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Presence
Current · Arkansas
Last published
2026
Sources
OpenAlex · ORCID
Refreshed
2026-10-06
J
Joshua Xu
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High Impact
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Also affiliated: The University of Sydney (2016); United States Food and Drug Administration (2008–2026); University Health Network (2022–2026); University of Calgary (2026); Duke University (2014); Fudan University (2022); Royal North Shore Hospital (2016); Government of the United States of America (2021); Princess Margaret Cancer Centre (2022–2026); Regenxbio (United States) (2024); University of Michigan–Flint (2016); State Key Laboratory of Genetic Engineering (2022); ICF International (United States) (2010–2012); McMaster University (2021–2022)
30 h-index
197 pubs
4,878 cited
Research Areas
Biomedical Subjects
Links
Biography and Research Information
OverviewAI-generated summary
Joshua Xu's research program investigates the application of high-throughput sequencing technologies and computational methods for gene expression analysis and predictive modeling. His work has focused on evaluating and comparing different platforms, such as microarrays and RNA sequencing, for their utility in clinical endpoint prediction and biomarker discovery.
Xu has been involved in collaborative studies, including the MicroArray Quality Control (MAQC)-II project, which aimed to establish best practices for developing and validating microarray-based predictive models. His research also extends to assessing the analytical validity of sequencing assays for precision oncology and exploring the integration of multi-omics data. He has co-authored numerous publications with key collaborators, including Leihong Wu, Weida Tong, and Binsheng Gong, primarily from the National Center for Toxicological Research, and Donald J. Johann from the University of Arkansas for Medical Sciences.
With a scholarly output reflected in 198 publications and an h-index of 30, Xu is recognized as a highly cited researcher. His work leverages artificial intelligence and machine learning techniques for applications such as species identification in food contaminants, demonstrating a broad interest in computational approaches to biological and toxicological research.
Metrics
- h-index: 30
- Publications: 197
- Citations: 4,878
Selected Publications
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Ensuring multiomics data reproducibility for artificial intelligence with reference materials as a common calibrator (2026)
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Does generative AI mean the “end of history” for pharmacovigilance automation? towards a framework for the future of human-AI systems (2026)
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Augmenting precision medicine via targeted RNA-Seq detection of expressed mutations (2025)
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Federated learning: a privacy-preserving approach to data-centric regulatory cooperation (2025)
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Zika and dengue viruses differentially modulate host mRNA processing factors defining its virulence (2025)
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Biomarkers of Neurotoxicity and Disease (2025)
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Leveraging FDA Labeling Documents and Large Language Model to Enhance Annotation, Profiling, and Classification of Drug Adverse Events with AskFDALabel (2025)
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Developing a Charlson Comorbidity Index for the American Indian Population Using the Epidemiologic Data from the Strong Heart Study (2024)
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Enhancing pharmacogenomic data accessibility and drug safety with large language models: a case study with Llama3.1 (2024)
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Targeted DNA-seq and RNA-seq of Reference Samples with Short-read and Long-read Sequencing (2024)
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Description and Validation of a Novel AI Tool, LabelComp, for the Identification of Adverse Event Changes in FDA Labeling (2024)
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Assessing the performance of large language models in literature screening for pharmacovigilance: a comparative study (2024)
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Automatic text classification of drug-induced liver injury using document-term matrix and XGBoost (2024)
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PERform: assessing model performance with predictivity and explainability readiness formula (2024)
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Towards accurate indel calling for oncopanel sequencing through an international pipeline competition at precisionFDA (2024)
Collaboration Network
Top Collaborators
Weida Tong
National Center for Toxicological Research
