Wen Zhang

Summary

Affiliation: University of Toronto
Country: Canada

Publications

  1. ncbi request reprint Monitoring G-protein-coupled receptor signaling with DNA microarrays and real-time polymerase chain reaction
    Tony Yuen
    Department of Neurology, Mount Sinai School of Medicine, New York, New York 10029, USA
    Methods Enzymol 345:556-69. 2002
  2. pmc The functional landscape of mouse gene expression
    Wen Zhang
    Banting and Best Department of Medical Research, University of Toronto, 1 King s College Circle, Toronto, ON M5S 1A8, Canada
    J Biol 3:21. 2004
  3. ncbi request reprint Genome-wide analysis of mouse transcripts using exon microarrays and factor graphs
    Brendan J Frey
    Electrical and Computer Engineering, University of Toronto, 10 King s College Rd, Toronto, Ontario M5S 3G4, Canada
    Nat Genet 37:991-6. 2005
  4. pmc Functional coordination of alternative splicing in the mammalian central nervous system
    Matthew Fagnani
    Banting and Best Department of Medical Research, Centre for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, Ontario, Canada, M5S 3E1
    Genome Biol 8:R108. 2007
  5. ncbi request reprint Exploration of essential gene functions via titratable promoter alleles
    Sanie Mnaimneh
    Banting and Best Department of Medical Research, University of Toronto, 112 College Street, Toronto, ON M5G 1L6, Canada
    Cell 118:31-44. 2004
  6. ncbi request reprint Revealing global regulatory features of mammalian alternative splicing using a quantitative microarray platform
    Qun Pan
    Banting and Best Department of Medical Research, University of Toronto, 112 College Street, Toronto, Ontario M5G 1L6, Canada
    Mol Cell 16:929-41. 2004
  7. ncbi request reprint Alternative splicing of conserved exons is frequently species-specific in human and mouse
    Qun Pan
    CH Best Institute, University of Toronto, 112 College Street, Toronto, Ontario, Canada M5G 1L6
    Trends Genet 21:73-7. 2005
  8. ncbi request reprint High-definition macromolecular composition of yeast RNA-processing complexes
    Nevan J Krogan
    Banting and Best Department of Medical Research, University of Toronto, 112 College Street, Toronto, Ontario M5G 1L6, Canada
    Mol Cell 13:225-39. 2004
  9. pmc Probing microRNAs with microarrays: tissue specificity and functional inference
    Tomas Babak
    Banting and Best Department of Medical Research, 112 College St, University of Toronto, Toronto, Ontario M5G 1L6, Canada
    RNA 10:1813-9. 2004
  10. ncbi request reprint Prediction and testing of novel transcriptional networks regulating embryonic stem cell self-renewal and commitment
    Emily Walker
    Institute of Biomaterials and Biomedical Engineering, University of Toronto, 164 College Street, Toronto, ON, M5S 3G9, Canada
    Cell Stem Cell 1:71-86. 2007

