Joshua Xu

发表

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.

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.

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

David P. Kreil, Steven P. Lund, Paweł P. Łabaj, 2014, Nature Communications.

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

May D. Wang, Wenwei Zhang, Simon M Lin, 2015, Genome Biology.

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

David P. Kreil, Paweł P. Łabaj, C. Furlanello, 2014, Nature Biotechnology.

A comprehensive study design reveals treatment-and transcript abundance – dependent concordance between RNA-seq and microarray data

David P. Kreil, Paweł P. Łabaj, Dalila, 2014 .

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

Leming Shi, W. Tong, J. Thierry-Mieg, 2014, Scientific Data.

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

W. Tong, H. Fang, R. Kelly, 2010, Human Genomics.

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

W. Xiao, W. Tong, H. Fang, 2015, Biomarkers in medicine.

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.

Landscape of circRNAs across 11 organs and 4 ages in Fischer 344 rats.

W. Tong, Joshua Xu, Binsheng Gong, 2020, Chemical research in toxicology.

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

W. Xiao, Tieliu Shi, Leming Shi, 2019, Science China Life Sciences.

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

Weida Tong, Hong Fang, Zhichao Liu, 2016, Drug discovery today.

SNPTrackTM : an integrated bioinformatics system for genetic association studies

Weida Tong, Huixiao Hong, Hong Fang, 2012, Human Genomics.

HetEnc: a deep learning predictive model for multi-type biological dataset

Joshua Xu, Leihong Wu, Xiangwen Liu, 2019, BMC Genomics.

Deep oncopanel sequencing reveals within block position-dependent quality degradation in FFPE processed samples

Thomas M. Blomquist, R. Sebra, Leming Shi, 2022, Genome biology.

DLI-IT: a deep learning approach to drug label identification through image and text embedding

W. Tong, Joshua Xu, J. Meehan, 2020, BMC Medical Informatics and Decision Making.

Trade-off Predictivity and Explainability for Machine-Learning Powered Predictive Toxicology: An in-Depth Investigation with Tox21 Data Sets.

I. Tetko, W. Tong, Joshua Xu, 2021, Chemical research in toxicology.

Trade off predictivity and explainability for ML-powered predictive toxicology: an in-depth investigation with Tox21 datasets

I. Tetko, W. Tong, Joshua Xu, 2022 .

Draft Genome Sequences of Two Methicillin-Resistant Clinical Staphylococcus aureus Isolates

Joshua Xu, Saeed A. Khan, K. Sung, 2016, Genome Announcements.

Draft Genome Sequence of Methicillin-Resistant Clinical Staphylococcus aureus Isolate 51S (Sequence Type 291)

Joshua Xu, Saeed A. Khan, K. Sung, 2015, Genome Announcements.

Author Correction: Towards accurate and reliable resolution of structural variants for clinical diagnosis

W. Tong, Joshua Xu, F. Sedlazeck, 2022, Genome Biology.

Optimized imaging methods for species-level identification of food-contaminating beetles

Himansu J Vyas, W. Tong, Joshua Xu, 2021, Scientific Reports.

CarcSeq measurement of rat mammary cancer driver mutations and relation to spontaneous mammary neoplasia.

Joshua Xu, Binsheng Gong, K. Harris, 2021, Toxicological sciences : an official journal of the Society of Toxicology.

Quartet DNA reference materials and datasets for comprehensively evaluating germline variants calling performance

K. Ye, Leming Shi, W. Tong, 2022, bioRxiv.

NeuroCORD: A Language Model to Facilitate COVID-19-Associated Neurological Disorder Studies

W. Tong, Joshua Xu, Leihong Wu, 2022, International journal of environmental research and public health.

Ratio-based quantitative multiomics profiling using universal reference materials empowers data integration

Ruiqiang Li, Leming Shi, W. Tong, 2022, bioRxiv.

Author Correction: The SEQC2 epigenomics quality control (EpiQC) study

Raymond G. Cavalcante, Paweł P. Łabaj, Matthew A. Campbell, 2021, Genome biology.

Quartet RNA reference materials and ratio-based reference datasets for reliable transcriptomic profiling

W. Xiao, Leming Shi, W. Tong, 2022, bioRxiv.

Impact of Sequencing Depth and Library Preparation on Toxicological Interpretation of RNA-Seq Data in a "Three-Sample" Scenario.

W. Tong, B. Ning, Joshua Xu, 2020, Chemical research in toxicology.

Development of benchmark datasets for text mining and sentiment analysis to accelerate regulatory literature review.

W. Tong, Lei Guo, Joshua Xu, 2022, Regulatory toxicology and pharmacology : RTP.

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

W. Xiao, Tieliu Shi, Leming Shi, 2019, Science China Life Sciences.

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

David P. Kreil, C. Mason, Leming Shi, 2014, Scientific Data.

A deep learning model to recognize food contaminating beetle species based on elytra fragments

Cesare Furlanello, Leihong Wu, Zhichao Liu, 2019, Comput. Electron. Agric..

