Tao Han

Summary

Affiliation: Food and Drug Administration
Country: USA

Publications

  1. pmc Characterization of whole genome amplified (WGA) DNA for use in genotyping assay development
    Tao Han
    Division of Systems Biology, National Center for Toxicological Research, FDA, Jefferson, AR 72079, USA
    BMC Genomics 13:217. 2012
  2. pmc Improvement in the reproducibility and accuracy of DNA microarray quantification by optimizing hybridization conditions
    Tao Han
    Center for Functional Genomics, National Center for Toxicological Research, US FDA, Jefferson, AR 72079, USA
    BMC Bioinformatics 7:S17. 2006
  3. doi request reprint Coupling global methylation and gene expression profiles reveal key pathophysiological events in liver injury induced by a methyl-deficient diet
    Volodymyr P Tryndyak
    Division of Biochemical Toxicology, National Center for Toxicological Research, Jefferson, AR 72079, USA
    Mol Nutr Food Res 55:411-8. 2011
  4. pmc Interstrain differences in the severity of liver injury induced by a choline- and folate-deficient diet in mice are associated with dysregulation of genes involved in lipid metabolism
    Volodymyr Tryndyak
    Division of Biochemical Toxicology, National Center for Toxicological Research, US Food and Drug Administration, Jefferson, Arkansas 72079, USA
    FASEB J 26:4592-602. 2012
  5. ncbi request reprint Microarray analysis of virulence gene profiles in Salmonella serovars from food/food animal environment
    Wen Zou
    Division of Personalized Nutrition and Medicine, National Center for Toxicological Research, Food and Drug Administration, Jefferson, AR 72079, United States
    J Infect Dev Ctries 5:94-105. 2011
  6. pmc Cross-platform comparability of microarray technology: intra-platform consistency and appropriate data analysis procedures are essential
    Leming Shi
    National Center for Toxicological Research, U S Food and Drug Administration, 3900 NCTR Road, Jefferson, Arkansas 72079, USA
    BMC Bioinformatics 6:S12. 2005
  7. doi request reprint Critical role of bioinformatics in translating huge amounts of next-generation sequencing data into personalized medicine
    Huixiao Hong
    Division of Bioinformatics and Biostatistics, National Center for Toxicological Research, US Food and Drug Administration, Jefferson, AR 72079, USA
    Sci China Life Sci 56:110-8. 2013
  8. pmc Elimination of laboratory ozone leads to a dramatic improvement in the reproducibility of microarray gene expression measurements
    William S Branham
    Center for Functional Genomics, Division of Systems Toxicology, National Center for Toxicological Research, US Food and Drug Administration, Jefferson, Arkansas 72079, USA
    BMC Biotechnol 7:8. 2007
  9. pmc Assessing batch effects of genotype calling algorithm BRLMM for the Affymetrix GeneChip Human Mapping 500 K array set using 270 HapMap samples
    Huixiao Hong
    Division of Systems Toxicology, National Center for Toxicological Research, US Food and Drug Administration, 3900 NCTR Road, Jefferson, AR 72079, USA
    BMC Bioinformatics 9:S17. 2008
  10. doi request reprint Difference in expression of hepatic microRNAs miR-29c, miR-34a, miR-155, and miR-200b is associated with strain-specific susceptibility to dietary nonalcoholic steatohepatitis in mice
    Igor P Pogribny
    Division of Biochemical Toxicology, National Center for Toxicological Research, Jefferson, AR 72079, USA
    Lab Invest 90:1437-46. 2010

