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List of works by Weida Tong

2012 Global Summit on Regulatory Science (GSRS-2012)—Modernizing Toxicology ⬇️

scientific article published on August 24, 2012

A Decade of Toxicogenomic Research and Its Contribution to Toxicological Science ⬇️

scientific article published on July 12, 2012

A Model to predict severity of drug-induced liver injury in humans

scientific article published on 15 June 2016

A Rat α-Fetoprotein Binding Activity Prediction Model to Facilitate Assessment of the Endocrine Disruption Potential of Environmental Chemicals

scientific article (publication date: 25 March 2016)

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

scientific article

A phenome-guided drug repositioning through a latent variable model

scientific article

A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages

scientific article

A strategy capitalizing on synergies: the Reporting Structure for Biological Investigation (RSBI) working group

scientific article published on January 2006

A systems approach for analysis of high content screening assay data with topic modeling

scientific article

A testing strategy to predict risk for drug-induced liver injury in humans using high-content screen assays and the 'rule-of-two' model

scientific article published on 11 June 2014

A unifying ontology to integrate histological and clinical observations for drug-induced liver injury

scientific article published on 08 February 2013

Alignment of Short Reads: A Crucial Step for Application of Next-Generation Sequencing Data in Precision Medicine

scientific article

An FDA bioinformatics tool for microbial genomics research on molecular characterization of bacterial foodborne pathogens using microarrays ⬇️

scientific article published on October 7, 2010

An approach to comparative analysis of chromatographic fingerprints for assuring the quality of botanical drugs

scientific article published on 01 May 2003

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

scientific article published on January 2007

An integrated study of acute effects of valproic acid in the liver using metabonomics, proteomics, and transcriptomics platforms

scientific article published in January 2006

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

scientific article

Application of dynamic topic models to toxicogenomics data

scientific article

Application of genome analysis strategies in the clinical testing for pediatric diseases

Applying network analysis and Nebula (neighbor-edges based and unbiased leverage algorithm) to ToxCast data

scientific article

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

scientific article

ArrayTrack: An FDA and Public Genomic Tool

scientific article published on January 2017

ArrayTrack: a free FDA bioinformatics tool to support emerging biomedical research -- an update ⬇️

scientific article published on August 1, 2010

ArrayTrack: an FDA and public genomic tool

2009 scientific article

Assessing QSAR Limitations - A Regulatory Perspective

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

scientific article

Assessing consistency between versions of genotype-calling algorithm Birdseed for the Genome-Wide Human SNP Array 6.0 using HapMap samples

scientific article published in January 2010

Assessing technical performance in differential gene expression experiments with external spike-in RNA control ratio mixtures

scientific article

Assessment of prediction confidence and domain extrapolation of two structure-activity relationship models for predicting estrogen receptor binding activity

scientific article

Asymmetric author-topic model for knowledge discovering of big data in toxicogenomics

scientific article

Biomarkers for drug-induced liver injury

scientific article published on April 2010

Building an organ-specific carcinogenic database for SAR analyses

scientific article published on 01 September 2004

Cancer genomics predicts disease relapse and therapeutic response to neoadjuvant chemotherapy of hormone sensitive breast cancers

scientific article published on 18 May 2020

Changes in the metabolome and microRNA levels in biological fluids might represent biomarkers of neurotoxicity: a trimethyltin study

journal article published in 2018

Chemical effects in biological systems--data dictionary (CEBS-DD): a compendium of terms for the capture and integration of biological study design description, conventional phenotypes, and 'omics data

scientific article

Chemometric analysis for identification of botanical raw materials for pharmaceutical use: a case study using Panax notoginseng

scientific article (publication date: 2014)

