Michael Q. Zhang

Orcid: 0000-0002-7022-6115

According to our database1, Michael Q. Zhang authored at least 69 papers between 1993 and 2024.

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Bibliography

2024
Exact Power Spectrum in a Minimal Hybrid Model of Stochastic Gene Expression Oscillations.
SIAM J. Appl. Math., 2024

2023
Dialog between artificial intelligence & natural intelligence.
Quant. Biol., December, 2023

Systematic comparison of genome information processing and boundary recognition tools used for genomic island detection.
Comput. Biol. Medicine, November, 2023

2022
HPVMD-C: a disease-based mutation database of human papillomavirus in China.
Database J. Biol. Databases Curation, 2022

2021
A personal journey on cracking the genomic codes.
Quant. Biol., 2021

Deciphering hierarchical organization of topologically associated domains through change-point testing.
BMC Bioinform., 2021

2020
2SigFinder: the combined use of small-scale and large-scale statistical testing for genomic island detection from a single genome.
BMC Bioinform., 2020

2019
Regulation by competition: a hidden layer of gene regulatory network.
Quant. Biol., 2019

2018
NONCODEV5: a comprehensive annotation database for long non-coding RNAs.
Nucleic Acids Res., 2018

CGmapTools improves the precision of heterozygous SNV calls and supports allele-specific methylation detection and visualization in bisulfite-sequencing data.
Bioinform., 2018

MTGIpick allows robust identification of genomic islands from a single genome.
Briefings Bioinform., 2018

DE MERVLs are Enriched Around Two-Cell-Specific Genes During Zygotic Genome Activation in Mouse.
Proceedings of the IEEE International Conference on Systems, Man, and Cybernetics, 2018

2017
HiC-3DViewer: a new tool to visualize Hi-C data in 3D space.
Quant. Biol., 2017

Web3DMol: interactive protein structure visualization based on WebGL.
Nucleic Acids Res., 2017

DIRECTION: a machine learning framework for predicting and characterizing DNA methylation and hydroxymethylation in mammalian genomes.
Bioinform., 2017

2016
Advances in computational ChIA-PET data analysis.
Quant. Biol., 2016

Developing bioimaging and quantitative methods to study 3D genome.
Quant. Biol., 2016

NONCODE 2016: an informative and valuable data source of long non-coding RNAs.
Nucleic Acids Res., 2016

2015
A novel method to identify topological domains using Hi-C data.
Quant. Biol., 2015

Integrative analysis of 111 reference human epigenomes Open.
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Nat., 2015

ChIP-Array 2: integrating multiple omics data to construct gene regulatory networks.
Nucleic Acids Res., 2015

MICC: an R package for identifying chromatin interactions from ChIA-PET data.
Bioinform., 2015

2013
Population dynamics of cancer cells with cell state conversions.
Quant. Biol., 2013

QB: A new inter- and multi-disciplinary forum for modeling, engineering and understanding life.
Quant. Biol., 2013

Computational Identification of Active Enhancers in Model Organisms.
Genom. Proteom. Bioinform., 2013

2012
Genome-Wide Localization of Protein-DNA Binding and Histone Modification by a Bayesian Change-Point Method with ChIP-seq Data.
PLoS Comput. Biol., 2012

Prioritizing Disease Genes and Understanding Disease Pathways.
Int. J. Knowl. Discov. Bioinform., 2012

Computational Modeling of Mammalian Promoters - (Invited Keynote Talk).
Proceedings of the Bioinformatics Research and Applications - 8th International Symposium, 2012

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 Res., 2011

Novel Markov model of induced pluripotency predicts gene expression changes in reprogramming.
BMC Syst. Biol., 2011

Histone modification profiles are predictive for tissue/cell-type specific expression of both protein-coding and microRNA genes.
BMC Bioinform., 2011

Correlated evolution of transcription factors and their binding sites.
Bioinform., 2011

SpliceTrap: a method to quantify alternative splicing under single cellular conditions.
Bioinform., 2011

