Yu Zhang

Summary

Affiliation: National Institutes of Health
Country: USA

Publications

  1. pmc Constraint and turnover in sex-biased gene expression in the genus Drosophila
    Yu Zhang
    Laboratory of Cellular and Developmental Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Department of Health and Human Services, Bethesda, Maryland 20892, USA
    Nature 450:233-7. 2007
  2. pmc Demasculinization of X chromosomes in the Drosophila genus
    David Sturgill
    Laboratory of Cellular and Developmental Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Department of Health and Human Services, Bethesda Maryland 20892, USA
    Nature 450:238-41. 2007
  3. pmc An evolutionary consequence of dosage compensation on Drosophila melanogaster female X-chromatin structure?
    Yu Zhang
    Laboratory of Cellular and Developmental Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892 8028, USA
    BMC Genomics 11:6. 2010
  4. pmc Expression in aneuploid Drosophila S2 cells
    Yu Zhang
    Laboratory of Cellular and Developmental Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland, United States of America
    PLoS Biol 8:e1000320. 2010
  5. pmc The gastric cardia is not a target for human papillomavirus-induced carcinogenesis
    Jill Koshiol
    Infections and Immunoepidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, 6120 Executive Boulevard, Room 7070, Rockville, MD 20852 7248, USA
    Cancer Epidemiol Biomarkers Prev 19:1137-9. 2010
  6. pmc No role for human papillomavirus in esophageal squamous cell carcinoma in China
    Jill Koshiol
    Division of Cancer Epidemiology and Genetics, Department of Health and Human Services, National Cancer Institute, National Institutes of Health, Bethesda, MD 20852 7248, USA
    Int J Cancer 127:93-100. 2010
  7. pmc A 220-nucleotide deletion of the intronic enhancer reveals an epigenetic hierarchy in immunoglobulin heavy chain locus activation
    Tirtha Chakraborty
    Laboratory of Cellular and Molecular Biology, National Institute on Aging, National Institutes of Health, Baltimore, MD 21224, USA
    J Exp Med 206:1019-27. 2009
  8. pmc Synthetic spike-in standards for RNA-seq experiments
    Lichun Jiang
    Section of Developmental Genomics, Laboratory of Cellular and Developmental Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
    Genome Res 21:1543-51. 2011
  9. ncbi request reprint Dosage compensation goes global
    Yu Zhang
    Laboratory of Cellular and Developmental Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
    Curr Opin Genet Dev 17:113-20. 2007
  10. ncbi request reprint Estimating system parameters from chaotic time series with synchronization optimized by a genetic algorithm
    Chao Tao
    Department of Surgery, Division of Otolaryngology Head and Neck Surgery, University of Wisconsin Medical School, Madison, Wisconsin 53792 7375, USA
    Phys Rev E Stat Nonlin Soft Matter Phys 76:016209. 2007

