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 विविध ChIPseq डेटा प्रकार के एक उपन्यास Bayesian बदलें बिंदु जीनोम चौड़ा विश्लेषण के लिए एल्गोरिथ्म 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
विविध ChIPseq डेटा प्रकार के एक उपन्यास Bayesian बदलें बिंदु जीनोम चौड़ा विश्लेषण के लिए एल्गोरिथ्म 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