Weida Tong

74 papers A* 1Journal 66Unranked 6
YearRankTypeTitle / Venue / Authors
2025 J jnl
Is regulatory science ready for artificial intelligence?
npj Digit. Medicine
Thomas Hartung, Maurice P. Whelan, Weida Tong, Robert M. Califf
2024 J jnl
Automatic text classification of drug-induced liver injury using document-term matrix and XGBoost.
Frontiers Artif. Intell.
Minjun Chen, Yue Wu, Byron Wingerd, Zhichao Liu, Joshua Xu, Shraddha Thakkar, Thomas J. Pedersen, Tom Donnelly, Nicholas Mann, Weida Tong, Russell D. Wolfinger, Wenjun Bao
2024 J jnl
Bridging organ transcriptomics for advancing multiple organ toxicity assessment with a generative AI approach.
npj Digit. Medicine
Ting Li, Xi Chen, Weida Tong
2023 J jnl
PLM-ARG: antibiotic resistance gene identification using a pretrained protein language model.
Bioinform.
Jun Wu, Jian Ouyang, Haipeng Qing, Jiajia Zhou, Ruth Roberts, Rania Siam, Lan Wang, Weida Tong, Zhichao Liu, Tieliu Shi
2023 J jnl
RxNorm for drug name normalization: a case study of prescription opioids in the FDA adverse events reporting system.
Frontiers Bioinform.
Huyen Le, Ru Chen, Stephen C. Harris, Hong Fang, Beverly Lyn-Cook, Huixiao Hong, Weigong Ge, Paul Rogers, Weida Tong, Wen Zou
2022 J jnl
Accurate species identification of food-contaminating beetles with quality-improved elytral images and deep learning.
Frontiers Artif. Intell.
Halil Bisgin, Tanmay Bera, Leihong Wu, Hongjian Ding, Neslihan Bisgin, Zhichao Liu, Monica Pava-Ripoll, Amy Barnes, James F. Campbell, Himansi Vyas, Cesare Furlanello, Weida Tong, Joshua Xu
2022 J jnl
Adaptability of AI for safety evaluation in regulatory science: A case study of drug-induced liver injury.
Frontiers Artif. Intell.
Skylar Connor, Ting Li, Ruth Roberts, Shraddha Thakkar, Zhichao Liu, Weida Tong
2022 J jnl
Best practice and reproducible science are required to advance artificial intelligence in real-world applications.
Briefings Bioinform.
Zhichao Liu, Ting Li, Skylar Connor, Shraddha Thakkar, Ruth Roberts, Weida Tong
2022 J jnl
Corrigendum: DeepCarc: Deep learning-powered carcinogenicity prediction using model-level representation.
Frontiers Artif. Intell.
Ting Li, Weida Tong, Ruth Roberts, Zhichao Liu, Shraddha Thakkar
2022 J jnl
DeepCausality: A general AI-powered causal inference framework for free text: A case study of LiverTox.
Frontiers Artif. Intell.
Xingqiao Wang, Xiaowei Xu, Weida Tong, Qi Liu, Zhichao Liu
2021 J jnl
BERT-Based Natural Language Processing of Drug Labeling Documents: A Case Study for Classifying Drug-Induced Liver Injury Risk.
Frontiers Artif. Intell.
Yue Wu, Zhichao Liu, Leihong Wu, Minjun Chen, Weida Tong
2021 J jnl
DICE: A Drug Indication Classification and Encyclopedia for AI-Based Indication Extraction.
Frontiers Artif. Intell.
Arjun Bhatt, Ruth Roberts, Xi Chen, Ting Li, Skylar Connor, Qais Hatim, Mike Mikailov, Weida Tong, Zhichao Liu
2021 J jnl
DeepCarc: Deep Learning-Powered Carcinogenicity Prediction Using Model-Level Representation.
Frontiers Artif. Intell.
