R. Perkins

发表

The MicroArray Quality Control (MAQC) project shows inter- and intraplatform reproducibility of gene expression measurements.

Hanlee P. Ji, G. M. Fischer, Stephen C. Harris, 2006, Nature biotechnology.

Comparing next-generation sequencing and microarray technologies in a toxicological study of the effects of aristolochic acid on rat kidneys.

Leming Shi, W. Tong, H. Fang, 2011, Chemical research in toxicology.

A comprehensive assessment of RNA-seq accuracy, reproducibility and information content by the Sequencing Quality Control consortium

David P. Kreil, Todd M. Smith, Thomas M. Blomquist, 2014, Nature Biotechnology.

Current Status of Methods for Defining the Applicability Domain of (Quantitative) Structure-Activity Relationships

Scott D. Kahn, G. Klopman, W. Tong, 2005, Alternatives to laboratory animals : ATLA.

The MicroArray Quality Control (MAQC)-II study of common practices for the development and validation of microarray-based predictive models

Kevin C. Dorff, Aaron M. Smalter, Stephen C. Harris, 2010, Nature Biotechnology.

QSAR Models Using a Large Diverse Set of Estrogens.

W. Tong, H. Fang, R. Perkins, 2001 .

Comparative molecular field analysis (CoMFA) model using a large diverse set of natural, synthetic and environmental chemicals for binding to the androgen receptor

H. Fang, H. Hong, R. Perkins, 2003, SAR and QSAR in environmental research.

The estrogen receptor relative binding affinities of 188 natural and xenochemicals: structural diversity of ligands.

H Fang, W S Branham, D M Sheehan, 2000, Toxicological sciences : an official journal of the Society of Toxicology.

Human sex hormone-binding globulin binding affinities of 125 structurally diverse chemicals and comparison with their binding to androgen receptor, estrogen receptor, and α-fetoprotein.

Weida Tong, Huixiao Hong, Hong Fang, 2015, Toxicological sciences : an official journal of the Society of Toxicology.

Next-Generation Sequencing: A Revolutionary Tool for Toxicogenomics

Leming Shi, W. Tong, H. Fang, 2011 .

ArrayTrack - Supporting Toxicogenomic Research at the FDA?s National Center for Toxicological Research (NCTR)

Stephen C. Harris, Leming Shi, W. Tong, 2003 .

Predicted changes in pre-mRNA secondary structure vary in their association with exon skipping for mutations in exons 2, 4, and 8 of the Hprt gene and exon 51 of the fibrillin gene.

R. Perkins, W. Tong, M. Tu, 2000, Mutation research.

Next-generation sequencing and its applications in molecular diagnostics

Leming Shi, W. Tong, H. Fang, 2011, Expert review of molecular diagnostics.

Quantitative structure‐activity relationship methods: Perspectives on drug discovery and toxicology

W. Tong, H. Fang, R. Perkins, 2003, Environmental toxicology and chemistry.

Text mining for identifying topics in the literatures about adolescent substance use and depression

James J. Chen, R. Perkins, Yijun Ding, 2016, BMC Public Health.

An investigation of biomarkers derived from legacy microarray data for their utility in the RNA-seq era

Weida Tong, Huixiao Hong, Leming Shi, 2014, Genome Biology.

Multiclass Decision Forest--a novel pattern recognition method for multiclass classification in microarray data analysis.

Weida Tong, Qian Xie, Huixiao Hong, 2004, DNA and cell biology.

Molecular Biomarkers for Personalized Medicine

Leming Shi, W. Tong, H. Fang, 2014 .

Prediction of estrogen receptor binding for 58,000 chemicals using an integrated system of a tree-based model with structural alerts.

Weida Tong, Qian Xie, Huixiao Hong, 2001, Environmental health perspectives.

Quantitative comparisons of in vitro assays for estrogenic activities.

H Fang, D M Sheehan, H. Fang, 2000, Environmental health perspectives.

Evaluation of Quantitative Structure—Activity Relationship Methods for Large-Scale Prediction of Chemicals Binding to the Estrogen Receptor.

William J. Welsh, Roger Perkins, Daniel M. Sheehan, 1998 .

Comparing genetic variants detected in the 1000 genomes project with SNPs determined by the International HapMap Consortium

W. Tong, W. Ge, H. Hong, 2015, Journal of Genetics.

The Reproducibility of Lists of Differentially Expressed Genes in Microarray Studies

Weida Tong, Qian Xie, Huixiao Hong, 2007 .

Technical Reproducibility of Genotyping SNP Arrays Used in Genome-Wide Association Studies

Christophe G. Lambert, Weida Tong, Huixiao Hong, 2012, PloS one.

Evaluating variations of genotype calling: a potential source of spurious associations in genome-wide association studies

Weida Tong, Huixiao Hong, Leming Shi, 2010, Journal of Genetics.

