Huixiao Hong

Summary

Affiliation: Food and Drug Administration
Country: USA

Publications

  1. ncbi request reprint Estimating relative noise to signal in DNA microarray data
    Huixiao Hong
    Division of Systems Biology, National Center for Toxicological Research, US Food and Drug Administration, Jefferson, Arkansas 72079, USA
    Int J Bioinform Res Appl 9:433-48. 2013
  2. doi request reprint Rat ╬▒-Fetoprotein binding affinities of a large set of structurally diverse chemicals elucidated the relationships between structures and binding affinities
    Huixiao Hong
    Division of Bioinformatics and Biostatistics, National Center for Toxicological Research, U S Food and Drug Administration, Jefferson, AK 72079, USA
    Chem Res Toxicol 25:2553-66. 2012
  3. 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
  4. 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
  5. 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
  6. doi request reprint The accurate prediction of protein family from amino acid sequence by measuring features of sequence fragments
    Huixiao Hong
    Division of Systems Toxicology, National Center for Toxicological Research, U S Food and Drug Administration, Jefferson, Arkansas 72079, USA
    J Comput Biol 16:1671-88. 2009
  7. pmc Assessing sources of inconsistencies in genotypes and their effects on genome-wide association studies with HapMap samples
    H Hong
    Division of Systems Toxicology, National Center for Toxicological Research, US Food and Drug Administration, Jefferson, AR, USA
    Pharmacogenomics J 10:364-74. 2010
  8. doi request reprint Molecular biomarkers: a US FDA effort
    Huixiao Hong
    Center for Toxicoinformatics, Division of Systems Toxicology, National Center for Toxicological Research, US FDA 3900 NCTR Road, Jefferson, AR, USA
    Biomark Med 4:215-25. 2010
  9. ncbi request reprint Evaluating variations of genotype calling: a potential source of spurious associations in genome-wide association studies
    Huixiao Hong
    Division of Systems Toxicology, National Center for Toxicological Research, US Food and Drug Administration, 3900 NCTR Road, Jefferson, AR 72079, USA
    J Genet 89:55-64. 2010
  10. doi request reprint Assessing consistency between versions of genotype-calling algorithm Birdseed for the Genome-Wide Human SNP Array 6.0 using HapMap samples
    Huixiao Hong
    Center for Toxicoinformatics, Division of Systems Toxicology, National Center for Toxicological Research, US Food and Drug Administration, Jefferson, AR 72079, USA
    Adv Exp Med Biol 680:355-60. 2010

