All Stories

  1. Disease category-specific annotation of variants using an ensemble learning framework

    Article • Briefings in Bioinformatics, October 2021, Oxford University Press (OUP)

    Dr Zhaohui S. Qin

  2. 20th International Workshop on Data Mining in Bioinformatics (BIOKDD 2021)

    Article • August 2021, ACM (Association for Computing Machinery)

    Da Yan, Dr Zhaohui S. Qin, Mohammed Zaki

  3. Plasma Metabolic Phenotypes of HPV-Associated versus Smoking-Associated Head and Neck Cancer and Patient Survival

    Article • Cancer Epidemiology Biomarkers & Prevention, August 2021, American Association for Cancer Research (AACR)

    Dr Zhaohui S. Qin

  4. LRcell: detecting the source of differential expression at the sub-cell type level from bulk RNA-seq data

    Article • August 2021, Cold Spring Harbor Laboratory Press

    Dr Zhaohui S. Qin

  5. EWASplus: a computational tool to expand EWAS coverage from the array to the whole epigenome.

    Article • Nature Communications, July 2021, Springer Science + Business Media

    Dr Zhaohui S. Qin

  6. Pan-cancer analysis of pathway-based gene expression pattern at the individual level reveals biomarkers of clinical prognosis

    Article • Cell Reports Methods, July 2021, Elsevier

    Dr Zhaohui S. Qin

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

    Article • Communications Biology, June 2021, Springer Science + Business Media

    Dr Zhaohui S. Qin

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

    Article • Nature Communications, November 2020, Springer Science + Business Media

    Dr Zhaohui S. Qin

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

    Article • Nature Communications, May 2020, Springer Science + Business Media

    Dr Zhaohui S. Qin

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

    Article • Proceedings of the National Academy of Sciences, February 2020, Proceedings of the National Academy of Sciences

    Dr Zhaohui S. Qin

  11. Application of topic models to a compendium of ChIP-Seq datasets uncovers recurrent transcriptional regulatory modules

    Article • Bioinformatics, January 2020, Oxford University Press (OUP)

    Dr Zhaohui S. Qin

  12. An Integrated System Biology Approach Yields Drug Repositioning Candidates for the Treatment of Heart Failure

    Article • Frontiers in Genetics, September 2019, Frontiers

    Dr Zhaohui S. Qin

  13. Regulatory annotation of genomic intervals based on tissue-specific expression QTLs

    Article • Bioinformatics, August 2019, Oxford University Press (OUP)

    Dr Zhaohui S. Qin

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

    Article • Epigenetics, June 2019, Taylor & Francis

    Dr Zhaohui S. Qin

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

    Article • IEEE/ACM Transactions on Computational Biology and Bioinformatics, January 2019, Institute of Electrical & Electronics Engineers (IEEE)

    Dr Zhaohui S. Qin, Ming Hu

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

    Article • Bioinformatics, November 2018, Oxford University Press (OUP)

    Dr Zhaohui S. Qin

  17. A comprehensive review of computational prediction of genome-wide features

    Article • Briefings in Bioinformatics, November 2018, Oxford University Press (OUP)

    Dr Zhaohui S. Qin

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

    Article • August 2018, Cold Spring Harbor Laboratory Press

    Axel Poulet, Dr Zhaohui S. Qin

  19. EWS/ETS-Driven Ewing Sarcoma Requires BET Bromodomain Proteins

    Article • Cancer Research, June 2018, American Association for Cancer Research (AACR)

    Dr Zhaohui S. Qin

  20. Use cloud-based distributed systems to speed up merging of large collection of VCF files.

    Article • GigaScience, May 2018, Oxford University Press (OUP)

    Dr Zhaohui S. Qin

  21. Special collection of bioinformatics in the era of precision medicine

    Article • Quantitative Biology, November 2017, Springer Science + Business Media

    Dr Zhaohui S. Qin

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

    Article • BMC Research Notes, October 2017, Springer Science + Business Media

    Dr Zhaohui S. Qin

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

    Article • Journal of Clinical Investigation, June 2017, American Society for Clinical Investigation