Classification of cDNA array genes that have a highly significant discriminative power due to their unique distribution in four brain regions

scientific article published on 01 October 2004

CoMPARA: Collaborative Modeling Project for Androgen Receptor Activity

scientific article published on 07 February 2020

Comparative Analysis of Predictive Models for Nongenotoxic Hepatocarcinogenicity Using Both Toxicogenomics and Quantitative Structure–Activity Relationships ⬇️

scientific article published on June 20, 2011

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

scientific article published in December 2015

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

scientific article published on 23 August 2011

Comparison of RNA-seq and microarray-based models for clinical endpoint prediction

scientific article published on 25 June 2015

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

scientific article

Comprehensive Assessments of RNA-seq by the SEQC Consortium: FDA-Led Efforts Advance Precision Medicine

scientific article

Comprehensive RNA-Seq transcriptomic profiling across 11 organs, 4 ages, and 2 sexes of Fischer 344 rats

scientific article

Comprehensively identifying and characterizing the missing gene sequences in human reference genome with integrated analytic approaches

scientific article published on 10 April 2013

Computational drug repositioning for rare diseases in the era of precision medicine

scientific article published on 18 October 2017

Computational prediction models for assessing endocrine disrupting potential of chemicals

scientific article published on 01 January 2018

Constructing a robust protein-protein interaction network by integrating multiple public databases ⬇️

scientific article published on October 18, 2011

Coordinated Regulation of UGT2B15 Expression by Long Noncoding RNA LINC00574 and hsa-miR-129-5p in HepaRG Cells

scientific article published on 21 February 2020

Correction to: Similarities and differences between variants called with human reference genome HG19 or HG38

scholarly article published in BMC Bioinformatics

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

scientific article published on 6 December 2008

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

scientific article

Cross-Platform Comparison of Microarray-Based Multiple-Class Prediction ⬇️

scientific article (publication date: 11 January 2011)

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

scientific article

Cross-platform ultradeep transcriptomic profiling of human reference RNA samples by RNA-Seq

scientific article

Current status of methods for defining the applicability domain of (quantitative) structure-activity relationships. The report and recommendations of ECVAM Workshop 52

scientific article (publication date: April 2005)

DILIrank: the largest reference drug list ranked by the risk for developing drug-induced liver injury in humans

scientific article published on 3 March 2016

DNA microarrays are predictive of cancer prognosis: a re-evaluation

scientific article published on 12 January 2010

Decision forest analysis of 61 single nucleotide polymorphisms in a case-control study of esophageal cancer; a novel method

scientific article published on 15 July 2005

Decision forest: combining the predictions of multiple independent decision tree models

scientific article published on March 2003

Development and Validation of Decision Forest Model for Estrogen Receptor Binding Prediction of Chemicals Using Large Data Sets

scientific article

Development of Decision Forest Models for Prediction of Drug-Induced Liver Injury in Humans Using A Large Set of FDA-approved Drugs.

scientific article published on 11 December 2017

Development of public toxicogenomics software for microarray data management and analysis

scientific article

Differential gene expression in mouse primary hepatocytes exposed to the peroxisome proliferator-activated receptor alpha agonists

scientific article

Direct comparison of performance of single nucleotide variant calling in human genome with alignment-based and assembly-based approaches

scientific article published on 8 September 2017

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

scientific article

Discovery of Transcriptional Targets Regulated by Nuclear Receptors Using a Probabilistic Graphical Model

scientific article published on 07 December 2015

Dissecting the Characteristics and Dynamics of Human Protein Complexes at Transcriptome Cascade Using RNA-Seq Data

scientific article

Drug-induced liver injury severity and toxicity (DILIst): binary classification of 1279 drugs by human hepatotoxicity

scientific article published on 01 November 2019

Drug-induced rhabdomyolysis: from systems pharmacology analysis to biochemical flux.

scientific article

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

scientific article published on 28 July 2013

Editorial: Integrative Toxicogenomics: Analytical Strategies to Amalgamate Exposure Effects With Genomic Sciences

scholarly article by Pierre R Bushel & Weida Tong published 2018 in Frontiers in Genetics

