Ming Zhan

Summary

Affiliation: National Institutes of Health
Country: USA

Publications

  1. pmc Expression profiling of human glial precursors
    James T Campanelli
    Q Therapeutics, Inc 615 Arapeen Dr, Ste 102, Salt Lake City, UT 84108, USA
    BMC Dev Biol 8:102. 2008
  2. ncbi request reprint Genomic studies to explore self-renewal and differentiation properties of embryonic stem cells
    Ming Zhan
    Bioinformatics Unit, Research Resources Branch, National Institute on Aging, NIH, Baltimore, MD, USA
    Front Biosci 13:276-83. 2008
  3. pmc Deciphering modular and dynamic behaviors of transcriptional networks
    Ming Zhan
    Bioinformatics Unit, Research Resources Branch, National Institute on Aging, NIH, 333 Cassell Drive, Baltimore, MD, 21224, USA
    Genomic Med 1:19-28. 2007
  4. ncbi request reprint Inferring regulatory networks
    Huai Li
    Bioinformatics Unit, Branch of Research Resources, National Institute on Aging, NIH, Baltimore, MD, USA
    Front Biosci 13:263-75. 2008
  5. pmc Evolutionarily conserved transcriptional co-expression guiding embryonic stem cell differentiation
    Yu Sun
    Bioinformatics Unit, Research Resources Branch, National Institute on Aging, NIH, Baltimore, MD, USA
    PLoS ONE 3:e3406. 2008
  6. pmc Cross-species transcriptional profiles establish a functional portrait of embryonic stem cells
    Yu Sun
    Bioinformatics Unit, Research Resources Branch, National Institute on Aging, National Institutes of Health, 333 Cassall Drive, Baltimore, MD 21224, USA
    Genomics 89:22-35. 2007
  7. pmc Genome wide profiling of human embryonic stem cells (hESCs), their derivatives and embryonal carcinoma cells to develop base profiles of U.S. Federal government approved hESC lines
    Ying Liu
    Laboratory of Neurosciences, National Institute on Aging Intramural Research Program, National Institutes of Health, Baltimore, Maryland 21224, USA
    BMC Dev Biol 6:20. 2006
  8. pmc Unraveling transcriptional regulatory programs by integrative analysis of microarray and transcription factor binding data
    Huai Li
    Bioinformatics Unit, Branch of Research Resources, National Institute on Aging, NIH, Baltimore, MD 21224, USA
    Bioinformatics 24:1874-80. 2008
  9. pmc LincRNA-p21 suppresses target mRNA translation
    Je Hyun Yoon
    Laboratory of Molecular Biology and Immunology, National Institute on Aging Intramural Research Program, National Institutes of Health, Baltimore, MD 21224, USA
    Mol Cell 47:648-55. 2012
  10. pmc Identification of a signature motif in target mRNAs of RNA-binding protein AUF1
    Krystyna Mazan-Mamczarz
    Laboratory of Cellular and Molecular Biology, National Institute on Aging, Intramural Research Program, National Institutes of Health, Baltimore, MD 21224, USA
    Nucleic Acids Res 37:204-14. 2009