Ting Li, Weida Tong, Ruth Roberts, Zhichao Liu, Shraddha Thakkar
2021 — conf
Discovering Drug-Drug Associations in the FDA Adverse Event Reporting System Database with Data Mining Approaches.
BIBM
Weizhong Zhao, Huyen Le, James J. Chen, Hesha J. Duggirala, Richard Forshee, Taxiarchis Botsis, Henry Francis, Huixiao Hong, Weida Tong, Yi-Ting Hwang, Wen Zou
2021 J jnl
InferBERT: A Transformer-Based Causal Inference Framework for Enhancing Pharmacovigilance.
Frontiers Artif. Intell.
Xingqiao Wang, Xiaowei Xu, Weida Tong, Ruth Roberts, Zhichao Liu
2021 — conf
Text Fingerprinting and Topic Mining in the Prescription Opioid Use Literature.
BIBM
Huyen Le, Junxiu Zhou, Weizhong Zhao, Roger Perkins, Weigong Ge, Beverly Lyn-Cook, Henry Francis, Huixiao Hong, Weida Tong, Wen Zou
2020 J jnl
DLI-IT: a deep learning approach to drug label identification through image and text embedding.
BMC Medical Informatics Decis. Mak.
Xiangwen Liu, Joe Meehan, Weida Tong, Leihong Wu, Xiaowei Xu, Joshua Xu
2020 J jnl
The need for standardisation in life science research - an approach to excellence and trust.
F1000Research
Susanne Hollmann, Andreas Kremer, Spela Baebler, Christophe Trefois, Kristina Gruden, Witold R. Rudnicki, Weida Tong, Aleksandra Gruca, Erik Bongcam-Rudloff, Chris T. A. Evelo, Alina S. Nechyporenko, Marcus Frohme, David Safránek, Babette Regierer, Domenica D'Elia
2019 J jnl
A deep learning model to recognize food contaminating beetle species based on elytra fragments.
Comput. Electron. Agric.
Leihong Wu, Zhichao Liu, Tanmay Bera, Hongjian Ding, Darryl Langley, Amy Barnes, Cesare Furlanello, Valerio Maggio, Weida Tong, Joshua Xu
2019 J jnl
Correction to: Similarities and differences between variants called with human reference genome HG19 or HG38.
BMC Bioinform.
Bohu Pan, Rebecca Kusko, Wenming Xiao, Yuanting Zheng, Zhichao Liu, Chunlin Xiao, Sugunadevi Sakkiah, Wenjing Guo, Ping Gong, Chaoyang Zhang, Weigong Ge, Leming Shi, Weida Tong, Huixiao Hong
2019 J jnl
Similarities and differences between variants called with human reference genome HG19 or HG38.
BMC Bioinform.
Bohu Pan, Rebecca Kusko, Wenming Xiao, Yuanting Zheng, Zhichao Liu, Chunlin Xiao, Sugunadevi Sakkiah, Wenjing Guo, Ping Gong, Chaoyang Zhang, Weigong Ge, Leming Shi, Weida Tong, Huixiao Hong
2019 J jnl
Study of serious adverse drug reactions using FDA-approved drug labeling and MedDRA.
BMC Bioinform.
Leihong Wu, Taylor Ingle, Zhichao Liu, Anna Zhao-Wong, Stephen C. Harris, Shraddha Thakkar, Guangxu Zhou, Junshuang Yang, Joshua Xu, Darshan Mehta, Weigong Ge, Weida Tong, Hong Fang
2017 — conf
Comprehensive analysis of pulmonary adenocarcinoma in situ (AIS) revealed new insights into lung cancer progression.
BIBM
Dan Li, William Yang, Yifan Zhang, Jack Y. Yang, Weida Tong, Renchu Guan, Mary Qu Yang
2017 J jnl
Integrating Drug's Mode of Action into Quantitative Structure-Activity Relationships for Improved Prediction of Drug-Induced Liver Injury.
