Michael Q. Zhang

Computational Biology and Bioinformatics, Cold Spring Harbor Laboratory

Affiliated withCold Spring Harbor Laboratory University of Texas at Dallas

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JoVE Journal Publications

ArticleTotal : 1	Year
Publication title Cited by 6	2012

Other Publications

Article	Year
Functional genomics as applied to mapping transcription regulatory networks. Current opinion in microbiology\| PubMed ID: 12057687	2002
GFScan: a gene family search tool at genomic DNA level. Genome research\| PubMed ID: 12097353	2002
Computational prediction of eukaryotic protein-coding genes. Nature reviews. Genetics\| PubMed ID: 12209144	2002
Extracting functional information from microarrays: a challenge for functional genomics. Proceedings of the National Academy of Sciences of the United States of America\| PubMed ID: 12271149	2002
Gene expression profiling in developing human hippocampus. Journal of neuroscience research\| PubMed ID: 12271469	2002
Direct coupling of the cell cycle and cell death machinery by E2F. Nature cell biology\| PubMed ID: 12389032	2002
The Argonaute family: tentacles that reach into RNAi, developmental control, stem cell maintenance, and tumorigenesis. Genes & development\| PubMed ID: 12414724	2002
Computational comparison of two mouse draft genomes and the human golden path. Genome biology\| PubMed ID: 12537546	2003
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\| PubMed ID: 12808131	2003
ESEfinder: A web resource to identify exonic splicing enhancers. Nucleic acids research\| PubMed ID: 12824367	2003
Computer software to find genes in plant genomic DNA. Methods in molecular biology (Clifton, N.J.)\| PubMed ID: 14501060	2003
Identifying cooperativity among transcription factors controlling the cell cycle in yeast. Nucleic acids research\| PubMed ID: 14627835	2003
Transcription factor binding element detection using functional clustering of mutant expression data. Nucleic acids research\| PubMed ID: 15115798	2004
Identifying combinatorial regulation of transcription factors and binding motifs. Genome biology\| PubMed ID: 15287978	2004
Similarity of position frequency matrices for transcription factor binding sites. Bioinformatics (Oxford, England)\| PubMed ID: 15319260	2005
DWE: discriminating word enumerator. Bioinformatics (Oxford, England)\| PubMed ID: 15333453	2005
Evidence and characteristics of putative human alpha recombination hotspots. Human molecular genetics\| PubMed ID: 15385449	2004
Genome-wide prediction and analysis of function-specific transcription factor binding sites. In silico biology\| PubMed ID: 15506990	2004
Interacting models of cooperative gene regulation. Proceedings of the National Academy of Sciences of the United States of America\| PubMed ID: 15534222	2004
The mouse genome: experimental examination of gene predictions and transcriptional start sites. Genome research\| PubMed ID: 15574821	2004
TRED: a Transcriptional Regulatory Element Database and a platform for in silico gene regulation studies. Nucleic acids research\| PubMed ID: 15608156	2005
From worm to human: bioinformatics approaches to identify FOXO target genes. Mechanisms of ageing and development\| PubMed ID: 15610780	2005
Identifying tissue-selective transcription factor binding sites in vertebrate promoters. Proceedings of the National Academy of Sciences of the United States of America\| PubMed ID: 15668401	2005
Mining ChIP-chip data for transcription factor and cofactor binding sites. Bioinformatics (Oxford, England)\| PubMed ID: 15961485	2005
Genome-wide promoter extraction and analysis in human, mouse, and rat. Genome biology\| PubMed ID: 16086854	2005
Distribution of SR protein exonic splicing enhancer motifs in human protein-coding genes. Nucleic acids research\| PubMed ID: 16147989	2005
Regulating gene expression through RNA nuclear retention. Cell\| PubMed ID: 16239143	2005
Large-scale structure of genomic methylation patterns. Genome research\| PubMed ID: 16365381	2006
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\| PubMed ID: 16606849	2006
Profiling alternatively spliced mRNA isoforms for prostate cancer classification. BMC bioinformatics\| PubMed ID: 16608523	2006
A clustering property of highly-degenerate transcription factor binding sites in the mammalian genome. Nucleic acids research\| PubMed ID: 16670430	2006
Characterization of RNase R-digested cellular RNA source that consists of lariat and circular RNAs from pre-mRNA splicing. Nucleic acids research\| PubMed ID: 16682442	2006
Adaptively inferring human transcriptional subnetworks. Molecular systems biology\| PubMed ID: 16760900	2006
Computational prediction of methylation status in human genomic sequences. Proceedings of the National Academy of Sciences of the United States of America\| PubMed ID: 16818882	2006
