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• affiliation:University of Missouri, Department of Computer Science / C.S. Bond Life Sciences Center, Columbia, MO, USA
• affiliation (former):Jilin University, College of Computer Science and Technology, Changchun, China
• affiliation (former):Oak Ridge National Laboratory, Life Sciences Division, Protein Informatics Group, Oak Ridge, TN, USA
• affiliation (PhD 1995):University of Illinois at Urbana-Champaign, IL, USA

• Dong Xu —disambiguation page
• Dong Xu0001 —University of Hong Kong, Department of Computer Science, Hong Kong(and 4 more)
• Dong Xu0003 — Shanghai Normal University, Shanghai, China
• Dong Xu0004 — Tsinghua University, Department of Precision Instrument, Beijing, China
• Dong Xu0005 —Beihang University, School of Automation Science and Electrical Engineering, Beijing, China(and 1 more)
• Dong Xu0006 —Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Hangzhou, China(and 1 more)
• Dong Xu0007 — University of Arizona, Department of Systems and Industrial Engineering, Tucson, AZ, USA
• Dong Xu0008 —Sanford-Burnham Medical Research Institute, San Diego, CA, USA(and 2 more)
• Dong Xu0009 — East China Normal University, School of Geographic Sciences, Key Laboratory of Geographic Information Science, Shanghai, China
• Dong Xu0010 — Harbin Engineering University, College of Computer Science and Technology, Harbin, China

• Dong Xu0011 — Wuhan University, State Key Laboratory of Information Engineering in Surveying Mapping and Remote Sensing, Wuhan, China
• Dong Xu0012 — University of Duisburg-Essen, Department of Communication Technology, Duisburg, Germany
• Dong Xu0013 —University of Science and Technology Beijing, National Engineering Research Center for Advanced Rolling and Intelligent Manufacturing, Beijing, China(and 1 more)
• Dong Xu0014 — Anhui University of Technology, Engineering Research Institute, Ma'anshan, China
• Dong Xu0015 — ZTE Corporation, Shanghai, China
• Dong Xu0016 — Chang Gung University, Taoyuan, Taiwan
• Dong Xu0017 —Beijing Normal University, Faculty of Geographical Science, State Key Laboratory of Remote Sensing Science, Beijing, China(and 2 more)
• Dong Xu0018 —Tongji University, School of Mechanical Engineering, Tongji, China(and 1 more)
• Dong Xu0019 — Northeastern University, College of Information Science and Engineering, Shenyang, China
• Dong Xu0020 — East China Jiaotong University, Department of Internet of Things, NanChang, China
• Dong Xu0021 — University of Virginia, Charlottesville, VA, USA
• Dong Xu0022 — Idaho State University, College of Pharmacy, Department of Biomedical and Pharmaceutical Sciences, Meridian, ID, USA
• Dong Xu0023 —Shenzhen University, National Engineering Laboratory for Big Data System Computing Technology, China(and 1 more)
• Dong Xu0024 — University of California - Merced (UCM), CA, USA

• Xu Dong —disambiguation page
• Xue Dong —disambiguation page
• Xudong Liu(aka: XuDong Liu, Xu-dong Liu, Xu-Dong Liu) —disambiguation page
• Dong-Ling Xu
• Jindong Xu(aka: Jin-dong Xu) —disambiguation page
• Dong Xue —disambiguation page
• Xudong Zhang(aka: Xu-Dong Zhang) —disambiguation page
• Xudong Zhang0001(aka: Xu-Dong Zhang0001) — Tsinghua University, Department of Electronic Engineering, Beijing, China
• Xudong Zhao(aka: Xu-Dong Zhao) —disambiguation page
• Xudong Zhao0001(aka: Xu-Dong Zhao0001) —Bohai University, College of Control Science and Engineering, Jinzhou, Liaoning, China(and 2 more)
• show all similar names

• 2026
• 
  [j118]
  Sohaib Asif,Fazal Hadi,Qurrat-ul-ain,Yuqi Yan,Vicky Yang Wang,Dong Xu:
  The impact of large language models on medical research and patient care: A systematic review of current trends, challenges, and future innovations.Comput. Sci. Rev.59:100847 (2026)
• 
  [j117]
  Muhammad Azam,Shuai Zeng,Hasanain Aldihis,Mihail Popescu,Dong Xu:
  Applications of Large Language Models and Prompt Optimization for Knowledge Extraction From Biological Pathway Figures.IEEE J. Biomed. Health Informatics30(2):1680-1692 (2026)
• 2025
• 
  [j116]
  Micheal Olaolu Arowolo,Sulaiman Olaniyi Abdulsalam,Rafiu Mope Isiaka,Kingsley Theophilus Igulu,Bukola Fatimah Balogun,Mihail Popescu,Dong Xu:
  Agentic RAG-Driven Multi-Omics Analysis for PI3K/AKT Pathway Deregulation in Precision Medicine.Algorithms18(9):545 (2025)
• 
  [j115]
  Longyi Li,Liyan Dong,Hao Zhang,Dong Xu,Yongli Li:
  spaLLM: enhancing spatial domain analysis in multi-omics data through large language model integration.Briefings Bioinform.26(4) (2025)
• 
  [j114]
  Mauminah Raina,Hao Cheng,Ricardo Melo Ferreira,Treyden Stansfield,Chandrima Modak,Ying-Hua Cheng,Hari Naga Sai Kiran Suryadevara,Dong Xu,Michael T. Eadon,Qin Ma,Juexin Wang:
  Relation equivariant graph neural networks to explore the mosaic-like tissue architecture of kidney diseases on spatially resolved transcriptomics.Bioinform.41(6) (2025)
• 
  [j113]
  Jinpu Li,Mauminah Raina,Yiqing Wang,Chunhui Xu,Li Su,Qi Guo,Ricardo Melo Ferreira,Michael T. Eadon,Qin Ma,Juexin Wang,Dong Xu:
  scBSP: a fast and accurate tool for identifying spatially variable features from high-resolution spatial omics data.Bioinform.41(10) (2025)
• 
  [j112]
  Yuanshu Li,Kexin Hong,Xiaohu Shi,Wei Pang,Yubin Xiao,Peng Zhao,Dong Xu,Chunli Song,Xu Zhou,You Zhou:
  A deep learning based approach for automatic cardiac events identification.Biomed. Signal Process. Control.100:107164 (2025)
