Michael Q. Zhang

Functional genomics as applied to mapping transcription regulatory networks.

GFScan: a gene family search tool at genomic DNA level.

Computational prediction of eukaryotic protein-coding genes.

Extracting functional information from microarrays: a challenge for functional genomics.

Gene expression profiling in developing human hippocampus.

Direct coupling of the cell cycle and cell death machinery by E2F.

The Argonaute family: tentacles that reach into RNAi, developmental control, stem cell maintenance, and tumorigenesis.

Computational comparison of two mouse draft genomes and the human golden path.

A global transcriptional regulatory role for c-Myc in Burkitt's lymphoma cells.

ESEfinder: A web resource to identify exonic splicing enhancers.

Computer software to find genes in plant genomic DNA.

Identifying cooperativity among transcription factors controlling the cell cycle in yeast.

Transcription factor binding element detection using functional clustering of mutant expression data.

Identifying combinatorial regulation of transcription factors and binding motifs.

Similarity of position frequency matrices for transcription factor binding sites.

DWE: discriminating word enumerator.

Evidence and characteristics of putative human alpha recombination hotspots.

Genome-wide prediction and analysis of function-specific transcription factor binding sites.

Interacting models of cooperative gene regulation.

The mouse genome: experimental examination of gene predictions and transcriptional start sites.

TRED: a Transcriptional Regulatory Element Database and a platform for in silico gene regulation studies.

From worm to human: bioinformatics approaches to identify FOXO target genes.

Identifying tissue-selective transcription factor binding sites in vertebrate promoters.

Mining ChIP-chip data for transcription factor and cofactor binding sites.

Genome-wide promoter extraction and analysis in human, mouse, and rat.

Distribution of SR protein exonic splicing enhancer motifs in human protein-coding genes.

Regulating gene expression through RNA nuclear retention.

Large-scale structure of genomic methylation patterns.

DNA motifs in human and mouse proximal promoters predict tissue-specific expression.

Profiling alternatively spliced mRNA isoforms for prostate cancer classification.

A clustering property of highly-degenerate transcription factor binding sites in the mammalian genome.

Characterization of RNase R-digested cellular RNA source that consists of lariat and circular RNAs from pre-mRNA splicing.

Adaptively inferring human transcriptional subnetworks.

Computational prediction of methylation status in human genomic sequences.

An increased specificity score matrix for the prediction of SF2/ASF-specific exonic splicing enhancers.

Predicting methylation status of CpG islands in the human brain.

A new method for detecting human recombination hotspots and its applications to the HapMap ENCODE data.

Computational prediction of novel components of lung transcriptional networks.

Pan-genome isolation of low abundance transcripts using SAGE tag.

Tissue-specific regulatory elements in mammalian promoters.

Computing exact P-values for DNA motifs.

Statistical significance of cis-regulatory modules.

Boosting with stumps for predicting transcription start sites.

Critical roles for Dicer in the female germline.

Analysis of the vertebrate insulator protein CTCF-binding sites in the human genome.

Predictive models of gene regulation: application of regression methods to microarray data.

A highly conserved regulatory element controls hematopoietic expression of GATA-2 in zebrafish.

Evolutionary impact of limited splicing fidelity in mammalian genes.

Dual-specificity splice sites function alternatively as 5' and 3' splice sites.

Neural potential of a stem cell population in the hair follicle.

Computational analyses of eukaryotic promoters.

OSCAR: one-class SVM for accurate recognition of cis-elements.

Prediction of transcription start sites based on feature selection using AMOSA.

Putative zinc finger protein binding sites are over-represented in the boundaries of methylation-resistant CpG islands in the human genome.

Identification of phylogenetically conserved microRNA cis-regulatory elements across 12 Drosophila species.

Genome-wide mapping and analysis of active promoters in mouse embryonic stem cells and adult organs.

Interferon regulatory factors are transcriptional regulators of adipogenesis.

Heat shock protein 90beta1 is essential for polyunsaturated fatty acid-induced mitochondrial Ca2+ efflux.