Pitfall of genome-wide association studies: Sources of inconsistency in genotypes and their effects

Weida Tong, Huixiao Hong, Leming Shi, 2012 .

Using Decision Forest to Classify Prostate Cancer Samples on the Basis of SELDI-TOF MS Data: Assessing Chance Correlation and Prediction Confidence

Weida Tong, Qian Xie, Huixiao Hong, 2004, Environmental health perspectives.

Receptor-Mediated Toxicity: QSARs for Estrogen Receptor Binding and Priority Setting of Potential Estrogenic Endocrine Disruptors

Weida Tong, Qian Xie, Huixiao Hong, 2004 .

Self-self hybridization as an alternative experiment design to dye swap for two-color microarrays.

Leming Shi, W. Tong, Y. Dragan, 2007, Omics : a journal of integrative biology.

Interpretation of Toxicogenomics Data

W. Tong, H. Fang, R. Perkins, 2010 .

Correlation analysis of external RNA controls reveals its utility for assessment of microarray assay.

Leming Shi, W. Tong, H. Fang, 2009, Analytical biochemistry.

Structure-activity relationships for a large diverse set of natural, synthetic, and environmental estrogens.

Q Xie, H Fang, D M Sheehan, 2001, Chemical research in toxicology.

Study of 202 natural, synthetic, and environmental chemicals for binding to the androgen receptor.

Weida Tong, Qian Xie, Huixiao Hong, 2003, Chemical research in toxicology.

Reproducible and reliable microarray results through quality control: good laboratory proficiency and appropriate data analysis practices are essential.

Weida Tong, Leming Shi, Hong Fang, 2008, Current opinion in biotechnology.

An integrated "4-phase" approach for setting endocrine disruption screening priorities--phase I and II predictions of estrogen receptor binding affinity

H Hong, W Tong, Q Xie, 2002, SAR and QSAR in environmental research.

QSAR Models Using a Large Diverse Set of Estrogens

Weida Tong, Leming Shi, Hong Fang, 2001, J. Chem. Inf. Comput. Sci..

Critical role of bioinformatics in translating huge amounts of next-generation sequencing data into personalized medicine

Tao Han, Jie Shen, Roger Perkins, 2013, Science China Life Sciences.

Omics Biomarkers in Risk Assessment: A Bioinformatics Perspective

Weida Tong, Huixiao Hong, Reagan Kelly, 2013 .

Consensus analysis of multiple classifiers using non-repetitive variables: Diagnostic application to microarray gene expression data

Weida Tong, Huixiao Hong, Roger Perkins, 2007, Comput. Biol. Chem..

Assessing sources of inconsistencies in genotypes and their effects on genome-wide association studies with HapMap samples

F. Goodsaid, H. Fang, W. Ge, 2010, The Pharmacogenomics Journal.

An integrated bioinformatics infrastructure essential for advancing pharmacogenomics and personalized medicine in the context of the FDA's Critical Path Initiative.

Weida Tong, Leming Shi, Hong Fang, 2007, Drug discovery today. Technologies.

An investigation of biomarkers derived from legacy microarray data for their utility in the RNA-seq era

Wenwei Zhang, Yanyan Zhang, Leming Shi, 2014, Genome Biology.

Whole genome sequencing of 35 individuals provides insights into the genetic architecture of Korean population

Weida Tong, Huixiao Hong, Roger Perkins, 2014, BMC Bioinformatics.

Cross-platform comparability of microarray technology: Intra-platform consistency and appropriate data analysis procedures are essential

Tao Han, James J. Chen, Weida Tong, 2005, BMC Bioinformatics.

Microarray scanner calibration curves: characteristics and implications

Tao Han, James J. Chen, Weida Tong, 2005, BMC Bioinformatics.

Structure‐activity relationship approaches and applications

Weida Tong, Leming Shi, Hong Fang, 2003, Environmental toxicology and chemistry.

Decision Forest Analysis of 61 Single Nucleotide Polymorphisms in a Case-Control Study of Esophageal Cancer; a novel method

Nan Hu, Weida Tong, Huixiao Hong, 2005, BMC Bioinformatics.

Kv1.3 Channel Gene-Targeted Deletion Produces “Super-Smeller Mice” with Altered Glomeruli, Interacting Scaffolding Proteins, and Biophysics

L. Kaczmarek, R. Perkins, R. Flavell, 2004, Neuron.

Very Important Pool (VIP) genes – an application for microarray-based molecular signatures

Weida Tong, Huixiao Hong, Leming Shi, 2008, BMC Bioinformatics.

The balance of reproducibility, sensitivity, and specificity of lists of differentially expressed genes in microarray studies

Catalin C. Barbacioru, Leming Shi, Hong Fang, 2008, BMC Bioinformatics.

