Michael Q. Zhang Computational Biology and Bioinformatics Cold Spring Harbor Laboratory Biography Publications Institution JoVE Articles Michael Q. Zhang has not added a biography. If you are Michael Q. Zhang and would like to personalize this page please email our Author Liaison for assistance. Publications Novel Foxo1-dependent Transcriptional Programs Control T(reg) Cell Function Nature. Nov, 2012 | Pubmed ID: 23135404 Regulatory Elements of Caenorhabditis Elegans Ribosomal Protein Genes BMC Genomics. Aug, 2012 | Pubmed ID: 22928635 Genome-wide Localization of Protein-DNA Binding and Histone Modification by a Bayesian Change-point Method with ChIP-seq Data PLoS Computational Biology. Jul, 2012 | Pubmed ID: 22844240 Chromatin State and MicroRNA Determine Different Gene Expression Dynamics Responsive to TNF Stimulation Genomics. Jul, 2012 | Pubmed ID: 22824656 Bivalent-like Chromatin Markers Are Predictive for Transcription Start Site Distribution in Human PloS One. 2012 | Pubmed ID: 22768038 H3K4 Demethylation by Jarid1a and Jarid1b Contributes to Retinoblastoma-mediated Gene Silencing During Cellular Senescence Proceedings of the National Academy of Sciences of the United States of America. Jun, 2012 | Pubmed ID: 22615382 Cell-type-based Analysis of MicroRNA Profiles in the Mouse Brain Neuron. Jan, 2012 | Pubmed ID: 22243745 A Highly Efficient and Effective Motif Discovery Method for ChIP-seq/ChIP-chip Data Using Positional Information Nucleic Acids Research. Apr, 2012 | Pubmed ID: 22228832 Novel Markov Model of Induced Pluripotency Predicts Gene Expression Changes in Reprogramming BMC Systems Biology. Dec, 2011 | Pubmed ID: 22784579 Inferring Haplotypes of Copy Number Variations from High-throughput Data with Uncertainty G3 (Bethesda, Md.). Jun, 2011 | Pubmed ID: 22384316 Identification of Novel Androgen-regulated Pathways and MRNA Isoforms Through Genome-wide Exon-specific Profiling of the LNCaP Transcriptome PloS One. 2011 | Pubmed ID: 22194994 Identification of Tumor Suppressors and Oncogenes from Genomic and Epigenetic Features in Ovarian Cancer PloS One. 2011 | Pubmed ID: 22174824 EpiRegNet: Constructing Epigenetic Regulatory Network from High Throughput Gene Expression Data for Humans Epigenetics : Official Journal of the DNA Methylation Society. Dec, 2011 | Pubmed ID: 22139581 Study of FoxA Pioneer Factor at Silent Genes Reveals Rfx-repressed Enhancer at Cdx2 and a Potential Indicator of Esophageal Adenocarcinoma Development PLoS Genetics. Sep, 2011 | Pubmed ID: 21935353 SpliceTrap: a Method to Quantify Alternative Splicing Under Single Cellular Conditions Bioinformatics (Oxford, England). Nov, 2011 | Pubmed ID: 21896509 Correlated Evolution of Transcription Factors and Their Binding Sites Bioinformatics (Oxford, England). Nov, 2011 | Pubmed ID: 21896508 Direct Cloning of Double-stranded RNAs from RNase Protection Analysis Reveals Processing Patterns of C/D Box SnoRNAs and Provides Evidence for Widespread Antisense Transcript Expression Nucleic Acids Research. Dec, 2011 | Pubmed ID: 21880592 Functional Mutation of SMAC/DIABLO, Encoding a Mitochondrial Proapoptotic Protein, Causes Human Progressive Hearing Loss DFNA64 American Journal of Human Genetics. Jul, 2011 | Pubmed ID: 21722859 ChIP-Array: Combinatory Analysis of ChIP-seq/chip and Microarray Gene Expression Data to Discover Direct/indirect Targets of a Transcription Factor Nucleic Acids Research. Jul, 2011 | Pubmed ID: 21586587 Histone Modification Profiles Are Predictive for Tissue/cell-type Specific Expression of Both Protein-coding and MicroRNA Genes BMC Bioinformatics. 2011 | Pubmed ID: 21569556 Comparison of Sequencing-based Methods to Profile DNA Methylation and Identification of Monoallelic Epigenetic Modifications Nature Biotechnology. Oct, 2010 | Pubmed ID: 20852635 A Long Nuclear-retained Non-coding RNA Regulates Synaptogenesis by Modulating Gene Expression The EMBO Journal. Sep, 2010 | Pubmed ID: 20729808 Development of the Human Cancer MicroRNA Network Silence. 