• 
  [j111]
  Yibo Chen,Gangqing Hu,Chun Xia,Lihua Yu,Mihail Popescu,Dong Xu:
  Large Language Models and Prompt-Based Learning: Frontiers and Challenges in Cross-Disciplinary Applications.Int. J. Artif. Intell. Robotics Res.2:2530001:1-2530001:15 (2025)
• 
  [j110]
  Jiabin Yu,Qi Liu,Chenjie Xu,Qinli Zhou,Jiajun Xu,Lingying Zhu,Chen Chen,Yahan Zhou,Binggang Xiao,Lin Zheng,Xiaofeng Zhou,Fengming Zhang,Yuhang Ye,Hongmei Mi,Dongping Zhang,Li Yang,Zhiwei Wu,Jiayi Wang,Ming Chen,Zhirui Zhou,Haoyang Wang,Vicky Y. Wang,Enyu Wang,Dong Xu:
  Deep learning-driven modality imputation and subregion segmentation to enhance high-grade glioma grading.BMC Medical Informatics Decis. Mak.25(1):200 (2025)
• 
  [j109]
  Li Su,Duolin Wang,Dong Xu:
  Bridging peptide presentation and T cell recognition with multi-task learning.Nat. Mac. Intell.7(2):170-171 (2025)
• 
  [j108]
  Yubin Xiao,Di Wang,Boyang Li,Huanhuan Chen,Wei Pang,Xuan Wu,Hao Li,Dong Xu,Yanchun Liang,You Zhou:
  Reinforcement Learning-Based Nonautoregressive Solver for Traveling Salesman Problems.IEEE Trans. Neural Networks Learn. Syst.36(7):13402-13416 (2025)
• 
  [i12]
  Jiacheng Xie,Yang Yu,Ziyang Zhang,Shuai Zeng,Jiaxuan He,Ayush Vasireddy,Xiaoting Tang,Congyu Guo,Lening Zhao,Congcong Jing,Guanghui An,Dong Xu:
  TCM-Ladder: A Benchmark for Multimodal Question Answering on Traditional Chinese Medicine.CoRRabs/2505.24063 (2025)
• 
  [i11]
  Jiacheng Xie,Ziyang Zhang,Biplab Poudel,Congyu Guo,Yang Yu,Guanghui An,Xiaoting Tang,Lening Zhao,Chunhui Xu,Dong Xu:
  TOM: An Open-Source Tongue Segmentation Method with Multi-Teacher Distillation and Task-Specific Data Augmentation.CoRRabs/2508.14932 (2025)
• 
  [i10]
  Jiacheng Xie,Shuai Zeng,Yang Yu,Xiaoting Tang,Guanghui An,Dong Xu:
  Leveraging Group Relative Policy Optimization to Advance Large Language Models in Traditional Chinese Medicine.CoRRabs/2510.17402 (2025)
• 
  [i9]
  Jiacheng Xie,Yang Yu,Yibo Chen,Hanyao Zhang,Lening Zhao,Jiaxuan He,Lei Jiang,Xiaoting Tang,Guanghui An,Dong Xu:
  BenCao: An Instruction-Tuned Large Language Model for Traditional Chinese Medicine.CoRRabs/2510.17415 (2025)
• 2024
• 
  [j107]
  Wenchuan Zhao,Yufeng Yu,Guosheng Liu,Yanchun Liang,Dong Xu,Xiaoyue Feng,Renchu Guan:
  MSI-DTI: predicting drug-target interaction based on multi-source information and multi-head self-attention.Briefings Bioinform.25(3) (2024)
• 
  [j106]
  Chunhui Xu,Trey Shaw,Sai Akhil Choppararu,Yiwei Lu,Shaik Naveed Farooq,Yongfang Qin,Matt Hudson,Brock Weekley,Michael Fisher,Fei He,Jose Roberto Da Silva Nascimento,Nicholas Wergeles,Trupti Joshi,Philip D. Bates,Abraham J. Koo,Doug K. Allen,Edgar B. Cahoon,Jay J. Thelen,Dong Xu:
  FatPlants: a comprehensive information system for lipid-related genes and metabolic pathways in plants.Database J. Biol. Databases Curation2024 (2024)
• 
  [j105]
  Muhammad Hassan,Yan Wang,Di Wang,Wei Pang,Daixi Li,You Zhou,Dong Xu,Sami Ur Rahman,Amin ur Rahman,Ahmed Fateh Ameen,Peiwu Qin:
  Deep learning model for human-intuitive shoeprint reconstruction.Expert Syst. Appl.249:123704 (2024)
• 
  [j104]
  Muhammad Hassan,Jieqiong Lin,Ahmed Ameen Fateh,Yijang Zhuang,Guojun Yun,Adnan Zeb,Dong Xu,Hongwu Zeng:
  Mapping brain development against neurological disorder using contrastive sharing.Expert Syst. Appl.256:124893 (2024)
• 
  [j103]
  Xiaosong Han,Mengchen Cao,Dong Xu,Xiaoyue Feng,Yanchun Liang,Xiaoduo Lang,Renchu Guan:
  SEOE: an option graph based semantically embedding method for prenatal depression detection.Frontiers Comput. Sci.18(6):186911 (2024)
• 
  [j102]
  Gang-Qing Hu,Li Liu,Dong Xu:
  On the Responsible Use of Chatbots in Bioinformatics.Genom. Proteom. Bioinform.22(1) (2024)
• 
  [j101]
  Yibo Chen,Jeffrey Gao,Marius Petruc,Richard D. Hammer,Mihail Popescu,Dong Xu:
  Iterative Prompt Refinement for Mining Gene Relationships from ChatGPT.Int. J. Artif. Intell. Robotics Res.1(2):2450005:1-2450005:29 (2024)
• 
  [j100]
  Yi He,Shuang Wang,Shuai Zeng,Jingxuan Zhu,Dong Xu,Weiwei Han,Juexin Wang:
  NRIMD, a Web Server for Analyzing Protein Allosteric Interactions Based on Molecular Dynamics Simulation.J. Chem. Inf. Model.64(19):7176-7183 (2024)
• 
  [j99]
  Jinge Wang,Zien Cheng,Qiuming Yao,Li Liu,Dong Xu,Gangqing Hu:
  Bioinformatics and biomedical informatics with ChatGPT: Year one review.Quant. Biol.12(4):345-359 (2024)
• 
  [j98]
  Muhammad Azam,Yibo Chen,Micheal Olaolu Arowolo,Haowang Liu,Mihail Popescu,Dong Xu:
  A comprehensive evaluation of large language models in mining gene relations and pathway knowledge.Quant. Biol.12(4):360-374 (2024)
• 
  [j97]
  Xuan Wu,Di Wang,Huanhuan Chen,Lele Yan,Yubin Xiao,Chunyan Miao,Hongwei Ge,Dong Xu,Yanchun Liang,Kangping Wang,Chunguo Wu,You Zhou:
  Neural Architecture Search for Text Classification With Limited Computing Resources Using Efficient Cartesian Genetic Programming.IEEE Trans. Evol. Comput.28(3):638-652 (2024)
• 
  [j96]
  Fei He,Kai Liu,Zhiyuan Yang,Yibo Chen,Richard D. Hammer,Dong Xu,Mihail Popescu:
  pathCLIP: Detection of Genes and Gene Relations From Biological Pathway Figures Through Image-Text Contrastive Learning.IEEE J. Biomed. Health Informatics28(8):5007-5019 (2024)
• 
  [c79]
  Ke Chen,Xiaosong Han,Xiaoran Li,Yanchun Liang,Dong Xu,Renchu Guan:
  PNESR-DDI: An Effective Drug-Drug Interaction Prediction Model Based on Pretraining Method and Enhanced Subgraph Reconstruction.BIBM2024:1874-1881
• 
  [c78]
