Zhang, Michael Q.
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Professor Michael Q. Zhang holds the Cecil H. and Ida Green Chair of Systems Biology Science. He also serves as director of the Center for Systems Biology. He is considered a leading scientist in computational biology and genomic research. Computational biology bridges the life sciences and quantitative sciences – mathematics, statistics and computer science – to understand living systems. His long-term research goal has been to use mathematical and statistical methods to identify functional elements in eucaryotic genomes, especially the genes and their control and regulatory elements.
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Works in Treasures @ UT Dallas are made available exclusively for educational purposes such as research or instruction. Literary rights, including copyright for published works held by the creator(s) or their heirs, or other third parties may apply. All rights are reserved unless otherwise indicated by the copyright owner(s).
Recent Submissions
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Integrating Hi-C and FISH Data for Modeling of the 3D Organization of Chromosomes
(Nature Publishing Group, 2019-05-03)The new advances in various experimental techniques that provide complementary information about the spatial conformations of chromosomes have inspired researchers to develop computational methods to fully exploit the ... -
Inhibiting the Integrated Stress Response Pathway Prevents Aberrant Chondrocyte Differentiation Thereby Alleviating Chondrodysplasia
The integrated stress response (ISR) is activated by diverse forms of cellular stress, including endoplasmic reticulum (ER) stress, and is associated with diseases. However, the molecular mechanism(s) whereby the ISR impacts ... -
Alterations of Specific Chromatin Conformation Affect ATRA-Induced Leukemia Cell Differentiation
Chromatin conformation plays a key role in regulating gene expression and controlling cell differentiation. However, the whole-genome chromatin conformation changes that occur during leukemia cell differentiation are poorly ... -
Relaxation Rates of Gene Expression Kinetics Reveal the Feedback Signs of Autoregulatory Gene Networks
The transient response to a stimulus and subsequent recovery to a steady state are the fundamental characteristics of a living organism. Here we study the relaxation kinetics of autoregulatory gene networks based on the ... -
FIND: DifFerential Chromatin INteractions Detection Using a Spatial Poisson Process
Polymer-based simulations and experimental studies indicate the existence of a spatial dependency between the adjacent DNA fibers involved in the formation of chromatin loops. However, the existing strategies for detecting ... -
Web3DMol: Interactive Protein Structure Visualization Based on WebGL
(Oxford University Press, 2017-05-08)A growing number of web-based databases and tools for protein research are being developed. There is now a widespread need for visualization tools to present the three-dimensional (3D) structure of proteins in web browsers. ... -
Super-Resolution Imaging of a 2.5 Kb Non-Repetitive DNA in situ in the Nuclear Genome Using Molecular Beacon Probes
(2018-08-31)High-resolution visualization of short non-repetitive DNA in situ in the nuclear genome is essential for studying looping interactions and chromatin organization in single cells. Recent advances in fluorescence in situ ... -
Reconstructing Cell Cycle Pseudo Time-Series Via Single-Cell Transcriptome Data
(Nature Publishing Group, 2018-08-24)Single-cell mRNA sequencing, which permits whole transcriptional profiling of individual cells, has been widely applied to study growth and development of tissues and tumors. Resolving cell cycle for such groups of cells ... -
ChIA-PET2: A Versatile and Flexible Pipeline for ChIA-PET Data Analysis
(Oxford University Press, 2016-09-12)ChIA-PET2 is a versatile and flexible pipeline for analyzing different types of ChIA-PET data from raw sequencing reads to chromatin loops. ChIA-PET2 integrates all steps required for ChIA-PET data analysis, including ... -
Emergent Lévy Behavior In Single-cell Stochastic Gene Expression
(American Physical Society, 2018-08-20)Single-cell gene expression is inherently stochastic; its emergent behavior can be defined in terms of the chemical master equation describing the evolution of the mRNA and protein copy numbers as the latter tends to ... -
De Novo Deciphering Three-Dimensional Chromatin Interaction and Topological Domains by Wavelet Transformation of Epigenetic Profiles
(Oxford University Press, 2016-04-07)Defining chromatin interaction frequencies and topological domains is a great challenge for the annotations of genome structures. Although the chromosome conformation capture (3C) and its derivative methods have been ... -
Chip-Array 2: Integrating Multiple Omics Data to Construct Gene Regulatory Networks
(2015-04-27)Transcription factors (TFs) play an important role in gene regulation. The interconnections among TFs, chromatin interactions, epigenetic marks and cisregulatory elements form a complex gene transcription apparatus. Our ... -
Quantitative Combination of Natural Anti-Oxidants Prevents Metabolic Syndrome by Reducing Oxidative Stress
(2015-06-26)Insulin resistance and abdominal obesity are present in the majority of people with the metabolic syndrome. Antioxidant therapy might be a useful strategy for type 2 diabetes and other insulin-resistant states. The combination ... -
3CPET: Finding Co-Factor Complexes from ChIA-Pet Data Using a Hierarchical Dirichlet Process
(BioMed Central Ltd, 2015-12-22)Various efforts have been made to elucidate the cooperating proteins involved in maintaining chromatin interactions; however, many are still unknown. Here, we present 3CPET, a tool based on a non-parametric Bayesian approach, ... -
Histone Deacetylases Positively Regulate Transcription Through the Elongation Machinery
(Elsevier B.V., 2015-11-17)Transcription elongation regulates the expression of many genes, including oncogenes. Histone deacetylase (HDAC) inhibitors (HDACIs) block elongation, suggesting that HDACs are involved in gene activation. To understand ... -
Fast Dimension Reduction and Integrative Clustering of Multi-Omics Data Using Low-Rank Approximation: Application to Cancer Molecular Classification
(BioMed Central, 2015-12-01)Background: One major goal of large-scale cancer omics study is to identify molecular subtypes for more accurate cancer diagnoses and treatments. To deal with high-dimensional cancer multi-omics data, a promising strategy ... -
Distinct and Predictive Histone Lysine Acetylation Patterns at Promoters, Enhancers, and Gene Bodies
(Genetics Society America, 2014-11-01)In eukaryotic cells, histone lysines are frequently acetylated. However, unlike modifications such as methylations, histone acetylation modifications are often considered redundant. As such, the functional roles of distinct ... -
Genome Wide Mapping of Foxo1 Binding-Sites in Murine T Lymphocytes
(Elsevier Inc, 2014-08-01)The Forkhead box O (Foxo) family of transcription factors has a critical role in controlling the development, differentiation, and function of T cells. However, the direct target genes of Foxo transcription factors in T ... -
Hsa-miR-1246, Hsa-miR-320a and Hsa-miR-196b-5p Inhibitors can Reduce the Cytotoxicity of Ebola Virus Glycoprotein in Vitro
(Science Press, 2014-09-12)Ebola virus (EBOV) causes a highly lethal hemorrhagic fever syndrome in humans and has been associated with mortality rates of up to 91% in Zaire, the most lethal strain. Though the viral envelope glycoprotein (GP) mediates ... -
Activity-Dependent FUS Dysregulation Disrupts Synaptic Homeostasis
(Natl Acad Sciences, 2014-10-16)The RNA-binding protein fused-in-sarcoma (FUS) has been associated with amyotrophic lateral sclerosis (ALS) and frontotemporal lobar degeneration (FTLD), two neurodegenerative disorders that share similar clinical and ...
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