Collaborators

Detail Information

Publications31

  1. ncbi request reprint Monitoring G-protein-coupled receptor signaling with DNA microarrays and real-time polymerase chain reaction
    Tony Yuen
    Department of Neurology, Mount Sinai School of Medicine, New York, New York 10029, USA
    Methods Enzymol 345:556-69. 2002
  2. pmc The functional landscape of mouse gene expression
    Wen Zhang
    Banting and Best Department of Medical Research, University of Toronto, 1 King s College Circle, Toronto, ON M5S 1A8, Canada
    J Biol 3:21. 2004
    ....
  3. ncbi request reprint Genome-wide analysis of mouse transcripts using exon microarrays and factor graphs
    Brendan J Frey
    Electrical and Computer Engineering, University of Toronto, 10 King s College Rd, Toronto, Ontario M5S 3G4, Canada
    Nat Genet 37:991-6. 2005
    ..GenRate also detected tens of thousands of potential new exons and reconciled discrepancies in current cDNA databases by 'stitching' new transcribed regions into previously annotated genes...
  4. pmc Functional coordination of alternative splicing in the mammalian central nervous system
    Matthew Fagnani
    Banting and Best Department of Medical Research, Centre for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, Ontario, Canada, M5S 3E1
    Genome Biol 8:R108. 2007
    ..However, the extent to which AS coordinates functions in a cell and tissue type specific manner is not known. Moreover, the sequence code that underlies cell and tissue type specific regulation of AS is poorly understood...
  5. ncbi request reprint Exploration of essential gene functions via titratable promoter alleles
    Sanie Mnaimneh
    Banting and Best Department of Medical Research, University of Toronto, 112 College Street, Toronto, ON M5G 1L6, Canada
    Cell 118:31-44. 2004
    ..We furthermore show that these strains are compatible with automated genetic analysis. This study underscores the importance of analyzing mutant phenotypes and provides a resource to complement the yeast knockout collection...
  6. ncbi request reprint Revealing global regulatory features of mammalian alternative splicing using a quantitative microarray platform
    Qun Pan
    Banting and Best Department of Medical Research, University of Toronto, 112 College Street, Toronto, Ontario M5G 1L6, Canada
    Mol Cell 16:929-41. 2004
    ..These results demonstrate the utility of our quantitative microarray platform and data for revealing important global regulatory features of AS...
  7. ncbi request reprint Alternative splicing of conserved exons is frequently species-specific in human and mouse
    Qun Pan
    CH Best Institute, University of Toronto, 112 College Street, Toronto, Ontario, Canada M5G 1L6
    Trends Genet 21:73-7. 2005
    ..The results thus provide evidence that species-specific AS of conserved exons constitutes an additional potential source of complexity and species-specific differences between mammals...
  8. ncbi request reprint High-definition macromolecular composition of yeast RNA-processing complexes
    Nevan J Krogan
    Banting and Best Department of Medical Research, University of Toronto, 112 College Street, Toronto, Ontario M5G 1L6, Canada
    Mol Cell 13:225-39. 2004
    ..This study provides a high-resolution overview of the modular topology of noncoding RNA-processing machinery...
  9. pmc Probing microRNAs with microarrays: tissue specificity and functional inference
    Tomas Babak
    Banting and Best Department of Medical Research, 112 College St, University of Toronto, Toronto, Ontario M5G 1L6, Canada
    RNA 10:1813-9. 2004
    ....
  10. ncbi request reprint Prediction and testing of novel transcriptional networks regulating embryonic stem cell self-renewal and commitment
    Emily Walker
    Institute of Biomaterials and Biomedical Engineering, University of Toronto, 164 College Street, Toronto, ON, M5S 3G9, Canada
    Cell Stem Cell 1:71-86. 2007
    ..By using this integrative approach, we have formulated novel networks describing gene repression of key developmental regulators in undifferentiated ESCs and successfully predicted the outcomes of genetic manipulation of these networks...
  11. pmc Zfp206 regulates ES cell gene expression and differentiation
    Wen Zhang
    Department of Molecular and Medical Genetics, University of Toronto, 4388 Medical Sciences Building, 1 King s College Circle, Toronto, ON M5S 1A8, Canada
    Nucleic Acids Res 34:4780-90. 2006