55 shared publications
In database
- An investigation of biomarkers derived from legacy microarray data for their utility in the RNA-seq era
- Assessing technical performance in differential gene expression experiments with external spike-in RNA control ratio mixtures
- Comparing SVM and ANN based Machine Learning Methods for Species Identification of Food Contaminating Beetles
- Correcting batch effects in large-scale multiomics studies using a reference-material-based ratio method
- Assessing batch effects of genotype calling algorithm BRLMM for the Affymetrix GeneChip Human Mapping 500 K array set using 270 HapMap samples
Showing 5 of 55 shared publications
Leihong Wu
National Center for Toxicological Research
40 shared publications
In database
- Comparing SVM and ANN based Machine Learning Methods for Species Identification of Food Contaminating Beetles
- Study of serious adverse drug reactions using FDA-approved drug labeling and MedDRA
- Trade-off Predictivity and Explainability for Machine-Learning Powered Predictive Toxicology: An in-Depth Investigation with Tox21 Data Sets
- Comprehensive Assessments of RNA-seq by the SEQC Consortium: FDA-Led Efforts Advance Precision Medicine
- Study of pharmacogenomic information in FDA-approved drug labeling to facilitate application of precision medicine
Showing 5 of 40 shared publications
Binsheng Gong
National Center for Toxicological Research
26 shared publications
In database
- The concordance between RNA-seq and microarray data depends on chemical treatment and transcript abundance
- Evaluating the analytical validity of circulating tumor DNA sequencing assays for precision oncology
- An investigation of biomarkers derived from legacy microarray data for their utility in the RNA-seq era
- A verified genomic reference sample for assessing performance of cancer panels detecting small variants of low allele frequency
- Comprehensive Assessments of RNA-seq by the SEQC Consortium: FDA-Led Efforts Advance Precision Medicine
Showing 5 of 26 shared publications
Hong Fang
National Center for Toxicological Research
17 shared publications
In database
- The concordance between RNA-seq and microarray data depends on chemical treatment and transcript abundance
- An investigation of biomarkers derived from legacy microarray data for their utility in the RNA-seq era
- Assessing batch effects of genotype calling algorithm BRLMM for the Affymetrix GeneChip Human Mapping 500 K array set using 270 HapMap samples
- Study of serious adverse drug reactions using FDA-approved drug labeling and MedDRA
- An FDA bioinformatics tool for microbial genomics research on molecular characterization of bacterial foodborne pathogens using microarrays
Showing 5 of 17 shared publications
Huixiao Hong
National Center for Toxicological Research
13 shared publications
In database
- The concordance between RNA-seq and microarray data depends on chemical treatment and transcript abundance
- Comparison of RNA-seq and microarray-based models for clinical endpoint prediction
- An investigation of biomarkers derived from legacy microarray data for their utility in the RNA-seq era
- Assessing technical performance in differential gene expression experiments with external spike-in RNA control ratio mixtures
- Correcting batch effects in large-scale multiomics studies using a reference-material-based ratio method
Showing 5 of 13 shared publications
Ying Yu
Shanghai Institutes for International Studies (CN)
13 shared publications
- Comparison of RNA-seq and microarray-based models for clinical endpoint prediction
- Correcting batch effects in large-scale multiomics studies using a reference-material-based ratio method
- Multi-omics data integration using ratio-based quantitative profiling with Quartet reference materials
- Quartet RNA reference materials improve the quality of transcriptomic data through ratio-based profiling
- Quartet DNA reference materials and datasets for comprehensively evaluating germline variant calling performance
Showing 5 of 13 shared publications
Wendell Jones
IQVIA (United States) (US)
12 shared publications
- Evaluating the analytical validity of circulating tumor DNA sequencing assays for precision oncology
- A verified genomic reference sample for assessing performance of cancer panels detecting small variants of low allele frequency
- Impact of RNA-seq data analysis algorithms on gene expression estimation and downstream prediction
- Advancing NGS quality control to enable measurement of actionable mutations in circulating tumor DNA
- Targeted DNA-seq and RNA-seq of Reference Samples with Short-read and Long-read Sequencing
Showing 5 of 12 shared publications
Rebecca Kusko
Cell Biotech (South Korea) (KR)
12 shared publications
- Evaluating the analytical validity of circulating tumor DNA sequencing assays for precision oncology
- A verified genomic reference sample for assessing performance of cancer panels detecting small variants of low allele frequency