Meta-Analysis of Pulsed-Field Gel Electrophoresis Fingerprints Based on a Constructed Salmonella Database

Wen Zou, Wei-Jiun Lin, Joe Meehan, 2013, PloS one.

Integrating Drug's Mode of Action into Quantitative Structure-Activity Relationships for Improved Prediction of Drug-Induced Liver Injury

Minjun Chen, Leihong Wu, Zhichao Liu, 2017, J. Chem. Inf. Model..

Evaluating the analytical validity of circulating tumor DNA sequencing assays for precision oncology

Paul M. Rindler, Ira W. Deveson, S. Cawley, 2021, Nature Biotechnology.

Gene Regulation Analysis Reveals Perturbations of Autism Spectrum Disorder during Neural System Development

Joshua Xu, Mary Yang, Dan Li, 2021, Genes.

The SEQC2 epigenomics quality control (EpiQC) study

Raymond G. Cavalcante, Paweł P. Łabaj, Matthew A. Campbell, 2021, Genome biology.

Towards accurate and reliable resolution of structural variants for clinical diagnosis

W. Tong, Joshua Xu, F. Sedlazeck, 2022, Genome Biology.

Liquid biopsy and its role in an advanced clinical trial for lung cancer

Erich A. Peterson, Joshua Xu, Mary Yang, 2018, Experimental biology and medicine.

Impact of RNA-seq data analysis algorithms on gene expression estimation and downstream prediction

May D. Wang, Weida Tong, Leming Shi, 2020, Scientific Reports.

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

Weida Tong, Huixiao Hong, Leihong Wu, 2016, Pharmaceutics.

ATP-Binding Cassette Genes Genotype and Expression: A Potential Association with Pancreatic Cancer Development and Chemoresistance?

Joshua Xu, Shiew-Mei Huang, Honggang Wang, 2014, Gastroenterology research and practice.

The FDA’s Experience with Emerging Genomics Technologies—Past, Present, and Future

W. Tong, Joshua Xu, Binsheng Gong, 2016, AAPS Journal.

Using synthetic chromosome controls to evaluate the sequencing of difficult regions within the human genome

Ira W. Deveson, N. Lennon, W. Tong, 2022, Genome biology.

The Sequencing Quality Control 2 study: establishing community standards for sequencing in precision medicine

W. Tong, Joshua Xu, T. Mercer, 2021, Genome biology.

A verified genomic reference sample for assessing performance of cancer panels detecting small variants of low allele frequency

David P. Kreil, Paweł P. Łabaj, Jeff S. Jasper, 2021, Genome biology.

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.

Linking Pharmacogenomic Information on Drug Safety and Efficacy with Ethnic Minority Populations

B. Ning, Joshua Xu, Zhichao Liu, 2020, Pharmaceutics.

Estimating Bacterial Concentrations in Fibrous Substrates Through a Combination of Scanning Electron Microscopy and ImageJ.

Joshua Xu, A. Fong, Sean W. Linder, 2019, Analytical chemistry.

The SEQC2 Epigenomics Quality Control (EpiQC) Study: Comprehensive Characterization of Epigenetic Methods, Reproducibility, and Quantification

Raymond G. Cavalcante, Paweł P. Łabaj, Matthew A. Campbell, 2020, bioRxiv.

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

James J. Chen, Weida Tong, Hong Fang, 2010, BMC Bioinformatics.

Cross-oncopanel study reveals high sensitivity and accuracy with overall analytical performance depending on genomic regions

Paul M. Rindler, David P. Kreil, Paweł P. Łabaj, 2021, Genome biology.

Technical advance in targeted NGS analysis enables identification of lung cancer risk-associated low frequency TP53, PIK3CA, and BRAF mutations in airway epithelial cells

Thomas M. Blomquist, J. Willey, Joshua Xu, 2019, BMC Cancer.

Correcting batch effects in large-scale multiomic studies using a reference-material-based ratio method

Leming Shi, W. Tong, H. Hong, 2022, bioRxiv.

Quantification of cancer driver mutations in human breast and lung DNA using targeted, error‐corrected CarcSeq

Joshua Xu, Binsheng Gong, K. Harris, 2020, Environmental and molecular mutagenesis.

FDA-led consortium studies advance quality control of targeted next generation sequencing assays for precision oncology

W. Tong, B. Ning, Joshua Xu, 2021, Precision cancer medicine.

Draft Genome Sequence of a Methicillin-Resistant Staphylococcus aureus ST1413 Strain for Studying Genetic Mechanisms of Antibiotic Resistance

Joshua Xu, Saeed A. Khan, K. Sung, 2014, Genome Announcements.

Differential gene expression in Staphylococcus aureus exposed to Orange II and Sudan III azo dyes

Joshua Xu, C. Cerniglia, W. Zou, 2015, Journal of Industrial Microbiology & Biotechnology.

DNA Sequence Analysis of Plasmids from Multidrug Resistant Salmonella enterica Serotype Heidelberg Isolates

Joshua Xu, Hailin Tang, D. David, 2012, PloS one.

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

Weida Tong, Hong Fang, Leihong Wu, 2019, BMC Bioinformatics.