    Dr Zhaohui S. Qin

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

    Article • Scientific Reports, April 2017, Springer Science + Business Media

    Oluwafemi Oluwole, Dr Zhaohui S. Qin

  25. Omicseq: searching omics data without using metadata

    Article • Nucleic Acids Research, April 2017, Oxford University Press (OUP)

    Dr Zhaohui S. Qin, Tianlei Xu, Michael Zwick

  26. 10.1038/srep46398

    Article • February 2017, Cold Spring Harbor Laboratory Press

    Dr Zhaohui S. Qin

  27. An approach of identifying differential nucleosome regions in multiple samples

    Article • BMC Genomics, February 2017, Springer Science + Business Media

    Dr Zhaohui S. Qin

  28. Computationally Tractable Multivariate HMM in Genome-Wide Mapping Studies

    Article • January 2017, Springer Science + Business Media

    Dr Zhaohui S. Qin

  29. Disease-specific non-coding variant annotation

    Article • December 2016, Springer Science + Business Media

    Dr Zhaohui S. Qin

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

    Article • Journal of Innate Immunity, November 2016, Karger Publishers

    Dr Zhaohui S. Qin

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

    Article • PeerJ, October 2016, PeerJ

    Dr Zhaohui S. Qin

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

    Article • Nature Communications, October 2016, Springer Science + Business Media

    Oluwafemi Oluwole, Dr Zhaohui S. Qin

  33. Use historical data to improve detection of differential expressed genes.

    Article • Statistics in Biosciences, July 2016, Springer Science + Business Media

    Dr Zhaohui S. Qin

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

    Article • Cell Discovery, May 2016, Nature

    Dr Zhaohui S. Qin

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

    Article • PLoS Genetics, May 2016, PLOS

    Dr Zhaohui S. Qin

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

    Article • Bioinformatics, December 2015, Oxford University Press (OUP)

    Dr Zhaohui S. Qin

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

    Article • Bioinformatics, October 2015, Oxford University Press (OUP)

    Dr Zhaohui S. Qin

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

    Article • PLoS Computational Biology, August 2015, PLOS

    Dr Zhaohui S. Qin

  39. Detection of differentially methylated regions from whole-genome bisulfite sequencing data without replicates

    Article • Nucleic Acids Research, July 2015, Oxford University Press (OUP)

    Tianlei Xu, Dr Zhaohui S. Qin

  40. Widespread Rearrangement of 3D Chromatin Organization Underlies Polycomb-Mediated Stress-Induced Silencing

    Article • Molecular Cell, April 2015, Elsevier

    Dr Zhaohui S. Qin

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

    Article • Nucleic Acids Research, February 2015, Oxford University Press (OUP)

    Dr Zhaohui S. Qin, Tianlei Xu

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

    Article • Bioinformatics, February 2015, Oxford University Press (OUP)

    Dr Zhaohui S. Qin

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

    Article • Science in China Series C Life Sciences, October 2014, Springer Science + Business Media

    Dr Zhaohui S. Qin

  44. Integrated Analysis of Whole-Genome Paired-End and Mate-Pair Sequencing Data for Identifying Genomic Structural Variations in Multiple Myeloma

    Article • Cancer Informatics, September 2014, Libertas Academica, Ltd.

    Dr Zhaohui S. Qin

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

    Article • Molecular and Cellular Endocrinology, September 2014, Elsevier

    Dr Zhaohui S. Qin

  46. Direct Amplification, Sequencing and Profiling of Chlamydia trachomatis Strains in Single and Mixed Infection Clinical Samples