An increased specificity score matrix for the prediction of SF2/ASF-specific exonic splicing enhancers. Human molecular genetics\| PubMed ID: 16825284	2006
Predicting methylation status of CpG islands in the human brain. Bioinformatics (Oxford, England)\| PubMed ID: 16837523	2006
A new method for detecting human recombination hotspots and its applications to the HapMap ENCODE data. American journal of human genetics\| PubMed ID: 16960799	2006
Computational prediction of novel components of lung transcriptional networks. Bioinformatics (Oxford, England)\| PubMed ID: 17050569	2007
Pan-genome isolation of low abundance transcripts using SAGE tag. FEBS letters\| PubMed ID: 17113583	2006
Tissue-specific regulatory elements in mammalian promoters. Molecular systems biology\| PubMed ID: 17224917	2007
Computing exact P-values for DNA motifs. Bioinformatics (Oxford, England)\| PubMed ID: 17237046	2007
Statistical significance of cis-regulatory modules. BMC bioinformatics\| PubMed ID: 17241466	2007
Boosting with stumps for predicting transcription start sites. Genome biology\| PubMed ID: 17274821	2007
Critical roles for Dicer in the female germline. Genes & development\| PubMed ID: 17369401	2007
Analysis of the vertebrate insulator protein CTCF-binding sites in the human genome. Cell\| PubMed ID: 17382889	2007
Predictive models of gene regulation: application of regression methods to microarray data. Methods in molecular biology (Clifton, N.J.)\| PubMed ID: 17634611	2007
A highly conserved regulatory element controls hematopoietic expression of GATA-2 in zebrafish. BMC developmental biology\| PubMed ID: 17708765	2007
Evolutionary impact of limited splicing fidelity in mammalian genes. Trends in genetics : TIG\| PubMed ID: 17719121	2007
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\| PubMed ID: 17848517	2007
Neural potential of a stem cell population in the hair follicle. Cell cycle (Georgetown, Tex.)\| PubMed ID: 17873521	2007
Computational analyses of eukaryotic promoters. BMC bioinformatics\| PubMed ID: 17903284	2007
OSCAR: one-class SVM for accurate recognition of cis-elements. Bioinformatics (Oxford, England)\| PubMed ID: 17921174	2007
Prediction of transcription start sites based on feature selection using AMOSA. Computational systems bioinformatics / Life Sciences Society. Computational Systems Bioinformatics Conference\| PubMed ID: 17951823	2007
Putative zinc finger protein binding sites are over-represented in the boundaries of methylation-resistant CpG islands in the human genome. PloS one\| PubMed ID: 18030324	2007
Identification of phylogenetically conserved microRNA cis-regulatory elements across 12 Drosophila species. Bioinformatics (Oxford, England)\| PubMed ID: 18037683	2008
Genome-wide mapping and analysis of active promoters in mouse embryonic stem cells and adult organs. Genome research\| PubMed ID: 18042645	2008
Interferon regulatory factors are transcriptional regulators of adipogenesis. Cell metabolism\| PubMed ID: 18177728	2008
Heat shock protein 90beta1 is essential for polyunsaturated fatty acid-induced mitochondrial Ca2+ efflux. The Journal of biological chemistry\| PubMed ID: 18178560	2008
扫描在 kilobase 分辨率的人类基因组。 Genome research\| PubMed ID: 18292219	2008
Using quality scores and longer reads improves accuracy of Solexa read mapping. BMC bioinformatics\| PubMed ID: 18307793	2008
CD36-dependent regulation of muscle FoxO1 and PDK4 in the PPAR delta/beta-mediated adaptation to metabolic stress. The Journal of biological chemistry\| PubMed ID: 18308721	2008
RNA landscape of evolution for optimal exon and intron discrimination. Proceedings of the National Academy of Sciences of the United States of America\| PubMed ID: 18391195	2008
Using CorePromoter to find human core promoters. Current protocols in bioinformatics / editoral board, Andreas D. Baxevanis ... [et al.]\| PubMed ID: 18428749	2005
Network-based global inference of human disease genes. Molecular systems biology\| PubMed ID: 18463613	2008
Identification of synaptic targets of Drosophila pumilio. PLoS computational biology\| PubMed ID: 18463699	2008
Combinatorial patterns of histone acetylations and methylations in the human genome. Nature genetics\| PubMed ID: 18552846	2008
Histone methylation marks play important roles in predicting the methylation status of CpG islands. Biochemical and biophysical research communications\| PubMed ID: 18656446	2008
Poly A- transcripts expressed in HeLa cells. PloS one\| PubMed ID: 18665230	2008
Regulation of the PDK4 isozyme by the Rb-E2F1 complex. The Journal of biological chemistry\| PubMed ID: 18667418	2008
ZOOM! Zillions of oligos mapped. Bioinformatics (Oxford, England)\| PubMed ID: 18684737	2008
Defining the regulatory network of the tissue-specific splicing factors Fox-1 and Fox-2. Genes & development\| PubMed ID: 18794351	2008