Detail Information

Publications39

  1. pmc Constraint and turnover in sex-biased gene expression in the genus Drosophila
    Yu Zhang
    Laboratory of Cellular and Developmental Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Department of Health and Human Services, Bethesda, Maryland 20892, USA
    Nature 450:233-7. 2007
    ..This higher divergence and turnover of genes with male-biased expression may be due to high transcription rates in the male germline, greater functional pleiotropy of genes expressed in females, and/or sexual competition...
  2. pmc Demasculinization of X chromosomes in the Drosophila genus
    David Sturgill
    Laboratory of Cellular and Developmental Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Department of Health and Human Services, Bethesda Maryland 20892, USA
    Nature 450:238-41. 2007
    ....
  3. pmc An evolutionary consequence of dosage compensation on Drosophila melanogaster female X-chromatin structure?
    Yu Zhang
    Laboratory of Cellular and Developmental Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892 8028, USA
    BMC Genomics 11:6. 2010
    ..The evolution of this system could result in neutral X chromatin changes that will be apparent in females...
  4. pmc Expression in aneuploid Drosophila S2 cells
    Yu Zhang
    Laboratory of Cellular and Developmental Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland, United States of America
    PLoS Biol 8:e1000320. 2010
    ..Our data indicate that expression dosage compensation dampens the effect of altered DNA copy number genome-wide. For the X chromosome, compensation includes fixed and dose-dependent components...
  5. pmc The gastric cardia is not a target for human papillomavirus-induced carcinogenesis
    Jill Koshiol
    Infections and Immunoepidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, 6120 Executive Boulevard, Room 7070, Rockville, MD 20852 7248, USA
    Cancer Epidemiol Biomarkers Prev 19:1137-9. 2010
    ..Given the availability of an effective HPV vaccine and its potential to prevent HPV-associated cancer, we decided to evaluate the prevalence of HPV DNA in GCA...
  6. pmc No role for human papillomavirus in esophageal squamous cell carcinoma in China
    Jill Koshiol
    Division of Cancer Epidemiology and Genetics, Department of Health and Human Services, National Cancer Institute, National Institutes of Health, Bethesda, MD 20852 7248, USA
    Int J Cancer 127:93-100. 2010
    ..HPV DNA contamination cannot be ruled out as an explanation for high HPV prevalence in ESCC tissue studies with less stringent tissue procurement and processing protocols...
  7. pmc A 220-nucleotide deletion of the intronic enhancer reveals an epigenetic hierarchy in immunoglobulin heavy chain locus activation
    Tirtha Chakraborty
    Laboratory of Cellular and Molecular Biology, National Institute on Aging, National Institutes of Health, Baltimore, MD 21224, USA
    J Exp Med 206:1019-27. 2009
    ..These observations define Emu-independent and Emu-dependent phases of locus activation that reveal an unappreciated epigenetic hierarchy in tissue-specific gene expression...
  8. pmc Synthetic spike-in standards for RNA-seq experiments
    Lichun Jiang
    Section of Developmental Genomics, Laboratory of Cellular and Developmental Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
    Genome Res 21:1543-51. 2011
    ..These quality metrics facilitate comparable analysis across different samples, protocols, and platforms...
  9. ncbi request reprint Dosage compensation goes global
    Yu Zhang
    Laboratory of Cellular and Developmental Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
    Curr Opin Genet Dev 17:113-20. 2007
    ..These approaches have resolved old controversies, suggested new questions, and promise to give us a more clear and comprehensive understanding of an old problem in molecular and cell biology...
  10. ncbi request reprint Estimating system parameters from chaotic time series with synchronization optimized by a genetic algorithm
    Chao Tao
    Department of Surgery, Division of Otolaryngology Head and Neck Surgery, University of Wisconsin Medical School, Madison, Wisconsin 53792 7375, USA
    Phys Rev E Stat Nonlin Soft Matter Phys 76:016209. 2007
    ..Finally, a Chua's circuit experiment shows the capacity of this method to estimate multiple parameters of real systems...
  11. ncbi request reprint Bayesian inference of epistatic interactions in case-control studies
    Yu Zhang
    Department of Statistics, The Pennsylvania State University, Thomas Building 422A, University Park, Pennsylvania 16802, USA
    Nat Genet 39:1167-73. 2007
    ....
  12. ncbi request reprint Molecular cloning and expression analysis of a monosaccharide transporter gene OsMST4 from rice (Oryza sativa L.)
    Yongqin Wang
    State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Datun Road, Beijing 100101, China
    Plant Mol Biol 65:439-51. 2007
    ..In addition, the cell type-specific expression patterns of OsMST4 in other sink and source tissues were also investigated, and its corresponding physiological roles were discussed...
  13. ncbi request reprint Evolution of genes and genomes on the Drosophila phylogeny