    Article • PLoS ONE, June 2014, PLOS

    Dr Zhaohui S. Qin

  47. H2B Ubiquitylation Promotes RNA Pol II Processivity via PAF1 and pTEFb

    Article • Molecular Cell, June 2014, Elsevier

    Dr Zhaohui S. Qin

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

    Article • Nature, April 2014, Nature

    Dr Zhaohui S. Qin

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

    Article • Nature Communications, January 2014, Nature

    Dr Zhaohui S. Qin

  50. Targeting MLL1 H3K4 Methyltransferase Activity in Mixed-Lineage Leukemia

    Article • Molecular Cell, January 2014, Elsevier

    Dr Zhaohui S. Qin

  51. EgoNet: identification of human disease ego-network modules

    Article • BMC Genomics, January 2014, Springer Science + Business Media

    Dr Zhaohui S. Qin

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

    Article • Genome Biology, January 2014, Springer Science + Business Media

    Dr Zhaohui S. Qin

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

    Article • Journal of Clinical Investigation, October 2013, American Society for Clinical Investigation

    Dr Zhaohui S. Qin

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

    Article • Genes & Development, July 2013, Cold Spring Harbor Laboratory Press

    Dr Zhaohui S. Qin

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

    Article • Quantitative Biology, June 2013, Springer Science + Business Media

    Dr Zhaohui S. Qin

  56. Bayesian Inference of Spatial Organizations of Chromosomes

    Article • PLoS Computational Biology, January 2013, PLOS

    Dr Zhaohui S. Qin

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

    Article • Bioinformatics, January 2013, Oxford University Press (OUP)

    Dr Zhaohui S. Qin

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

    Article • BMC Systems Biology, January 2013, Springer Science + Business Media

    Dr Zhaohui S. Qin

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

    Article • Molecular Cell, January 2013, Elsevier

    Dr Zhaohui S. Qin

  60. Exploring the Cooccurrence Patterns of Multiple Sets of Genomic Intervals

    Article • BioMed Research International, January 2013, Hindawi Publishing Corporation

    Dr Zhaohui S. Qin

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

    Article • Frontiers in Bioscience, January 2013, Frontiers in Bioscience

    Dr Zhaohui S. Qin

  62. Gene Density, Transcription, and Insulators Contribute to the Partition of the Drosophila Genome into Physical Domains

    Article • Molecular Cell, November 2012, Elsevier

    Dr Zhaohui S. Qin

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

    Article • October 2012, Institute of Electrical & Electronics Engineers (IEEE)

    Dr Zhaohui S. Qin

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

    Article • Bioinformatics, September 2012, Oxford University Press (OUP)

    Dr Zhaohui S. Qin

  65. The Histone Acetyltransferase MOF Is a Key Regulator of the Embryonic Stem Cell Core Transcriptional Network

    Article • Cell Stem Cell, August 2012, Elsevier

    Dr Zhaohui S. Qin

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

    Article • Statistics in Biosciences, June 2012, Springer Science + Business Media

    Dr Zhaohui S. Qin

  67. GPUmotif: An Ultra-Fast and Energy-Efficient Motif Analysis Program Using Graphics Processing Units

    Article • PLoS ONE, May 2012, PLOS

    Dr Zhaohui S. Qin

  68. Cooperation between Polycomb and androgen receptor during oncogenic transformation

    Article • Genome Research, December 2011, Cold Spring Harbor Laboratory Press

    Dr Zhaohui S. Qin

  69. FOXP3 Orchestrates H4K16 Acetylation and H3K4 Trimethylation for Activation of Multiple Genes by Recruiting MOF and Causing Displacement of PLU-1

    Article • Molecular Cell, December 2011, Elsevier

    Dr Zhaohui S. Qin

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

    Article • Bioinformatics, November 2011, Oxford University Press (OUP)