Detail Information

Publications19

  1. pmc Characterization of whole genome amplified (WGA) DNA for use in genotyping assay development
    Tao Han
    Division of Systems Biology, National Center for Toxicological Research, FDA, Jefferson, AR 72079, USA
    BMC Genomics 13:217. 2012
    ..However, the uniformity and fidelity of the amplification process across the genome has not been extensively characterized...
  2. pmc Improvement in the reproducibility and accuracy of DNA microarray quantification by optimizing hybridization conditions
    Tao Han
    Center for Functional Genomics, National Center for Toxicological Research, US FDA, Jefferson, AR 72079, USA
    BMC Bioinformatics 7:S17. 2006
    ..A successful microarray experiment, however, involves many steps: well-designed oligonucleotide probes, printing, RNA extraction and labeling, hybridization, and imaging. Optimization is essential to generate reliable microarray data...
  3. doi request reprint Coupling global methylation and gene expression profiles reveal key pathophysiological events in liver injury induced by a methyl-deficient diet
    Volodymyr P Tryndyak
    Division of Biochemical Toxicology, National Center for Toxicological Research, Jefferson, AR 72079, USA
    Mol Nutr Food Res 55:411-8. 2011
    ..However, whether methyl deficiency affects the methylation status of gene promoters has not been explored...
  4. pmc Interstrain differences in the severity of liver injury induced by a choline- and folate-deficient diet in mice are associated with dysregulation of genes involved in lipid metabolism
    Volodymyr Tryndyak
    Division of Biochemical Toxicology, National Center for Toxicological Research, US Food and Drug Administration, Jefferson, Arkansas 72079, USA
    FASEB J 26:4592-602. 2012
    ..These findings suggest that the PPARĪ±-regulated metabolism network is one of the key mechanisms determining interstrain susceptibility and severity of NAFLD in mice...
  5. ncbi request reprint Microarray analysis of virulence gene profiles in Salmonella serovars from food/food animal environment
    Wen Zou
    Division of Personalized Nutrition and Medicine, National Center for Toxicological Research, Food and Drug Administration, Jefferson, AR 72079, United States
    J Infect Dev Ctries 5:94-105. 2011
    ....
  6. pmc Cross-platform comparability of microarray technology: intra-platform consistency and appropriate data analysis procedures are essential
    Leming Shi
    National Center for Toxicological Research, U S Food and Drug Administration, 3900 NCTR Road, Jefferson, Arkansas 72079, USA
    BMC Bioinformatics 6:S12. 2005
    ..Nucleic Acids Res., 31, 5676-5684, 2003), portrays a disturbingly negative picture of the cross-platform comparability, and, hence, the reliability of microarray technology...
  7. doi request reprint Critical role of bioinformatics in translating huge amounts of next-generation sequencing data into personalized medicine
    Huixiao Hong
    Division of Bioinformatics and Biostatistics, National Center for Toxicological Research, US Food and Drug Administration, Jefferson, AR 72079, USA
    Sci China Life Sci 56:110-8. 2013
    ..We review some key bioinformatics tasks, issues, and challenges in contexts of IT requirements, data quality, analysis tools and pipelines, and validation of biomarkers...
  8. pmc Elimination of laboratory ozone leads to a dramatic improvement in the reproducibility of microarray gene expression measurements
    William S Branham
    Center for Functional Genomics, Division of Systems Toxicology, National Center for Toxicological Research, US Food and Drug Administration, Jefferson, Arkansas 72079, USA
    BMC Biotechnol 7:8. 2007
    ..Cyanine 3 (Cy3) is much less affected by atmospheric ozone. Degradation of the Cy5 signal relative to the Cy3 signal in 2-color microarrays will adversely reduce the Cy5/Cy3 ratio resulting in unreliable microarray data...
  9. pmc Assessing batch effects of genotype calling algorithm BRLMM for the Affymetrix GeneChip Human Mapping 500 K array set using 270 HapMap samples
    Huixiao Hong
    Division of Systems Toxicology, National Center for Toxicological Research, US Food and Drug Administration, 3900 NCTR Road, Jefferson, AR 72079, USA
    BMC Bioinformatics 9:S17. 2008
    ..In this paper, we analyzed both the batch size and batch composition for effects on the genotype calling algorithm BRLMM using raw data of 270 HapMap samples analyzed with the Affymetrix Human Mapping 500 K array set...
  10. doi request reprint Difference in expression of hepatic microRNAs miR-29c, miR-34a, miR-155, and miR-200b is associated with strain-specific susceptibility to dietary nonalcoholic steatohepatitis in mice