  Yibo Chen,Dong Xu,Richard D. Hammer,Mihail Popescu:
  Predicting Gene Relations with a Graph Transformer Network Integrating DNA, Protein, and Descriptive Data.BIBM2024:3101-3104
• 
  [c77]
  Sohaib Asif,Vicky Yang Wang,Dong Xu:
  LungX-Net: Lung Cancer Diagnosis from CT and Histopathological Images via Attention Based Multi-Level Feature Fusion Network.BIBM2024:6334-6341
• 
  [c76]
  Muhammad Azam,Fei He,Krpns Santosh,Dong Xu,Mihail Popescu:
  Evaluation and Integration of Advanced AI Chatbots for Biological Pathway Curation.BIBM2024:6342-6348
• 
  [c75]
  Shuai Zeng,Duolin Wang,Lei Jiang,Dong Xu:
  Prompt-Based Learning on Large Protein Language Models Improves Signal Peptide Prediction.RECOMB2024:400-405
• 
  [i8]
  Jinge Wang,Zien Cheng,Qiuming Yao,Li Liu,Dong Xu,Gangqing Hu:
  Bioinformatics and Biomedical Informatics with ChatGPT: Year One Review.CoRRabs/2403.15274 (2024)
• 2023
• 
  [j95]
  Zhengzhong Qiu,Wei Bi,Dong Xu,Hua Guo,Hongwei Ge,Yanchun Liang,Heow Pueh Lee,Chunguo Wu:
  Efficient Self-learning Evolutionary Neural Architecture Search.Appl. Soft Comput.146:110671 (2023)
• 
  [j94]
  Zhenhao Wang,Rui Xu,Tingyuan Nie,Dong Xu:
  Semi-supervised active learning hypothesis verification for improved geometric expression in three-dimensional object recognition.Eng. Appl. Artif. Intell.120:105956 (2023)
• 
  [j93]
  Jihong Ouyang,Dong Mao,Zeqi Guo,Siguang Liu,Dong Xu,Wenting Wang:
  Contrastive self-supervised learning for diabetic retinopathy early detection.Medical Biol. Eng. Comput.61(9):2441-2452 (2023)
• 
  [j92]
  Yuexu Jiang,Lei Jiang,Chopparapu Sai Akhil,Duolin Wang,Ziyang Zhang,Weinan Zhang,Dong Xu:
  MULocDeep web service for protein localization prediction and visualization at subcellular and suborganellar levels.Nucleic Acids Res.51(W1):343-349 (2023)
• 
  [j91]
  Duolin Wang,Fei He,Yang Yu,Dong Xu:
  Meta-learning for T cell receptor binding specificity and beyond.Nat. Mac. Intell.5(4):337-339 (2023)
• 
  [j90]
  Jianing Qiu,Lin Li,Jiankai Sun,Jiachuan Peng,Peilun Shi,Ruiyang Zhang,Yinzhao Dong,Kyle Lam,Frank P.-W. Lo,Bo Xiao,Wu Yuan,Ningli Wang,Dong Xu,Benny P. L. Lo:
  Large AI Models in Health Informatics: Applications, Challenges, and the Future.IEEE J. Biomed. Health Informatics27(12):6074-6087 (2023)
• 
  [j89]
  Yuanxun Zhang,Prasad Calyam,Trupti Joshi,Satish S. Nair,Dong Xu:
  Domain-Specific Topic Model for Knowledge Discovery in Computational and Data-Intensive Scientific Communities.IEEE Trans. Knowl. Data Eng.35(2):1402-1420 (2023)
• 
  [i7]
  Jianing Qiu,Lin Li,Jiankai Sun,Jiachuan Peng,Peilun Shi,Ruiyang Zhang,Yinzhao Dong,Kyle Lam,Frank P.-W. Lo,Bo Xiao,Wu Yuan,Dong Xu,Benny Lo:
  Large AI Models in Health Informatics: Applications, Challenges, and the Future.CoRRabs/2303.11568 (2023)
• 
  [i6]
  Yubin Xiao,Di Wang,Huanhuan Chen,Boyang Li,Wei Pang,Xuan Wu,Hao Li,Dong Xu,Yanchun Liang,You Zhou:
  Reinforcement Learning-based Non-Autoregressive Solver for Traveling Salesman Problems.CoRRabs/2308.00560 (2023)
• 
  [i5]
  Fei He,Zhiyuan Yang,Mingyue Gao,Biplab Poudel,Newgin Sam Ebin Sam Dhas,Rajan Gyawali,Ashwin Dhakal,Jianlin Cheng,Dong Xu:
  Adapting Segment Anything Model (SAM) through Prompt-based Learning for Enhanced Protein Identification in Cryo-EM Micrographs.CoRRabs/2311.16140 (2023)
• 2022
• 
  [j88]
  Shuangquan Zhang,Anjun Ma,Jing Zhao,Dong Xu,Qin Ma,Yan Wang:
  Assessing deep learning methods in cis-regulatory motif finding based on genomic sequencing data.Briefings Bioinform.23(1) (2022)
• 
  [j87]
  Renchu Guan,Haoyu Pang,Yanchun Liang,Zhongjun Shao,Xin Gao,Dong Xu,Xiaoyue Feng:
  Discovering trends and hotspots of biosafety and biosecurity research via machine learning.Briefings Bioinform.23(5) (2022)
• 
  [j86]
  Haocheng Gu,Hao Cheng,Anjun Ma,Yang Li,Juexin Wang,Dong Xu,Qin Ma:
  scGNN 2.0: a graph neural network tool for imputation and clustering of single-cell RNA-Seq data.Bioinform.38(23):5322-5325 (2022)
• 
  [j85]
  Muhammad Hassan,Yan Wang,Di Wang,Wei Pang,Kangping Wang,Daixi Li,You Zhou,Dong Xu:
  Restorable-inpainting: A novel deep learning approach for shoeprint restoration.Inf. Sci.600:22-42 (2022)
• 
  [j84]
  Muhammad Hassan,Yan Wang,Wei Pang,Di Wang,Daixi Li,You Zhou,Dong Xu:
  IPAS-Net: A deep-learning model for generating high-fidelity shoeprints from low-quality images with no natural references.J. King Saud Univ. Comput. Inf. Sci.34(6 Part A):2743-2757 (2022)
• 
  [j83]
  Tianyu Cui,Yiying Dou,Puwen Tan,Zhen Ni,Tianyuan Liu,Duolin Wang,Yan Huang,Kaican Cai,Xiaoyang Zhao,Dong Xu,Hao Lin,Dong Wang:
  RNALocate v2.0: an updated resource for RNA subcellular localization with increased coverage and annotation.Nucleic Acids Res.50(D1):333-339 (2022)
• 
  [j82]
  Yuning Yang,Jiawen Yu,Zhe Liu,Xi Wang,Han Wang,Zhiqiang Ma,Dong Xu:
  An Improved Topology Prediction of Alpha-Helical Transmembrane Protein Based on Deep Multi-Scale Convolutional Neural Network.IEEE ACM Trans. Comput. Biol. Bioinform.19(1):295-304 (2022)
• 
  [c74]
  Han Wang,Hangxu Zhu,Wenhao Li,Ming Liu,Li Zhang,Dong Xu:
  Predicting Compound-Protein Interaction by Deepening the Systemic Background via Molecular Network Feature Embedding.BIBM2022:346-353
• 
  [c73]
  Clement Essien,Fei He,Mark Hannink,Mihail Popescu,Dong Xu:
  Extraction of Gene Regulatory Relation Using BioBERT.BIBM2022:3351-3355
• 
  [c72]
  Stuart Aldrich,Micheal Olaolu Arowolo,Fei He,Mihail Popescu,Dong Xu:
  Comprehensive Assessment of OCR Tools for Gene Name Recognition in Biological Pathway Figures.BIBM2022:3574-3579
• 
  [c71]
  Yibo Chen,Dong Xu,Mihail Popescu:
  Integration of Gene Regulatory Pathways Found in the Literature in a Graph Database.BIBM2022:3791-3793
• 
  [c70]
  Lei Jiang,Yuexu Jiang,Cankun Wang,Clement Essien,Juexin Wang,Anjun Ma,Qin Ma,Dong Xu:
  Machine learning development environment for single-cell sequencing data analyses.BIBM2022:3824-3826
• 
  [c69]
  Negin Manshour,Yang Yu,Wenyuan Qin,Fei He,Duolin Wang,Dong Xu:
  Evaluating template-based and template-free protein-peptide complex structure prediction using AlphaFold2.BIBM2022:3856
• 
  [c68]
  Junlin Wang,Wenbo Wang,Yi Shang,Dong Xu:
  New Heuristic Methods for Protein Model Quality Assessment via Two-Stage Machine Learning and Hierarchical Ensemble.CogMI2022:84-90
• 2021
• 
  [j81]
  Komal Vekaria,Prasad Calyam,Sai Swathi Sivarathri,Songjie Wang,Yuanxun Zhang,Ashish Pandey,Cong Chen,Dong Xu,Trupti Joshi,Satish S. Nair:
  Recommender-as-a-service with chatbot guided domain-science knowledge discovery in a science gateway.Concurr. Comput. Pract. Exp.33(19) (2021)
• 
  [j80]
  Rui Gao,Shoufeng Li,Xiaohu Shi,Yanchun Liang,Dong Xu:
  Overlapping Community Detection Based on Membership Degree Propagation.Entropy23(1):15 (2021)
• 
  [j79]
  Ye Han,Fei He,Yongbing Chen,Wenyuan Qin,Helong Yu,Dong Xu:
  Quality Assessment of Protein Docking Models Based on Graph Neural Network.Frontiers Bioinform.1 (2021)
• 
  [j78]
  Shuai Zeng,Ziting Mao,Yijie Ren,Duolin Wang,Dong Xu,Trupti Joshi:
  G2PDeep: a web-based deep-learning framework for quantitative phenotype prediction and discovery of genomic markers.Nucleic Acids Res.49(Webserver-Issue):228-236 (2021)
• 
  [j77]
  Chao Fang,Dong Xu,Jing Su,Jonathan R. Dry,Bolan Linghu:
  DeePaN: deep patient graph convolutional network integrating clinico-genomic evidence to stratify lung cancers for immunotherapy.npj Digit. Medicine4 (2021)
• 
  [j76]
  Matthew Dickinson,Saptarshi Debroy,Prasad Calyam,Samaikya Valluripally,Yuanxun Zhang,Ronny Bazan Antequera,Trupti Joshi,Tommi A. White,Dong Xu:
  Multi-Cloud Performance and Security Driven Federated Workflow Management.IEEE Trans. Cloud Comput.9(1):240-257 (2021)
• 
  [c67]
  Fei He,Joshua Thompson,Ziting Mao,Yijie Ren,Yulia I. Nussbaum,Olha Kholod,Dmitriy Shin,Mark Hannink,Mihail Popescu,Dong Xu:
  Identifying Genes and Their Interactions from Pathway Figures and Text in Biomedical Articles.BIBM2021:398-405
• 
  [c66]
  Xiaosong Han,Xiaoran Li,Yanchun Liang,Xinghao Wang,Dong Xu,Renchu Guan:
  Acupuncture and Tuina Knowledge Graph for Ancient Literature of Traditional Chinese Medicine.BIBM2021:674-677
• 
  [c65]
  Joshua Thompson,Haoyu Dong,Kai Liu,Fei He,Mihail Popescu,Dong Xu:
  A Rule-Based Approach for Generating Synthetic Biological Pathways.CIBB2021:105-116
• 
  [c64]
  Yijie Ren,Fei He,Jing Qu,Yifan Li,Joshua Thompson,Mark Hannink,Mihail Popescu,Dong Xu:
  Text Mining Enhancements for Image Recognition of Gene Names and Gene Relations.CIBB2021:132-142
• 2020
• 
  [j75]
  Yuexu Jiang,Yanchun Liang,Duolin Wang,Dong Xu,Trupti Joshi:
  A dynamic programing approach to integrate gene expression data and network information for pathway model generation.Bioinform.36(1):169-176 (2020)
• 
  [j74]
  Chao Fang,Zhaoyu Li,Dong Xu,Yi Shang:
  MUFold-SSW: a new web server for predicting protein secondary structures, torsion angles and turns.Bioinform.36(4):1293-1295 (2020)
• 
  [j73]
  Bowen Tang,Skyler T. Kramer,Meijuan Fang,Yingkun Qiu,Zhen Wu,Dong Xu:
  A self-attention based message passing neural network for predicting molecular lipophilicity and aqueous solubility.J. Cheminformatics12(1):15 (2020)
• 
  [j72]
  Duolin Wang,Dongpeng Liu,Jiakang Yuchi,Fei He,Yuexu Jiang,Siteng Cai,Jingyi Li,Dong Xu:
  MusiteDeep: a deep-learning based webserver for protein post-translational modification site prediction and visualization.Nucleic Acids Res.48(Webserver-Issue):W140-W146 (2020)
• 
  [j71]
  Wenbo Wang,Junlin Wang,Dong Xu,Yi Shang:
  Two New Heuristic Methods for Protein Model Quality Assessment.IEEE ACM Trans. Comput. Biol. Bioinform.17(4):1430-1439 (2020)
• 
  [j70]
  Ming Liu,Zhiqian Zhou,Penghui Shang,Dong Xu:
  Fuzzified Image Enhancement for Deep Learning in Iris Recognition.IEEE Trans. Fuzzy Syst.28(1):92-99 (2020)
• 
  [i4]
  Muhammad Hassan,Yan Wang,Di Wang,Daixi Li,Yanchun Liang,You Zhou,Dong Xu:
  Deep Learning Analysis and Age Prediction from Shoeprints.CoRRabs/2011.03794 (2020)

• 2019
• 
  [j69]
  Duolin Wang,Yanchun Liang,Dong Xu:
  Capsule network for protein post-translational modification site prediction.Bioinform.35(14):2386-2394 (2019)
• 
  [j68]
  Liu Yang,Dong Xu:
  Sliding mode control with PI-based saturation for nano-positioning.Int. J. Wirel. Mob. Comput.16(3):204-210 (2019)
• 
  [j67]
  Wenbo Wang,Zhaoyu Li,Junlin Wang,Dong Xu,Yi Shang:
  PSICA: a fast and accurate web service for protein model quality analysis.Nucleic Acids Res.47(Webserver-Issue):W443-W450 (2019)
• 
  [j66]
  Son P. Nguyen,Zhaoyu Li,Dong Xu,Yi Shang:
  New Deep Learning Methods for Protein Loop Modeling.IEEE ACM Trans. Comput. Biol. Bioinform.16(2):596-606 (2019)
• 
  [j65]
  Chao Fang,Yi Shang,Dong Xu:
  Prediction of Protein Backbone Torsion Angles Using Deep Residual Inception Neural Networks.IEEE ACM Trans. Comput. Biol. Bioinform.16(3):1020-1028 (2019)
• 
  [c63]