Collaborators

Detail Information

Publications35

  1. pmc Expression profiling of human glial precursors
    James T Campanelli
    Q Therapeutics, Inc 615 Arapeen Dr, Ste 102, Salt Lake City, UT 84108, USA
    BMC Dev Biol 8:102. 2008
    ..We have generated gene expression databases for human glial precursors, neuronal precursors, astrocyte precursors and neural stem cells and focused on comparing the profile of glial precursors with that of other populations...
  2. ncbi request reprint Genomic studies to explore self-renewal and differentiation properties of embryonic stem cells
    Ming Zhan
    Bioinformatics Unit, Research Resources Branch, National Institute on Aging, NIH, Baltimore, MD, USA
    Front Biosci 13:276-83. 2008
    ..In this article, various aspects of genomic and transcriptomic studies on ESCs are reviewed, and important findings regarding ESC self-renewal and differentiation are highlighted and discussed...
  3. pmc Deciphering modular and dynamic behaviors of transcriptional networks
    Ming Zhan
    Bioinformatics Unit, Research Resources Branch, National Institute on Aging, NIH, 333 Cassell Drive, Baltimore, MD, 21224, USA
    Genomic Med 1:19-28. 2007
    ..We also demonstrate how these computational algorithms can be applied in systems biology studies as on disease, stem cells, and drug discovery...
  4. ncbi request reprint Inferring regulatory networks
    Huai Li
    Bioinformatics Unit, Branch of Research Resources, National Institute on Aging, NIH, Baltimore, MD, USA
    Front Biosci 13:263-75. 2008
    ..Popular solutions to each of these problems and their relative merits are discussed...
  5. pmc Evolutionarily conserved transcriptional co-expression guiding embryonic stem cell differentiation
    Yu Sun
    Bioinformatics Unit, Research Resources Branch, National Institute on Aging, NIH, Baltimore, MD, USA
    PLoS ONE 3:e3406. 2008
    ..Cross-species examination of transcriptional co-expression allows elucidation of fundamental and species-specific mechanisms regulating ESC self-renewal or differentiation...
  6. pmc Cross-species transcriptional profiles establish a functional portrait of embryonic stem cells
    Yu Sun
    Bioinformatics Unit, Research Resources Branch, National Institute on Aging, National Institutes of Health, 333 Cassall Drive, Baltimore, MD 21224, USA
    Genomics 89:22-35. 2007
    ..The data and analyses resulting from this study provide a framework for new hypotheses and research directions and a public resource for functional genomics of ESCs...
  7. pmc Genome wide profiling of human embryonic stem cells (hESCs), their derivatives and embryonal carcinoma cells to develop base profiles of U.S. Federal government approved hESC lines
    Ying Liu
    Laboratory of Neurosciences, National Institute on Aging Intramural Research Program, National Institutes of Health, Baltimore, Maryland 21224, USA
    BMC Dev Biol 6:20. 2006
    ....
  8. pmc Unraveling transcriptional regulatory programs by integrative analysis of microarray and transcription factor binding data
    Huai Li
    Bioinformatics Unit, Branch of Research Resources, National Institute on Aging, NIH, Baltimore, MD 21224, USA
    Bioinformatics 24:1874-80. 2008
    ..Unraveling the transcriptional regulatory program mediated by transcription factors (TFs) is a fundamental objective of computational biology, yet still remains a challenge...
  9. pmc LincRNA-p21 suppresses target mRNA translation
    Je Hyun Yoon
    Laboratory of Molecular Biology and Immunology, National Institute on Aging Intramural Research Program, National Institutes of Health, Baltimore, MD 21224, USA
    Mol Cell 47:648-55. 2012
    ..We propose that HuR controls translation of a subset of target mRNAs by influencing lincRNA-p21 levels. Our findings uncover a role for lincRNA as a posttranscriptional inhibitor of translation...
  10. pmc Identification of a signature motif in target mRNAs of RNA-binding protein AUF1
    Krystyna Mazan-Mamczarz
    Laboratory of Cellular and Molecular Biology, National Institute on Aging, Intramural Research Program, National Institutes of Health, Baltimore, MD 21224, USA
    Nucleic Acids Res 37:204-14. 2009
    ....
  11. pmc Aging studies in Drosophila melanogaster
    Yaning Sun
    Translational Gerontology Branch, National Institute on Aging, Baltimore, MD, USA
    Methods Mol Biol 1048:77-93. 2013
    ..We also describe some commonly used assays to measure changes in physiological and behavioral functions of Drosophila in aging, such as stress resistance and locomotor activity. ..
  12. ncbi request reprint Mechanisms controlling embryonic stem cell self-renewal and differentiation
    Yu Sun
    Bioinformatics Unit, Research Resources Branch, National Institute on Aging, NIH, Baltimore, MD 21224, USA
    Crit Rev Eukaryot Gene Expr 16:211-31. 2006
    ..Here, we review recent findings on mechanisms controlling ES cell development. By integrating data from different sources, we present a global picture of how ES cells reach the decision of self-renewal or differentiation...
  13. pmc Exploring pathways from gene co-expression to network dynamics
    Huai Li
    Bioinformatics Unit, Branch of Research Resources, National Institute on Aging, National Institutes of Health, Baltimore, MD, USA
    Methods Mol Biol 541:249-67. 2009