Integrative bioinformatics analysis of transcriptional regulatory programs in breast cancer cells. BMC bioinformatics\| PubMed ID: 18823535	2008
High-resolution human core-promoter prediction with CoreBoost_HM. Genome research\| PubMed ID: 18997002	2009
Multi-stage analysis of gene expression and transcription regulation in C57/B6 mouse liver development. Genomics\| PubMed ID: 19015022	2009
The Seventh Asia Pacific Bioinformatics Conference (APBC2009). BMC bioinformatics\| PubMed ID: 19208108	2009
Gene set-based module discovery in the breast cancer transcriptome. BMC bioinformatics\| PubMed ID: 19243633	2009
Determination of enriched histone modifications in non-genic portions of the human genome. BMC genomics\| PubMed ID: 19335899	2009
The transcriptome of human CD34+ hematopoietic stem-progenitor cells. Proceedings of the National Academy of Sciences of the United States of America\| PubMed ID: 19416867	2009
An integrative genomics approach identifies Hypoxia Inducible Factor-1 (HIF-1)-target genes that form the core response to hypoxia. Nucleic acids research\| PubMed ID: 19491311	2009
High definition profiling of mammalian DNA methylation by array capture and single molecule bisulfite sequencing. Genome research\| PubMed ID: 19581485	2009
Updates to the RMAP short-read mapping software. Bioinformatics (Oxford, England)\| PubMed ID: 19736251	2009
SFSSClass: an integrated approach for miRNA based tumor classification. BMC bioinformatics\| PubMed ID: 20122194	2010
Transcriptome study for early hematopoiesis--achievement, challenge and new opportunity. Journal of cellular physiology\| PubMed ID: 20143329	2010
Development of the human cancer microRNA network. Silence\| PubMed ID: 20226080	2010
A long nuclear-retained non-coding RNA regulates synaptogenesis by modulating gene expression. The EMBO journal\| PubMed ID: 20729808	2010
Comparison of sequencing-based methods to profile DNA methylation and identification of monoallelic epigenetic modifications. Nature biotechnology\| PubMed ID: 20852635	2010
Histone modification profiles are predictive for tissue/cell-type specific expression of both protein-coding and microRNA genes. BMC bioinformatics\| PubMed ID: 21569556	2011
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\| PubMed ID: 21586587	2011
Functional mutation of SMAC/DIABLO, encoding a mitochondrial proapoptotic protein, causes human progressive hearing loss DFNA64. American journal of human genetics\| PubMed ID: 21722859	2011
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\| PubMed ID: 21880592	2011
Correlated evolution of transcription factors and their binding sites. Bioinformatics (Oxford, England)\| PubMed ID: 21896508	2011
SpliceTrap: a method to quantify alternative splicing under single cellular conditions. Bioinformatics (Oxford, England)\| PubMed ID: 21896509	2011
Study of FoxA pioneer factor at silent genes reveals Rfx-repressed enhancer at Cdx2 and a potential indicator of esophageal adenocarcinoma development. PLoS genetics\| PubMed ID: 21935353	2011
EpiRegNet: constructing epigenetic regulatory network from high throughput gene expression data for humans. Epigenetics : official journal of the DNA Methylation Society\| PubMed ID: 22139581	2011
Identification of tumor suppressors and oncogenes from genomic and epigenetic features in ovarian cancer. PloS one\| PubMed ID: 22174824	2011
Identification of novel androgen-regulated pathways and mRNA isoforms through genome-wide exon-specific profiling of the LNCaP transcriptome. PloS one\| PubMed ID: 22194994	2011
A highly efficient and effective motif discovery method for ChIP-seq/ChIP-chip data using positional information. Nucleic acids research\| PubMed ID: 22228832	2012
Cell-type-based analysis of microRNA profiles in the mouse brain. Neuron\| PubMed ID: 22243745	2012
Inferring haplotypes of copy number variations from high-throughput data with uncertainty. G3 (Bethesda, Md.)\| PubMed ID: 22384316	2011
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\| PubMed ID: 22615382	2012
Bivalent-like chromatin markers are predictive for transcription start site distribution in human. PloS one\| PubMed ID: 22768038	2012
Novel Markov model of induced pluripotency predicts gene expression changes in reprogramming. BMC systems biology\| PubMed ID: 22784579	2011
Chromatin state and microRNA determine different gene expression dynamics responsive to TNF stimulation. Genomics\| PubMed ID: 22824656	2012
Genome-wide localization of protein-DNA binding and histone modification by a Bayesian change-point method with ChIP-seq data. PLoS computational biology\| PubMed ID: 22844240	2012
Regulatory elements of Caenorhabditis elegans ribosomal protein genes. BMC genomics\| PubMed ID: 22928635	2012
Novel Foxo1-dependent transcriptional programs control T(reg) cell function. Nature\| PubMed ID: 23135404	2012