  Yulia Innokenteva,Olha Kholod,Fei He,Duolin Wang,Richard D. Hammer,Dong Xu,Dmitriy Shin:
  An Informatics Framework for Knowledge Representation and Reconciliation of Disease Pathways.AMIA2019
• 
  [c62]
  Fei He,Duolin Wang,Yulia Innokenteva,Olha Kholod,Dmitriy Shin,Dong Xu:
  Extracting Molecular Entities and Their Interactions from Pathway Figures Based on Deep Learning.BCB2019:397-404
• 
  [c61]
  Han Wang,Yuning Yang,Jiawen Yu,Xi Wang,Dawei Zhao,Dong Xu,Pingping Sun:
  DMCTOP: Topology Prediction of Alpha-Helical Transmembrane Protein Based on Deep Multi-Scale Convolutional Neural Network.BIBM2019:36-43
• 
  [c60]
  Fei He,Rui Wang,Yanxin Gao,Duolin Wang,Yang Yu,Dong Xu,Xiaowei Zhao:
  Protein Ubiquitylation and Sumoylation Site Prediction Based on Ensemble and Transfer Learning.BIBM2019:117-123
• 
  [c59]
  Fei He,Duolin Wang,Yulia Innokenteva,Olha Kholod,Dmitriy Shin,Dong Xu:
  Extracting Molecular Entities and Their Interactions from Pathway Figures Based on Deep Learning.BIBM2019:1191-1193
• 
  [c58]
  Clement Essien,Duolin Wang,Dong Xu:
  Capsule Network for Predicting Zinc Binding Sites in Metalloproteins.BIBM2019:2337-2341
• 
  [c57]
  Xue Gu,Ziyao Meng,Yanchun Liang,Dong Xu,Han Huang,Xiaosong Han,Chunguo Wu:
  ESAE: Evolutionary Strategy-Based Architecture Evolution.BIC-TA (1)2019:193-208
• 
  [c56]
  Yuexu Jiang,Duolin Wang,Dong Xu:
  DeepDom: Predicting protein domain boundary from sequence alone using stacked bidirectional.PSB2019:66-75
• 
  [c55]
  Pericles S. Giannaris,Cynthia Tang,Olha Kholod,Steve Hanson,Chi-Ren Shyu,Richard D. Hammer,Dong Xu,Dmitriy Shin:
  Modeling of Contextual Information in Knowledge Graphs of Diagnostic Reports.SWH@ISWC2019:20-29
• 
  [i3]
  Ming Liu,Dongpeng Liu,Guangyu Sun,Yi Zhao,Duolin Wang,Fangxing Liu,Xiang Fang,Qing He,Dong Xu:
  Detection of Malfunctioning Smart Electricity Meter.CoRRabs/1907.11377 (2019)
• 2018
• 
  [j64]
  Juexin Wang,Robert Sheridan,Selçuk Onur Sümer,Nikolaus Schultz,Dong Xu,Jianjiong Gao:
  G2S: a web-service for annotating genomic variants on 3D protein structures.Bioinform.34(11):1949-1950 (2018)
• 
  [j63]
  R. Shyama Prasad Rao,Ning Zhang,Dong Xu,Ian Max Møller:
  CarbonylDB: a curated data-resource of protein carbonylation sites.Bioinform.34(14):2518-2520 (2018)
• 
  [j62]
  Donghui Wang,Yanchun Liang,Dong Xu,Xiaoyue Feng,Renchu Guan:
  A content-based recommender system for computer science publications.Knowl. Based Syst.157:1-9 (2018)
• 
  [j61]
  Saad M. Khan,Jason E. Denney,Michael X. Wang,Dong Xu:
  Whole-exome sequencing and microRNA profiling reveal PI3K/AKT pathway's involvement in juvenile myelomonocytic leukemia.Quant. Biol.6(1):85-97 (2018)
• 
  [j60]
  Ronny Bazan Antequera,Prasad Calyam,Saptarshi Debroy,Longhai Cui,Sripriya Seetharam,Matthew Dickinson,Trupti Joshi,Dong Xu,Tsegereda Beyene:
  ADON: Application-Driven Overlay Network-as-a-Service for Data-Intensive Science.IEEE Trans. Cloud Comput.6(3):640-655 (2018)
• 
  [c54]
  Yuexu Jiang,Duolin Wang,Dong Xu,Trupti Joshi:
  Integrating Gene Expression Data and Pathway Knowledge for In Silico Hypothesis Generation with IMPRes.BIBM2018:102-107
• 
  [c53]
  Shuai Zeng,Zhen Lyu,Siva Ratna Kumari Narisetti,Dong Xu,Trupti Joshi:
  Knowledge Base Commons (KBCommons) v1.0: A multi OMICS' web-based data integration framework for biological discoveries.BIBM2018:589-594
• 
  [c52]
  Sadia Akter,Dong Xu,Susan C. Nagel,Trupti Joshi:
  A Data Mining Approach for Biomarker Discovery Using Transcriptomics in Endometriosis.BIBM2018:969-972
• 
  [c51]
  Yuanxun Zhang,Prasad Calyam,Trupti Joshi,Satish S. Nair,Dong Xu:
  Domain-specific Topic Model for Knowledge Discovery through Conversational Agents in Data Intensive Scientific Communities.IEEE BigData2018:4886-4895
• 2017
• 
  [j59]
  Jianjiong Gao,Andreas Prlic,Chunxiao Bi,Wolfgang Bluhm,Dimitris Dimitropoulos,Dong Xu,Philip E. Bourne,Peter W. Rose:
  BioJava-ModFinder: identification of protein modifications in 3D structures from the Protein Data Bank.Bioinform.33(13):2047-2049 (2017)
• 
  [j58]
  Duolin Wang,Shuai Zeng,Chunhui Xu,Wangren Qiu,Yanchun Liang,Trupti Joshi,Dong Xu:
  MusiteDeep: a deep-learning framework for general and kinase-specific phosphorylation site prediction.Bioinform.33(24):3909-3916 (2017)
• 
  [j57]
  Xiaoyue Feng,Yanchun Liang,Xiaohu Shi,Dong Xu,Xu Wang,Renchu Guan:
  Overfitting Reduction of Text Classification Based on AdaBELM.Entropy19(7):330 (2017)
• 
  [j56]
  Li Zhang,Han Wang,Lun Yan,Lingtao Su,Dong Xu:
  OMPcontact: An Outer Membrane Protein Inter-Barrel Residue Contact Prediction Method.J. Comput. Biol.24(3):217-228 (2017)
• 
  [c50]
  Fei He,Lingling Bao,Rui Wang,Jiagen Li,Dong Xu,Xiaowei Zhao:
  A multimodal deep architecture for large-scale protein ubiquitylation site prediction.BIBM2017:108-113
• 
  [c49]
  Yuexu Jiang,Yanchun Liang,Duolin Wang,Dong Xu,Trupti Joshi:
  IMPRes: Integrative MultiOmics pathway resolution algorithm and tool.BIBM2017:2260
• 
  [c48]
  Saad M. Khan,Gavin C. Conant,Dong Xu:
  Effects of evolutionary pressure on histone modifications.BIBM2017:2267
• 
  [c47]
  Chunhui Xu,Wangren Qiu,Xuan Xiao,Dong Xu:
  Computational prediction of ubiquitination protein using evolutionary profiles and functional domains.BIBM2017:2296
• 
  [c46]
  Penghui Shang,Duolin Wang,Dongpeng Liu,Dong Xu:
  A deep-learning framework for amidation site prediction.BIBM2017:2302
• 
  [c45]
  Lingtao Su,Dong Xu,Guixia Liu:
  A new method for disease-related gene prioritization.BIBM2017:2315
• 
  [c44]
  Juexin Wang,Zhen Lyu,Shakhawat Hossain,Gary Stacey,Dong Xu,Trupti Joshi:
  SoyTSN: A web-based prediction tool for soybean tissue specific network within SoyKB.BIBM2017:2326
• 
  [c43]
  Chao Fang,Yi Shang,Dong Xu:
  A New Deep Neighbor Residual Network for Protein Secondary Structure Prediction.ICTAI2017:66-71
• 
  [c42]
  Zhaoyu Li,Son P. Nguyen,Dong Xu,Yi Shang:
  Protein Loop Modeling Using Deep Generative Adversarial Network.ICTAI2017:1085-1091
• 
  [i2]
  Chao Fang,Yi Shang,Dong Xu:
  MUFold-SS: Protein Secondary Structure Prediction Using Deep Inception-Inside-Inception Networks.CoRRabs/1709.06165 (2017)
• 2016
• 
  [j55]
  Chao Wang,Haicang Zhang,Wei-Mou Zheng,Dong Xu,Jianwei Zhu,Bing Wang,Kang Ning,Shiwei Sun,Shuai Cheng Li,Dongbo Bu:
  FALCON@home: a high-throughput protein structure prediction server based on remote homologue recognition.Bioinform.32(3):462-464 (2016)
• 
  [j54]
  Yang Liu,Saad M. Khan,Juexin Wang,Mats Rynge,Yuanxun Zhang,Shuai Zeng,Shiyuan Chen,João V. Maldonado dos Santos,Babu Valliyodan,Prasad Calyam,Nirav C. Merchant,Henry T. Nguyen,Dong Xu,Trupti Joshi:
  PGen: large-scale genomic variations analysis workflow and browser in SoyKB.BMC Bioinform.17(S-13):337 (2016)
• 
  [j53]
  Hao Zhang,Yanpu Li,Yuanning Liu,Haiming Liu,Hongyu Wang,Wen Jin,Yanmei Zhang,Chao Zhang,Dong Xu:
  Role of plant MicroRNA in cross-species regulatory networks of humans.BMC Syst. Biol.10:60 (2016)
• 
  [j52]
  Hongbo Li,Yanchun Liang,Ning Zhang,Jinsong Guo,Dong Xu,Zhanshan Li:
  Improving degree-based variable ordering heuristics for solving constraint satisfaction problems.J. Heuristics22(2):125-145 (2016)
• 
  [c41]
  Matthew Dickinson,Saptarshi Debroy,Prasad Calyam,Samaikya Valluripally,Yuanxun Zhang,Trupti Joshi,Dong Xu:
  End-to-End Security Formalization and Alignment for Federated Workflow Management.CLOUD2016:59-67
• 
  [c40]
  Zainab Al-Taie,Nattaphon Thanintorn,Ilker Ersoy,Richard D. Hammer,Dong Xu,Trupti Joshi,Dmitriy Shin:
  Complexity Reduction and Visualization of RDF Knowledge Networks for Precision medicine.AMIA2016
• 
  [c39]
  Guitao Cao,Jie Ding,Ye Duan,Liping Tu,Jiatuo Xu,Dong Xu:
  Classification of tongue images based on doublet and color space dictionary.BIBM2016:1170-1175
• 
  [c38]
  Dan Meng,Guitao Cao,Ye Duan,Minghua Zhu,Liping Tu,Jiatuo Xu,Dong Xu:
  A deep tongue image features analysis model for medical application.BIBM2016:1918-1922
• 
  [c37]
  Nattaphon Thanintorn,Juexin Wang,Ilker Ersoy,Zainab Al-Taie,Yuexu Jiang,Duolin Wang,Megha Verma,Trupti Joshi,Richard D. Hammer,Dong Xu,Dmitriy Shin:
  RDF Sketch Maps - Knowledge Complexity Reduction for Precision Medicine Analytics.PSB2016:417-428
• 
  [r1]
  Qiuming Yao,Jianjiong Gao,Dong Xu:
  Musite: Tool for Predicting Protein Phosphorylation Sites.Encyclopedia of Algorithms2016:1393-1397
• 2015
• 
  [j51]
  Dong Xu,Kun Huang,Jeanette Schmidt:
  Guest Editors Introduction to the Special Issue on Software and Databases.IEEE ACM Trans. Comput. Biol. Bioinform.12(4):793-794 (2015)
• 2014
• 
  [j50]
  Rui Liu,Xiangtian Yu,Xiaoping Liu,Dong Xu,Kazuyuki Aihara,Luonan Chen:
  Identifying critical transitions of complex diseases based on a single sample.Bioinform.30(11):1579-1586 (2014)
• 
  [j49]
  Trupti Joshi,Robert Williamson,Kapil Patil,Suwit Viyanon,Xiangge Li,Yufu Zhang,Wenchuan Qi,Dong Li,Jeremy Zimmer,Uday Illindala,Shawn Foley,Robert Campbell,Ye Duan,Dong Xu:
  Virtual physical examination (VPE): a multimedia system for education in medicine.Int. J. Funct. Informatics Pers. Medicine4(3/4):181-197 (2014)
• 
  [j48]
  Qiuming Yao,Huangyi Ge,Shangquan Wu,Ning Zhang,Wei Chen,Chunhui Xu,Jianjiong Gao,Jay J. Thelen,Dong Xu:
  P³DB 3.0: From plant phosphorylation sites to protein networks.Nucleic Acids Res.42(Database-Issue):1206-1213 (2014)
• 
  [j47]
  Trupti Joshi,Michael R. Fitzpatrick,Shiyuan Chen,Yang Liu,Hongxin Zhang,Ryan Z. Endacott,Eric C. Gaudiello,Gary Stacey,Henry T. Nguyen,Dong Xu:
  Soybean knowledge base (SoyKB): a web resource for integration of soybean translational genomics and molecular breeding.Nucleic Acids Res.42(Database-Issue):1245-1252 (2014)
• 
  [c36]
  Yan Chen,Yi Shang,Dong Xu:
  Multi-dimensional scaling and MODELLER-based evolutionary algorithms for protein model refinement.IEEE Congress on Evolutionary Computation2014:1038-1045
• 
  [c35]
  Son P. Nguyen,Yi Shang,Dong Xu:
  DL-PRO: A novel deep learning method for protein model quality assessment.IJCNN2014:2071-2078
• 
  [i1]
  Jianjiong Gao,Chao Zhang,Martijn P. van Iersel,Li Zhang,Dong Xu,Nikolaus Schultz,Alexander R. Pico:
  BridgeDb app: unifying identifier mapping services for Cytoscape.F1000Research3:148 (2014)
• 2013
• 
  [j46]
  Chao Zhang,Jiguang Wang,Kristina Hanspers,Dong Xu,Luonan Chen,Alexander R. Pico:
  NOA: a cytoscape plugin for network ontology analysis.Bioinform.29(16):2066-2067 (2013)
• 
  [j45]
  Trupti Joshi,Babu Valliyodan,Jeng-Hung Wu,Suk-Ha Lee,Dong Xu,Henry T. Nguyen:
  Genomic differences between cultivated soybean, G. max and its wild relative G. soja.BMC Genom.14(S-1):S5 (2013)
• 
  [j44]
  Hao Zhang,Zhi Li,Yanpu Li,Yuanning Liu,Junxin Liu,Xin Li,Tingjie Shen,Yunna Duan,Minggang Hu,Dong Xu:
  A computational method for predicting regulation of human microRNAs on the influenza virus genome.BMC Syst. Biol.7(S-2):S3 (2013)
• 