Emerging efforts for discovering new biomarkers of liver disease and hepatotoxicity

scientific article published on 01 January 2014

Emerging technologies for food and drug safety

scientific article published on 23 July 2018

Endocrine Disrupting Chemicals Mediated through Binding Androgen Receptor Are Associated with Diabetes Mellitus

scientific article published on 23 December 2017

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

scientific article published on 3 August 2016

Estimating relative noise to signal in DNA microarray data

scientific article

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

scientific article

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

scientific article

Evaluation of Bioinformatics Approaches for Next-Generation Sequencing Analysis of microRNAs with a Toxicogenomics Study Design

scientific article published on 6 February 2018

Evaluation of external RNA controls for the assessment of microarray performance

scientific article published on September 2006

Evaluation of gene expression data generated from expired Affymetrix GeneChip® microarrays using MAQC reference RNA samples

scientific article

Evaluation of multiple mechanism-based toxicity endpoints in primary cultured human hepatocytes for the identification of drugs with clinical hepatotoxicity: Results from 152 marketed drugs with known liver injury profiles

scientific article published on 12 November 2015

Evaluations of the trans-sulfuration pathway in multiple liver toxicity studies

scientific article published on 6 December 2008

Experimental Data Extraction and in Silico Prediction of the Estrogenic Activity of Renewable Replacements for Bisphenol A.

scientific article

FAIRsharing, a cohesive community approach to the growth in standards, repositories and policies

FDA drug labeling: rich resources to facilitate precision medicine, drug safety, and regulatory science

scientific article published on 15 June 2016

FDA-approved drug labeling for the study of drug-induced liver injury

article

Five-Feature Model for Developing the Classifier for Synergistic vs. Antagonistic Drug Combinations Built by XGBoost

scientific article published on 09 July 2019

GOFFA: gene ontology for functional analysis--a FDA gene ontology tool for analysis of genomic and proteomic data

scientific article

Gaining Confidence on Molecular Classification through Consensus Modeling and Validation

scientific article published on January 2006

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

scientific article

Global Summit on Regulatory Science 2013.

scientific article published on 13 August 2014

High daily dose and being a substrate of cytochrome P450 enzymes are two important predictors of drug-induced liver injury

scientific article published on 24 January 2014

High lipophilicity and high daily dose of oral medications are associated with significant risk for drug-induced liver injury

scientific article published on 27 May 2013

Homology Model and Ligand Binding Interactions of the Extracellular Domain of the Human <i>α</i>4<i>β</i>2 Nicotinic Acetylcholine Receptor

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

scientific article

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

scientific article published on 27 October 2014

ISA software suite: supporting standards-compliant experimental annotation and enabling curation at the community level

scientific article (publication date: 15 September 2010)

In silico drug repositioning – what we need to know ⬇️

scientific article published on August 28, 2012

In vitro to in vivo extrapolation for drug-induced liver injury using a pair ranking method

scientific article published on 11 January 2017

Incorporating the human gene annotations in different databases significantly improved transcriptomic and genetic analyses

scientific article published on 19 February 2013

Inhibition of bile salt transport by drugs associated with liver injury in primary hepatocytes from human, monkey, dog, rat, and mouse

scientific article published on 19 March 2016

Integrating adverse outcome pathways (AOPs) and high throughput in vitro assays for better risk evaluations, a study with drug-induced liver injury (DILI)

scientific article published on 08 November 2019

Integrating time-course microarray gene expression profiles with cytotoxicity for identification of biomarkers in primary rat hepatocytes exposed to cadmium

scientific article

Investigating drug repositioning opportunities in FDA drug labels through topic modeling ⬇️

scientific article published on September 11, 2012

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

scientific article

Is toxicogenomics a more reliable and sensitive biomarker than conventional indicators from rats to predict drug-induced liver injury in humans?

scientific article published on 13 December 2011

Lessons Learned from Two Decades of Anticancer Drugs

scientific article

Long noncoding RNA LINC00844-mediated molecular network regulates expression of drug metabolizing enzymes and nuclear receptors in human liver cells

scientific article published on 28 March 2020

Machine Learning Methods for Predicting HLA-Peptide Binding Activity

scientific article

Mechanistic roles of microRNAs in hepatocarcinogenesis: A study of thioacetamide with multiple doses and time-points of rats

scientific article

Mechanistically linked serum miRNAs distinguish between drug induced and fatty liver disease of different grades

scientific article published on 5 April 2016

Meeting report: Validation of toxicogenomics-based test systems: ECVAM-ICCVAM/NICEATM considerations for regulatory use.