J. Chem. Inf. Model.
Leihong Wu, Zhichao Liu, Scott M. Auerbach, Ruili Huang, Minjun Chen, Kristin McEuen, Joshua Xu, Hong Fang, Weida Tong
2017 — conf
Protein-Protein Interaction Extraction Using Attention-Based Convolution Neural Networks.
BCB
Hao Zhang, Mary Qu Yang, Xiaoyue Feng, William Yang, Weida Tong, Renchu Guan
2017 J jnl
Scaling bioinformatics applications on HPC.
BMC Bioinform.
Mike Mikailov, Fu-Jyh Luo, Stuart Barkley, Lohit Valleru, Stephen Whitney, Zhichao Liu, Shraddha Thakkar, Weida Tong, Nicholas Petrick
2017 — conf
Toward precision breast cancer survival prediction utilizing combined whole genome-wide expression and somatic mutation analysis.
BIBM
Yifan Zhang, William Yang, Dan Li, Jack Y. Yang, Renchu Guan, Weida Tong, Mary Qu Yang
2016 J jnl
A novel procedure on next generation sequencing data analysis using text mining algorithm.
BMC Bioinform.
Weizhong Zhao, James J. Chen, Roger Perkins, Yuping Wang, Zhichao Liu, Huixiao Hong, Weida Tong, Wen Zou
2016 A* conf
An Image Analysis Environment for Species Identification of Food Contaminating Beetles.
AAAI
Daniel Martin, Hongjian Ding, Leihong Wu, Howard Semey, Amy Barnes, Darryl Langley, Su Inn Park, Zhichao Liu, Weida Tong, Joshua Xu
2016 J jnl
Application of dynamic topic models to toxicogenomics data.
BMC Bioinform.
Mikyung Lee, Zhichao Liu, Ruili Huang, Weida Tong
2016 J jnl
Erratum to: A novel procedure on next generation sequencing data analysis using text mining algorithm.
BMC Bioinform.
Weizhong Zhao, James J. Chen, Roger Perkins, Yuping Wang, Zhichao Liu, Huixiao Hong, Weida Tong, Wen Zou
2015 J jnl
Understanding and predicting binding between human leukocyte antigens (HLAs) and peptides by network analysis.
BMC Bioinform.
Heng Luo, Hao Ye, Hui Wen Ng, Leming Shi, Weida Tong, William Mattes, Donna Mendrick, Huixiao Hong
2014 J jnl
A phenome-guided drug repositioning through a latent variable model.
BMC Bioinform.
Halil Bisgin, Zhichao Liu, Hong Fang, Reagan J. Kelly, Xiaowei Xu, Weida Tong
2014 J jnl
Advances in translational bioinformatics facilitate revealing the landscape of complex disease mechanisms.
BMC Bioinform.
Jack Y. Yang, A. Keith Dunker, Jun S. Liu, Xiang Qin, Hamid R. Arabnia, William Yang, Andrzej Niemierko, Zhongxue Chen, Zuojie Luo, Liangjiang Wang, Yunlong Liu, Dong Xu, Youping Deng, Weida Tong, Mary Qu Yang
2014 J jnl
Competitive molecular docking approach for predicting estrogen receptor subtype α agonists and antagonists.
BMC Bioinform.
Hui Wen Ng, Wenqian Zhang, Mao Shu, Heng Luo, Weigong Ge, Roger Perkins, Weida Tong, Huixiao Hong
2014 J jnl
Identification of genes and pathways involved in kidney renal clear cell carcinoma.
BMC Bioinform.
William Yang, Kenji Yoshigoe, Xiang Qin, Jun S. Liu, Jack Y. Yang, Andrzej Niemierko, Youping Deng, Yunlong Liu, A. Keith Dunker, Zhongxue Chen, Liangjiang Wang, Dong Xu, Hamid R. Arabnia, Weida Tong, Mary Qu Yang
2014 J jnl
Mining hidden knowledge for drug safety assessment: topic modeling of LiverTox as a case study.
BMC Bioinform.
