Choi, Hyungwon, Nesvizhskii, Alexey I., Ghosh, Debashis, Qin, Zhaohui S.
Motivation: Chromatin immunoprecipitation (ChIP) experiments followed by array hybridization, or ChIP-chip, is a powerful approach for identifying transcription factor binding sites (TFBS) and has...
Gene Expression, Zuoshuang Xiang, Zhaohui S. Qin, Yongqun He
CRCView: a web server for analyzing and visualizing microarray gene expression data using model-based clustering
BIOINFORMATICS ORIGINAL PAPER Genetics and population analysis (2008)
Zhaohui S. Qin, Shyam Gopalakrishnan, Gonçalo R. Abecasis
An efficient comprehensive search algorithm for tagSNP selection using linkage disequilibrium criteria Vol. 22 no. 2 2006, pages 220–225 doi:10.1093/bioinformatics/bti762
Xin Lu, Wen Zhang, Zhaohui S. Qin, Jun S. Liu
A Periodic-Normal Mixture (PNM) model is proposed to fit the yeast cell cycle data of Cho et al. and Spellmen et al. and to resynchronize the transcription profiles of cell-cycle related genes....
TAGSNP SELECTION BASED ON PAIRWISE LD CRITERIA AND POWER ANALYSIS IN ASSOCIATION STUDIES (2008)
Shyam Gopalakrishnan, Zhaohui S. Qin, Shyam Gopalakrishnan, Zhaohui S Qin
TagSNP selection is an important step in designing case control association studies. Among selection methods that have proliferated, the ones based on pairwise LD measurement are attractive for the...
Abstract Several studies have been conducted to assess the influence of genetic variation on genome-wide gene expression profiles measured by the microarray technologies. Due to substantial noise in...
Xiang, Zuoshuang, Qin, Zhaohui S., He, Yongqun
Summary: CRCView is a user-friendly point-and-click web server for analyzing and visualizing microarray gene expression data using a Dirichlet process mixture model-based clustering algorithm....
Operon Prediction for Sequenced Bacterial Genomes without Experimental Information � † (2006)
Nicholas H. Bergman, Karla D. Passalacqua, Philip C. Hanna, Zhaohui S. Qin
Various computational approaches have been proposed for operon prediction, but most algorithms rely on experimental or functional data that are only available for a small subset of sequenced genomes....
Nicholas H. Bergman, Karla D. Passalacqua, Philip C. Hanna, Zhaohui S. Qin, Nicholas H. Bergman, Ph. D
Various computational approaches have been proposed for operon prediction, but most algorithms rely on experimental or functional data that are only available for a small subset of sequenced genomes....
A comparison of phasing algorithms for trios and unrelated individuals (2006)
Jonathan Marchini, David Cutler, Nick Patterson, Matthew Stephens, Eleazar Eskin, Eran Halperin, ...
Knowledge of haplotype phase is valuable for many analysis methods in the study of disease, population, and evolutionary genetics. Considerable research effort has been devoted to the development of...
Qin, Zhaohui S., Gopalakrishnan, Shyam, Abecasis, Gonçalo R.
Motivation: Selecting SNP markers for genome-wide association studies is an important and challenging task. The goal is to minimize the number of markers selected for genotyping in a particular...
Clustering microarray gene expression data using weighted Chinese restaurant process (2006)
Motivation: Clustering microarray gene expression data is a powerful tool for elucidating co-regulatory relationships among genes. Many different clustering techniques have been successfully applied...
Zhu, Dongxiao, Hero, Alfred O, Qin, Zhaohui S, Swaroop, Anand
Many exploratory microarray data analysis tools such as gene clustering and relevance networks rely on detecting pairwise gene co-expression. Traditional screening of pairwise co-expression either...
Structural comparison of metabolic networks in selected single cell organisms (2005)
Abstract Background There has been tremendous interest in the study of biological network structure. An array of measurements has been conceived to assess the topological properties of these...
BMC Bioinformatics BioMed Central (2005)
Dongxiao Zhu, Zhaohui S Qin, Dongxiao Zhu, Zhaohui S Qin
Research article Structural comparison of metabolic networks in selected single cell organisms
Dongxiao Zhu, Alfred O Hero, Zhaohui S Qin
Many exploratory microarray data analysis tools such as gene clustering and relevance networks rely on detecting pairwise gene co-expression. Traditional screening of pairwise co-expression either...
Statistical resynchronization and bayesian detection of periodically expressed genes (2004)
Xin Lu, Wen Zhang, Zhaohui S. Qin, Kurt E. Kwast, Jun S. Liu
We propose a periodic±normal mixture (PNM) model to ®t transcription pro®les of periodically expressed (PE) genes in cell cycle microarray experiments. The model leads to a principled statistical...