    Dr Zhaohui S. Qin

  71. Coordinated Regulation of Polycomb Group Complexes through microRNAs in Cancer

    Article • Cancer Cell, August 2011, Elsevier

    Dr Zhaohui S. Qin

  72. Deep sequencing reveals distinct patterns of DNA methylation in prostate cancer

    Article • Genome Research, July 2011, Cold Spring Harbor Laboratory Press

    Dr Zhaohui S. Qin

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

    Article • Molecular Endocrinology, April 2011, Endocrine Society

    Dr Zhaohui S. Qin

  74. SAINT: probabilistic scoring of affinity purification–mass spectrometry data

    Article • Nature Methods, December 2010, Nature

    Dr Zhaohui S. Qin

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

    Article • Genes, September 2010, MDPI AG

    Dr Zhaohui S. Qin

  76. A Global Protein Kinase and Phosphatase Interaction Network in Yeast

    Article • Science, May 2010, American Association for the Advancement of Science

    Dr Zhaohui S. Qin

  77. An Integrated Network of Androgen Receptor, Polycomb, and TMPRSS2-ERG Gene Fusions in Prostate Cancer Progression

    Article • Cancer Cell, May 2010, Elsevier

    Dr Zhaohui S. Qin

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

    Article • Journal of Computational Biology, February 2010, Mary Ann Liebert Inc

    Dr Zhaohui S. Qin

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

    Article • Nucleic Acids Research, January 2010, Oxford University Press (OUP)

    Dr Zhaohui S. Qin

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

    Article • BMC Bioinformatics, January 2010, Springer Science + Business Media

    Dr Zhaohui S. Qin

  81. Global Gene Expression Analysis Reveals Evidence for Decreased Lipid Biosynthesis and Increased Innate Immunity in Uninvolved Psoriatic Skin

    Article • Journal of Investigative Dermatology, December 2009, Elsevier

    Dr Zhaohui S. Qin

  82. 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

    Article • Endocrinology, August 2009, Endocrine Society

    Dr Zhaohui S. Qin

  83. Drug–Drug Interaction Prediction Assessment

    Article • Journal of Biopharmaceutical Statistics, June 2009, Taylor & Francis

    Dr Zhaohui S. Qin

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

    Article • Bioinformatics, May 2009, Oxford University Press (OUP)

    Dr Zhaohui S. Qin

  85. Progress toward personalized medicine for glaucoma

    Article • Expert Review of Ophthalmology, April 2009, Informa Healthcare

    Dr Zhaohui S. Qin

  86. Query Large Scale Microarray Compendium Datasets Using a Model-Based Bayesian Approach with Variable Selection

    Article • PLoS ONE, February 2009, PLOS

    Dr Zhaohui S. Qin

  87. A new probabilistic rule for drug–dug interaction prediction

    Article • Journal of Pharmacokinetics and Pharmacodynamics, January 2009, Springer Science + Business Media

    Dr Zhaohui S. Qin

  88. Advances in Statistical Bioinformatics

    Article • January 2009, Cambridge University Press

    Dr Zhaohui S. Qin

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

    Article • Journal of Microbiological Methods, October 2008, Elsevier

    Dr Zhaohui S. Qin

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

    Article • American Journal of Medical Genetics Part B Neuropsychiatric Genetics, July 2008, Wiley

    Dr Zhaohui S. Qin

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

    Article • Nature, October 2007, Nature

    Rachelle Gaudet, Dr Zhaohui S. Qin

  92. A second generation human haplotype map of over 3.1 million SNPs

    Article • Nature, October 2007, Nature

    Dr Zhaohui S. Qin

  93. p53-Mediated Activation of miRNA34 Candidate Tumor-Suppressor Genes

    Article • Current Biology, August 2007, Elsevier

    Dr Zhaohui S. Qin

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

    Article • Bioinformatics, May 2007, Oxford University Press (OUP)

    Dr Zhaohui S. Qin

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

    Article • BMC Proceedings, January 2007, Springer Science + Business Media

    Dr Zhaohui S. Qin

  96. Operon Prediction for Sequenced Bacterial Genomes without Experimental Information

    Article • Applied and Environmental Microbiology, November 2006, ASM Journals

    Dr Zhaohui S. Qin

  97. Clustering microarray gene expression data using weighted Chinese restaurant process

    Article • Bioinformatics, June 2006, Oxford University Press (OUP)

    Dr Zhaohui S. Qin

  98. A Comparison of Phasing Algorithms for Trios and Unrelated Individuals

    Article • The American Journal of Human Genetics, March 2006, Elsevier

    Dr Zhaohui S. Qin

  99. Energy, quiescence and the cellular basis of animal life spans

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

    Dr Zhaohui S. Qin

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

    Article • December 2005, World Scientific Pub Co Pte Lt

    Dr Zhaohui S. Qin

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

    Article • Bioinformatics, November 2005, Oxford University Press (OUP)