Ke Yu, Jie Zhang, Minjun Chen, Xiaowei Xu, Ayako Suzuki, Katarina Ilic, Weida Tong
2014 J jnl
Of text and gene - using text mining methods to uncover hidden knowledge in toxicogenomics.
BMC Syst. Biol.
Mikyung Lee, Zhichao Liu, Reagan J. Kelly, Weida Tong
2014 J jnl
Whole genome sequencing of 35 individuals provides insights into the genetic architecture of Korean population.
BMC Bioinform.
Wenqian Zhang, Joe Meehan, Zhenqiang Su, Hui Wen Ng, Mao Shu, Heng Luo, Weigong Ge, Roger Perkins, Weida Tong, Huixiao Hong
2013 J jnl
A systems approach for analysis of high content screening assay data with topic modeling.
BMC Bioinform.
Halil Bisgin, Minjun Chen, Yuping Wang, Reagan J. Kelly, Hong Fang, Xiaowei Xu, Weida Tong
2013 J jnl
Estimating relative noise to signal in DNA microarray data.
Int. J. Bioinform. Res. Appl.
Huixiao Hong, Qilong Hong, Jie Liu, Weida Tong, Leming Shi
2013 J jnl
Homology modeling, molecular docking, and molecular dynamics simulations elucidated α-fetoprotein binding modes.
BMC Bioinform.
Jie Shen, Wenqian Zhang, Hong Fang, Roger Perkins, Weida Tong, Huixiao Hong
2012 J jnl
Investigating drug repositioning opportunities in FDA drug labels through topic modeling.
BMC Bioinform.
Halil Bisgin, Zhichao Liu, Reagan J. Kelly, Hong Fang, Xiaowei Xu, Weida Tong
2011 J jnl
Constructing a robust protein-protein interaction network by integrating multiple public databases.
BMC Bioinform.
Venkata Swamy Martha, Zhichao Liu, Li Guo, Zhenqiang Su, Yanbin Ye, Hong Fang, Don Ding, Weida Tong, Xiaowei Xu
2011 J jnl
Mining FDA drug labels using an unsupervised learning technique - topic modeling.
BMC Bioinform.
Halil Bisgin, Zhichao Liu, Hong Fang, Xiaowei Xu, Weida Tong
2011 J jnl
Selecting a single model or combining multiple models for microarray-based classifier development? - A comparative analysis based on large and diverse datasets generated from the MAQC-II project.
BMC Bioinform.
Minjun Chen, Leming M. Shi, Reagan J. Kelly, Roger Perkins, Hong Fang, Weida Tong
2011 — ch.
The MicroArray Quality Control (MAQC) Project and Cross-Platform Analysis of Microarray Data.
Handbook of Statistical Bioinformatics
Zhining Wen, Zhenqiang Su, Jie Liu, Baitang Ning, Lei Guo, Weida Tong, Leming M. Shi
2011 J jnl
Translating Clinical Findings into Knowledge in Drug Safety Evaluation - Drug Induced Liver Injury Prediction System (DILIps).
PLoS Comput. Biol.
Zhichao Liu, Qiang Shi, Don Ding, Reagan J. Kelly, Hong Fang, Weida Tong
2010 J jnl
An FDA bioinformatics tool for microbial genomics research on molecular characterization of bacterial foodborne pathogens using microarrays.
BMC Bioinform.
Hong Fang, Joshua Xu, Don Ding, Scott A. Jackson, Isha R. Patel, Jonathan G. Frye, Wen Zou, Rajesh Nayak, Steven L. Foley, James J. Chen, Zhenqiang Su, Yanbin Ye, Steve Turner, Steve Harris, Guangxu Zhou, Carl Cerniglia, Weida Tong
2010 J jnl
Evaluation of gene expression data generated from expired Affymetrix GeneChip
BMC Bioinform.
Zhining Wen, Charles Wang, Quan Shi, Ying Huang, Zhenqiang Su, Huixiao Hong, Weida Tong, Leming Shi
2010 J jnl
ISA software suite: supporting standards-compliant experimental annotation and enabling curation at the community level.