Detail Information

Publications41

  1. ncbi request reprint Estimating relative noise to signal in DNA microarray data
    Huixiao Hong
    Division of Systems Biology, National Center for Toxicological Research, US Food and Drug Administration, Jefferson, Arkansas 72079, USA
    Int J Bioinform Res Appl 9:433-48. 2013
    ..Relative noise was estimated for both data sets, and the results were consistent with the observations in the original papers, demonstrating the proposed method is reliable for estimating relative noise in microarray data. ..
  2. doi request reprint Rat ╬▒-Fetoprotein binding affinities of a large set of structurally diverse chemicals elucidated the relationships between structures and binding affinities
    Huixiao Hong
    Division of Bioinformatics and Biostatistics, National Center for Toxicological Research, U S Food and Drug Administration, Jefferson, AK 72079, USA
    Chem Res Toxicol 25:2553-66. 2012
    ..The data assist in elucidating binding interactions and mechanisms between chemicals and rat AFP and, in turn, assist in the evaluation of the endocrine disrupting potential of chemicals...
  3. 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...
  4. 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...
  5. 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...
  6. doi request reprint The accurate prediction of protein family from amino acid sequence by measuring features of sequence fragments
    Huixiao Hong
    Division of Systems Toxicology, National Center for Toxicological Research, U S Food and Drug Administration, Jefferson, Arkansas 72079, USA
    J Comput Biol 16:1671-88. 2009
    ..9941 was achieved. This study demonstrates that SVM based methods can accurately recognize and predict the protein family to which a sequence belongs based solely on its primary amino acid sequence...
  7. pmc Assessing sources of inconsistencies in genotypes and their effects on genome-wide association studies with HapMap samples
    H Hong
    Division of Systems Toxicology, National Center for Toxicological Research, US Food and Drug Administration, Jefferson, AR, USA
    Pharmacogenomics J 10:364-74. 2010
    ..Our studies show that inconsistencies between SNP arrays and between genotype calling algorithms are potential sources for the lack of reproducibility in GWAS results...
  8. doi request reprint Molecular biomarkers: a US FDA effort
    Huixiao Hong
    Center for Toxicoinformatics, Division of Systems Toxicology, National Center for Toxicological Research, US FDA 3900 NCTR Road, Jefferson, AR, USA
    Biomark Med 4:215-25. 2010
    ..Specific FDA programs and research projects related to molecular biomarkers are also discussed for supporting regulatory review in the future...
  9. ncbi request reprint Evaluating variations of genotype calling: a potential source of spurious associations in genome-wide association studies
    Huixiao Hong
    Division of Systems Toxicology, National Center for Toxicological Research, US Food and Drug Administration, 3900 NCTR Road, Jefferson, AR 72079, USA
    J Genet 89:55-64. 2010
    ..The effect of the threshold was much larger than the effect of the size. Moreover, the heterozygous calls had lower consistency compared to the homozygous calls...
  10. doi request reprint Assessing consistency between versions of genotype-calling algorithm Birdseed for the Genome-Wide Human SNP Array 6.0 using HapMap samples
    Huixiao Hong
    Center for Toxicoinformatics, Division of Systems Toxicology, National Center for Toxicological Research, US Food and Drug Administration, Jefferson, AR 72079, USA
    Adv Exp Med Biol 680:355-60. 2010
    ..Our results revealed that genotypes called from version-1 and version-2 of Birdseed were slightly different and the inconsistency in genotypes propagated to the downstream association analysis...
  11. doi request reprint Mold(2), molecular descriptors from 2D structures for chemoinformatics and toxicoinformatics
    Huixiao Hong
    Center for Toxicoinformatics, Division of Systems Toxicology, National Center for Toxicological Research, National Center for Toxicological Research, U S Food and Drug Administration, Jefferson, Arkansas 72079, USA
    J Chem Inf Model 48:1337-44. 2008
    ..High reproducibility and reliability are expected because Mold (2) does not require 3D structures. Mold (2) is freely available to the public ( http://www.fda.gov/nctr/science/centers/toxicoinformatics/index.htm)...
  12. pmc Assessment of prediction confidence and domain extrapolation of two structure-activity relationship models for predicting estrogen receptor binding activity
    Weida Tong
    Center for Toxicoinformatics, National Center for Toxicological Research, Food and Drug Administration, Jefferson, Arkansas 72079, USA
    Environ Health Perspect 112:1249-54. 2004
    ....
  13. ncbi request reprint Development of public toxicogenomics software for microarray data management and analysis
    Weida Tong
    Center for Toxicoinformatics, Division of Biometry and Risk Assessment, NCTR, 3900 NCTR Road, HFT 020, Jefferson, AR 72079, USA
    Mutat Res 549:241-53. 2004
    ..ArrayTrack is publicly available online and the prospective user can also request a local installation version by contacting the authors...
  14. pmc Very Important Pool (VIP) genes--an application for microarray-based molecular signatures
    Zhenqiang Su
    Center for Toxicoinformatics, National Center for Toxicological Research NCTR, U, S, Food and Drug Administration FDA, 3900 NCTR Road, Jefferson, AR 72079, USA
    BMC Bioinformatics 9:S9. 2008
