J
Joshua Xu Data-verified
Affiliation confirmed via AI analysis of OpenAlex, ORCID, and web sources.
High Impact
Researcher
faculty
31 h-index
198 pubs
5,923 cited
Research Areas
Links
Biography and Research Information
OverviewAI-generated summary
Joshua Xu's research focuses on the development and application of high-throughput sequencing and multi-omics data integration for toxicological assessment and precision medicine. His work investigates methods to improve the accuracy and reliability of genomic analyses, particularly in the context of clinical diagnosis and predictive toxicology. This includes developing and validating reference materials and ratio-based quantitative profiling techniques to correct for batch effects and enhance the quality of transcriptomic and epigenomic data.
Dr. Xu has published extensively on topics related to evaluating analytical validity of DNA sequencing assays, resolving structural variants, and integrating multi-omics data. His research also explores the trade-offs between predictivity and explainability in machine learning models used for predictive toxicology, with applications to large-scale data sets. He collaborates with researchers at the National Center for Toxicological Research and the University of Arkansas for Medical Sciences, contributing to a network focused on advancing toxicological research and its applications in human health.
With an h-index of 31 and nearly 200 publications, Dr. Xu is recognized as a highly cited researcher. His work directly supports the goals of regulatory agencies like the U.S. Food and Drug Administration by providing robust methodologies for assessing the performance of genomic assays and for understanding the complex interactions of environmental factors and biological systems.
Metrics
- h-index: 31
- Publications: 198
- Citations: 5,923
Selected Publications
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Federated learning: a privacy-preserving approach to data-centric regulatory cooperation (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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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)
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A framework enabling LLMs into regulatory environment for transparency and trustworthiness and its application to drug labeling document (2024)
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Extend the benchmarking indel set by manual review using the individual cell line sequencing data from the Sequencing Quality Control 2 (SEQC2) project (2024)
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RxBERT: Enhancing drug labeling text mining and analysis with AI language modeling (2023)
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Measurement and Mitigation of Bias in Artificial Intelligence: A Narrative Literature Review for Regulatory Science (2023)
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Quartet DNA reference materials and datasets for comprehensively evaluating germline variant calling performance (2023)
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Author Correction: Quartet RNA reference materials improve the quality of transcriptomic data through ratio-based profiling (2023)
Collaboration Network
Top Collaborators
Weida Tong
United States Food and Drug Administration (US)
27 shared publications
- Towards accurate and reliable resolution of structural variants for clinical diagnosis
- Correcting batch effects in large-scale multiomics studies using a reference-material-based ratio method
- Trade-off Predictivity and Explainability for Machine-Learning Powered Predictive Toxicology: An in-Depth Investigation with Tox21 Data Sets
- Quartet DNA reference materials and datasets for comprehensively evaluating germline variant calling performance
- Measurement and Mitigation of Bias in Artificial Intelligence: A Narrative Literature Review for Regulatory Science
Showing 5 of 27 shared publications
Leihong Wu
National Center for Toxicological Research
15 shared publications
In database
- Trade-off Predictivity and Explainability for Machine-Learning Powered Predictive Toxicology: An in-Depth Investigation with Tox21 Data Sets
- Measurement and Mitigation of Bias in Artificial Intelligence: A Narrative Literature Review for Regulatory Science
- Advancing NGS quality control to enable measurement of actionable mutations in circulating tumor DNA
- A Weakly Supervised Deep Learning Framework for Whole Slide Classification to Facilitate Digital Pathology in Animal Study
- RxBERT: Enhancing drug labeling text mining and analysis with AI language modeling
Showing 5 of 15 shared publications
Binsheng Gong
National Center for Toxicological Research
11 shared publications
In database
- 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
- Deep oncopanel sequencing reveals within block position-dependent quality degradation in FFPE processed samples
- CarcSeq Measurement of Rat Mammary Cancer Driver Mutations and Relation to Spontaneous Mammary Neoplasia
- Ultra-deep sequencing data from a liquid biopsy proficiency study demonstrating analytic validity
Showing 5 of 11 shared publications
Wanwan Hou
Fudan University (CN)
10 shared publications
- Multi-omics data integration using ratio-based quantitative profiling with Quartet reference materials
- Correcting batch effects in large-scale multiomics studies using a reference-material-based ratio method
- 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 10 shared publications
Rebecca Kusko
9 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 9 shared publications
Ying Yu
State Key Laboratory of Genetic Engineering
9 shared publications
- Multi-omics data integration using ratio-based quantitative profiling with Quartet reference materials
- Correcting batch effects in large-scale multiomics studies using a reference-material-based ratio method
- 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 9 shared publications
Jingcheng Yang
Fudan University (CN)
9 shared publications
- Multi-omics data integration using ratio-based quantitative profiling with Quartet reference materials
- Correcting batch effects in large-scale multiomics studies using a reference-material-based ratio method
- 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 9 shared publications
Luyao Ren
Fudan University (CN)
9 shared publications
- Multi-omics data integration using ratio-based quantitative profiling with Quartet reference materials
- Correcting batch effects in large-scale multiomics studies using a reference-material-based ratio method
- 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 9 shared publications
Yaqing Liu
Fudan University (CN)
8 shared publications
- Multi-omics data integration using ratio-based quantitative profiling with Quartet reference materials
- Correcting batch effects in large-scale multiomics studies using a reference-material-based ratio method
- 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 8 shared publications
Zehui Cao
State Key Laboratory of Genetic Engineering
8 shared publications
- Multi-omics data integration using ratio-based quantitative profiling with Quartet reference materials
- Correcting batch effects in large-scale multiomics studies using a reference-material-based ratio method
- 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 8 shared publications
Wendell Jones
7 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
- Ultra-deep sequencing data from a liquid biopsy proficiency study demonstrating analytic validity
- Targeted DNA-seq and RNA-seq of Reference Samples with Short-read and Long-read Sequencing
Showing 5 of 7 shared publications
Tim R. Mercer
The University of Queensland (AU)
7 shared publications
- Towards accurate and reliable resolution of structural variants for clinical diagnosis
- The Sequencing Quality Control 2 study: establishing community standards for sequencing in precision medicine
- Advancing NGS quality control to enable measurement of actionable mutations in circulating tumor DNA
- Ultra-deep sequencing data from a liquid biopsy proficiency study demonstrating analytic validity
- Using synthetic chromosome controls to evaluate the sequencing of difficult regions within the human genome
Showing 5 of 7 shared publications
Lianhua Dong
National Institute of Metrology (CN)
7 shared publications
- Multi-omics data integration using ratio-based quantitative profiling with Quartet reference materials
- Correcting batch effects in large-scale multiomics studies using a reference-material-based ratio method
- 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 7 shared publications
Naixin Zhang
Fudan University (CN)
7 shared publications
- Correcting batch effects in large-scale multiomics studies using a reference-material-based ratio method
- 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
- Author Correction: Quartet RNA reference materials improve the quality of transcriptomic data through ratio-based profiling
Showing 5 of 7 shared publications
Qingwang Chen
Fudan University (CN)
6 shared publications
- Correcting batch effects in large-scale multiomics studies using a reference-material-based ratio method
- 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
- Correcting batch effects in large-scale multiomic studies using a reference-material-based ratio method
Showing 5 of 6 shared publications
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