Bioinform.
Philippe Rocca-Serra, Marco Brandizi, Eamonn Maguire, Nataliya Sklyar, Chris F. Taylor, Kimberly Begley, Dawn Field, Stephen C. Harris, Winston Hide, Oliver Hofmann, Steffen Neumann, Peter Sterk, Weida Tong, Susanna-Assunta Sansone
2010 J jnl
The EDKB: an established knowledge base for endocrine disrupting chemicals.
BMC Bioinform.
Don Ding, Lei Xu, Hong Fang, Huixiao Hong, Roger Perkins, Steve Harris, Edward D. Bearden, Leming Shi, Weida Tong
2010 J jnl
Two new ArrayTrack libraries for personalized biomedical research.
BMC Bioinform.
Joshua Xu, Carolyn Wise, Vijayalakshmi Varma, Hong Fang, Baitang Ning, Huixiao Hong, Weida Tong, Jim Kaput
2009 — conf
Accurate Prediction and Recognition of Subfamilies of G Protein-Coupled Receptors from Amino Acid Sequences.
BIOCOMP
Huixiao Hong, Qilong Hong, Weida Tong
2009 J jnl
The Accurate Prediction of Protein Family from Amino Acid Sequence by Measuring Features of Sequence Fragments.
J. Comput. Biol.
Huixiao Hong, Qilong Hong, Roger Perkins, Leming M. Shi, Hong Fang, Zhenqiang Su, Yvonne P. Dragan, James C. Fuscoe, Weida Tong
2008 J jnl
Assessing batch effects of genotype calling algorithm BRLMM for the Affymetrix GeneChip Human Mapping 500 K array set using 270 HapMap samples.
BMC Bioinform.
Huixiao Hong, Zhenqiang Su, Weigong Ge, Leming M. Shi, Roger Perkins, Hong Fang, Joshua Xu, James J. Chen, Tao Han, Jim Kaput, James C. Fuscoe, Weida Tong
2008 J jnl
Mold
J. Chem. Inf. Model.
Huixiao Hong, Qian Xie, Weigong Ge, Feng Qian, Hong Fang, Leming Shi, Zhenqiang Su, Roger Perkins, Weida Tong
2008 J jnl
Very Important Pool (VIP) genes - an application for microarray-based molecular signatures.
BMC Bioinform.
Zhenqiang Su, Huixiao Hong, Hong Fang, Leming M. Shi, Roger Perkins, Weida Tong
2007 J jnl
Consensus analysis of multiple classifiers using non-repetitive variables: Diagnostic application to microarray gene expression data.
Comput. Biol. Chem.
Zhenqiang Su, Huixiao Hong, Roger Perkins, Xueguang Shao, Wensheng Cai, Weida Tong
2006 J jnl
Differential gene expression in mouse primary hepatocytes exposed to the peroxisome proliferator-activated receptor alpha agonists.
BMC Bioinform.
Lei Guo, Hong Fang, Jim Collins, Xiao-hui Fan, Stacey L. Dial, Alex Wong, Kshama Mehta, Ernice Blann, Leming M. Shi, Weida Tong, Yvonne P. Dragan
2006 J jnl
GOFFA: Gene Ontology For Functional Analysis - A FDA Gene Ontology Tool for Analysis of Genomic and Proteomic Data.
BMC Bioinform.
Hongmei Sun, Hong Fang, Tao Chen, Roger Perkins, Weida Tong
2006 J jnl
Integrating time-course microarray gene expression profiles with cytotoxicity for identification of biomarkers in primary rat hepatocytes exposed to cadmium.
Bioinform.
Yongxi Tan, Leming M. Shi, Saber M. Hussain, Jun Xu, Weida Tong, John M. Frazier, Charles Wang
2006 J jnl
Microarray analysis distinguishes differential gene expression patterns from large and small colony
BMC Bioinform.