    Andrew G Clark
    Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14853, USA
    Nature 450:203-18. 2007
    ..These may prove to underlie differences in the ecology and behaviour of these diverse species...
  14. doi request reprint Evolution of protein-coding genes in Drosophila
    Amanda M Larracuente
    Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
    Trends Genet 24:114-23. 2008
    ....
  15. doi request reprint Tree-guided Bayesian inference of population structures
    Yu Zhang
    Department of Statistics, The Pennsylvania State University, State College, PA, USA
    Bioinformatics 24:965-71. 2008
    ..As a result, they can lose sensitivity and specificity in detecting subtle stratifications. In addition, when a large number of genetic markers are used, many existing algorithms perform rather inefficiently...
  16. ncbi request reprint [Expression profile of clock genes during the process of embryonic stem cells differentiation]
    Shu Xie
    Department of Neurobiology, Xuanwu Hospital, Capital Medical University, Beijing 100053, China
    Zhonghua Yi Xue Za Zhi 87:3203-7. 2007
    ..To analysis the expression profile of7 clock genes during mouse embryonic stem cell (mES) differentiation...
  17. ncbi request reprint The molecular mechanism governing the oncogenic potential of SOX2 in breast cancer
    Yupeng Chen
    Department of Biochemistry and Molecular Biology, Peking University Health Science Center, Beijing, China
    J Biol Chem 283:17969-78. 2008
    ..Our experiments not only determined a role for SOX2 in mammary tumorigenesis but also revealed another activity of the multifunctional protein, beta-catenin...
  18. doi request reprint YY1 restrained cell senescence through repressing the transcription of p16
    Xiuli Wang
    Institute of Genetics and Cytology, Northeast Normal University, Changchun 130024, P R China
    Biochim Biophys Acta 1783:1876-83. 2008
    ..Overall, data from this study suggest that YY1, HDAC3 and HDAC4 restrained cell senescence by repressing p16(INK4a) expression through an epigenetic modification of histones...
  19. doi request reprint Farnesoid X receptor induces GLUT4 expression through FXR response element in the GLUT4 promoter
    Hong Shen
    Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, China
    Cell Physiol Biochem 22:1-14. 2008
    ..All these data thereby implied that FXR is a new transcription factor of GLUT4, further elucidating the potential role for FXR in glucose metabolism...
  20. ncbi request reprint A collection of 10,096 indica rice full-length cDNAs reveals highly expressed sequence divergence between Oryza sativa indica and japonica subspecies
    Xiaohui Liu
    National Center for Gene Research and Shanghai Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 500 Caobao Road, Shanghai 200233, China
    Plant Mol Biol 65:403-15. 2007
    ..These variations might distinguish the phenotypic changes of the two cultivated rice subspecies indica and japonica. Analysis of these cDNAs extends known rice genes and identifies new ones in rice...
  21. ncbi request reprint Improving the prediction of human microRNA target genes by using ensemble algorithm
    Xingqi Yan
    The National Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and Peking Union Medical College, Tsinghua University, Beijing, China
    FEBS Lett 581:1587-93. 2007
    ..Finally, we applied our algorithm on the whole prediction data set provided by miRanda website. The results are available at http://www.biosino.org/~kanghu/mRTP/mRTP.html...
  22. ncbi request reprint Molecular cloning and characterization of CT120, a novel membrane-associated gene involved in amino acid transport and glutathione metabolism
    Xianghuo He
    State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Shanghai 200032, People s Republic of China
    Biochem Biophys Res Commun 297:528-36. 2002
    ....
  23. ncbi request reprint Sequence and analysis of rice chromosome 4
    Qi Feng
    National Center for Gene Research, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 500 Caobao Road, Shanghai 200233, China
    Nature 420:316-20. 2002
    ..By contrast, there is little conservation in gene order between rice and Arabidopsis...
  24. ncbi request reprint Sequence variations of simple sequence repeats on chromosome-4 in two subspecies of the Asian cultivated rice
    Can Li
    National Center for Gene Research, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 500 Caobao Road, Shanghai 200233, China
    Theor Appl Genet 108:392-400. 2004
    ..These results provide a great opportunity for SSR-based marker development and comparative genome analysis of the two subspecies of the Asian cultivated rice...
  25. ncbi request reprint Biodegradation of polycyclic aromatic hydrocarbons by Pichia anomala
    Feng Pan
    State Key Laboratory of Environmental Aquatic Chemistry, Research Center for Eco Environmental Sciences, Chinese Academy of Sciences, P O Box 2871, Beijing 100085, PR China
    Biotechnol Lett 26:803-6. 2004
    ..Chrysene, which remained in the mixture even after 96 h, could be degraded along with naphthalene. Chrysene at 0.7 and 1 mg l(-1), in the presence of 4.3 and 65 mg naphthalene l(-1), respectively, was removed within 96 h...