- Advancing NGS quality control to enable measurement of actionable mutations in circulating tumor DNA
- Deep oncopanel sequencing reveals within block position-dependent quality degradation in FFPE processed samples
- FDA-led consortium studies advance quality control of targeted next generation sequencing assays for precision oncology
Showing 5 of 12 shared publications
Wanwan Hou
Fudan University (CN)
12 shared publications
- Correcting batch effects in large-scale multiomics studies using a reference-material-based ratio method
- Multi-omics data integration using ratio-based quantitative profiling with Quartet reference materials
- Quartet RNA reference materials improve the quality of transcriptomic data through ratio-based profiling
- Quartet DNA reference materials and datasets for comprehensively evaluating germline variant calling performance
- Quartet DNA reference materials and datasets for comprehensively evaluating germline variants calling performance
Showing 5 of 12 shared publications
Jingcheng Yang
Fudan University (CN)
11 shared publications
- Correcting batch effects in large-scale multiomics studies using a reference-material-based ratio method
- Multi-omics data integration using ratio-based quantitative profiling with Quartet reference materials
- Quartet RNA reference materials improve the quality of transcriptomic data through ratio-based profiling
- Quartet DNA reference materials and datasets for comprehensively evaluating germline variant calling performance
- Quartet DNA reference materials and datasets for comprehensively evaluating germline variants calling performance
Showing 5 of 11 shared publications
Luyao Ren
Fudan University (CN)
11 shared publications
- Correcting batch effects in large-scale multiomics studies using a reference-material-based ratio method
- Multi-omics data integration using ratio-based quantitative profiling with Quartet reference materials
- Quartet RNA reference materials improve the quality of transcriptomic data through ratio-based profiling
- Quartet DNA reference materials and datasets for comprehensively evaluating germline variant calling performance
- Quartet DNA reference materials and datasets for comprehensively evaluating germline variants calling performance
Showing 5 of 11 shared publications
James C. Willey
University of Toledo (US)
10 shared publications
- Evaluating the analytical validity of circulating tumor DNA sequencing assays for precision oncology
- Technical advance in targeted NGS analysis enables identification of lung cancer risk-associated low frequency TP53, PIK3CA, and BRAF mutations in airway epithelial cells
- Advancing NGS quality control to enable measurement of actionable mutations in circulating tumor DNA
- Augmenting precision medicine via targeted RNA-Seq detection of expressed mutations
- Abstract 3539: Impact of formalin time on targeted NGS performance in FFPE tissue
Showing 5 of 10 shared publications
Erin L. Crawford
University of Toledo (US)
10 shared publications
- Technical advance in targeted NGS analysis enables identification of lung cancer risk-associated low frequency TP53, PIK3CA, and BRAF mutations in airway epithelial cells
- Advancing NGS quality control to enable measurement of actionable mutations in circulating tumor DNA
- Deep oncopanel sequencing reveals within block position-dependent quality degradation in FFPE processed samples
- Deep oncopanel sequencing reveals fixation time- and within block position-dependent quality degradation in FFPE processed samples
- Abstract 3539: Impact of formalin time on targeted NGS performance in FFPE tissue
Showing 5 of 10 shared publications
Yaqing Liu
Fudan University (CN)
10 shared publications
- Correcting batch effects in large-scale multiomics studies using a reference-material-based ratio method
- Multi-omics data integration using ratio-based quantitative profiling with Quartet reference materials
- Quartet RNA reference materials improve the quality of transcriptomic data through ratio-based profiling
- Quartet DNA reference materials and datasets for comprehensively evaluating germline variant calling performance
- Author Correction: Quartet RNA reference materials improve the quality of transcriptomic data through ratio-based profiling
Showing 5 of 10 shared publications
Zehui Cao
Fudan University (CN)
10 shared publications
- Correcting batch effects in large-scale multiomics studies using a reference-material-based ratio method
- Multi-omics data integration using ratio-based quantitative profiling with Quartet reference materials
- Quartet RNA reference materials improve the quality of transcriptomic data through ratio-based profiling
- Author Correction: Quartet RNA reference materials improve the quality of transcriptomic data through ratio-based profiling
- Quartet RNA reference materials and ratio-based reference datasets for reliable transcriptomic profiling
Showing 5 of 10 shared publications
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