Advancing NGS quality control to enable measurement of actionable mutations in circulating tumor DNA

Ira W. Deveson, Thomas M. Blomquist, W. Jones, 2021, Cell reports methods.

Advancing quality-control for NGS measurement of actionable mutations in circulating tumor DNA

T. Richmond, W. Jones, J. Willey, 2021, bioRxiv.

Global transcriptomic analyses of Salmonella enterica in Iron-depleted and Iron-rich growth conditions

Joshua Xu, C. Grim, A. Ottesen, 2019, BMC Genomics.

Assessment of clonal expansion using CarcSeq measurement of lung cancer driver mutations and correlation with mouse strain- and sex-related incidence of spontaneous lung neoplasia.

Joshua Xu, Binsheng Gong, K. Harris, 2021, Toxicological sciences : an official journal of the Society of Toxicology.

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.

FDALabel for drug repurposing studies and beyond

Stephen C. Harris, W. Tong, H. Fang, 2020, Nature Biotechnology.

Species Identification of Food Contaminating Beetles by Recognizing Patterns in Microscopic Images of Elytra Fragments

Weida Tong, Halil Bisgin, Joshua Xu, 2016, PloS one.

Comparing SVM and ANN based Machine Learning Methods for Species Identification of Food Contaminating Beetles

W. Tong, Joshua Xu, Zhichao Liu, 2018, Scientific Reports.

Deep oncopanel sequencing reveals fixation time- and within block position-dependent quality degradation in FFPE processed samples

Thomas M. Blomquist, C. Mason, R. Sebra, 2021, bioRxiv.

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

Stephen C. Harris, W. Tong, H. Fang, 2020, Drug discovery today.

Global transcriptomic analyses of Salmonella enterica in Iron-depleted and Iron-rich growth conditions

Joshua Xu, C. Grim, A. Ottesen, 2019, BMC Genomics.

Two new ArrayTrack libraries for personalized biomedical research

Weida Tong, Huixiao Hong, Hong Fang, 2010, BMC Bioinformatics.

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

Stephen C. Harris, W. Tong, H. Fang, 2019, BMC Bioinformatics.

Classifying Free Texts Into Predefined Sections Using AI in Regulatory Documents: A Case Study with Drug Labeling Documents.

W. Tong, Joshua Xu, Leihong Wu, 2023, Chemical Research in Toxicology.

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

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

A Weakly Supervised Deep Learning Framework for Whole Slide Classification to Facilitate Digital Pathology in Animal Study

W. Tong, Joshua Xu, Nicole Bussola, 2023, Chemical research in toxicology.

Ultra-deep sequencing data from a liquid biopsy proficiency study demonstrating analytic validity

W. Jones, W. Tong, Joshua Xu, 2022, Scientific Data.

Multi-omics data integration using ratio-based quantitative profiling with Quartet reference materials.

W. Tong, H. Hong, Joshua Xu, 2023, Nature biotechnology.

Quartet RNA reference materials improve the quality of transcriptomic data through ratio-based profiling.

W. Tong, J. Thierry-Mieg, H. Hong, 2023, Nature biotechnology.

Correcting batch effects in large-scale multiomics studies using a reference-material-based ratio method

W. Tong, H. Hong, Joshua Xu, 2023, Genome Biology.

An Image Analysis Environment for Species Identification of Food Contaminating Beetles

Weida Tong, Daniel Martin, Leihong Wu, 2016, AAAI.

Impact of Sequencing Depth and Library Preparation on Toxicological Interpretation of RNA-Seq Data in a "Three-Sample" Scenario.

W. Tong, B. Ning, Joshua Xu, 2020, Chemical research in toxicology.

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.

Transcriptomic Response of Human Nosocomial Pathogen Pseudomonas aeruginosa Biofilms Following Continuous Exposure to Antibiotic-Impregnated Catheters

Joshua Xu, Saeed A. Khan, K. Sung, 2022, Data.

Quartet DNA reference materials and datasets for comprehensively evaluating germline variant calling performance

W. Tong, H. Hong, Joshua Xu, 2023, Genome Biology.

Single-cell RNA-sequencing and subcellular spatial transcriptomics facilitate the translation of liver microphysiological systems for regulatory application

W. Tong, Joshua Xu, Binsheng Gong, 2023, Journal of pharmaceutical analysis.

Microarray analysis of virulence gene profiles in Salmonella serovars from food/food animal environment.

Rajesh Nayak, Hong Fang, Joshua Xu, 2011, Journal of infection in developing countries.

Automatic text classification of drug-induced liver injury using document-term matrix and XGBoost

Joshua Xu, S. Thakkar, Yue Wu, 2024, Frontiers in artificial intelligence.

RxBERT: Enhancing drug labeling text mining and analysis with AI language modeling

Joshua Xu, Oanh Dang, Leihong Wu, 2023, Experimental biology and medicine.

Targeted DNA-seq and RNA-seq of Reference Samples with Short-read and Long-read Sequencing

David P. Kreil, Paweł P. Łabaj, Hagen U. Tilgner, 2024, Scientific data.