    ..The analysis using these newly developed algorithms show the great usefulness of computational systems biology approaches for biological and medical research...
  14. pmc Enhanced translation by Nucleolin via G-rich elements in coding and non-coding regions of target mRNAs
    Kotb Abdelmohsen
    Laboratory of Molecular Biology and Immunology, National Institute on Aging Intramural Research Program, NIH, Baltimore, MD 21224, USA
    Nucleic Acids Res 39:8513-30. 2011
    ..In summary, nucleolin binds G-rich sequences in the CR and UTRs of target mRNAs, many of which encode cancer proteins, and enhances their translation...
  15. ncbi request reprint The discovery of transcriptional modules by a two-stage matrix decomposition approach
    Huai Li
    Bioinformatics Unit, Branch of Research Resources, National Institute on Aging, NIH, Baltimore, MD 21224, USA
    Bioinformatics 23:473-9. 2007
    ..Unraveling such transcriptional modules is important for understanding biological network, deciphering regulatory mechanisms and identifying biomarkers...
  16. pmc The human glucocorticoid receptor as an RNA-binding protein: global analysis of glucocorticoid receptor-associated transcripts and identification of a target RNA motif
    Faoud T Ishmael
    Division of Allergy and Clinical Immunology, The Johns Hopkins Asthma and Allergy Center, Baltimore, MD 21224, USA
    J Immunol 186:1189-98. 2011
    ..These results indicate that cytoplasmic GR interacts with a subset of mRNA through specific sequences and can regulate turnover rates, suggesting a novel posttranscriptional role for GR as an RNA-binding protein...
  17. pmc NF90 selectively represses the translation of target mRNAs bearing an AU-rich signature motif
    Yuki Kuwano
    RNA Regulation Section, Laboratory of Cellular and Molecular Biology and Bioinformatics Unit, Research Resources Branch, National Institute on Aging Intramural Research Program, National Institutes of Health, Baltimore, MD 21224, USA
    Nucleic Acids Res 38:225-38. 2010
    ..In summary, we have identified an AU-rich RNA motif present in NF90 target mRNAs and have obtained evidence that NF90 represses the translation of this subset of mRNAs...
  18. pmc Temporal and spatial transcriptional profiles of aging in Drosophila melanogaster
    Ming Zhan
    Bioinformatics Unit, Branch of Research Resources, National Institute on Aging, NIH, Baltimore, MD 21224, USA
    Genome Res 17:1236-43. 2007
    ..The spatial and temporal transcriptome data presented in this study provide a basis and a valuable resource for further genetic and genomic investigation of tissue-specific regulation of aging...
  19. pmc Transcriptome coexpression map of human embryonic stem cells
    Huai Li
    Bioinformatics Unit, Branch of Research Resources, National Institute on Aging, NIH, Baltimore, MD 21224, USA
    BMC Genomics 7:103. 2006
    ..However, no systematic analysis has yet addressed whether gene expression in human ES cells may be regulated in chromosomal domains, and no chromosomal domains of coexpression have been identified...
  20. pmc The B-MYB transcriptional network guides cell cycle progression and fate decisions to sustain self-renewal and the identity of pluripotent stem cells
    Ming Zhan
    Bioinformatics Unit, National Institute on Aging, National Institutes of Health, Baltimore, Maryland, United States of America
    PLoS ONE 7:e42350. 2012
    ..These results coupled with functional studies demonstrate that B-MYB not only controls and accelerates cell cycle progression in ESCs it contributes to fate decisions and maintenance of pluripotent stem cell identity...
  21. pmc Ribosomal protein mRNAs are primary targets of regulation in RNase-L-induced senescence
    Jesper B Andersen
    Marlene and Stewart Greenebaum Cancer Center, University of Maryland Baltimore, School of Medicine, Baltimore, MD 21201, USA
    RNA Biol 6:305-15. 2009
    ..Our data support a model in which the RNase-L-mediated degradation of RP mRNAs inhibits translation, and may contribute to its antiproliferative, senescence inducing and tumor suppressor activities...
  22. pmc Functional significance for a heterogenous ribonucleoprotein A18 signature RNA motif in the 3'-untranslated region of ataxia telangiectasia mutated and Rad3-related (ATR) transcript
    Ruiqing Yang
    Department of Radiation Oncology, the Marlene and Stewart Greenebaum Cancer Center, University of Maryland School of Medicine, Baltimore, Maryland 21201, USA
    J Biol Chem 285:8887-93. 2010
    ..hnRNP A18 could thus become a new target to trigger ATR activity as back-up stress response mechanisms to functionally compensate for absent or defective responders...
  23. pmc Gene expression atlas of the mouse central nervous system: impact and interactions of age, energy intake and gender
    Xiangru Xu
    Laboratory of Neurosciences, National Institute on Aging Intramural Research Program, 5600 Nathan Shock Drive, Baltimore, MD 21224, USA
    Genome Biol 8:R234. 2007
    ..The structural and functional complexity of the mammalian central nervous system (CNS) is organized and modified by complicated molecular signaling processes that are poorly understood...
  24. ncbi request reprint Mitochondrial UCP4 mediates an adaptive shift in energy metabolism and increases the resistance of neurons to metabolic and oxidative stress
