje Cell Vulnerability in a Mouse Model of Niemann-Pick Type C Disease

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

Hierarchical hidden Markov model with application to joint analysis of ChIP-chip and ChIP-seq data

High throughput screening of co-expressed gene pairs with controlled false discovery rate (FDR) and minimum acceptable strength (MAS).

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

Identifying tagging SNPs for African specific genetic variation from the African Diaspora Genome

Impaired replication elongation in Tetrahymena mutants deficient in histone H3 Lys 27 monomethylation

Improved classification of mass spectrometry database search results using newer machine learning approaches

Improving Hierarchical Models Using Historical Data with Applications in High-Throughput Genomics Data Analysis

Incorporating genotyping uncertainty in haplotype inference for single-nucleotide polymorphisms

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

Insulator function and topological domain border strength scale with architectural protein occupancy

Integrated analysis of whole-genome paired-end and mate-pair sequencing data for identifying genomic structural variations in multiple myeloma

MLL1 and MLL1 fusion proteins have distinct functions in regulating leukemic transcription program

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

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

Multipoint Metropolis Method with Application to Hybrid Monte Carlo

OUP accepted manuscript

Omicseq: a web-based search engine for exploring omics datasets.

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

One Size Doesn't Fit All - RefEditor: Building Personalized Diploid Reference Genome to Improve Read Mapping and Genotype Calling in Next Generation Sequencing Studies

Operon prediction for sequenced bacterial genomes without experimental information

Optimized distributed systems achieve significant performance improvement on sorted merging of massive VCF files.

PM-Seq: Using Finite Poisson Mixture Models for RNA-Seq Data Analysis and Transcript Expression Level Quantification

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