Haplotype Inference and Its Application in Linkage Disequilibrium Mapping. - Tianhua Niu; Xin Lu; Hosung Kang; Zhaohui S. Qin; Jun S. Liu (Computational Methods for SNPs and Haplotype Inference, 2002)

Dynamic Programming Algorithms for Haplotype Block Partitioning and Tag SNP Selection Using Haplotype Data or Genotype Data. - Kui Zhang; Ting Chen 006; Michael S. Waterman; Zhaohui S. Qin; Jun S. Liu; Fengzhu Sun (Computational Methods for SNPs and Haplotype Inference, 2002)

Statistical Resynchronization and Detection of Periodic Transcripts. - Xin Lu; Wen Zhang; Zhaohui S. Qin; Jun S. Liu (CSB, 2003)

HapBlock: haplotype block partitioning and tag SNP selection software using a set of dynamic programming algorithms. - Kui Zhang; Zhaohui S. Qin; Ting Chen 006; Jun S. Liu; Michael S. Waterman; Fengzhu Sun (Bioinform., 2005)

Structural comparison of metabolic networks in selected single cell organisms. - Dongxiao Zhu; Zhaohui S. Qin (BMC Bioinform., 2005)

High Throughput Screening of Co-Expressed Gene Pairs with Controlled False Discovery Rate (FDR) and Minimum Acceptable Strength (MAS). - Dongxiao Zhu; Alfred O. Hero III; Zhaohui S. Qin; Anand Swaroop (J. Comput. Biol., 2005)

TagSNP Selection Based on Pairwise LD Criteria and Power Analysis in Association Studies. - Shyam Gopalakrishnan; Zhaohui S. Qin (Pacific Symposium on Biocomputing, 2006)

Clustering microarray gene expression data using weighted Chinese restaurant process. - Zhaohui S. Qin (Bioinform., 2006)

An efficient comprehensive search algorithm for tagSNP selection using linkage disequilibrium criteria. - Zhaohui S. Qin; Shyam Gopalakrishnan; Gonçalo R. Abecasis (Bioinform., 2006)

CRCView: a web server for analyzing and visualizing microarray gene expression data using model-based clustering. - Zuoshuang Xiang; Zhaohui S. Qin; Yongqun He (Bioinform., 2007)

Data Analysis and Graphics Using R: An Example-Based Approach, Second Edition.: John Maindonald and John Braun. - Zhaohui S. Qin (Briefings Bioinform., 2008)

Hierarchical hidden Markov model with application to joint analysis of ChIP-chip and ChIP-seq data. - Hyungwon Choi; Alexey I. Nesvizhskii; Debashis Ghosh; Zhaohui S. Qin (Bioinform., 2009)

HPeak: an HMM-based algorithm for defining read-enriched regions in ChIP-Seq data. - Zhaohui S. Qin; Jianjun Yu; Jincheng Shen; Christopher A. Maher; Ming Hu 001; Shanker Kalyana-Sundaram; Jindan Yu; Arul M. Chinnaiyan (BMC Bioinform., 2010)

A Double-Layered Mixture Model for the Joint Analysis of DNA Copy Number and Gene Expression Data. - Hyungwon Choi; Zhaohui S. Qin; Debashis Ghosh (J. Comput. Biol., 2010)

Read-mapping using personalized diploid reference genome for RNA sequencing data reduced bias for detecting allele-specific expression. - Shuai Yuan; Zhaohui S. Qin (BIBM Workshops, 2012)

HiCNorm: removing biases in Hi-C data via Poisson regression. - Ming Hu 001; Ke Deng; Siddarth Selvaraj; Zhaohui S. Qin; Bing Ren; Jun S. Liu (Bioinform., 2012)

Using Poisson mixed-effects model to quantify transcript-level gene expression in RNA-Seq. - Ming Hu 001; Yu Zhu; Jeremy M. G. Taylor; Jun S. Liu; Zhaohui S. Qin (Bioinform., 2012)

Sparsely correlated hidden Markov models with application to genome-wide location studies. - Hyungwon Choi; Damian Fermin; Alexey I. Nesvizhskii; Debashis Ghosh; Zhaohui S. Qin (Bioinform., 2013)

A genome-wide MeSH-based literature mining system predicts implicit gene-to-gene relationships and networks. - Zuoshuang Xiang; Tingting Qin; Zhaohui S. Qin; Yongqun He (BMC Syst. Biol., 2013)

Bayesian Inference of Spatial Organizations of Chromosomes. - Ming Hu 001; Ke Deng; Zhaohui S. Qin; Jesse R. Dixon; Siddarth Selvaraj; Jennifer Fang; Bing Ren; Jun S. Liu (PLoS Comput. Biol., 2013)

Understanding spatial organizations of chromosomes via statistical analysis of Hi-C data. - Ming Hu 001; Ke Deng; Zhaohui S. Qin; Jun S. Liu (Quant. Biol., 2013)

A novel statistical method for quantitative comparison of multiple ChIP-seq datasets. - Li Chen 029; Chi Wang 003; Zhaohui S. Qin; Hao Wu 003 (Bioinform., 2015)

One Size Doesn't Fit All - RefEditor: Building Personalized Diploid Reference Genome to Improve Read Mapping and Genotype Calling in Next Generation Sequencing Studies. - Shuai Yuan; H. Richard Johnston; Guosheng Zhang; Yun Li; Yi-Juan Hu; Zhaohui S. Qin (PLoS Comput. Biol., 2015)