    Igor P Pogribny
    Division of Biochemical Toxicology, National Center for Toxicological Research, Jefferson, AR 72079, USA
    Lab Invest 90:1437-46. 2010
    ..More important, our data provide a mechanistic link between alterations in miRNA expression and pathophysiological and pathomorphological features of NASH...
  11. pmc Technical reproducibility of genotyping SNP arrays used in genome-wide association studies
    Huixiao Hong
    Center of Excellence for Bioinformatics, Division of Systems Biology, National Center for Toxicological Research, US Food and Drug Administration, Jefferson, Arizona, United States of America
    PLoS ONE 7:e44483. 2012
    ..e. the odds ratio) and the minor allele frequencies are low...
  12. pmc Identification and categorization of liver toxicity markers induced by a related pair of drugs
    Ching Wei Chang
    Division of Personalized Nutrition and Medicine, National Center for Toxicological Research, FDA, Jefferson, AR 72079, USA E mail
    Int J Mol Sci 12:4609-24. 2011
    ..The gene Vars2 (valyl-tRNA synthetase 2) was identified in both animals and the pathway to which it belongs, the aminoacyl-tRNA biosynthesis pathway, was one of the three most significant tolcapone-specific pathways identified...
  13. pmc Microarray scanner calibration curves: characteristics and implications
    Leming Shi
    National Center for Toxicological Research, U S Food and Drug Administration, 3900 NCTR Road, Jefferson, Arkansas 72079, USA
    BMC Bioinformatics 6:S11. 2005
    ..Microarray-based measurement of mRNA abundance assumes a linear relationship between the fluorescence intensity and the dye concentration. In reality, however, the calibration curve can be nonlinear...
  14. ncbi request reprint Gene expression profiling reveals underlying molecular mechanisms of the early stages of tamoxifen-induced rat hepatocarcinogenesis
    Igor P Pogribny
    Division of Biochemical Toxicology, National Center for Toxicological Research, Jefferson, AR 72079, USA
    Toxicol Appl Pharmacol 225:61-9. 2007
    ..The early appearance of these alterations suggests their importance in the mechanism of neoplastic cell transformation induced by tamoxifen...
  15. ncbi request reprint An integrated study of acute effects of valproic acid in the liver using metabonomics, proteomics, and transcriptomics platforms
    Laura K Schnackenberg
    Division of Systems Toxicology, National Center for Toxicological Research, Food and Drug Administration, Jefferson, Arkansas, 72079, USA
    OMICS 10:1-14. 2006
    ..The combined studies indicated a perturbation in the glycogenolysis pathway following administration of VPA...
  16. doi request reprint Epigenetic alterations in the brains of Fisher 344 rats induced by long-term administration of folate/methyl-deficient diet
    Igor P Pogribny
    Division of Biochemical Toxicology, National Center for Toxicological Research, Jefferson, AR 72079, USA
    Brain Res 1237:25-34. 2008
    ..Together, these data suggest that the proper maintenance of the epigenomic landscape in normal brain depends on the adequate supply of essential nutrients involved in the metabolism of methyl groups...
  17. pmc The MicroArray Quality Control (MAQC) project shows inter- and intraplatform reproducibility of gene expression measurements
    Leming Shi
    National Center for Toxicological Research, US Food and Drug Administration, Jefferson, Arkansas 72079, USA
    Nat Biotechnol 24:1151-61. 2006
    ..This study provides a resource that represents an important first step toward establishing a framework for the use of microarrays in clinical and regulatory settings...
  18. pmc A microarray study of MPP+-treated PC12 Cells: Mechanisms of toxicity (MOT) analysis using bioinformatics tools
    Zengjun Xu
    Division of Neurotoxicology, National Center for Toxicological Research, U S Food and Drug Administration, 3900 NCTR Road, Jefferson, Arkansas 72079, USA
    BMC Bioinformatics 6:S8. 2005
    ..MPP+ depletes dopamine content and elicits cell death in PC12 cells. However, the mechanism of MPP+-induced neurotoxicity is still unclear...
  19. ncbi request reprint QA/QC: challenges and pitfalls facing the microarray community and regulatory agencies
    Leming Shi
    US Food and Drug Administration, Center for Toxicoinformatics, Division of Systems Toxicology, National Center for Toxicological Research, HFT 020, 3900 NCTR Road, Jefferson, AR 72079, USA
    Expert Rev Mol Diagn 4:761-77. 2004
    ..These fundamental issues must be adequately addressed before microarray technology can be transformed from a research tool to clinical practices...