Tong, Weida

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

MAQC Consortium, Shi, L., Shi, L., Reid, L. H., Jones, W. D., Shippy, R., Warrington, J. A., Baker, S. C., Collins, P. J., de Longueville, F., et al. (2006) · Nature Biotechnology

Gene expression and cancer classificationMolecular Biology Techniques and Applications

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Transparency and reproducibility in artificial intelligence

Haibe-Kains, B., Adam, G. A., Hosny, A., Khodakarami, F., Massive Analysis Quality Control (MAQC) Society Board of Directors, Shraddha, T., Kusko, R., Sansone, S.-A., Tong, W., Wolfinger, R. D., et al. (2020) · Nature

Explainable Artificial Intelligence (XAI)Ethics and Social Impacts of AI

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

Wang, C., Gong, B., Bushel, P. R., Thierry-Mieg, J., Thierry-Mieg, D., Xu, J., Fang, H., Hong, H., Shen, J., Su, Z., et al. (2014) · Nature Biotechnology

Gene expression and cancer classificationGenomics and Phylogenetic Studies

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Toward interoperable bioscience data

Sansone, S.-A., Rocca-Serra, P., Field, D., Maguire, E., Taylor, C., Hofmann, O., Fang, H., Neumann, S., Tong, W., Amaral-Zettler, L., et al. (2012) · Nature Genetics

Research Data Management PracticesScientific Computing and Data Management

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

Chen, M., Vijay, V., Shi, Q., Liu, Z., Fang, H., & Tong, W. (2011) · Drug Discovery Today

Drug-Induced Hepatotoxicity and ProtectionPharmacovigilance and Adverse Drug Reactions

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

Chen, M., Suzuki, A., Thakkar, S., Yu, K., Hu, C., & Tong, W. (2016) · Drug Discovery Today

Drug-Induced Hepatotoxicity and ProtectionComputational Drug Discovery Methods

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

Yu, Y., Fuscoe, J. C., Zhao, C., Guo, C., Jia, M., Qing, T., Bannon, D. I., Lancashire, L., Bao, W., Du, T., et al. (2014) · Nature Communications

Genomics and Phylogenetic StudiesGene expression and cancer classification

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

Zhang, W., Yu, Y., Hertwig, F., Thierry-Mieg, J., Zhang, W., Thierry-Mieg, D., Wang, J., Furlanello, C., Devanarayan, V., Cheng, J., et al. (2015) · Genome Biology

Gene expression and cancer classificationNeuroblastoma Research and Treatments

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

Thakkar, S., Li, T., Liu, Z., Wu, L., Roberts, R., & Tong, W. (2020) · Drug Discovery Today

Drug-Induced Hepatotoxicity and ProtectionComputational Drug Discovery Methods

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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

Hong, H., Branham, W. S., Ng, H. W., Moland, C. L., Dial, S. L., Fang, H., Perkins, R., Sheehan, D., & Tong, W. (2015) · Toxicological Sciences

Effects and risks of endocrine disrupting chemicalsEstrogen and related hormone effects

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

Wu, L., Ingle, T., Liu, Z., Zhao-Wong, A., Harris, S., Thakkar, S., Zhou, G., Yang, J., Xu, J., Mehta, D., et al. (2019) · BMC Bioinformatics

Pharmacovigilance and Adverse Drug ReactionsBiomedical Text Mining and Ontologies

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

Fang, H., Harris, S. C., Liu, Z., Zhou, G., Zhang, G., Xu, J., Rosario, L., Howard, P. C., & Tong, W. (2016) · Drug Discovery Today

Pharmacovigilance and Adverse Drug ReactionsPharmaceutical industry and healthcare

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DICTrank: The largest reference list of 1318 human drugs ranked by risk of drug-induced cardiotoxicity using FDA labeling

Qu, Y., Li, T., Liu, Z., Li, D., & Tong, W. (2023) · Drug Discovery Today

Chemotherapy-induced cardiotoxicity and mitigationPharmacovigilance and Adverse Drug Reactions

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

Hong, H., Branham, W. S., Dial, S. L., Moland, C. L., Fang, H., Shen, J., Perkins, R., Sheehan, D., & Tong, W. (2012) · Chemical Research in Toxicology

Effects and risks of endocrine disrupting chemicalsEstrogen and related hormone effects

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BERT-Based Natural Language Processing of Drug Labeling Documents: A Case Study for Classifying Drug-Induced Liver Injury Risk

Wu, Y., Liu, Z., Wu, L., Chen, M., & Tong, W. (2021) · Frontiers in Artificial Intelligence

Topic ModelingDrug-Induced Hepatotoxicity and Protection

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Generation of a drug-induced renal injury list to facilitate the development of new approach methodologies for nephrotoxicity

Connor, S., Li, T., Qu, Y., Roberts, R. A., & Tong, W. (2024) · Drug Discovery Today

Acute Kidney Injury ResearchAnimal testing and alternatives

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Leveraging FDA Labeling Documents and Large Language Model to Enhance Annotation, Profiling, and Classification of Drug Adverse Events with AskFDALabel

Wu, L., Fang, H., Qu, Y., Xu, J., & Tong, W. (2025) · Drug Safety

Pharmacovigilance and Adverse Drug ReactionsBiomedical Text Mining and Ontologies

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FDALabel for drug repurposing studies and beyond

Fang, H., Harris, S., Liu, Z., Thakkar, S., Yang, J., Ingle, T., Xu, J., Lesko, L., Rosario, L., & Tong, W. (2020) · Nature Biotechnology

Computational Drug Discovery MethodsPharmacovigilance and Adverse Drug Reactions

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A framework enabling LLMs into regulatory environment for transparency and trustworthiness and its application to drug labeling document

Wu, L., Xu, J., Thakkar, S., Gray, M., Qu, Y., Li, D., & Tong, W. (2024) · Regulatory Toxicology and Pharmacology

Topic ModelingArtificial Intelligence in Healthcare and Education

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

Wu, L., Gray, M., Dang, O., Xu, J., Fang, H., & Tong, W. (2023) · Experimental Biology and Medicine

Pharmacovigilance and Adverse Drug ReactionsBiomedical Text Mining and Ontologies

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

Chen, M., Wu, Y., Wingerd, B., Liu, Z., Xu, J., Thakkar, S., Pedersen, T. J., Donnelly, T., Mann, N., Tong, W., et al. (2024) · Frontiers in Artificial Intelligence

Pharmacovigilance and Adverse Drug ReactionsText and Document Classification Technologies

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