Tao Han, Jianyong Wang, Weida Tong, Martha M. Moore, James C. Fuscoe, Tao Chen
2005 J jnl
Bioinformatics approaches for cross-species liver cancer analysis based on microarray gene expression profiling.
BMC Bioinform.
Hong Fang, Weida Tong, Roger Perkins, Leming M. Shi, Huixiao Hong, X. Cao, Qian Xie, S. H. Yim, J. M. Ward, Henry C. Pitot, Yvonne P. Dragan
2005 J jnl
Cross-platform comparability of microarray technology: Intra-platform consistency and appropriate data analysis procedures are essential.
BMC Bioinform.
Leming M. Shi, Weida Tong, Hong Fang, Uwe Scherf, Jing Han, Raj K. Puri, Felix W. Frueh, Federico M. Goodsaid, Lei Guo, Zhenqiang Su, Tao Han, James C. Fuscoe, Z. Alex Xu, Tucker A. Patterson, Huixiao Hong, Qian Xie, Roger Perkins, James J. Chen, Daniel A. Casciano
2005 J jnl
Decision Forest Analysis of 61 Single Nucleotide Polymorphisms in a Case-Control Study of Esophageal Cancer; a novel method.
BMC Bioinform.
Qian Xie, Luke D. Ratnasinghe, Huixiao Hong, Roger Perkins, Ze-Zhong Tang, Nan Hu, Philip R. Taylor, Weida Tong
2005 J jnl
Microarray scanner calibration curves: characteristics and implications.
BMC Bioinform.
Leming M. Shi, Weida Tong, Zhenqiang Su, Tao Han, Jing Han, Raj K. Puri, Hong Fang, Felix W. Frueh, Federico M. Goodsaid, Lei Guo, William S. Branham, James J. Chen, Z. Alex Xu, Stephen C. Harris, Huixiao Hong, Qian Xie, Roger Perkins, James C. Fuscoe
2005 J jnl
Quality control and quality assessment of data from surface-enhanced laser desorption/ionization (SELDI) time-of flight (TOF) mass spectrometry (MS).
BMC Bioinform.
Huixiao Hong, Yvonne P. Dragan, Joshua Epstein, Candee Teitel, Bangzheng Chen, Qian Xie, Hong Fang, Leming M. Shi, Roger Perkins, Weida Tong
2004 J jnl
Multi-class tumor classification by discriminant partial least squares using microarray gene expression data and assessment of classification models.
Comput. Biol. Chem.
Yongxi Tan, Leming M. Shi, Weida Tong, G. T. Gene Hwang, Charles Wang
2003 J jnl
An Approach to Comparative Analysis of Chromatographic Fingerprints for Assuring the Quality of Botanical Drugs.
J. Chem. Inf. Comput. Sci.
Yiyu Cheng, Minjun Chen, Weida Tong
2003 J jnl
Decision Forest: Combining the Predictions of Multiple Independent Decision Tree Models.
J. Chem. Inf. Comput. Sci.
Weida Tong, Huixiao Hong, Hong Fang, Qian Xie, Roger Perkins
2001 J jnl
QSAR Models Using a Large Diverse Set of Estrogens.
J. Chem. Inf. Comput. Sci.
Leming M. Shi, Hong Fang, Weida Tong, Jie Wu, Roger Perkins, Robert M. Blair, William S. Branham, Stacey L. Dial, Carrie L. Moland, Daniel M. Sheehan
1998 J jnl
Evaluation of Quantitative Structure-Activity Relationship Methods for Large-Scale Prediction of Chemicals Binding to the Estrogen Receptor.
J. Chem. Inf. Comput. Sci.
Weida Tong, David R. Lowis, Roger Perkins, Yu Chen, William J. Welsh, Dean W. Goddette, Trevor W. Heritage, Daniel M. Sheehan
1995 J jnl
The Role of the Carboxylate Ion in Models of Acyl-Chymotrypsin.
J. Comput. Chem.
Weida Tong, Valerian T. D'Souza