    ..Together, these data indicate that Zfp206 is a regulator of ES cell differentiation that controls a set of genes expressed very early in development, most of which themselves appear to be regulators...
  12. ncbi request reprint A panoramic view of yeast noncoding RNA processing
    Wen Tao Peng
    Banting and Best Department of Medical Research, University of Toronto, 112 College Street, M5G 1L6, Toronto, Ontario, Canada
    Cell 113:919-33. 2003
    ..These data present a global view of yeast noncoding RNA processing and confirm that many currently uncharacterized yeast proteins are involved in biogenesis of noncoding RNA...
  13. ncbi request reprint A combined 1H-NMR spectroscopy- and mass spectrometry-based metabolomic study of the PPAR-alpha null mutant mouse defines profound systemic changes in metabolism linked to the metabolic syndrome
    Helen J Atherton
    Department of Biochemistry, University of Cambridge, Cambridge, UK
    Physiol Genomics 27:178-86. 2006
    ..Furthermore, despite PPAR-alpha being weakly expressed in adipose tissue, a profound metabolic perturbation was detected in this tissue...
  14. pmc Statistical resynchronization and Bayesian detection of periodically expressed genes
    Xin Lu
    Department of Statistics, Harvard University, Cambridge, MA 02138, USA
    Nucleic Acids Res 32:447-55. 2004
    ....
  15. ncbi request reprint Subtractive transcriptomics: establishing polarity drives in vitro human endothelial morphogenesis
    David A Glesne
    Biosciences Division, Argonne National Laboratory, Argonne, Illinois 60439, USA
    Cancer Res 66:4030-40. 2006
    ....
  16. ncbi request reprint Bim and Noxa are candidates to mediate the deleterious effect of the NF-kappa B subunit RelA in cerebral ischemia
    Ioana Inta
    Department of Neurology, University of Heidelberg, 69120 Heidelberg, Germany
    J Neurosci 26:12896-903. 2006
    ..Thus, the deleterious function in cerebral ischemia is specific for the NF-kappaB subunit RelA and may be mediated through Bim and Noxa...
  17. ncbi request reprint Increased expression of integrin beta1 subunit enhances p21WAF1/Cip1 transcription through the Sp1 sites and p300-mediated histone acetylation in human hepatocellular carcinoma cells
    Zhengyu Fang
    Department of Biochemistry and Molecular Biology, Shanghai Medical College, Fudan University, 138 Yi Xue Yuan Road, Shanghai 200032, PR China
    J Cell Biochem 101:654-64. 2007
    ..Therefore, these findings presented the mechanisms by which integrin beta1 induced the elevated p21 expression in hepatic cancer cells...
  18. ncbi request reprint Kruppel-like factor 4 is acetylated by p300 and regulates gene transcription via modulation of histone acetylation
    Paul M Evans
    Department of Biochemistry and Molecular Biology, Sealy Center for Cancer Cell Biology, University of Texas Medical Branch, 301 University Boulevard, Galveston, TX 77555, USA
    J Biol Chem 282:33994-4002. 2007
    ..Our results suggest that KLF4 might function as an activator or repressor of transcription depending on whether it interacts with co-activators such as p300 and CREB-binding protein or co-repressors such as HDAC3...
  19. ncbi request reprint Positive expression of E-cadherin suppresses cell adhesion to fibronectin via reduction of alpha5beta1 integrin in human breast carcinoma cells
    Heng Wu
    Key Laboratory of Glycoconjugate Research, Ministry of Health, Department of Biochemistry and Molecular Biology, Shanghai Medical College, Fudan University, 138 Yi Xue Yuan Road, Shanghai, 200032, People s Republic of China
    J Cancer Res Clin Oncol 132:795-803. 2006
    ..Taken together, these results indicated that positive expression of E-cadherin inhibits the cell adhesion to extracellular matrix mediated by alpha5beta1 integrin signaling...
  20. pmc Distinct functions of homeodomain-containing and homeodomain-less isoforms encoded by homothorax
    Barbara Noro
    Department of Biochemistry and Molecular Biophysics, Columbia University, New York, New York 10032, USA
    Genes Dev 20:1636-50. 2006
    ..We further demonstrate that the mouse ortholog of hth, Meis1, also encodes a HDless isoform, suggesting that homeodomain-less variants of this gene family are evolutionarily ancient...
  21. pmc Novel cross talk of Kruppel-like factor 4 and beta-catenin regulates normal intestinal homeostasis and tumor repression
    Wen Zhang
    Sealy Center for Cancer Cell Biology, University of Texas Medical Branch, Galveston, TX 77555 1048, USA