Pathway Analysis Revealed Potential Diverse Health Impacts of Flavonoids that Bind Estrogen Receptors

Weida Tong, Huixiao Hong, Roger Perkins, 2016, International journal of environmental research and public health.

The Current Status of DNA Microarrays

Weida Tong, Leming Shi, Roger Perkins, 2009 .

ArrayTrack--supporting toxicogenomic research at the U.S. Food and Drug Administration National Center for Toxicological Research.

Weida Tong, Qian Xie, Huixiao Hong, 2003, Environmental health perspectives.

An in silico ensemble method for lead discovery: decision forest

H Hong, W Tong, Q Xie, 2005, SAR and QSAR in environmental research.

Gene expression profile exploration of a large dataset on chronic fatigue syndrome.

Weida Tong, Qian Xie, Hong Fang, 2006, Pharmacogenomics.

Mold2, Molecular Descriptors from 2D Structures for Chemoinformatics and Toxicoinformatics

Weida Tong, Huixiao Hong, Leming Shi, 2008, J. Chem. Inf. Model..

Homology modeling, molecular docking, and molecular dynamics simulations elucidated α-fetoprotein binding modes

Weida Tong, Huixiao Hong, Hong Fang, 2013, BMC Bioinformatics.

Evaluation of Quantitative Structure-Activity Relationship Methods for Large-Scale Prediction of Chemicals Binding to the Estrogen Receptor

Yu Chen, William J. Welsh, Weida Tong, 1998, J. Chem. Inf. Comput. Sci..

Assessing batch effects of genotype calling algorithm BRLMM for the Affymetrix GeneChip Human Mapping 500 K array set using 270 HapMap samples

Tao Han, James J. Chen, Weida Tong, 2008, BMC Bioinformatics.

A heuristic approach to determine an appropriate number of topics in topic modeling

Weizhong Zhao, Roger Perkins, Yijun Ding, 2015, BMC Bioinformatics.

Development of public toxicogenomics software for microarray data management and analysis.

Weida Tong, Qian Xie, Huixiao Hong, 2004, Mutation research.

A novel procedure on next generation sequencing data analysis using text mining algorithm

W. Tong, James J. Chen, H. Hong, 2016, BMC Bioinformatics.

Estrogenic activity data extraction and in silico prediction show the endocrine disruption potential of bisphenol A replacement compounds.

Weida Tong, Huixiao Hong, Roger Perkins, 2015, Chemical research in toxicology.

QSAR Models for Binding of Estrogenic Compounds to Estrogen Receptor α and β Subtypes.

Roger Perkins, Li Xing, William J Welsh, 1997, Endocrinology.

Quantitative structure-activity relationships (QSARs) for estrogen binding to the estrogen receptor: predictions across species.

W S Branham, D M Sheehan, R. Perkins, 1997, Environmental health perspectives.

Erratum to: A novel procedure on next generation sequencing data analysis using text mining algorithm

W. Tong, James J. Chen, H. Hong, 2016, BMC Bioinform..

Phytoestrogens and mycoestrogens bind to the rat uterine estrogen receptor.

Weida Tong, Leming Shi, Hong Fang, 2002, The Journal of nutrition.

The Accurate Prediction of Protein Family from Amino Acid Sequence by Measuring Features of Sequence Fragments

Weida Tong, Huixiao Hong, Leming Shi, 2009, J. Comput. Biol..

QSAR models for binding of estrogenic compounds to estrogen receptor alpha and beta subtypes.

D M Sheehan, R. Perkins, W. Welsh, 1997, Endocrinology.

Mold2 Molecular Descriptors for QSAR

Svetoslav H. Slavov, Weida Tong, Huixiao Hong, 2012 .

Versatility or Promiscuity: The Estrogen Receptors, Control of Ligand Selectivity and an Update on Subtype Selective Ligands

Weida Tong, Huixiao Hong, Roger Perkins, 2014, International journal of environmental research and public health.

Bioinformatics approaches for cross-species liver cancer analysis based on microarray gene expression profiling

Weida Tong, Huixiao Hong, Leming Shi, 2005, BMC Bioinformatics.

Approaches and Practical Considerations for the Analysis of Toxicogenomics Data

Weida Tong, Huixiao Hong, Leming Shi, 2011 .

Competitive molecular docking approach for predicting estrogen receptor subtype α agonists and antagonists

W. Tong, W. Ge, H. Hong, 2014, BMC Bioinformatics.

5.21 – Computational Toxicology☆

Weida Tong, Huixiao Hong, S. Thakkar, 2018 .

Homology modeling, molecular docking, and molecular dynamics simulations elucidated α-fetoprotein binding modes

W. Tong, H. Fang, H. Hong, 2013, BMC Bioinformatics.

EADB: an estrogenic activity database for assessing potential endocrine activity.