EGO: A Biomedical Ontology for Integrative Epigenome Representation and Analysis. - Yongqun He; Zhaohui S. Qin; Jie Zheng 001 (ICBO/BioCreative, 2016)

traseR: an R package for performing trait-associated SNP enrichment analysis in genomic intervals. - Li Chen 029; Zhaohui S. Qin (Bioinform., 2016)

Bayesian inference with historical data-based informative priors improves detection of differentially expressed genes. - Ben Li; Zhaonan Sun; Qing He; Yu Zhu; Zhaohui S. Qin (Bioinform., 2016)

A hidden Markov random field-based Bayesian method for the detection of long-range chromosomal interactions in Hi-C data. - Zheng Xu 010; Guosheng Zhang; Fulai Jin; Mengjie Chen; Terrence S. Furey; Patrick F. Sullivan; Zhaohui S. Qin; Ming Hu 001; Yun Li (Bioinform., 2016)

High Performance Merging of Massive Data from Genome-Wide Association Studies. - Xiaobo Sun; Fusheng Wang 001; Zhaohui S. Qin (DMAH@VLDB, 2017)

Omicseq: a web-based search engine for exploring omics datasets. - Xiaobo Sun; William S. Pittard; Tianlei Xu; Li Chen 029; Michael E. Zwick; Xiaoqian Jiang; Fusheng Wang 001; Zhaohui S. Qin (Nucleic Acids Res., 2017)

Special collection of bioinformatics in the era of precision medicine. - Zhaohui S. Qin (Quant. Biol., 2017)

Probabilistic and machine learning-based retrieval approaches for biomedical dataset retrieval. - Payam Karisani; Zhaohui S. Qin; Eugene Agichtein (Database J. Biol. Databases Curation, 2018)

RT States: systematic annotation of the human genome using cell type-specific replication timing programs. - Axel Poulet; Ben Li; Tristan Dubos; Juan Carlos Rivera-Mulia; David M. Gilbert; Zhaohui S. Qin (Bioinform., 2019)

A comprehensive review of computational prediction of genome-wide features. - Tianlei Xu; Xiaoqi Zheng; Ben Li; Peng Jin; Zhaohui S. Qin; Hao Wu 003 (Briefings Bioinform., 2020)

Regulatory annotation of genomic intervals based on tissue-specific expression QTLs. - Tianlei Xu; Peng Jin; Zhaohui S. Qin (Bioinform., 2020)

Application of topic models to a compendium of ChIP-Seq datasets uncovers recurrent transcriptional regulatory modules. - Guodong Yang; Aiqun Ma; Zhaohui S. Qin; Li Chen 029 (Bioinform., 2020)

Proceedings of the 2019 MidSouth Computational Biology and Bioinformatics Society (MCBIOS) Conference. - Jonathan D. Wren; Yongsheng Bai; Zhaohui S. Qin; Da Yan 001; Ramin Homayouni (BMC Bioinform., 2020)

Inferring Spatial Organization of Individual Topologically Associated Domains via Piecewise Helical Model. - Rongrong Zhang; Ming Hu 001; Yu Zhu; Zhaohui S. Qin; Ke Deng; Jun S. Liu (IEEE ACM Trans. Comput. Biol. Bioinform., 2020)

Systematic Exploration in Tissue-Pathway Associations of Complex Traits Using Comprehensive eQTLs Catalog. - Boqi Wang; James Yang; Steven Qiu; Yongsheng Bai; Zhaohui S. Qin (Frontiers Big Data, 2021)

A wonderful time - exciting progress made in the past 20 years in genetics powered by the Human Genome Project. - Zhaohui S. Qin (Quant. Biol., 2021)

Disease category-specific annotation of variants using an ensemble learning framework. - Zhen Cao; Yanting Huang; Ran Duan; Peng Jin; Zhaohui S. Qin; Shihua Zhang (Briefings Bioinform., 2022)

LRcell: detecting the source of differential expression at the sub-cell-type level from bulk RNA-seq data. - Wenjing Ma; Sumeet Sharma; Peng Jin; Shannon L. Gourley; Zhaohui S. Qin (Briefings Bioinform., 2022)

Guest Editorial for Selected Papers From BIOKDD 2021. - Da Yan 001; Zhaohui S. Qin; Debswapna Bhattacharya; Jake Y. Chen (IEEE ACM Trans. Comput. Biol. Bioinform., 2022)

Editorial: AI and data science in drug development and public health: Highlights from the MCBIOS 2022 conference. - Ramin Homayouni; Prashanti Manda; Aik Choon Tan; Zhaohui S. Qin (Frontiers Big Data, 2023)

A novel classification framework for genome-wide association study of whole brain MRI images using deep learning. - Shaojun Yu; Junjie Wu; Yumeng Shao; Deqiang Qiu; Zhaohui S. Qin (PLoS Comput. Biol., 2024)

Controllable Data Generation by Deep Learning: A Review. - Shiyu Wang 002; Yuanqi Du; Xiaojie Guo 002; Bo Pan; Zhaohui S. Qin; Liang Zhao 002 (ACM Comput. Surv., 2024)

A review on knowledge graphs for healthcare: Resources, applications, and promises. - Hejie Cui; Jiaying Lu 001; Ran Xu 002; Shiyu Wang 002; Wenjing Ma; Yue Yu 001; Shaojun Yu; Xuan Kan; Chen Ling 003; Liang Zhao 002; Zhaohui S. Qin; Joyce C. Ho; et al. (J. Biomed. Informatics, 2025)