Dr Zhaohui S. Qin
Emory University
Faculty Member, Statistics
United States
My co-authors include
Rachelle Gaudet
Ming Hu
Oluwafemi Oluwole
My Publications
Disease-specific non-coding variant annotation
December 2016
DIVAN is a machine learning-based algorithm that is capable of predicting whether a mutation that occur anywhere in the genome is likely to be disease-associated. It is related to popular algorithm...
Omicseq: searching omics data without using metadata
Nucleic Acids Research
April 2017
Omicseq is a search engine for omics datasets such as ChIP-seqm RNA-seq and DNase-seq. The key idea is to rank among all the public datasets given a query gene name of pathway name. Unlike existing...
Application of topic models to a compendium of ChIP-Seq datasets uncovers recurrent tra...
Bioinformatics
January 2020
Regulatory annotation of genomic intervals based on tissue-specific expression QTLs
Bioinformatics
August 2019
Use cloud-based distributed systems to speed up merging of large collection of VCF files.
GigaScience
May 2018
Sorted merge is very slow when the number of objects is large. Merging VCF file is a prime example and commonly faced in large scale sequencing-based genetics study. We showed ways to do this in th...
EWASplus: a computational tool to expand EWAS coverage from the array to the whole epig...
Nature Communications
July 2021
Existing EWAS only cover 2% of all CpGs in teh genome. EWASplus enables EWAS to be performed on all CpGs in the genome, which can significantly boost the discovery power of EWAS so new biomedical i...
Pan-cancer analysis of pathway-based gene expression pattern at the individual level re...
Cell Reports Methods
July 2021
An Integrated System Biology Approach Yields Drug Repositioning Candidates for the Trea...
Frontiers in Genetics
September 2019
RT States: systematic annotation of the human genome using cell type-specific replicati...
Bioinformatics
November 2018
Our work is similar to chromatin states, which use histone mark ChIP-seq data from multiple cell types to annotate the human genome, Here, we instead using replication timing data as the source of ...
LRcell: detecting the source of differential expression at the sub-cell type level from...
August 2021
Disease category-specific annotation of variants using an ensemble learning framework
Briefings in Bioinformatics
October 2021
20th International Workshop on Data Mining in Bioinformatics (BIOKDD 2021)
August 2021
Plasma Metabolic Phenotypes of HPV-Associated versus Smoking-Associated Head and Neck C...
Cancer Epidemiology Biomarkers & Prevention
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