    Dr Zhaohui S. Qin

  102. Improved Classification of Mass Spectrometry Database Search Results Using Newer Machine Learning Approaches

    Article • Molecular & Cellular Proteomics, November 2005, American Society for Biochemistry & Molecular Biology (ASBMB)

    Dr Zhaohui S. Qin

  103. A haplotype map of the human genome

    Article • Nature, October 2005, Nature

    Dr Zhaohui S. Qin

  104. High Throughput Screening of Co-Expressed Gene Pairs with Controlled False Discovery Rate (FDR) and Minimum Acceptable Strength (MAS)

    Article • Journal of Computational Biology, September 2005, Mary Ann Liebert Inc

    Dr Zhaohui S. Qin

  105. Protein Tyrosine Phosphatase Gene PTPN22 Polymorphism in Psoriasis: Lack of Evidence for Association

    Article • Journal of Investigative Dermatology, August 2005, Wiley

    Dr Zhaohui S. Qin

  106. Fine Mapping of the Psoriasis Susceptibility Gene PSORS1: A Reassessment of Risk Associated with a Putative Risk Haplotype Lacking HLA-Cw6

    Article • Journal of Investigative Dermatology, May 2005, Elsevier

    Dr Zhaohui S. Qin

  107. Article • BMC Bioinformatics, January 2005, Springer Science + Business Media

    Dr Zhaohui S. Qin

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

    Article • Bioinformatics, August 2004, Oxford University Press (OUP)

    Dr Zhaohui S. Qin

  109. Haplotype Block Partitioning and Tag SNP Selection Using Genotype Data and Their Applications to Association Studies

    Article • Genome Research, May 2004, Cold Spring Harbor Laboratory Press

    Dr Zhaohui S. Qin

  110. Incorporating Genotyping Uncertainty in Haplotype Inference for Single-Nucleotide Polymorphisms

    Article • The American Journal of Human Genetics, March 2004, Elsevier

    Dr Zhaohui S. Qin

  111. Statistical resynchronization and Bayesian detection of periodically expressed genes

    Article • Nucleic Acids Research, January 2004, Oxford University Press (OUP)

    Dr Zhaohui S. Qin

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

    Article • January 2004, Springer Science + Business Media

    Dr Zhaohui S. Qin

  113. Haplotype Inference and Its Application in Linkage Disequilibrium Mapping

    Article • January 2004, Springer Science + Business Media

    Dr Zhaohui S. Qin

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

    Article • Nature Biotechnology, March 2003, Nature

    Dr Zhaohui S. Qin

  115. Scale Mixture Models with Applications to Bayesian Inference

    Article • January 2003, American Institute of Physics

    Dr Zhaohui S. Qin

  116. Partition-Ligation–Expectation-Maximization Algorithm for Haplotype Inference with Single-Nucleotide Polymorphisms

    Article • The American Journal of Human Genetics, November 2002, Elsevier

    Dr Zhaohui S. Qin

  117. Bayesian Haplotype Inference for Multiple Linked Single-Nucleotide Polymorphisms

    Article • The American Journal of Human Genetics, January 2002, Elsevier

    Dr Zhaohui S. Qin

  118. Multipoint Metropolis Method with Application to Hybrid Monte Carlo

    Article • Journal of Computational Physics, September 2001, Elsevier

    Dr Zhaohui S. Qin

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

    Article • Cambridge University Press

    Dr Zhaohui S. Qin

  120. Plate section

    Article • Cambridge University Press

    Dr Zhaohui S. Qin

  121. Preface

    Article • Cambridge University Press

    Dr Zhaohui S. Qin

  122. Statistical resynchronization and detection of periodic transcripts

    Article • Institute of Electrical & Electronics Engineers (IEEE)

    Dr Zhaohui S. Qin