Research Topics
| Huixiao HongSummaryAffiliation: Food and Drug Administration Country: USA Publications
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Detail Information
Publications
Critical role of bioinformatics in translating huge amounts of next-generation sequencing data into personalized medicineHuixiao 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...
Technical reproducibility of genotyping SNP arrays used in genome-wide association studiesHuixiao 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...- Assessing batch effects of genotype calling algorithm BRLMM for the Affymetrix GeneChip Human Mapping 500 K array set using 270 HapMap samplesHuixiao 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... - The accurate prediction of protein family from amino acid sequence by measuring features of sequence fragmentsHuixiao 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... - Mold(2), molecular descriptors from 2D structures for chemoinformatics and toxicoinformaticsHuixiao 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)... - Assessing sources of inconsistencies in genotypes and their effects on genome-wide association studies with HapMap samplesH 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... - Molecular biomarkers: a US FDA effortHuixiao 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... 
Evaluating variations of genotype calling: a potential source of spurious associations in genome-wide association studiesHuixiao 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...- Assessing consistency between versions of genotype-calling algorithm Birdseed for the Genome-Wide Human SNP Array 6.0 using HapMap samplesHuixiao 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... - Assessment of prediction confidence and domain extrapolation of two structure-activity relationship models for predicting estrogen receptor binding activityWeida Tong
Center for Toxicoinformatics, National Center for Toxicological Research, Food and Drug Administration, Jefferson, Arkansas 72079, USA
Environ Health Perspect 112:1249-54. 2004.... - Development of public toxicogenomics software for microarray data management and analysisWeida 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... - Cross-platform comparability of microarray technology: intra-platform consistency and appropriate data analysis procedures are essentialLeming 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... - Very Important Pool (VIP) genes--an application for microarray-based molecular signaturesZhenqiang 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... - Next-generation sequencing and its applications in molecular diagnosticsZhenqiang 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... - The balance of reproducibility, sensitivity, and specificity of lists of differentially expressed genes in microarray studiesLeming 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... - Evaluation of gene expression data generated from expired Affymetrix GeneChip® microarrays using MAQC reference RNA samplesZhining 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... - Decision forest: combining the predictions of multiple independent decision tree modelsWeida 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... - Comparing next-generation sequencing and microarray technologies in a toxicological study of the effects of aristolochic acid on rat kidneysZhenqiang 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... - Correlation analysis of external RNA controls reveals its utility for assessment of microarray assayXiaohui 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... - The MicroArray Quality Control (MAQC)-II study of common practices for the development and validation of microarray-based predictive modelsLeming 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... - ArrayTrack--supporting toxicogenomic research at the U.S. Food and Drug Administration National Center for Toxicological ResearchWeida 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... - Study of 202 natural, synthetic, and environmental chemicals for binding to the androgen receptorHong 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... - Multiclass Decision Forest--a novel pattern recognition method for multiclass classification in microarray data analysisHuixiao 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... - 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... - Rat α-Fetoprotein Binding Affinities of a Large Set of Structurally Diverse Chemicals Elucidated the Relationships between Structures and Binding AffinitiesHuixiao Hong
Division of Bioinformatics and Biostatistics, National Center for Toxicological Research, U S Food and Drug Administration, Jefferson, Arkansas 72079, United States
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... - Two new ArrayTrack libraries for personalized biomedical researchJoshua 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... - Using decision forest to classify prostate cancer samples on the basis of SELDI-TOF MS data: assessing chance correlation and prediction confidenceWeida 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... - Decision forest analysis of 61 single nucleotide polymorphisms in a case-control study of esophageal cancer; a novel methodQian Xie
Division of Bioinformatics, Z tech at FDA s National Center for Toxicological Research, Jefferson, AR 72079, USA
BMC Bioinformatics 6:S4. 2005.... - Evaluation of external RNA controls for the assessment of microarray performanceWeida 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... - Microarray scanner calibration curves: characteristics and implicationsLeming 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... - The EDKB: an established knowledge base for endocrine disrupting chemicalsDon 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... - Studies on abacavir-induced hypersensitivity reaction: a successful example of translation of pharmacogenetics to personalized medicineYongli 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... - The MicroArray Quality Control (MAQC) project shows inter- and intraplatform reproducibility of gene expression measurementsLeming 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... - Prediction of estrogen receptor binding for 58,000 chemicals using an integrated system of a tree-based model with structural alertsHuixiao 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... - Voluntary exploratory data submissions to the US FDA and the EMA: experience and impactFederico 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.... - Biomarkers for drug-induced liver injuryQiang 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...