    Dong Liu
    Laboratory of Neurosciences, National Institute on Aging Intramural Research Program, Baltimore, MD, USA
    Neuromolecular Med 8:389-414. 2006
    ..By shifting energy metabolism to reduce ROS production and cellular reliance on mitochondrial respiration, UCP4 can protect neurons against oxidative stress and calcium overload...
  25. ncbi request reprint Systematic intervention of transcription for identifying network response to disease and cellular phenotypes
    Huai Li
    Bioinformatics Unit, Branch of Research Resources, National Institute on Aging NIH, Baltimore, MD 21224, USA
    Bioinformatics 22:96-102. 2006
    ..Here, we addressed this issue by developing an algorithm to mimic the behavior of regulatory networks in silico and to identify the dynamic response to disease and changing cellular conditions...
  26. ncbi request reprint Conservation and variation of gene regulation in embryonic stem cells assessed by comparative genomics
    Ming Zhan
    Bioinformatics Unit, Branch of Research Resources, National Institute on Aging, NIH, Baltimore, MD, 21224, USA
    Cell Biochem Biophys 43:379-405. 2005
    ..These results provide a framework for examining the current reported differences between rodent and human ES cells and define targets for future perturbation studies...
  27. pmc RNA binding activity of the recessive parkinsonism protein DJ-1 supports involvement in multiple cellular pathways
    Marcel P van der Brug
    Cell Biology and Gene Expression Unit, Laboratory of Neurogenetics, National Institute on Aging, 35 Convent Drive, Bethesda, MD 20892 3707, USA
    Proc Natl Acad Sci U S A 105:10244-9. 2008
    ..These data implicate a single mechanism for the pleiotropic effects of DJ-1 in different model systems, namely that the protein binds multiple RNA targets in an oxidation-dependent manner...
  28. pmc En masse nascent transcription analysis to elucidate regulatory transcription factors
    Jinshui Fan
    Laboratory of Cellular and Molecular Biology, National Institute on Aging Intramural Research Program, National Institutes of Health, Baltimore, MD 21224, USA
    Nucleic Acids Res 34:1492-500. 2006
    ..The strategies described here permit the successful identification of the TFs responsible for implementing adaptive gene expression programs in response to cellular stimulation...
  29. pmc Identification and functional outcome of mRNAs associated with RNA-binding protein TIA-1
    Isabel Lopez de Silanes
    Laboratory of Cellular and Molecular Biology, Intramural Research Program, National Institute on Aging NIH, 5600 Nathan Shock Drive, Baltimore, MD 21224, USA
    Mol Cell Biol 25:9520-31. 2005
    ..In summary, we report a signature motif present in mRNAs that associate with TIA-1 and provide support to the notion that TIA-1 represses the translation of target transcripts...
  30. ncbi request reprint Novel anticholinesterases based on the molecular skeletons of furobenzofuran and methanobenzodioxepine
    Weiming Luo
    Drug Design and Development Section, Laboratory of Neurosciences, National Institute on Aging, National Institutes of Health, 5600 Nathan Shock Drive, Baltimore, Maryland 21224, USA
    J Med Chem 48:986-94. 2005
    ....
  31. ncbi request reprint Characterization of progenitor-cell-specific genes identified by subtractive suppression hybridization
    Jingli Cai
    Laboratoryof Neurosciences, National Institute on Aging, Baltimore, MD 21224, USA
    Dev Neurosci 26:131-47. 2004
    ..Overall, our results show that SSH can be used to identify lineage- and stage-specific markers and that extracellular matrix molecules likely play important roles in the migration and differentiation of GRPs...
  32. pmc Identification of a target RNA motif for RNA-binding protein HuR
    Isabel Lopez de Silanes
    Laboratory of Cellular and Molecular Biology, National Institute on Aging Intramural Research Program, National Institutes of Health, Baltimore, MD 21224, USA
    Proc Natl Acad Sci U S A 101:2987-92. 2004
    ..This study describes an HuR target RNA motif and presents a general strategy for identifying target motifs for RNA-binding proteins...
  33. ncbi request reprint Whole genome analysis of human neural stem cells derived from embryonic stem cells and stem and progenitor cells isolated from fetal tissue
    Soojung Shin
    Stem Cells and Regenerative Medicine, Invitrogen, Carlsbad, California, USA
    Stem Cells 25:1298-306. 2007
    ..Disclosure of potential conflicts of interest is found at the end of this article...
  34. ncbi request reprint Copper homeostasis gene discovery in Drosophila melanogaster
    Melanie Norgate
    Department of Genetics, The University of Melbourne, Parkville, VIC 3010, Australia
    Biometals 20:683-97. 2007
    ..Building on this information, there is great potential for the further use of Drosophila for copper homeostasis gene discovery...
  35. pmc Elucidation of a C-rich signature motif in target mRNAs of RNA-binding protein TIAR
    Henry S Kim
    Department of Biochemistry and Molecular Biology, Monash University, Victoria, Australia
    Mol Cell Biol 27:6806-17. 2007
    ..In sum, we report the identification of a C-rich signature motif present in TIAR target mRNAs whose association with TIAR decreases following exposure to a stress-causing agent...