A method for finding novel associations between genome-wide copy number and dna methylation patterns.
Proceedings of the 2011 IEEE International Workshop on Genomic Signal Processing and Statistics, 2011

Computational Promoter Prediction in a Vertebrate Genome.
Proceedings of the Handbook of Statistical Bioinformatics., 2011

2010
SFSSClass: an integrated approach for miRNA based tumor classification.
BMC Bioinform., 2010

2009
Challenges in Understanding Genome-Wide DNA Methylation.
J. Comput. Sci. Technol., 2009

The Seventh Asia Pacific Bioinformatics Conference (APBC2009).
BMC Bioinform., 2009

Gene set-based module discovery in the breast cancer transcriptome.
BMC Bioinform., 2009

Updates to the RMAP short-read mapping software.
Bioinform., 2009

2008
Identification of Synaptic Targets of <i>Drosophila</i> Pumilio.
PLoS Comput. Biol., 2008

Using quality scores and longer reads improves accuracy of Solexa read mapping.
BMC Bioinform., 2008

Integrative bioinformatics analysis of transcriptional regulatory programs in breast cancer cells.
BMC Bioinform., 2008

Identification of phylogenetically conserved microRNA <i>cis</i>-regulatory elements across 12 <i>Drosophila</i> species.
Bioinform., 2008

ZOOM! Zillions of oligos mapped.
Bioinform., 2008

Multiobjective fuzzy biclustering in microarray data: Method and a new performance measure.
Proceedings of the IEEE Congress on Evolutionary Computation, 2008

2007
Neighbor number, valley seeking and clustering.
Pattern Recognit. Lett., 2007

TRED: a transcriptional regulatory element database, new entries and other development.
Nucleic Acids Res., 2007

Computational analyses of eukaryotic promoters.
BMC Bioinform., 2007

Statistical significance of cis-regulatory modules.
BMC Bioinform., 2007

Computing exact <i>P</i>-values for DNA motifs.
Bioinform., 2007

Computational prediction of novel components of lung transcriptional networks.
Bioinform., 2007

OSCAR: One-class SVM for accurate recognition of <i>cis</i>-elements.
Bioinform., 2007

2006
Profiling alternatively spliced mRNA isoforms for prostate cancer classification.
BMC Bioinform., 2006

Predicting methylation status of CpG islands in the human brain.
Bioinform., 2006

Analysis and visualization of DNA spectrograms: open possibilities for the genome research.
Proceedings of the 14th ACM International Conference on Multimedia, 2006

2005
TRED: a Transcriptional Regulatory Element Database and a platform for <i>in silico</i> gene regulation studies.
Nucleic Acids Res., 2005

DWE: Discriminating Word Enumerator.
Bioinform., 2005

Similarity of position frequency matrices for transcription factor binding sites.
Bioinform., 2005

Computational Molecular Biology of Genome Expression and Regulation.
Proceedings of the Pattern Recognition and Machine Intelligence, 2005

Mining ChIP-chip data for transcription factor and cofactor binding sites.
Proceedings of the Proceedings Thirteenth International Conference on Intelligent Systems for Molecular Biology 2005, 2005

2004
Genome-wide prediction and analysis of function-specific transcription factor binding sites.
Silico Biol., 2004

2003
ESEfinder: a web resource to identify exonic splicing enhancers.
Nucleic Acids Res., 2003

2001
Promoter Extraction from GenBank (PEG): automatic extraction of eukaryotic promoter sequences in large sets of genes.
Bioinform., 2001

Identifying the 3'-terminal exon in human DNA.
Bioinform., 2001

2000
Discriminant Analysis and Its Application in DNA Sequence Motif Recognition.
Briefings Bioinform., 2000

1999
Promoter Analysis of Co-regulated Genes in the Yeast Genome.
Comput. Chem., 1999

SCPD: a promoter database of the yeast Saccharomyces cerevisiae.
Bioinform., 1999

1993
A weight array method for splicing signal analysis.
Comput. Appl. Biosci., 1993


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