    ..However, improving the ability to identify differentiating genes remains a challenge in bioinformatics...
  15. 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...
  16. doi request reprint Next-generation sequencing and its applications in molecular diagnostics
    Zhenqiang Su
    Z Tech, an ICF International Company at US FDA s National Center for Toxicological Research, 3900 NCTR Road, Jefferson, AR 72079, USA
    Expert Rev Mol Diagn 11:333-43. 2011
    ..The challenges in the analysis of NGS data and their potential applications in clinical diagnosis are also discussed...
  17. ncbi request reprint Quantitative structure-activity relationship models for predicting drug-induced liver injury based on FDA-approved drug labeling annotation and using a large collection of drugs
    Minjun Chen
    Division of Bioinformatics and Biostatistics, National Center for Toxicological Research, U S Food and Drug Administration, Jefferson, Arkansas 72079
    Toxicol Sci 136:242-9. 2013
    ....
  18. pmc The balance of reproducibility, sensitivity, and specificity of lists of differentially expressed genes in microarray studies
    Leming Shi
    National Center for Toxicological Research, US Food and Drug Administration, 3900 NCTR Road, Jefferson, AR 72079, USA
    BMC Bioinformatics 9:S10. 2008
    ..The resultant variety of existing and emerging methods exacerbates confusion and continuing debate in the microarray community on the appropriate choice of methods for identifying reliable DEG lists...
  19. ncbi request reprint Study of 202 natural, synthetic, and environmental chemicals for binding to the androgen receptor
    Hong Fang
    Northrop Grumman Information Technology, Jefferson, Arkansas 72079, USA
    Chem Res Toxicol 16:1338-58. 2003
    ..The SAR studies of ligand binding characteristics for AR are compared to our previously reported results for estrogen receptor binding...
  20. pmc Evaluation of gene expression data generated from expired Affymetrix GeneChip® microarrays using MAQC reference RNA samples
    Zhining Wen
    Division of Systems Biology, National Center for Toxicological Research NCTR, US Food and Drug Administration FDA, 3900 NCTR Road, Jefferson, AR 72079, USA
    BMC Bioinformatics 11:S10. 2010
    ..Experiments were conducted to answer these questions...
  21. doi request reprint Comparing next-generation sequencing and microarray technologies in a toxicological study of the effects of aristolochic acid on rat kidneys
    Zhenqiang Su
    ICF International at FDA s National Center for Toxicological Research, 3900 NCTR Road, Jefferson, Arkansas 72079, USA
    Chem Res Toxicol 24:1486-93. 2011
    ..However, there is clearly a need for future investigations to better understand the advantages and limitations of RNA-Seq in toxicogenomics studies and environmental health research...
  22. ncbi request reprint Decision forest: combining the predictions of multiple independent decision tree models
    Weida Tong
    Center for Toxicoinformatics, Division of Biometry and Risk Assessment, National Center for Toxicological Research, Jefferson, Arkansas 72079, USA
    J Chem Inf Comput Sci 43:525-31. 2003
    ..An example will be presented for prediction of binding affinity of 232 chemicals to the estrogen receptor...
  23. ncbi request reprint Multiclass Decision Forest--a novel pattern recognition method for multiclass classification in microarray data analysis
    Huixiao Hong
    Bioinformatics Laboratory, National Center for Toxicological Research, FDA, Jefferson, Arkansas 72079, USA
    DNA Cell Biol 23:685-94. 2004
    ..The results demonstrated that the multiclass DF is an effective classification method for analysis of gene expression data for the purpose of molecular diagnostics...
  24. pmc ArrayTrack--supporting toxicogenomic research at the U.S. Food and Drug Administration National Center for Toxicological Research
    Weida Tong
    Center for Toxicoinformatics, Division of Biometry and Risk Assessment, National Center for Toxicological Research, U S Food and Drug Administration, 3900 NCTR Road, Jefferson, AR 72079, USA
    Environ Health Perspect 111:1819-26. 2003
    ..Using ArrayTrack, we can select an analysis method from the TOOL and apply the method to selected microarray data stored in the MicroarrayDB; the analysis results can be linked directly to gene information in the LIB...
  25. doi request reprint Correlation analysis of external RNA controls reveals its utility for assessment of microarray assay
    Xiaohui Fan
    National Center for Toxicological Research, US Food and Drug Administration, Jefferson, AR 72079, USA
    Anal Biochem 385:203-7. 2009
    ..The proposed approach is sensitive to identifying outlying assays and is not dependent on the choice of normalization method...
  26. pmc The MicroArray Quality Control (MAQC)-II study of common practices for the development and validation of microarray-based predictive models
    Leming Shi
    National Center for Toxicological Research, US Food and Drug Administration, Jefferson, Arkansas, USA
    Nat Biotechnol 28:827-38. 2010
    ..The conclusions and recommendations from MAQC-II should be useful for regulatory agencies, study committees and independent investigators that evaluate methods for global gene expression analysis...
  27. 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...
  28. pmc Quality control and quality assessment of data from surface-enhanced laser desorption/ionization (SELDI) time-of flight (TOF) mass spectrometry (MS)
    Huixiao Hong
    Division of Bioinformatics, Z tech at FDA s National Center for Toxicological Research, Jefferson, Arkansas 72079, USA
