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Author Details

Michael Q Zhang
The University of Texas at Dallas
2011
37
18
PMIDPaper TitleJournal TitlePublished Year
37278656Enterococcus faecalis Strains with Compromised CRISPR-Cas Defense Emerge under Antibiotic Selection for a CRISPR-Targeted Plasmid.Appl Environ Microbiol2023
37547001Chromatin-associated RNA Dictates the ecDNA Interactome in the Nucleus.bioRxiv2023
36108240Prostate Cancer Transcriptomic Regulation by the Interplay of Germline Risk Alleles, Somatic Mutations, and 3D Genomic Architecture.Cancer Discov2022
35348640HPVMD-C: a disease-based mutation database of human papillomavirus in China.Database (Oxford)2022
34301239Single-cell alternative polyadenylation analysis delineates GABAergic neuron types.BMC Biol2021
33838653Deciphering hierarchical organization of topologically associated domains through change-point testing.BMC Bioinformatics2021
34404448Quantifying the phase separation property of chromatin-associated proteins under physiological conditions using an anti-1,6-hexanediol index.Genome Biol2021
34608315SEAM is a spatial single nuclear metabolomics method for dissecting tissue microenvironment.Nat Methods2021
32343676The landscape of RNA polymerase II-associated chromatin interactions in prostate cancer.J Clin Invest2020
33256598Highly diversified core promoters in the human genome and their effects on gene expression and disease predisposition.BMC Genomics2020
32735574Model-based analysis of chromatin interactions from dCas9-Based CAPTURE-3C-seq.PLoS One2020
32553668Beta-amyloid deposition around hepatic bile ducts is a novel pathobiological and diagnostic feature of biliary atresia.J Hepatol2020
32138752Multiplexed capture of spatial configuration and temporal dynamics of locus-specific 3D chromatin by biotinylated dCas9.Genome Biol2020
323496772SigFinder: the combined use of small-scale and large-scale statistical testing for genomic island detection from a single genome.BMC Bioinformatics2020
30799483SuperCT: a supervised-learning framework for enhanced characterization of single-cell transcriptomic profiles.Nucleic Acids Res2019
31869986Single-cell stochastic gene expression kinetics with coupled positive-plus-negative feedback.Phys Rev E2019
28025178MTGIpick allows robust identification of genomic islands from a single genome.Brief Bioinform2018
29927077CAPTURE: In Situ Analysis of Chromatin Composition of Endogenous Genomic Loci by Biotinylated dCas9.Curr Protoc Mol Biol2018
30352805Global transcriptional activity dynamics reveal functional enhancer RNAs.Genome Res2018
29659575Synergistic co-regulation and competition by a SOX9-GLI-FOXA phasic transcriptional network coordinate chondrocyte differentiation transitions.PLoS Genet2018
29561359Comparative transcriptome profiling of the human and mouse dorsal root ganglia: an RNA-seq-based resource for pain and sensory neuroscience research.Pain2018
28860207PAF1 regulation of promoter-proximal pause release via enhancer activation.Science2017
29347590Emergent Lévy behavior in single-cell stochastic gene expression.Phys Rev E2017
29167445Stochastic fluctuations can reveal the feedback signs of gene regulatory networks at the single-molecule level.Sci Rep2017
28841410In Situ Capture of Chromatin Interactions by Biotinylated dCas9.Cell2017
25958398Design and bioinformatics analysis of genome-wide CLIP experiments.Nucleic Acids Res2015
28348816Genome-wide analysis of the response to nitric oxide in uropathogenic <i>Escherichia coli</i> CFT073.Microb Genom2015
26549458Histone Deacetylases Positively Regulate Transcription through the Elongation Machinery.Cell Rep2015
26210472Reconfigurable hybrid interface for molecular marker diagnostics and in-situ reporting.Biosens Bioelectron2015
25916854ChIP-Array 2: integrating multiple omics data to construct gene regulatory networks.Nucleic Acids Res2015
25825433Genome Modification in Enterococcus faecalis OG1RF Assessed by Bisulfite Sequencing and Single-Molecule Real-Time Sequencing.J Bacteriol2015
24798576Assembly and validation of versatile transcription activator-like effector libraries.Sci Rep2014
23685394Computational identification of active enhancers in model organisms.Genomics Proteomics Bioinformatics2013
23924514ProteoMirExpress: inferring microRNA and protein-centered regulatory networks from high-throughput proteomic and mRNA expression data.Mol Cell Proteomics2013
21586587ChIP-Array: combinatory analysis of ChIP-seq/chip and microarray gene expression data to discover direct/indirect targets of a transcription factor.Nucleic Acids Res2011
21896508Correlated evolution of transcription factors and their binding sites.Bioinformatics2011
22139581EpiRegNet: constructing epigenetic regulatory network from high throughput gene expression data for humans.Epigenetics2011
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Collaborators

Yong Chen
Rowan University
Co-authored papers 7
Panwen Wang
Co-authored papers 4
Tae Hoon Kim
Co-authored papers 3
Jiapei Yuan
UT Southwestern Medical Center
Co-authored papers 2
GuemHee Baek
UT Southwestern Medical Center
Co-authored papers 2
Ram S Mani
UT Southwestern Medical Center
Co-authored papers 2
Paul C Boutros
University of California los angeles
Co-authored papers 2
Zhenyu Xuan
Co-authored papers 2
Kathleen E Houlahan
University of California los angeles
Co-authored papers 2
Susmita G Ramanand
UT Southwestern Medical Center
Co-authored papers 2
Pak C Sham
the University of Hong Kong
Co-authored papers 1
Ganesh V Raj
University of Texas Southwestern Medical Center at Dallas
Co-authored papers 1
Huimin Xia
Guangzhou Women and Children's Medical Center, Guangzhou Medical University
Co-authored papers 1
Xiang-Dong Fu
Co-authored papers 1
Gary C Hon
Cecil H. and Ida Green Center for Reproductive Biology Sciences
Co-authored papers 1
Suzanne Carreira
The Institute of Cancer Research
Co-authored papers 1
Adam Sharp
The Institute for Cancer Research
Co-authored papers 1
Wei Yuan
The Institute for Cancer Research
Co-authored papers 1
In-Hyun Park
Yale School of Medicine
Co-authored papers 1
Mohammed Kanchwala
The University of Texas Southwestern Medical Center
Co-authored papers 1
Maryou B Lambros
The Institute of Cancer Research
Co-authored papers 1
Dong-Er Zhang
Moores Cancer Center, University of California San Diego
Co-authored papers 1
Z Josh Huang
Duke University School of Medicine
Co-authored papers 1
Anirban Paul
Penn State College of Medicine
Co-authored papers 1
Yunpeng Gao
University of Texas Southwestern Medical Center at Dallas
Co-authored papers 1
Kelly Daescu
Center for Systems Biology, University of Texas at Dallas
Co-authored papers 1
Jun Qin
Co-authored papers 1
Tao Wang
University of Texas Southwestern Medical Center
Co-authored papers 1
Ali Shilatifard
Northwestern University Feinberg School of Medicine
Co-authored papers 1
Stuart H Orkin
Boston Children's Hospital and Dana-Farber Cancer Institute, Harvard Medical School
Co-authored papers 1
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