scientific article

Meta-analysis of microarray data using a pathway-based approach identifies a 37-gene expression signature for systemic lupus erythematosus in human peripheral blood mononuclear cells ⬇️

scientific article published on May 30, 2011

Microarray analysis distinguishes differential gene expression patterns from large and small colony Thymidine kinase mutants of L5178Y mouse lymphoma cells

scientific article

Microarray scanner calibration curves: characteristics and implications

scientific article published on 15 July 2005

Mining FDA drug labels using an unsupervised learning technique - topic modeling ⬇️

scientific article published on October 18, 2011

Mining hidden knowledge for drug safety assessment: topic modeling of LiverTox as a case study

scientific article

Modeling Chemical Interaction Profiles: I. Spectral Data-Activity Relationship and Structure-Activity Relationship Models for Inhibitors and Non-inhibitors of Cytochrome P450 CYP3A4 and CYP2D6 Isozymes ⬇️

scientific article published on March 15, 2012

Modeling Chemical Interaction Profiles: II. Molecular Docking, Spectral Data-Activity Relationship, and Structure-Activity Relationship Models for Potent and Weak Inhibitors of Cytochrome P450 CYP3A4 Isozyme ⬇️

scientific article published on March 15, 2012

Mold(2), molecular descriptors from 2D structures for chemoinformatics and toxicoinformatics

scientific article

Molecular biomarkers: a US FDA effort

scientific article published on April 2010

Molecular docking to identify associations between drugs and class I human leukocyte antigens for predicting idiosyncratic drug reactions.

scientific article

Molecular regulation of miRNAs and potential biomarkers in the progression of hepatic steatosis to NASH

scientific article

Multi-class cancer classification by total principal component regression (TPCR) using microarray gene expression data

scientific article

Multi-class tumor classification by discriminant partial least squares using microarray gene expression data and assessment of classification models

scientific article

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

scientific article

Multiple microRNAs function as self-protective modules in acetaminophen-induced hepatotoxicity in humans

scientific article

NETBAGs: a network-based clustering approach with gene signatures for cancer subtyping analysis

scientific article published on 26 October 2015

Next generation sequencing for profiling expression of miRNAs: technical progress and applications in drug development ⬇️

scientific article published on October 1, 2011

Next-generation sequencing and its applications in molecular diagnostics

scientific article published on April 2011

Of text and gene--using text mining methods to uncover hidden knowledge in toxicogenomics

scientific article

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

scientific article published on 26 March 2016

Performance comparison of one-color and two-color platforms within the MicroArray Quality Control (MAQC) project

scientific article published on 01 September 2006

Persistent Organic Pollutants in Food: Contamination Sources, Health Effects and Detection Methods

scientific article published on 08 November 2019

Perspectives on validation of high-throughput assays supporting 21st century toxicity testing

scientific article (publication date: 2013)

Phytoestrogens and mycoestrogens bind to the rat uterine estrogen receptor

scientific article published on 01 April 2002

Potential Reuse of Oncology Drugs in the Treatment of Rare Diseases

scientific article

Predicting idiosyncratic drug-induced liver injury: some recent advances

scientific article published on 23 May 2014

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

scientific article

Profiling of the Tox21 10K compound library for agonists and antagonists of the estrogen receptor alpha signaling pathway

scientific article

QA/QC issues to aid regulatory acceptance of microarray gene expression data

scientific article

QA/QC: challenges and pitfalls facing the microarray community and regulatory agencies

scientific article

QSAR Models at the US FDA/NCTR.

scientific article published on January 2016

QuaPra: Efficient transcript assembly and quantification using quadratic programming with Apriori algorithm

scientific article published on 22 May 2019

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

scientific article published on 15 July 2005

Quantitative structure-activity relationship methods: perspectives on drug discovery and toxicology

scientific article

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

scientific article published on 31 August 2013

Rat toxicogenomic study reveals analytical consistency across microarray platforms

scientific article

Rat α-Fetoprotein Binding Affinities of a Large Set of Structurally Diverse Chemicals Elucidated the Relationships between Structures and Binding Affinities ⬇️

scientific article published on October 12, 2012

Regulatory bioinformatics for food and drug safety

scientific article published on 18 May 2016

Regulatory landscape of dietary supplements and herbal medicines from a global perspective

scientific article published on 16 April 2020

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

scientific article

SNPTrack™ : an integrated bioinformatics system for genetic association studies

scientific article

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 ⬇️

scientific article published on October 18, 2011

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

scientific article published on 01 January 2007

Sequencing XMET genes to promote genotype-guided risk assessment and precision medicine

scientific article published on 20 May 2019

Significant variations in alternative splicing patterns and expression profiles between human-mouse orthologs in early embryos

scientific article published on 4 July 2016

Similarities and differences between variants called with human reference genome HG19 or HG38