    BMC Bioinformatics 6:S5. 2005
    ..The use of SELDI data for biomarker identification requires application of rigorous procedures to detect and discard low quality spectra prior to data analysis...
  29. pmc Two new ArrayTrack libraries for personalized biomedical research
    Joshua Xu
    Z Tech Corporation, ICF International company at NCTR, National Center for Toxicological Research, 3900 NCTR Rd, Jefferson, AR 72079, USA
    BMC Bioinformatics 11:S6. 2010
    ..An efficient data mining strategy and a set of sophisticated tools are necessary to help better understand and utilize the findings from genetic association studies...
  30. pmc Using decision forest to classify prostate cancer samples on the basis of SELDI-TOF MS data: assessing chance correlation and prediction confidence
    Weida Tong
    Center for Toxicoinformatics, Division of Biometry and Risk Assessment, National Center for Toxicological Research FDA, 3900 NCTR Road, HFT020, Jefferson, AK 72079, USA
    Environ Health Perspect 112:1622-7. 2004
    ..DF should be equally applicable to other omics data such as gene expression data or metabolomic data. The DF algorithm is available upon request...
  31. pmc Decision forest analysis of 61 single nucleotide polymorphisms in a case-control study of esophageal cancer; a novel method
    Qian Xie
    Division of Bioinformatics, Z tech at FDA s National Center for Toxicological Research, Jefferson, AR 72079, USA
    BMC Bioinformatics 6:S4. 2005
    ....
  32. ncbi request reprint Evaluation of external RNA controls for the assessment of microarray performance
    Weida Tong
    National Center for Toxicological Research, US Food and Drug Administration, 3900 NCTR Rd, Jefferson, Arkansas 72079, USA
    Nat Biotechnol 24:1132-9. 2006
    ..This multiplatform investigation of the behavior and utility of ERCs provides a basis for articulating specific recommendations for their future use in evaluating assay performance across multiple platforms...
  33. pmc The EDKB: an established knowledge base for endocrine disrupting chemicals
    Don Ding
    Division of Bioinformatics, Z Tech Corporation, ICF International Company at NCTR FDA, Jefferson, AR 72079, USA
    BMC Bioinformatics 11:S5. 2010
    ..This paper demonstrates the utility of EDKB database, an integral part of the EDKB project, for understanding and prioritizing EDs for testing...
  34. 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...
  35. ncbi request reprint Toxicogenomics and cancer susceptibility: advances with next-generation sequencing
    Baitang Ning
    a National Center for Toxicological Research, Food and Drug Administration, Jefferson, Arkansas, USA
    J Environ Sci Health C Environ Carcinog Ecotoxicol Rev 32:121-58. 2014
    ..These new findings should benefit public health by providing insights in understanding cancer biology, and in improving cancer diagnosis and therapy. ..
  36. doi request reprint Toward predictive models for drug-induced liver injury in humans: are we there yet?
    Minjun Chen
    Division of Bioinformatics and Biostatistics, National Center for Toxicological Research, The US Food and Drug Administration, Jefferson, AR, USA
    Biomark Med 8:201-13. 2014
    ....
  37. doi request reprint Studies on abacavir-induced hypersensitivity reaction: a successful example of translation of pharmacogenetics to personalized medicine
    Yongli Guo
    Division of Systems Biology, National Center for Toxicological Research, The US Food and Drug Administration, Jefferson, AR 72079, USA
    Sci China Life Sci 56:119-24. 2013
    ..The studies of abacavir-induced HSR and the implementation of the HLA-B*57:01 screening in the clinic represent a successful example of the use of pharmacogenetics for personalized diagnosis and therapy...
  38. pmc Prediction of estrogen receptor binding for 58,000 chemicals using an integrated system of a tree-based model with structural alerts
    Huixiao Hong
    R O W Sciences, Inc, Jefferson, Arkansas 72079, USA
    Environ Health Perspect 110:29-36. 2002
    ..The general approach for predicting ER binding reported here may be applied to other receptors and/or reversible binding mechanisms involved in endocrine disruption...
  39. ncbi request reprint Voluntary exploratory data submissions to the US FDA and the EMA: experience and impact
    Federico M Goodsaid
    Genomics Group, Office of Clinical Pharmacology, Office of Translational Sciences, Center for Drug Evaluation and Research, US FDA, Building 51, 10903 New Hampshire Avenue, Silver Spring, Maryland 20903 002, USA
    Nat Rev Drug Discov 9:435-45. 2010
    ....
  40. doi request reprint Biomarkers for drug-induced liver injury
    Qiang Shi
    Center for Toxicoinformatics, Division of Systems Toxicology, National Center for Toxicological Research, US Food and Drug Administration, 3900 NCTR Road, Jefferson, AR 72079, USA
    Expert Rev Gastroenterol Hepatol 4:225-34. 2010
    ..This review summarizes the current practice and future perspectives for DILI biomarkers...
  41. ncbi request reprint EADB: an estrogenic activity database for assessing potential endocrine activity
    Jie Shen
    Division of Bioinformatics and Biostatistics, National Center for Toxicological Research, U S Food and Drug Administration, Jefferson, Arkansas 72079
    Toxicol Sci 135:277-91. 2013
    ..A set of tools allow users to access EADB and evaluate potential endocrine activity of chemicals. As a case study, a classification model was developed using EADB for predicting ER binding of chemicals. ..