2010 | Pubmed ID: 20226080 Transcriptome Study for Early Hematopoiesis--achievement, Challenge and New Opportunity Journal of Cellular Physiology. Jun, 2010 | Pubmed ID: 20143329 SFSSClass: an Integrated Approach for MiRNA Based Tumor Classification BMC Bioinformatics. 2010 | Pubmed ID: 20122194 Updates to the RMAP Short-read Mapping Software Bioinformatics (Oxford, England). Nov, 2009 | Pubmed ID: 19736251 High Definition Profiling of Mammalian DNA Methylation by Array Capture and Single Molecule Bisulfite Sequencing Genome Research. Sep, 2009 | Pubmed ID: 19581485 An Integrative Genomics Approach Identifies Hypoxia Inducible Factor-1 (HIF-1)-target Genes That Form the Core Response to Hypoxia Nucleic Acids Research. Aug, 2009 | Pubmed ID: 19491311 The Transcriptome of Human CD34+ Hematopoietic Stem-progenitor Cells Proceedings of the National Academy of Sciences of the United States of America. May, 2009 | Pubmed ID: 19416867 Determination of Enriched Histone Modifications in Non-genic Portions of the Human Genome BMC Genomics. 2009 | Pubmed ID: 19335899 Gene Set-based Module Discovery in the Breast Cancer Transcriptome BMC Bioinformatics. 2009 | Pubmed ID: 19243633 The Seventh Asia Pacific Bioinformatics Conference (APBC2009) BMC Bioinformatics. 2009 | Pubmed ID: 19208108 Multi-stage Analysis of Gene Expression and Transcription Regulation in C57/B6 Mouse Liver Development Genomics. Mar, 2009 | Pubmed ID: 19015022 High-resolution Human Core-promoter Prediction with CoreBoost_HM Genome Research. Feb, 2009 | Pubmed ID: 18997002 Integrative Bioinformatics Analysis of Transcriptional Regulatory Programs in Breast Cancer Cells BMC Bioinformatics. 2008 | Pubmed ID: 18823535 Defining the Regulatory Network of the Tissue-specific Splicing Factors Fox-1 and Fox-2 Genes & Development. Sep, 2008 | Pubmed ID: 18794351 ZOOM! Zillions of Oligos Mapped Bioinformatics (Oxford, England). Nov, 2008 | Pubmed ID: 18684737 Regulation of the PDK4 Isozyme by the Rb-E2F1 Complex The Journal of Biological Chemistry. Oct, 2008 | Pubmed ID: 18667418 Poly A- Transcripts Expressed in HeLa Cells PloS One. 2008 | Pubmed ID: 18665230 Histone Methylation Marks Play Important Roles in Predicting the Methylation Status of CpG Islands Biochemical and Biophysical Research Communications. Sep, 2008 | Pubmed ID: 18656446 Combinatorial Patterns of Histone Acetylations and Methylations in the Human Genome Nature Genetics. Jul, 2008 | Pubmed ID: 18552846 Identification of Synaptic Targets of Drosophila Pumilio PLoS Computational Biology. Feb, 2008 | Pubmed ID: 18463699 Network-based Global Inference of Human Disease Genes Molecular Systems Biology. 2008 | Pubmed ID: 18463613 RNA Landscape of Evolution for Optimal Exon and Intron Discrimination Proceedings of the National Academy of Sciences of the United States of America. Apr, 2008 | Pubmed ID: 18391195 CD36-dependent Regulation of Muscle FoxO1 and PDK4 in the PPAR Delta/beta-mediated Adaptation to Metabolic Stress The Journal of Biological Chemistry. May, 2008 | Pubmed ID: 18308721 Using Quality Scores and Longer Reads Improves Accuracy of Solexa Read Mapping BMC Bioinformatics. 2008 | Pubmed ID: 18307793 Genome Research. May, 2008 | Pubmed ID: 18292219 Heat Shock Protein 90beta1 is Essential for Polyunsaturated Fatty Acid-induced Mitochondrial Ca2+ Efflux The Journal of Biological Chemistry. Mar, 2008 | Pubmed ID: 18178560 Interferon Regulatory Factors Are Transcriptional Regulators of Adipogenesis Cell Metabolism. Jan, 2008 | Pubmed ID: 18177728 Genome-wide Mapping and Analysis of Active Promoters in Mouse Embryonic Stem Cells and Adult Organs Genome Research. Jan, 2008 | Pubmed ID: 18042645 Identification of Phylogenetically Conserved MicroRNA Cis-regulatory Elements Across 12 Drosophila Species Bioinformatics (Oxford, England). Jan, 2008 | Pubmed ID: 18037683 Putative Zinc Finger Protein Binding Sites Are Over-represented in the Boundaries of Methylation-resistant CpG Islands in the Human Genome PloS One. 2007 | Pubmed ID: 18030324 Prediction of Transcription Start Sites Based on Feature Selection Using AMOSA Computational Systems Bioinformatics / Life Sciences Society. Computational Systems Bioinformatics Conference. 