Weida Tong, Huixiao Hong, Hong Fang, 2013, Toxicological sciences : an official journal of the Society of Toxicology.

The EDKB: an established knowledge base for endocrine disrupting chemicals

Lei Xu, Weida Tong, Huixiao Hong, 2010, BMC Bioinformatics.

Decision Forest: Combining the Predictions of Multiple Independent Decision Tree Models

Weida Tong, Huixiao Hong, Hong Fang, 2003, J. Chem. Inf. Comput. Sci..

Regulatory application of SAR/QSAR for priority setting of endocrine disruptors: A perspective

Weida Tong, Qian Xie, Huixiao Hong, 2003 .

Development of Quantitative Structure-Activity Relationships ( QSARs ) and Their Use for Priority Setting in the Testing Strategy of Endocrine Disruptors

Weida Tong, Qian Xie, Huixiao Hong, 2002 .

GOFFA: Gene Ontology For Functional Analysis – A FDA Gene Ontology Tool for Analysis of Genomic and Proteomic Data

Tao Chen, Weida Tong, Hong Fang, 2006, BMC Bioinformatics.

Comparison of Estrogen Receptor α and β Subtypes Based on Comparative Molecular Field Analysis (CoMFA)

William J. Welsh, Weida Tong, Roger Perkins, 1999 .

ArrayTrack: an FDA and public genomic tool.

Weida Tong, Leming Shi, Hong Fang, 2009, Methods in molecular biology.

Comparing genetic variants detected in the 1000 genomes project with SNPs determined by the International HapMap Consortium

W. Tong, W. Ge, H. Hong, 2015, Journal of Genetics.

Quality control metrics improve repeatability and reproducibility of single-nucleotide variants derived from whole-genome sequencing

H Hong, W Tong, W Zhang, 2014, The Pharmacogenomics Journal.

Critical role of bioinformatics in translating huge amounts of next-generation sequencing data into personalized medicine

Leming Shi, W. Tong, H. Hong, 2013, Science China Life Sciences.

DNA Microarrays Are Predictive of Cancer Prognosis: A Re-evaluation

Weida Tong, Leming Shi, Yiyu Cheng, 2010, Clinical Cancer Research.

Selecting a single model or combining multiple models for microarray-based classifier development? – A comparative analysis based on large and diverse datasets generated from the MAQC-II project

Weida Tong, Leming Shi, Hong Fang, 2011, BMC Bioinformatics.

Quality control and quality assessment of data from surface-enhanced laser desorption/ionization (SELDI) time-of flight (TOF) mass spectrometry (MS)

Weida Tong, Huixiao Hong, Leming Shi, 2005, BMC Bioinformatics.

ArrayTrack: An FDA and Public Genomic Tool.

Weida Tong, Leming Shi, Hong Fang, 2017, Methods in molecular biology.

Discovering functional modules by topic modeling RNA-Seq based toxicogenomic data.

Weida Tong, Roger Perkins, Ke Yu, 2014, Chemical research in toxicology.

QSARs for Endocrine Disruption Priority Setting Database 2: The Integrated 4‐Phase Model

Weida Tong, Hong Fang, Roger Perkins, 2003 .

Gaining Confidence on Molecular Classification through Consensus Modeling and Validation

Huixiao Hong, Weida Tong, Roger Perkins, 2006, Toxicology mechanisms and methods.

Investigation of reproducibility of differentially expressed genes in DNA microarrays through statistical simulation

Weida Tong, Leming Shi, Hong Fang, 2009, BMC proceedings.

Multiclass Decision Forest--a novel pattern recognition method for multiclass classification in microarray data analysis.

Leming Shi, W. Tong, H. Fang, 2004, DNA and cell biology.

The MicroArray Quality Control (MAQC)-II study of common practices for the development and validation of microarray-based predictive models

Todd H. Stokes, Kevin C. Dorff, Aaron M. Smalter, 2010, Nature Biotechnology.

Assessment of Prediction Confidence and Domain Extrapolation of Two Structure–Activity Relationship Models for Predicting Estrogen Receptor Binding Activity

Weida Tong, Qian Xie, Huixiao Hong, 2004, Environmental health perspectives.

Comparison of estrogen receptor alpha and beta subtypes based on comparative molecular field analysis (CoMFA).

D M Sheehan, R. Perkins, W. Welsh, 1999, SAR and QSAR in environmental research.

Human sex hormone-binding globulin binding affinities of 125 structurally diverse chemicals and comparison with their binding to androgen receptor, estrogen receptor, and α-fetoprotein.

W. Tong, H. Fang, H. Hong, 2015, Toxicological sciences : an official journal of the Society of Toxicology.

A novel procedure on next generation sequencing data analysis using text mining algorithm

W. Tong, James J. Chen, H. Hong, 2016, BMC Bioinformatics.