扫描在 kilobase 分辨率的人类基因组。

Using quality scores and longer reads improves accuracy of Solexa read mapping.

CD36-dependent regulation of muscle FoxO1 and PDK4 in the PPAR delta/beta-mediated adaptation to metabolic stress.

RNA landscape of evolution for optimal exon and intron discrimination.

Using CorePromoter to find human core promoters.

Network-based global inference of human disease genes.

Identification of synaptic targets of Drosophila pumilio.

Combinatorial patterns of histone acetylations and methylations in the human genome.

Histone methylation marks play important roles in predicting the methylation status of CpG islands.

Poly A- transcripts expressed in HeLa cells.

Regulation of the PDK4 isozyme by the Rb-E2F1 complex.

ZOOM! Zillions of oligos mapped.

Defining the regulatory network of the tissue-specific splicing factors Fox-1 and Fox-2.

Integrative bioinformatics analysis of transcriptional regulatory programs in breast cancer cells.

High-resolution human core-promoter prediction with CoreBoost_HM.

Multi-stage analysis of gene expression and transcription regulation in C57/B6 mouse liver development.

The Seventh Asia Pacific Bioinformatics Conference (APBC2009).

Gene set-based module discovery in the breast cancer transcriptome.

Determination of enriched histone modifications in non-genic portions of the human genome.

The transcriptome of human CD34+ hematopoietic stem-progenitor cells.

An integrative genomics approach identifies Hypoxia Inducible Factor-1 (HIF-1)-target genes that form the core response to hypoxia.

High definition profiling of mammalian DNA methylation by array capture and single molecule bisulfite sequencing.

Updates to the RMAP short-read mapping software.

SFSSClass: an integrated approach for miRNA based tumor classification.

Transcriptome study for early hematopoiesis--achievement, challenge and new opportunity.

Development of the human cancer microRNA network.

A long nuclear-retained non-coding RNA regulates synaptogenesis by modulating gene expression.

Comparison of sequencing-based methods to profile DNA methylation and identification of monoallelic epigenetic modifications.

Histone modification profiles are predictive for tissue/cell-type specific expression of both protein-coding and microRNA genes.

ChIP-Array: combinatory analysis of ChIP-seq/chip and microarray gene expression data to discover direct/indirect targets of a transcription factor.

Functional mutation of SMAC/DIABLO, encoding a mitochondrial proapoptotic protein, causes human progressive hearing loss DFNA64.

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.

Correlated evolution of transcription factors and their binding sites.

SpliceTrap: a method to quantify alternative splicing under single cellular conditions.

Study of FoxA pioneer factor at silent genes reveals Rfx-repressed enhancer at Cdx2 and a potential indicator of esophageal adenocarcinoma development.

EpiRegNet: constructing epigenetic regulatory network from high throughput gene expression data for humans.

Identification of tumor suppressors and oncogenes from genomic and epigenetic features in ovarian cancer.

Identification of novel androgen-regulated pathways and mRNA isoforms through genome-wide exon-specific profiling of the LNCaP transcriptome.

A highly efficient and effective motif discovery method for ChIP-seq/ChIP-chip data using positional information.

Cell-type-based analysis of microRNA profiles in the mouse brain.

Inferring haplotypes of copy number variations from high-throughput data with uncertainty.

H3K4 demethylation by Jarid1a and Jarid1b contributes to retinoblastoma-mediated gene silencing during cellular senescence.

Bivalent-like chromatin markers are predictive for transcription start site distribution in human.

Novel Markov model of induced pluripotency predicts gene expression changes in reprogramming.

Chromatin state and microRNA determine different gene expression dynamics responsive to TNF stimulation.

Genome-wide localization of protein-DNA binding and histone modification by a Bayesian change-point method with ChIP-seq data.

Regulatory elements of Caenorhabditis elegans ribosomal protein genes.

Novel Foxo1-dependent transcriptional programs control T(reg) cell function.