The Block Partitioning Results Using Different � and � a (2004)
Kui Zhang, Zhaohui S. Qin, Jun S. Liu, Ting Chen, Michael S. Waterman, Fengzhu Sun, ...
service This article cites 49 articles, 10 of which can be accessed free at:
Statistical resynchronization and Bayesian detection of periodically expressed genes (2004)
Lu, Xin, Zhang, Wen, Qin, Zhaohui S., Kwast, Kurt E., Liu, Jun S.
We propose a periodic–normal mixture (PNM) model to fit transcription profiles of periodically expressed (PE) genes in cell cycle microarray experiments. The model leads to a principled statistical...
Zhang, Kui, Qin, Zhaohui S., Liu, Jun S., Chen, Ting, Waterman, Michael S., Sun, Fengzhu
Recent studies have revealed that linkage disequilibrium(LD) patterns vary across the human genome with some regions of high LD interspersed by regions of low LD. A small fraction of SNPs (tag SNPs)...
Zhang, Kui, Qin, Zhaohui S., Liu, Jun S., Chen, Ting, Waterman, Michael S., Sun, Fengzhu
Recent studies have revealed that linkage disequilibrium (LD) patterns vary across the human genome with some regions of high LD interspersed by regions of low LD. A small fraction of SNPs (tag SNPs)...
Statistical resynchronization and Bayesian detection of periodically expressed genes
Lu, Xin, Zhang, Wen, Qin, Zhaohui S., Kwast, Kurt E., Liu, Jun S.
We propose a periodic–normal mixture (PNM) model to fit transcription profiles of periodically expressed (PE) genes in cell cycle microarray experiments. The model leads to a principled statistical...
Zhang, Kui, Qin, Zhaohui S., Liu, Jun S., Chen, Ting, Waterman, Michael S., Sun, Fengzhu
Recent studies have revealed that linkage disequilibrium (LD) patterns vary across the human genome with some regions of high LD interspersed by regions of low LD. A small fraction of SNPs (tag SNPs)...
A Comparison of Phasing Algorithms for Trios and Unrelated Individuals
Marchini, Jonathan, Cutler, David, Patterson, Nick, Stephens, Matthew, Eskin, Eleazar, Halperin, Eran, ...
Knowledge of haplotype phase is valuable for many analysis methods in the study of disease, population, and evolutionary genetics. Considerable research effort has been devoted to the development of...
Statistical resynchronization and Bayesian detection of periodically expressed genes
Lu, Xin, Zhang, Wen, Qin, Zhaohui S., Kwast, Kurt E., Liu, Jun S.
We propose a periodic–normal mixture (PNM) model to fit transcription profiles of periodically expressed (PE) genes in cell cycle microarray experiments. The model leads to a principled statistical...
Bayesian Haplotype Inference for Multiple Linked Single-Nucleotide Polymorphisms
Niu, Tianhua, Qin, Zhaohui S., Xu, Xiping, Liu, Jun S.
Haplotypes have gained increasing attention in the mapping of complex-disease genes, because of the abundance of single-nucleotide polymorphisms (SNPs) and the limited power of conventional...
Zhang, Kui, Qin, Zhaohui S., Liu, Jun S., Chen, Ting, Waterman, Michael S., Sun, Fengzhu
Recent studies have revealed that linkage disequilibrium (LD) patterns vary across the human genome with some regions of high LD interspersed by regions of low LD. A small fraction of SNPs (tag SNPs)...
Incorporating Genotyping Uncertainty in Haplotype Inference for Single-Nucleotide Polymorphisms
Kang, Hosung, Qin, Zhaohui S., Niu, Tianhua, Liu, Jun S.
The accuracy of the vast amount of genotypic information generated by high-throughput genotyping technologies is crucial in haplotype analyses and linkage-disequilibrium mapping for complex diseases....
A Comparison of Phasing Algorithms for Trios and Unrelated Individuals
Marchini, Jonathan, Cutler, David, Patterson, Nick, Stephens, Matthew, Eskin, Eleazar, Halperin, Eran, ...
Knowledge of haplotype phase is valuable for many analysis methods in the study of disease, population, and evolutionary genetics. Considerable research effort has been devoted to the development of...
Operon Prediction for Sequenced Bacterial Genomes without Experimental Information▿ †
Bergman, Nicholas H., Passalacqua, Karla D., Hanna, Philip C., Qin, Zhaohui S.
Various computational approaches have been proposed for operon prediction, but most algorithms rely on experimental or functional data that are only available for a small subset of sequenced genomes....
Several studies have been conducted to assess the influence of genetic variation on genome-wide gene expression profiles measured by the microarray technologies. Due to substantial noise in...
In microarray gene expression data analysis, it is often of interest to identify genes that share similar expression profiles with a particular gene such as a key regulatory protein. Multiple studies...