2007 | Pubmed ID: 17951823 OSCAR: One-class SVM for Accurate Recognition of Cis-elements Bioinformatics (Oxford, England). Nov, 2007 | Pubmed ID: 17921174 Computational Analyses of Eukaryotic Promoters BMC Bioinformatics. 2007 | Pubmed ID: 17903284 Neural Potential of a Stem Cell Population in the Hair Follicle Cell Cycle (Georgetown, Tex.). Sep, 2007 | Pubmed ID: 17873521 Dual-specificity Splice Sites Function Alternatively As 5' and 3' Splice Sites Proceedings of the National Academy of Sciences of the United States of America. Sep, 2007 | Pubmed ID: 17848517 Evolutionary Impact of Limited Splicing Fidelity in Mammalian Genes Trends in Genetics : TIG. Oct, 2007 | Pubmed ID: 17719121 A Highly Conserved Regulatory Element Controls Hematopoietic Expression of GATA-2 in Zebrafish BMC Developmental Biology. 2007 | Pubmed ID: 17708765 Predictive Models of Gene Regulation: Application of Regression Methods to Microarray Data Methods in Molecular Biology (Clifton, N.J.). 2007 | Pubmed ID: 17634611 Analysis of the Vertebrate Insulator Protein CTCF-binding Sites in the Human Genome Cell. Mar, 2007 | Pubmed ID: 17382889 Critical Roles for Dicer in the Female Germline Genes & Development. Mar, 2007 | Pubmed ID: 17369401 Boosting with Stumps for Predicting Transcription Start Sites Genome Biology. 2007 | Pubmed ID: 17274821 Statistical Significance of Cis-regulatory Modules BMC Bioinformatics. 2007 | Pubmed ID: 17241466 Computing Exact P-values for DNA Motifs Bioinformatics (Oxford, England). Mar, 2007 | Pubmed ID: 17237046 Tissue-specific Regulatory Elements in Mammalian Promoters Molecular Systems Biology. 2007 | Pubmed ID: 17224917 Computational Prediction of Novel Components of Lung Transcriptional Networks Bioinformatics (Oxford, England). Jan, 2007 | Pubmed ID: 17050569 Pan-genome Isolation of Low Abundance Transcripts Using SAGE Tag FEBS Letters. Dec, 2006 | Pubmed ID: 17113583 A New Method for Detecting Human Recombination Hotspots and Its Applications to the HapMap ENCODE Data American Journal of Human Genetics. Oct, 2006 | Pubmed ID: 16960799 Predicting Methylation Status of CpG Islands in the Human Brain Bioinformatics (Oxford, England). Sep, 2006 | Pubmed ID: 16837523 An Increased Specificity Score Matrix for the Prediction of SF2/ASF-specific Exonic Splicing Enhancers Human Molecular Genetics. Aug, 2006 | Pubmed ID: 16825284 Computational Prediction of Methylation Status in Human Genomic Sequences Proceedings of the National Academy of Sciences of the United States of America. Jul, 2006 | Pubmed ID: 16818882 Adaptively Inferring Human Transcriptional Subnetworks Molecular Systems Biology. 2006 | Pubmed ID: 16760900 Characterization of RNase R-digested Cellular RNA Source That Consists of Lariat and Circular RNAs from Pre-mRNA Splicing Nucleic Acids Research. 2006 | Pubmed ID: 16682442 A Clustering Property of Highly-degenerate Transcription Factor Binding Sites in the Mammalian Genome Nucleic Acids Research. 2006 | Pubmed ID: 16670430 Profiling Alternatively Spliced MRNA Isoforms for Prostate Cancer Classification BMC Bioinformatics. 2006 | Pubmed ID: 16608523 DNA Motifs in Human and Mouse Proximal Promoters Predict Tissue-specific Expression Proceedings of the National Academy of Sciences of the United States of America. Apr, 2006 | Pubmed ID: 16606849 Large-scale Structure of Genomic Methylation Patterns Genome Research. Feb, 2006 | Pubmed ID: 16365381 Using CorePromoter to Find Human Core Promoters Current Protocols in Bioinformatics / Editoral Board, Andreas D. Baxevanis ... [et Al.]. Jul, 2005 | Pubmed ID: 18428749 Regulating Gene Expression Through RNA Nuclear Retention Cell. Oct, 2005 | Pubmed ID: 16239143 Distribution of SR Protein Exonic Splicing Enhancer Motifs in Human Protein-coding Genes Nucleic Acids Research. 2005 | Pubmed ID: 16147989 Genome-wide Promoter Extraction and Analysis in Human, Mouse, and Rat Genome Biology. 