Michael Q. Zhang

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