Structural Changes Due to Antagonist Binding in Ligand Binding Pocket of Androgen Receptor Elucidated Through Molecular Dynamics Simulations.

scientific article

Structure-activity relationship approaches and applications

scientific article

Structures of androgen receptor bound with ligands: advancing understanding of biological functions and drug discovery

scientific article published on 19 May 2016

Study of 202 Natural, Synthetic, and Environmental Chemicals for Binding to the Androgen Receptor ⬇️

scientific article published on October 1, 2003

Study of pharmacogenomic information in FDA-approved drug labeling to facilitate application of precision medicine

scientific article published on 04 February 2020

Study of serious adverse drug reactions using FDA-approved drug labeling and MedDRA

Technical reproducibility of genotyping SNP arrays used in genome-wide association studies

scientific article

The EDKB: an established knowledge base for endocrine disrupting chemicals

scientific article

The FDA's Experience with Emerging Genomics Technologies-Past, Present, and Future

scientific article published on 26 April 2016

The Liver Toxicity Knowledge Base (LKTB) and drug-induced liver injury (DILI) classification for assessment of human liver injury

scientific article published on 21 September 2017

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

scientific article

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

scientific article

The accurate prediction of protein family from amino acid sequence by measuring features of sequence fragments

scientific article published in December 2009

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

scientific article

The concordance between RNA-seq and microarray data depends on chemical treatment and transcript abundance

scientific article

The first RSBI (ISA-TAB) workshop: "can a simple format work for complex studies?".

scientific article

The international MAQC Society launches to enhance reproducibility of high-throughput technologies

scientific article published in December 2017

Toward Clinical Implementation of Next-Generation Sequencing-Based Genetic Testing in Rare Diseases: Where Are We?

scientific article published on 14 October 2019

Toward a checklist for exchange and interpretation of data from a toxicology study

scientific article

Toward interoperable bioscience data

scientific article (publication date: 27 January 2012)

Toward predictive models for drug-induced liver injury in humans: are we there yet?

scientific article published on January 2014

Towards interoperable reporting standards for omics data: hopes and hurdles

scientific article (publication date: March 2009)

Towards the development of an omics data analysis framework

scientific article published on 19 February 2020

Toxicogenomics: A 2020 Vision

scientific article published on 26 December 2018

Transcriptional Responses Reveal Similarities Between Preclinical Rat Liver Testing Systems.

scientific article

Transcriptomic profiling of rat liver samples in a comprehensive study design by RNA-Seq

scientific article

Translating Clinical Findings into Knowledge in Drug Safety Evaluation - Drug Induced Liver Injury Prediction System (DILIps) ⬇️

scientific article published on December 15, 2011

Two new ArrayTrack libraries for personalized biomedical research ⬇️

scientific article published on October 7, 2010

Understanding and predicting binding between human leukocyte antigens (HLAs) and peptides by network analysis

scientific article

Using decision forest to classify prostate cancer samples on the basis of SELDI-TOF MS data: assessing chance correlation and prediction confidence

scientific article

Versatility or promiscuity: the estrogen receptors, control of ligand selectivity and an update on subtype selective ligands

scientific article

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

scientific article

Voluntary exploratory data submissions to the US FDA and the EMA: experience and impact

scientific article published in June 2010

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

scientific article

atBioNet– an integrated network analysis tool for genomics and biomarker discovery ⬇️

scientific article published on July 20, 2012

ebTrack: an environmental bioinformatics system built upon ArrayTrack

scientific article

miRNAs and their application in drug-induced liver injury

scientific article published on January 2014

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