2005 | Pubmed ID: 16086854 Mining ChIP-chip Data for Transcription Factor and Cofactor Binding Sites Bioinformatics (Oxford, England). Jun, 2005 | Pubmed ID: 15961485 Identifying Tissue-selective Transcription Factor Binding Sites in Vertebrate Promoters Proceedings of the National Academy of Sciences of the United States of America. Feb, 2005 | Pubmed ID: 15668401 From Worm to Human: Bioinformatics Approaches to Identify FOXO Target Genes Mechanisms of Ageing and Development. Jan, 2005 | Pubmed ID: 15610780 TRED: a Transcriptional Regulatory Element Database and a Platform for in Silico Gene Regulation Studies Nucleic Acids Research. Jan, 2005 | Pubmed ID: 15608156 DWE: Discriminating Word Enumerator Bioinformatics (Oxford, England). Jan, 2005 | Pubmed ID: 15333453 Similarity of Position Frequency Matrices for Transcription Factor Binding Sites Bioinformatics (Oxford, England). Feb, 2005 | Pubmed ID: 15319260 The Mouse Genome: Experimental Examination of Gene Predictions and Transcriptional Start Sites Genome Research. Dec, 2004 | Pubmed ID: 15574821 Interacting Models of Cooperative Gene Regulation Proceedings of the National Academy of Sciences of the United States of America. Nov, 2004 | Pubmed ID: 15534222 Genome-wide Prediction and Analysis of Function-specific Transcription Factor Binding Sites In Silico Biology. 2004 | Pubmed ID: 15506990 Evidence and Characteristics of Putative Human Alpha Recombination Hotspots Human Molecular Genetics. Nov, 2004 | Pubmed ID: 15385449 Identifying Combinatorial Regulation of Transcription Factors and Binding Motifs Genome Biology. 2004 | Pubmed ID: 15287978 Transcription Factor Binding Element Detection Using Functional Clustering of Mutant Expression Data Nucleic Acids Research. 2004 | Pubmed ID: 15115798 Identifying Cooperativity Among Transcription Factors Controlling the Cell Cycle in Yeast Nucleic Acids Research. Dec, 2003 | Pubmed ID: 14627835 Computer Software to Find Genes in Plant Genomic DNA Methods in Molecular Biology (Clifton, N.J.). 2003 | Pubmed ID: 14501060 ESEfinder: A Web Resource to Identify Exonic Splicing Enhancers Nucleic Acids Research. Jul, 2003 | Pubmed ID: 12824367 A Global Transcriptional Regulatory Role for C-Myc in Burkitt's Lymphoma Cells Proceedings of the National Academy of Sciences of the United States of America. Jul, 2003 | Pubmed ID: 12808131 Computational Comparison of Two Mouse Draft Genomes and the Human Golden Path Genome Biology. 2003 | Pubmed ID: 12537546 The Argonaute Family: Tentacles That Reach into RNAi, Developmental Control, Stem Cell Maintenance, and Tumorigenesis Genes & Development. Nov, 2002 | Pubmed ID: 12414724 Direct Coupling of the Cell Cycle and Cell Death Machinery by E2F Nature Cell Biology. Nov, 2002 | Pubmed ID: 12389032 Gene Expression Profiling in Developing Human Hippocampus Journal of Neuroscience Research. Oct, 2002 | Pubmed ID: 12271469 Extracting Functional Information from Microarrays: a Challenge for Functional Genomics Proceedings of the National Academy of Sciences of the United States of America. Oct, 2002 | Pubmed ID: 12271149 Computational Prediction of Eukaryotic Protein-coding Genes Nature Reviews. Genetics. Sep, 2002 | Pubmed ID: 12209144 GFScan: a Gene Family Search Tool at Genomic DNA Level Genome Research. Jul, 2002 | Pubmed ID: 12097353 Functional Genomics As Applied to Mapping Transcription Regulatory Networks Current Opinion in Microbiology. Jun, 2002 | Pubmed ID: 12057687 A Novel Bayesiana Algoritmo de Mudança-ponto para Genome-wide Análise de tipos de dados ChIPseq Diversos Haipeng Xing1, Willey Liao1,2, Yifan Mo1,2, Michael Q. Zhang2,3 1Department of Applied Mathematics & Statistics, Stony Brook University, 2Computational Biology and Bioinformatics, Cold Spring Harbor Laboratory, 3Department of Molecular and Cell Biology, University of Texas at Dallas JoVE 4273 Biology
A Novel Bayesiana Algoritmo de Mudança-ponto para Genome-wide Análise de tipos de dados ChIPseq Diversos Haipeng Xing1, Willey Liao1,2, Yifan Mo1,2, Michael Q. Zhang2,3 1Department of Applied Mathematics & Statistics, Stony Brook University, 2Computational Biology and Bioinformatics, Cold Spring Harbor Laboratory, 3Department of Molecular and Cell Biology, University of Texas at Dallas JoVE 4273 Biology
