Author details

Full Name

Joshua Xu

Affiliation

ORCID

Career Start Year

2008

Papers

H Index

Expertise

CM4AI Collaborator

PMID	Paper Title	Journal Title	Published Year
37487037	Classifying Free Texts Into Predefined Sections Using AI in Regulatory Documents: A Case Study with Drug Labeling Documents.	Chem Res Toxicol	2023
36372266	Development of benchmark datasets for text mining and sentiment analysis to accelerate regulatory literature review.	Regul Toxicol Pharmacol	2023
37679543	Multi-omics data integration using ratio-based quantitative profiling with Quartet reference materials.	Nat Biotechnol	2023
37679545	Quartet RNA reference materials improve the quality of transcriptomic data through ratio-based profiling.	Nat Biotechnol	2023
37674217	Correcting batch effects in large-scale multiomics studies using a reference-material-based ratio method.	Genome Biol	2023
38018360	Measurement and Mitigation of Bias in Artificial Intelligence: A Narrative Literature Review for Regulatory Science.		2023
38012772	Quartet DNA reference materials and datasets for comprehensively evaluating germline variant calling performance.	Genome Biol	2023
37577388	Single-cell RNA-sequencing and subcellular spatial transcriptomics facilitate the translation of liver microphysiological systems for regulatory application.	J Pharm Anal	2023
37783850	Author Correction: Quartet RNA reference materials improve the quality of transcriptomic data through ratio-based profiling.	Nat Biotechnol	2023
38062992	Assessments of tumor mutational burden estimation by targeted panel sequencing: A comprehensive simulation analysis.	Exp Biol Med (Maywood)	2023
37540590	A Weakly Supervised Deep Learning Framework for Whole Slide Classification to Facilitate Digital Pathology in Animal Study.	Chem Res Toxicol	2023
35241127	Towards accurate and reliable resolution of structural variants for clinical diagnosis.	Genome Biol	2022
35768876	Deep oncopanel sequencing reveals within block position-dependent quality degradation in FFPE processed samples.	Genome Biol	2022
36034596	Accurate species identification of food-contaminating beetles with quality-improved elytral images and deep learning.	Front Artif Intell	2022
36011614	NeuroCORD: A Language Model to Facilitate COVID-19-Associated Neurological Disorder Studies.	Int J Environ Res Public Health	2022
35680918	Ultra-deep multi-oncopanel sequencing of benchmarking samples with a wide range of variant allele frequencies.	Sci Data	2022
35418127	Ultra-deep sequencing data from a liquid biopsy proficiency study demonstrating analytic validity.	Sci Data	2022
36127716	Author Correction: Towards accurate and reliable resolution of structural variants for clinical diagnosis.	Genome Biol	2022
35022065	Using synthetic chromosome controls to evaluate the sequencing of difficult regions within the human genome.	Genome Biol	2022
34935280	A targeted simulation-extrapolation method for evaluating biomarkers based on new technologies in precision medicine.	Pharmaceutical Statistics	2022
34749795	The Sequencing Quality Control 2 study: establishing community standards for sequencing in precision medicine.	Genome Biol	2021
35475002	Advancing NGS quality control to enable measurement of actionable mutations in circulating tumor DNA.	Cell Rep Methods	2021
33846644	Evaluating the analytical validity of circulating tumor DNA sequencing assays for precision oncology.	Nat Biotechnol	2021
33846381	Optimized imaging methods for species-level identification of food-contaminating beetles.	Sci Rep	2021
33513003	Trade-off Predictivity and Explainability for Machine-Learning Powered Predictive Toxicology: An in-Depth Investigation with Tox21 Data Sets.	Chem Res Toxicol	2021
33822199	CarcSeq Measurement of Rat Mammary Cancer Driver Mutations and Relation to Spontaneous Mammary Neoplasia.	Toxicological Sciences	2021
33863366	A verified genomic reference sample for assessing performance of cancer panels detecting small variants of low allele frequency.	Genome Biol	2021
33863344	Cross-oncopanel study reveals high sensitivity and accuracy with overall analytical performance depending on genomic regions.	Genome Biol	2021
33354967	Impact of Sequencing Depth and Library Preparation on Toxicological Interpretation of RNA-Seq Data in a "Three-Sample" Scenario.	Chem Res Toxicol	2021
32692164	Landscape of circRNAs Across 11 Organs and 4 Ages in Fischer 344 Rats.	Chem Res Toxicol	2021
35282311	FDA-led consortium studies advance quality control of targeted next generation sequencing assays for precision oncology.	Precis Cancer Med	2021
34949218	Author Correction: The SEQC2 epigenomics quality control (EpiQC) study.	Genome Biol	2021
34373914	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.	Toxicological Sciences	2021
34946850	Gene Regulation Analysis Reveals Perturbations of Autism Spectrum Disorder during Neural System Development.	Genes	2021
34872606	The SEQC2 epigenomics quality control (EpiQC) study.	Genome Biol	2021
32940377	Quantification of cancer driver mutations in human breast and lung DNA using targeted, error-corrected CarcSeq.	Environ Mol Mutagen	2020
32293428	DLI-IT: a deep learning approach to drug label identification through image and text embedding.	BMC Med Inform Decis Mak	2020
32032705	Study of pharmacogenomic information in FDA-approved drug labeling to facilitate application of precision medicine.	Drug Discov Today	2020
33235392	FDALabel for drug repurposing studies and beyond.	Nat Biotechnol	2020
33113799	Linking Pharmacogenomic Information on Drug Safety and Efficacy with Ethnic Minority Populations.	Pharmaceutics	2020
31195964	Global transcriptomic analyses of Salmonella enterica in Iron-depleted and Iron-rich growth conditions.	BMC Genomics	2019
31711466	Technical advance in targeted NGS analysis enables identification of lung cancer risk-associated low frequency TP53, PIK3CA, and BRAF mutations in airway epithelial cells.	BMC Cancer	2019
30871458	Study of serious adverse drug reactions using FDA-approved drug labeling and MedDRA.	BMC Bioinformatics	2019
31114935	Sequencing XMET genes to promote genotype-guided risk assessment and precision medicine.	Sci China Life Sci	2019
31395005	HetEnc: a deep learning predictive model for multi-type biological dataset.	BMC Genomics	2019
30835114	Estimating Bacterial Concentrations in Fibrous Substrates Through a Combination of Scanning Electron Microscopy and ImageJ.	Analytical Chemistry	2019
29695741	Comparing SVM and ANN based Machine Learning Methods for Species Identification of Food Contaminating Beetles.	Sci Rep	2018
29951521	Advancing Genomics for Drug Development and Safety Evaluation.	International Journal of Genomics	2018
28350954	Integrating Drug's Mode of Action into Quantitative Structure-Activity Relationships for Improved Prediction of Drug-Induced Liver Injury.	J Chem Inf Model	2017
27603930	Correction: Species Identification of Food Contaminating Beetles by Recognizing Patterns in Microscopic Images of Elytra Fragments.	PLoS One	2016