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Journal Articles
- 2024
[j64]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:
Automatic text classification of drug-induced liver injury using document-term matrix and XGBoost. Frontiers Artif. Intell. 7 (2024)- [j63]Ting Li
, Xi Chen, Weida Tong:
Bridging organ transcriptomics for advancing multiple organ toxicity assessment with a generative AI approach. npj Digit. Medicine 7(1) (2024) - 2023
- [j62]Jun Wu, Jian Ouyang, Haipeng Qing, Jiajia Zhou, Ruth Roberts, Rania Siam, Lan Wang, Weida Tong, Zhichao Liu, Tieliu Shi:
PLM-ARG: antibiotic resistance gene identification using a pretrained protein language model. Bioinform. 39(11) (2023) - [j61]Huyen Le, Ru Chen, Stephen C. Harris, Hong Fang, Beverly Lyn-Cook, Huixiao Hong, Weigong Ge, Paul Rogers, Weida Tong, Wen Zou:
RxNorm for drug name normalization: a case study of prescription opioids in the FDA adverse events reporting system. Frontiers Bioinform. 3 (2023) - 2022
- [j60]Zhichao Liu, Ting Li, Skylar Connor, Shraddha Thakkar, Ruth Roberts, Weida Tong:
Best practice and reproducible science are required to advance artificial intelligence in real-world applications. Briefings Bioinform. 23(4) (2022) - [j59]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:
Accurate species identification of food-contaminating beetles with quality-improved elytral images and deep learning. Frontiers Artif. Intell. 5 (2022) - [j58]Skylar Connor, Ting Li, Ruth Roberts, Shraddha Thakkar, Zhichao Liu, Weida Tong:
Adaptability of AI for safety evaluation in regulatory science: A case study of drug-induced liver injury. Frontiers Artif. Intell. 5 (2022) - [j57]Ting Li, Weida Tong, Ruth Roberts, Zhichao Liu, Shraddha Thakkar:
Corrigendum: DeepCarc: Deep learning-powered carcinogenicity prediction using model-level representation. Frontiers Artif. Intell. 5 (2022) - [j56]Xingqiao Wang, Xiaowei Xu, Weida Tong, Qi Liu, Zhichao Liu:
DeepCausality: A general AI-powered causal inference framework for free text: A case study of LiverTox. Frontiers Artif. Intell. 5 (2022) - 2021
- [j55]Xingqiao Wang, Xiaowei Xu, Weida Tong, Ruth Roberts, Zhichao Liu:
InferBERT: A Transformer-Based Causal Inference Framework for Enhancing Pharmacovigilance. Frontiers Artif. Intell. 4: 659622 (2021) - [j54]Arjun Bhatt, Ruth Roberts, Xi Chen, Ting Li, Skylar Connor, Qais Hatim, Mike Mikailov, Weida Tong, Zhichao Liu:
DICE: A Drug Indication Classification and Encyclopedia for AI-Based Indication Extraction. Frontiers Artif. Intell. 4: 711467 (2021) - [j53]Yue Wu, Zhichao Liu, Leihong Wu, Minjun Chen, Weida Tong:
BERT-Based Natural Language Processing of Drug Labeling Documents: A Case Study for Classifying Drug-Induced Liver Injury Risk. Frontiers Artif. Intell. 4: 729834 (2021) - [j52]Ting Li, Weida Tong, Ruth Roberts, Zhichao Liu, Shraddha Thakkar:
DeepCarc: Deep Learning-Powered Carcinogenicity Prediction Using Model-Level Representation. Frontiers Artif. Intell. 4: 757780 (2021) - 2020
- [j51]Xiangwen Liu, Joe Meehan, Weida Tong, Leihong Wu, Xiaowei Xu, Joshua Xu:
DLI-IT: a deep learning approach to drug label identification through image and text embedding. BMC Medical Informatics Decis. Mak. 20(1): 68 (2020) - 2019
- [j50]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:
Correction to: Similarities and differences between variants called with human reference genome HG19 or HG38. BMC Bioinform. 20(1): 252:1 (2019) - [j49]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:
Similarities and differences between variants called with human reference genome HG19 or HG38. BMC Bioinform. 20-S(2): 17-29 (2019) - [j48]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:
Study of serious adverse drug reactions using FDA-approved drug labeling and MedDRA. BMC Bioinform. 20-S(2): 129-139 (2019) - [j47]Leihong Wu, Zhichao Liu, Tanmay Bera, Hongjian Ding, Darryl Langley, Amy Barnes, Cesare Furlanello, Valerio Maggio, Weida Tong, Joshua Xu:
A deep learning model to recognize food contaminating beetle species based on elytra fragments. Comput. Electron. Agric. 166 (2019) - 2017
- [j46]Mike Mikailov, Fu-Jyh Luo, Stuart Barkley, Lohit Valleru, Stephen Whitney, Zhichao Liu, Shraddha Thakkar, Weida Tong, Nicholas Petrick:
Scaling bioinformatics applications on HPC. BMC Bioinform. 18(14): 163-169 (2017) - [j45]Leihong Wu, Zhichao Liu, Scott M. Auerbach, Ruili Huang, Minjun Chen, Kristin McEuen, Joshua Xu, Hong Fang, Weida Tong:
Integrating Drug's Mode of Action into Quantitative Structure-Activity Relationships for Improved Prediction of Drug-Induced Liver Injury. J. Chem. Inf. Model. 57(4): 1000-1006 (2017) - 2016
- [j44]Weizhong Zhao, James J. Chen, Roger Perkins, Yuping Wang, Zhichao Liu, Huixiao Hong, Weida Tong, Wen Zou:
A novel procedure on next generation sequencing data analysis using text mining algorithm. BMC Bioinform. 17: 213 (2016) - [j43]Weizhong Zhao, James J. Chen, Roger Perkins, Yuping Wang, Zhichao Liu, Huixiao Hong, Weida Tong, Wen Zou:
Erratum to: A novel procedure on next generation sequencing data analysis using text mining algorithm. BMC Bioinform. 17: 301 (2016) - [j42]Mikyung Lee, Zhichao Liu, Ruili Huang, Weida Tong:
Application of dynamic topic models to toxicogenomics data. BMC Bioinform. 17(S-13): 368 (2016) - 2015
- [j41]Heng Luo, Hao Ye, Hui Wen Ng, Leming Shi, Weida Tong, William Mattes, Donna Mendrick, Huixiao Hong:
Understanding and predicting binding between human leukocyte antigens (HLAs) and peptides by network analysis. BMC Bioinform. 16(S13): S9 (2015) - 2014
- [j40]Halil Bisgin, Zhichao Liu, Hong Fang, Reagan Kelly, Xiaowei Xu, Weida Tong:
A phenome-guided drug repositioning through a latent variable model. BMC Bioinform. 15: 267 (2014) - [j39]Hui Wen Ng, Wenqian Zhang, Mao Shu, Heng Luo, Weigong Ge, Roger Perkins, Weida Tong, Huixiao Hong:
Competitive molecular docking approach for predicting estrogen receptor subtype α agonists and antagonists. BMC Bioinform. 15(S-11): S4 (2014) - [j38]Wenqian Zhang, Joe Meehan, Zhenqiang Su, Hui Wen Ng, Mao Shu, Heng Luo, Weigong Ge, Roger Perkins, Weida Tong, Huixiao Hong:
Whole genome sequencing of 35 individuals provides insights into the genetic architecture of Korean population. BMC Bioinform. 15(S-11): S6 (2014) - [j37]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:
Advances in translational bioinformatics facilitate revealing the landscape of complex disease mechanisms. BMC Bioinform. 15(S-17): I1 (2014) - [j36]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:
Identification of genes and pathways involved in kidney renal clear cell carcinoma. BMC Bioinform. 15(S-17): S2 (2014) - [j35]Ke Yu, Jie Zhang, Minjun Chen, Xiaowei Xu, Ayako Suzuki, Katarina Ilic, Weida Tong:
Mining hidden knowledge for drug safety assessment: topic modeling of LiverTox as a case study. BMC Bioinform. 15(S-17): S6 (2014) - [j34]Mikyung Lee, Zhichao Liu, Reagan Kelly, Weida Tong:
Of text and gene - using text mining methods to uncover hidden knowledge in toxicogenomics. BMC Syst. Biol. 8: 93 (2014) - 2013
- [j33]Halil Bisgin, Minjun Chen, Yuping Wang, Reagan Kelly, Hong Fang, Xiaowei Xu, Weida Tong:
A systems approach for analysis of high content screening assay data with topic modeling. BMC Bioinform. 14(S-14): S11 (2013) - [j32]Jie Shen, Wenqian Zhang, Hong Fang, Roger Perkins, Weida Tong, Huixiao Hong:
Homology modeling, molecular docking, and molecular dynamics simulations elucidated α-fetoprotein binding modes. BMC Bioinform. 14(S-14): S6 (2013) - [j31]Huixiao Hong, Qilong Hong, Jie Liu, Weida Tong, Leming Shi:
Estimating relative noise to signal in DNA microarray data. Int. J. Bioinform. Res. Appl. 9(5): 433-448 (2013) - 2012
- [j30]Halil Bisgin, Zhichao Liu, Reagan Kelly, Hong Fang, Xiaowei Xu, Weida Tong:
Investigating drug repositioning opportunities in FDA drug labels through topic modeling. BMC Bioinform. 13(S-15): S6 (2012) - 2011
- [j29]Halil Bisgin, Zhichao Liu, Hong Fang, Xiaowei Xu, Weida Tong:
Mining FDA drug labels using an unsupervised learning technique - topic modeling. BMC Bioinform. 12(S-10): S11 (2011) - [j28]Minjun Chen, Leming M. Shi, Reagan Kelly, Roger Perkins, Hong Fang, Weida Tong:
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. 12(S-10): S3 (2011) - [j27]Venkata Swamy Martha, Zhichao Liu, Li Guo, Zhenqiang Su, Yanbin Ye, Hong Fang, Don Ding, Weida Tong, Xiaowei Xu:
Constructing a robust protein-protein interaction network by integrating multiple public databases. BMC Bioinform. 12(S-10): S7 (2011) - [j26]Zhichao Liu, Qiang Shi, Don Ding, Reagan Kelly, Hong Fang, Weida Tong:
Translating Clinical Findings into Knowledge in Drug Safety Evaluation - Drug Induced Liver Injury Prediction System (DILIps). PLoS Comput. Biol. 7(12) (2011) - 2010
- [j25]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:
ISA software suite: supporting standards-compliant experimental annotation and enabling curation at the community level. Bioinform. 26(18): 2354-2356 (2010) - [j24]Zhining Wen, Charles Wang, Quan Shi, Ying Huang, Zhenqiang Su, Huixiao Hong, Weida Tong, Leming Shi:
Evaluation of gene expression data generated from expired Affymetrix GeneChip® microarrays using MAQC reference RNA samples. BMC Bioinform. 11(S-6): S10 (2010) - [j23]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:
An FDA bioinformatics tool for microbial genomics research on molecular characterization of bacterial foodborne pathogens using microarrays. BMC Bioinform. 11(S-6): S4 (2010) - [j22]Don Ding, Lei Xu, Hong Fang, Huixiao Hong, Roger Perkins, Steve Harris, Edward D. Bearden, Leming Shi, Weida Tong:
The EDKB: an established knowledge base for endocrine disrupting chemicals. BMC Bioinform. 11(S-6): S5 (2010) - [j21]Joshua Xu, Carolyn Wise, Vijayalakshmi Varma, Hong Fang, Baitang Ning, Huixiao Hong, Weida Tong, Jim Kaput:
Two new ArrayTrack libraries for personalized biomedical research. BMC Bioinform. 11(S-6): S6 (2010) - 2009
- [j20]Huixiao Hong, Qilong Hong, Roger Perkins, Leming M. Shi, Hong Fang, Zhenqiang Su, Yvonne P. Dragan, James C. Fuscoe, Weida Tong:
The Accurate Prediction of Protein Family from Amino Acid Sequence by Measuring Features of Sequence Fragments. J. Comput. Biol. 16(12): 1671-1688 (2009) - 2008
- [j19]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:
Assessing batch effects of genotype calling algorithm BRLMM for the Affymetrix GeneChip Human Mapping 500 K array set using 270 HapMap samples. BMC Bioinform. 9(S-9) (2008) - [j18]Zhenqiang Su, Huixiao Hong, Hong Fang, Leming M. Shi, Roger Perkins, Weida Tong:
Very Important Pool (VIP) genes - an application for microarray-based molecular signatures. BMC Bioinform. 9(S-9) (2008) - [j17]Huixiao Hong, Qian Xie, Weigong Ge, Feng Qian, Hong Fang, Leming Shi, Zhenqiang Su, Roger Perkins, Weida Tong:
Mold2, Molecular Descriptors from 2D Structures for Chemoinformatics and Toxicoinformatics. J. Chem. Inf. Model. 48(7): 1337-1344 (2008) - 2007
- [j16]Zhenqiang Su, Huixiao Hong, Roger Perkins, Xueguang Shao, Wensheng Cai, Weida Tong:
Consensus analysis of multiple classifiers using non-repetitive variables: Diagnostic application to microarray gene expression data. Comput. Biol. Chem. 31(1): 48-56 (2007) - 2006
- [j15]Yongxi Tan, Leming M. Shi, Saber M. Hussain, Jun Xu, Weida Tong, John M. Frazier, Charles Wang:
Integrating time-course microarray gene expression profiles with cytotoxicity for identification of biomarkers in primary rat hepatocytes exposed to cadmium. Bioinform. 22(1): 77-87 (2006) - [j14]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:
Differential gene expression in mouse primary hepatocytes exposed to the peroxisome proliferator-activated receptor alpha agonists. BMC Bioinform. 7(S-2) (2006) - [j13]Tao Han, Jianyong Wang, Weida Tong, Martha M. Moore, James C. Fuscoe, Tao Chen:
Microarray analysis distinguishes differential gene expression patterns from large and small colony Thymidine kinase mutants of L5178Y mouse lymphoma cells. BMC Bioinform. 7(S-2) (2006) - [j12]Hongmei Sun, Hong Fang, Tao Chen, Roger Perkins, Weida Tong:
GOFFA: Gene Ontology For Functional Analysis - A FDA Gene Ontology Tool for Analysis of Genomic and Proteomic Data. BMC Bioinform. 7(S-2) (2006) - 2005
- [j11]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:
Bioinformatics approaches for cross-species liver cancer analysis based on microarray gene expression profiling. BMC Bioinform. 6(S-2) (2005) - [j10]Huixiao Hong, Yvonne P. Dragan, Joshua Epstein, Candee Teitel, Bangzheng Chen, Qian Xie, Hong Fang, Leming M. Shi, Roger Perkins, Weida Tong:
Quality control and quality assessment of data from surface-enhanced laser desorption/ionization (SELDI) time-of flight (TOF) mass spectrometry (MS). BMC Bioinform. 6(S-2) (2005) - [j9]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:
Cross-platform comparability of microarray technology: Intra-platform consistency and appropriate data analysis procedures are essential. BMC Bioinform. 6(S-2) (2005) - [j8]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:
Microarray scanner calibration curves: characteristics and implications. BMC Bioinform. 6(S-2) (2005) - [j7]Qian Xie, Luke D. Ratnasinghe, Huixiao Hong, Roger Perkins, Ze-Zhong Tang, Nan Hu, Philip R. Taylor, Weida Tong:
Decision Forest Analysis of 61 Single Nucleotide Polymorphisms in a Case-Control Study of Esophageal Cancer; a novel method. BMC Bioinform. 6(S-2) (2005) - 2004
- [j6]Yongxi Tan, Leming M. Shi, Weida Tong, G. T. Gene Hwang, Charles Wang:
Multi-class tumor classification by discriminant partial least squares using microarray gene expression data and assessment of classification models. Comput. Biol. Chem. 28(3): 235-243 (2004) - 2003
- [j5]Weida Tong, Huixiao Hong, Hong Fang, Qian Xie, Roger Perkins:
Decision Forest: Combining the Predictions of Multiple Independent Decision Tree Models. J. Chem. Inf. Comput. Sci. 43(2): 525-531 (2003) - [j4]Yiyu Cheng, Minjun Chen, Weida Tong:
An Approach to Comparative Analysis of Chromatographic Fingerprints for Assuring the Quality of Botanical Drugs. J. Chem. Inf. Comput. Sci. 43(3): 1068-1076 (2003) - 2001
- [j3]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:
QSAR Models Using a Large Diverse Set of Estrogens. J. Chem. Inf. Comput. Sci. 41(1): 186-195 (2001) - 1998
- [j2]Weida Tong, David R. Lowis, Roger Perkins, Yu Chen, William J. Welsh, Dean W. Goddette, Trevor W. Heritage, Daniel M. Sheehan:
Evaluation of Quantitative Structure-Activity Relationship Methods for Large-Scale Prediction of Chemicals Binding to the Estrogen Receptor. J. Chem. Inf. Comput. Sci. 38(4): 669-677 (1998) - 1995
- [j1]Weida Tong, Valerian T. D'Souza:
The Role of the Carboxylate Ion in Models of Acyl-Chymotrypsin. J. Comput. Chem. 16(6): 705-714 (1995)
Conference and Workshop Papers
- 2021
- [c7]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:
Discovering Drug-Drug Associations in the FDA Adverse Event Reporting System Database with Data Mining Approaches. BIBM 2021: 1197-1204 - [c6]Huyen Le, Junxiu Zhou, Weizhong Zhao, Roger Perkins, Weigong Ge, Beverly Lyn-Cook, Henry Francis, Huixiao Hong, Weida Tong, Wen Zou:
Text Fingerprinting and Topic Mining in the Prescription Opioid Use Literature. BIBM 2021: 2741-2748 - 2017
- [c5]Hao Zhang, Mary Qu Yang, Xiaoyue Feng, William Yang, Weida Tong, Renchu Guan:
Protein-Protein Interaction Extraction Using Attention-Based Convolution Neural Networks. BCB 2017: 770-771 - [c4]Dan Li, William Yang, Yifan Zhang, Jack Y. Yang, Weida Tong, Renchu Guan, Mary Qu Yang:
Comprehensive analysis of pulmonary adenocarcinoma in situ (AIS) revealed new insights into lung cancer progression. BIBM 2017: 792-797 - [c3]Yifan Zhang, William Yang, Dan Li, Jack Y. Yang, Renchu Guan, Weida Tong, Mary Qu Yang:
Toward precision breast cancer survival prediction utilizing combined whole genome-wide expression and somatic mutation analysis. BIBM 2017: 830-835 - 2016
- [c2]Daniel Martin, Hongjian Ding, Leihong Wu, Howard Semey, Amy Barnes, Darryl Langley, Su Inn Park, Zhichao Liu, Weida Tong, Joshua Xu:
An Image Analysis Environment for Species Identification of Food Contaminating Beetles. AAAI 2016: 4375-4376 - 2009
- [c1]Huixiao Hong, Qilong Hong, Weida Tong:
Accurate Prediction and Recognition of Subfamilies of G Protein-Coupled Receptors from Amino Acid Sequences. BIOCOMP 2009: 3-9
Parts in Books or Collections
- 2011
- [p1]Zhining Wen, Zhenqiang Su, Jie Liu, Baitang Ning, Lei Guo, Weida Tong, Leming M. Shi:
The MicroArray Quality Control (MAQC) Project and Cross-Platform Analysis of Microarray Data. Handbook of Statistical Bioinformatics 2011: 171-192
Informal and Other Publications
- 2020
- [i1]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:
The need for standardisation in life science research - an approach to excellence and trust. F1000Research 9: 1398 (2020)
Coauthor Index
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