    Mol Cell Biol 26:2055-64. 2006
    ..Our findings suggest that the cross talk of KLF4 and beta-catenin plays a critical role in homeostasis of the normal intestine as well as in tumorigenesis of colorectal cancers...
  22. ncbi request reprint Gene expression profiling in a renal cell carcinoma cell line: dissecting VHL and hypoxia-dependent pathways
    Yide Jiang
    Genzyme Molecular Oncology, Framingham, MA 01701, USA
    Mol Cancer Res 1:453-62. 2003
    ....
  23. ncbi request reprint Integrin beta1 subunit overexpressed in the SMMC-7721 cells regulates the promoter activity of p21(CIP1) and enhances its transcription
    Yu Long Liang
    Department of Biochemistry and Molecular Biology, Shanghai Medical College, Fudan University, 138 Yi Xue Yuan Road, Shanghai 200032, PR China
    FEBS Lett 558:107-13. 2004
    ....
  24. ncbi request reprint Tumor necrosis factor-like weak inducer of apoptosis-induced neurodegeneration
    Ioana Potrovita
    Department of Neurology, University of Heidelberg, D 69120 Heidelberg, Germany
    J Neurosci 24:8237-44. 2004
    ..In summary, our data show that TWEAK induces neuronal cell death and is involved in neurodegeneration in vivo...
  25. ncbi request reprint Preparation of cardiovascular disease-related genes microarray and its application in exploring ligustrazine-induced changes in endothelial gene expression
    Zesong Li
    Beijing Institute of Radiation Medicine, 100850 Beijing, China
    Pol J Pharmacol 56:427-33. 2004
    ..This also demonstrates the use of oligonucleotide microarray technology as an approach to studying targets of active components of Traditional Chinese Medicine...
  26. ncbi request reprint Neuronal activation of NF-kappaB contributes to cell death in cerebral ischemia
    Wen Zhang
    Department of Neurology, University of Heidelberg, Heidelberg, Germany
    J Cereb Blood Flow Metab 25:30-40. 2005
    ..In summary, the data show that NF-kappaB is activated in neurons and astrocytes during cerebral ischemia and that NF-kappaB activation in neurons contributes to the ischemic damage...
  27. ncbi request reprint Expression profiling of homocysteine junction enzymes in the NCI60 panel of human cancer cell lines
    Wen Zhang
    Department of Biochemistry, University of Nebraska, Lincoln, Nebraska, USA
    Cancer Res 65:1554-60. 2005
    ....
  28. ncbi request reprint Down-regulation of PTEN expression due to loss of promoter activity in human hepatocellular carcinoma cell lines
    Dong Zhu Ma
    Minstry of Health Key Laboratory of Glycocojugate Research, Department of Biochemistry and Molecular Biology, Shanghai Medical College, Fudan University, 138 Yixueyuan Road, Shanghai 200032, China
    World J Gastroenterol 11:4472-7. 2005
    ..To investigate the regulation of phosphatase and tensin homolog deleted on chromosome ten (PTEN) gene expression in human hepatocellular carcinoma (HCC) cell lines...
  29. ncbi request reprint Clinical evaluation of oligonucleotide microarrays for the detection of HBV mutants associated with lamivudine resistance
    Li Yan Chen
    Beijing Institute of Radiation Medicine, Beijing 100850, China
    Pharmacogenomics 6:721-30. 2005
    ..The aim of the present study was to evaluate the clinical application of an oligonucleotide microarray in detecting HBV mutants associated with lamivudine resistance...
  30. ncbi request reprint Supranormal myocardial creatine and phosphocreatine concentrations lead to cardiac hypertrophy and heart failure: insights from creatine transporter-overexpressing transgenic mice
    Julie Wallis
    Department of Cardiovascular Medicine, University of Oxford, Oxford, England
    Circulation 112:3131-9. 2005
    ..Previously, it has not been possible to increase myocardial creatine and phosphocreatine concentrations to supranormal levels because they are subject to tight regulation by the sarcolemmal creatine transporter (CrT)...
  31. pmc Variation in homeodomain DNA binding revealed by high-resolution analysis of sequence preferences
    Michael F Berger
    Division of Genetics, Department of Medicine, Brigham and Women s Hospital and Harvard Medical School, Boston, MA 02115, USA
    Cell 133:1266-76. 2008
    ..Our results provide an unprecedented level of resolution in the analysis of this simple domain structure and suggest that variation in sequence recognition may be a factor in its functional diversity and evolutionary success...