  26. ncbi request reprint Zebrafish Dpr2 inhibits mesoderm induction by promoting degradation of nodal receptors
    Lixia Zhang
    Laboratory of Developmental Biology, Ministry of Education MOE, Department of Biological Sciences and Biotechnology, Tsinghua University, Beijing 100084, China
    Science 306:114-7. 2004
    ..Dpr2 is localized in late endosomes, binds to the TGFbeta receptors ALK5 and ALK4, and accelerates lysosomal degradation of these receptors...
  27. ncbi request reprint Pur alpha and Sp8 as opposing regulators of neural gata2 expression
    William Todd Penberthy
    Department of Molecular, Cell, and Developmental Biology, University of California Los Angeles, Los Angeles, CA 90095 1606, USA
    Dev Biol 275:225-34. 2004
    ....
  28. ncbi request reprint [Study on the gene expression profiling of caudal nuclei in Parkinson disease]
    Yan Ning Cai
    Department of Neurological Molecular Biology, Institute of Geriatrics, Xuewu Hospital, Capital Medical University, Beijing 100053, China
    Zhonghua Yi Xue Za Zhi 84:1191-3. 2004
  29. pmc An Eulerian path approach to local multiple alignment for DNA sequences
    Yu Zhang
    Department of Mathematics, University of Southern California, 1042 West 36th Place, DRB289, Los Angeles, CA 90089 1113, USA
    Proc Natl Acad Sci U S A 102:1285-90. 2005
    ..We compare the results with Alus marked by repeatmasker, where the two programs are in good agreement. Our method is robust under various conditions and superior to other methods in terms of efficiency and accuracy...
  30. ncbi request reprint Cloning and characterization of mouse homolog of the CXC chemokine receptor CXCR1
    Wenxian Fu
    Department of Immunology, Peking University Health Science Center, Beijing 100083, China
    Cytokine 31:9-17. 2005
    ....
  31. pmc Serial analysis of gene expression study of a hybrid rice strain (LYP9) and its parental cultivars
    Jingyue Bao
    Beijing Genomics Institute, Chinese Academy of Sciences, Beijing 101300, China
    Plant Physiol 138:1216-31. 2005
    ..Our study adds a new set of data crucial for the understanding of molecular mechanisms of heterosis and gene regulation networks of the cultivated rice...
  32. ncbi request reprint Estimating immunoregulatory gene networks in human herpesvirus type 6-infected T cells
    Tomoiku Takaku
    First Department of Internal Medicine, Tokyo Medical University, Tokyo, Japan
    Biochem Biophys Res Commun 336:469-77. 2005
    ..This study describes a novel approach to find genes related with the complex host-virus interaction using microarray data employing the Bayesian statistical framework...
  33. ncbi request reprint Genetic analysis of Arabidopsis GATA transcription factor gene family reveals a nitrate-inducible member important for chlorophyll synthesis and glucose sensitivity
    Yong Mei Bi
    Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, Canada N1G 2W1
    Plant J 44:680-92. 2005
    ..These observations suggest a function for GNC in regulating carbon and nitrogen metabolism...
  34. ncbi request reprint Refinement of optical map assemblies
    Anton Valouev
    MCB 1050 Childs Way, Los Angeles, CA 90089 2910, USA
    Bioinformatics 22:1217-24. 2006
    ..Optical maps are assembled to cover the whole genome, and the accuracy of assembly is critical...
  35. pmc Differentiation of Escherichia coli pathotypes by oligonucleotide spotted array
    Raghavan U M Palaniappan
    Department of Population Medicine and Diagnostic Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY 14853, USA
    J Clin Microbiol 44:1495-501. 2006
    ..coli pathotypes and could also have a significant impact on the epidemiological analysis of E. coli infections...
  36. ncbi request reprint Effect of tea polyphenol on cytokine gene expression in rats with alcoholic liver disease
    Xing Guo Zhang
    Department of Pharmacology, First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310003, China
    Hepatobiliary Pancreat Dis Int 5:268-72. 2006
    ..Green tea polyphenols have both antioxidant and antiinflammatory properties. This study was designed to evaluate the effect of tea polyphenol (TP) on alcohol-induced liver injury in rats...
  37. pmc A coalescence-guided hierarchical Bayesian method for haplotype inference
    Yu Zhang
    Department of Statistics, Harvard University, Cambridge, MA 02138, USA
    Am J Hum Genet 79:313-22. 2006
    ....
  38. ncbi request reprint Inhibition of adenovirus-mediated human MAGE-D1 on angiogenesis in vitro and in vivo
    Wei Gan Shen
    Medical College of Yangzhou University, 16 Huai Hai Road, Yangzhou 225000, Jiangsu Province, PR China
    Mol Cell Biochem 300:89-99. 2007
    ....
  39. ncbi request reprint A new haplogroup pattern displayed in Fujian Han in China
    Min Yu
    Department of Biology, Harbin Medical University, China
    J Hum Genet 47:95-8. 2002
    ..In addition, M122C frequency was only 22.78%, and M45A and M103T were default. The distinctive haplogroup frequencies (H1, H5, and H6/7/8) imply that the haplogroup pattern is a relatively ancestral and interim type...