  [j43]
  Qingguo Wang,Charles Shang,Dong Xu,Yi Shang:
  New MDS and Clustering Based Algorithms for protein Model Quality Assessment and Selection.Int. J. Artif. Intell. Tools22(5) (2013)
• 
  [j42]
  Yuanning Liu,Ya-Ping Chang,Dong Xu,Zhi Li,Hao Zhang,Jie Li,Mingyao Tian:
  Optimised design of siRNA based on multi-featured comparison and analysis of H1N1 virus.Int. J. Data Min. Bioinform.7(4):345-357 (2013)
• 
  [j41]
  Yuanning Liu,Yaping Chang,Chao Zhang,Qingkai Wei,Jingbo Chen,Hui-Ling Chen,Dong Xu:
  Influence of mRNA Features on siRNA Interference Efficacy.J. Bioinform. Comput. Biol.11(3) (2013)
• 
  [c34]
  Trupti Joshi,Michael R. Fitzpatrick,Shiyuan Chen,Yang Liu,Hongxin Zhang,Ryan Z. Endacott,Eric C. Gaudiello,Gary Stacey,Henry T. Nguyen,Dong Xu:
  Soybean knowledge base (SoyKB): Bridging the gap between soybean translational genomics and breeding.BIBM2013:42-44
• 2012
• 
  [j40]
  Chao Zhang,Kristina Hanspers,Allan Kuchinsky,Nathan Salomonis,Dong Xu,Alexander R. Pico:
  Mosaic: making biological sense of complex networks.Bioinform.28(14):1943-1944 (2012)
• 
  [j39]
  Trupti Joshi,Kapil Patil,Michael R. Fitzpatrick,D. Franklin Levi,Qiuming Yao,Jeffrey R. Cook,Zheng Wang,Marc Libault,Laurent Brechenmacher,Babu Valliyodan,Xiaolei Wu,Jianlin Cheng,Gary Stacey,Henry T. Nguyen,Dong Xu:
  Soybean Knowledge Base (SoyKB): a web resource for soybean translational genomics.BMC Genom.13(S-1):S15 (2012)
• 
  [j38]
  Ratchadaporn Kanawong,Wentao Xu,Dong Xu,Shao Li,Tao Ma,Ye Duan:
  An automatic tongue detection and segmentation framework for computer-aided tongue image analysis.Int. J. Funct. Informatics Pers. Medicine4(1):56-68 (2012)
• 
  [j37]
  Chao Zhang,Guolu Zheng,Shunfu Xu,Dong Xu:
  Computational Challenges in Characterization of Bacteria and Bacteria-Host Interactions Based on Genomic Data.J. Comput. Sci. Technol.27(2):225-239 (2012)
• 
  [c33]
  Tayo Obafemi-Ajayi,Ratchadaporn Kanawong,Dong Xu,Shao Li,Ye Duan:
  Features for automated tongue image shape classification.BIBM Workshops2012:273-279
• 
  [c32]
  Ratchadaporn Kanawong,Tayo Obafemi-Ajayi,Jun Yu,Dong Xu,Shao Li,Ye Duan:
  ZHENG classification in Traditional Chinese Medicine based on modified specular-free tongue images.BIBM Workshops2012:288-294
• 
  [c31]
  Hao Zhang,Xin Li,Yuanning Liu,Zhi Li,Minggang Hu,Dong Xu:
  Human encoded miRNAs that regulate the inflenenza virus genome.ISB2012:22-25
• 
  [c30]
  Jingfen Zhang,Dong Xu:
  Protein Structure Prediction and Clustering Using MUFOLD.ISBRA2012:328-329
• 
  [c29]
  Jianjiong Gao,Dong Xu:
  Correlation Between Posttranslational Modification and Intrinsic Disorder in Protein.Pacific Symposium on Biocomputing2012:94-103
• 2011
• 
  [j36]
  Guan Ning Lin,Chao Zhang,Dong Xu:
  Polytomy identification in microbial phylogenetic reconstruction.BMC Syst. Biol.5(S-3):S2 (2011)
• 
  [j35]
  Liupu Wang,Juexin Wang,Michael Wang,Yanchun Liang,Dong Xu:
  User experience evaluation of Google search for obtaining medical knowledge: a case study.Int. J. Data Min. Bioinform.5(6):626-639 (2011)
• 
  [j34]
  Qingguo Wang,Yi Shang,Dong Xu:
  Improving a Consensus Approach for Protein Structure Selection by Removing Redundancy.IEEE ACM Trans. Comput. Biol. Bioinform.8(6):1708-1715 (2011)
• 
  [c28]
  Juexin Wang,Fan Zhang,Yan Wang,Yuan Fu,Dong Xu,Yanchun Liang:
  Identification of Salt Tolerance Genes in Rice from Microarray Data using SVM-RFE.BICoB2011:30-35
• 
  [c27]
  Qingguo Wang,Yi Shang,Dong Xu:
  A Hybrid Consensus and Clustering Method for Protein Structure Selection.ICTAI2011:1-8
• 2010
• 
  [j33]
  Dongyu Zhao,Yan Wang,Di Luo,Xiaohu Shi,Liupu Wang,Dong Xu,Jun Yu,Yanchun Liang:
  PMirP: A pre-microRNA prediction method based on structure-sequence hybrid features.Artif. Intell. Medicine49(2):127-132 (2010)
• 
  [j32]
  Trupti Joshi,Zhe Yan,Marc Libault,Dong-Hoon Jeong,Sunhee Park,Pamela J. Green,D. Janine Sherrier,Andrew Farmer,Greg May,Blake C. Meyers,Dong Xu,Gary Stacey:
  Prediction of novel miRNAs and associated target genes inGlycine max.BMC Bioinform.11(S-1):14 (2010)
• 
  [j31]
  Jianjiong Gao,Dong Xu:
  The Musite open-source framework for phosphorylation-site prediction.BMC Bioinform.11(S-12):S9 (2010)
• 
  [j30]
  Guan Ning Lin,Zheng Wang,Dong Xu,Jianlin Cheng:
  SeqRate: sequence-based protein folding type classification and rates prediction.BMC Bioinform.11(S-3):1 (2010)
• 
  [j29]
  Gyan Prakash Srivastava,Ping Li,Jingdong Liu,Dong Xu:
  Identification of transcription factor's targets using tissue-specific transcriptomic data in Arabidopsis thaliana.BMC Syst. Biol.4(S-2):S2 (2010)
• 
  [j28]
  Gyan Prakash Srivastava,Jing Qiu,Dong Xu:
  Genome-wide functional annotation by integrating multiple microarray datasets using meta-analysis.Int. J. Data Min. Bioinform.4(4):357-376 (2010)
• 
  [j27]
  Chi-Ren Shyu,Bin Pang,Pin-Hao Chi,Nan Zhao,Dmitry Korkin,Dong Xu:
  ProteinDBS v2.0: a web server for global and local protein structure search.Nucleic Acids Res.38(Web-Server-Issue):53-58 (2010)
• 
  [c26]
  Trupti Joshi,Qiuming Yao,D. Franklin Levi,Laurent Brechenmacher,Babu Valliyodan,Gary Stacey,Henry T. Nguyen,Dong Xu:
  SoyMetDB: The soybean metabolome database.BIBM2010:203-208
• 
  [c25]
  Chao Zhang,Shunfu Xu,Dong Xu:
  Detection and application of CagA sequence markers for assessing risk factor of gastric cancer caused by Helicobacter pylori.BIBM2010:485-488
• 
  [c24]
  Qingguo Wang,Yi Shang,Dong Xu:
  Protein structure selection based on consensus.IEEE Congress on Evolutionary Computation2010:1-7
• 
  [p1]
  Zhao Song,Luonan Chen,Dong Xu:
  Bioinformatics Methods for Protein Identification Using Peptide Mass Fingerprinting.Proteome Bioinformatics2010:7-22

• 2009
• 
  [j26]
  Guan Ning Lin,Zhipeng Cai,Guohui Lin,Sounak Chakraborty,Dong Xu:
  ComPhy: prokaryotic composite distance phylogenies inferred from whole-genome gene sets.BMC Bioinform.10(S-1) (2009)
• 
  [j25]
  Dong Xu:
  Mutual understanding between Traditional Chinese Medicine and systems biology: gaps, challenges and opportunities.Int. J. Funct. Informatics Pers. Medicine2(3):248-260 (2009)
• 
  [j24]
  Jianjiong Gao,Ganesh Kumar Agrawal,Jay J. Thelen,Dong Xu:
  P³DB: a plant protein phosphorylation database.Nucleic Acids Res.37(Database-Issue):960-962 (2009)
• 
  [c23]
  Guan Ning Lin,Zheng Wang,Dong Xu,Jianlin Cheng:
  Sequence-Based Prediction of Protein Folding Rates Using Contacts, Secondary Structures and Support Vector Machines.BIBM2009:3-8
• 
  [c22]
  Jianjiong Gao,Ganesh Kumar Agrawal,Jay J. Thelen,Zoran Obradovic,A. Keith Dunker,Dong Xu:
  A New Machine Learning Approach for Protein Phosphorylation Site Prediction in Plants.BICoB2009:18-29
• 
  [e1]
  Dacheng Tao,Dong Xu,Xuelong Li:
  Semantic Mining Technologies for Multimedia Databases.IGI Global2009, ISBN978-1-60566-188-9[contents]
• 2008
• 
  [b1]
  Dong Xu,James M. Keller,Mihail Popescu,Rajkumar Bondugula:
  Applications of Fuzzy Logic in Bioinformatics.Series on Advances in Bioinformatics and Computational Biology 9,WorldScientific2008, ISBN978-1-84816-258-7, pp. 1-248
• 
  [j23]
  Christopher A. Bottoms,Dong Xu:
  Wanted: unique names for unique atom positions. PDB-wide analysis of diastereotopic atom names of small molecules containing diphosphate.BMC Bioinform.9(S-9) (2008)
• 
  [j22]
  Chao Zhang,Trupti Joshi,Guan Ning Lin,Dong Xu:
  An integrated probabilistic approach for gene function prediction using multiple sources of high-throughput data.Int. J. Comput. Biol. Drug Des.1(3):254-274 (2008)
• 
  [j21]
  Robin Kramer,Dong Xu:
  Projecting Gene Expression Trajectories through Inducing Differential Equations from Microarray Time Series Experiments.J. Signal Process. Syst.50(3):321-329 (2008)
• 
  [c21]
  Qingguo Wang,Yi Shang,Dong Xu:
  A new clustering-based method for protein structure selection.IJCNN2008:2891-2898
• 2007
• 
  [c20]
  Mihail Popescu,Dong Xu,Erik Taylor:
  GoFuzzKegg: Mapping Genes to KEGG Pathways Using an Ontological Fuzzy Rule System.CIBCB2007:298-303
• 
  [c19]
  Mihail Popescu,Dong Xu:
  Mapping Genes to Pathways Using Ontological Fuzzy Rule Systems.FUZZ-IEEE2007:1-6
• 2006
• 
  [j20]
  Yong Wang,Trupti Joshi,Xiang-Sun Zhang,Dong Xu,Luonan Chen:
  Inferring gene regulatory networks from multiple microarray datasets.Bioinform.22(19):2413-2420 (2006)
• 
  [j19]
  Pin-Hao Chi,Chi-Ren Shyu,Dong Xu:
  A fast SCOP fold classification system using content-based E-Predict algorithm.BMC Bioinform.7:362 (2006)
• 
  [j18]
  Xiaomeng Wu,Xiu-Feng Wan,Gang Wu,Dong Xu,Guohui Lin:
  Phylogenetic analysis using complete signature information of whole genomes and clustered Neighbour-Joining method.Int. J. Bioinform. Res. Appl.2(3):219-248 (2006)
• 
  [j17]
  X.-F. Wan,J. Zhou,Dong Xu:
  CodonO: a new informatics method for measuring synonymous codon usage bias within and across genomes.Int. J. Gen. Syst.35(1):109-125 (2006)
• 
  [j16]
  Xiu-Feng Wan,Guohui Lin,Dong Xu:
  Rnall: an Efficient Algorithm for Predicting Rna Local Secondary Structural Landscape in Genomes.J. Bioinform. Comput. Biol.4(5):1015-1032 (2006)
• 
  [c18]
  Zhao Song,Luonan Chen,Chao Zhang,Dong Xu:
  Design and Implementation of Probability-Based Scoring Function for Peptide Mass Fingerprinting Protein Identification.EMBC2006:4556-4559
• 
  [c17]
  Rajkumar Bondugula,Dong Xu,Yi Shang:
  A Fast Algorithm for Low-Resolution Protein Structure Prediction.EMBC2006:5826-5829
• 
  [c16]
  Dong Xu,Rajkumar Bondugula,Mihail Popescu,James M. Keller:
  Bioinformatics and Fuzzy Logic.FUZZ-IEEE2006:817-824
• 
  [c15]
  Robin Kramer,Victor Olman,Ying Xu,Dong Xu:
  DigitalTree: A Tool for Displaying Biological Data in Tree Structure.International Conference on Computational Science (2)2006:855-862
• 
  [c14]
  Yong Wang,Trupti Joshi,Dong Xu,Xiang-Sun Zhang,Luonan Chen:
  Supervised Inference of Gene Regulatory Networks by Linear Programming.ICIC (3)2006:551-561
• 2005
• 
  [j15]
  Trupti Joshi,Yu Chen,Nickolai Alexandrov,Dong Xu:
  Cellular function prediction and biological pathway discovery in Arabidopsis thaliana using microarray data.Int. J. Bioinform. Res. Appl.1(3):335-350 (2005)
• 
  [j14]
  Zhi-Zhong Chen,Guohui Lin,Romeo Rizzi,Jianjun Wen,Dong Xu,Ying Xu,Tao Jiang:
  More Reliable Protein NMR Peak Assignment via Improved 2-Interval Scheduling.J. Comput. Biol.12(2):129-146 (2005)
• 
  [c13]
  Rajkumar Bondugula,Ognen Duzlevski,Dong Xu:
  Profiles and fuzzy K-nearest neighbor algorithm for protein secondary structure prediction.APBC2005:85-94
• 
  [c12]
  Xiaomeng Wu,Guohui Lin,Xiu-Feng Wan,Dong Xu:
  Whole Genome Phylogeny Based on Clustered Signature String Composition.CSB Workshops2005:53-54
• 2004
• 
  [j13]
  Jun-tao Guo,Kyle Ellrott,Won Jae Chung,Dong Xu,Sergei Passovets,Ying Xu:
  PROSPECT-PSPP: an automatic computational pipeline for protein structure prediction.Nucleic Acids Res.32(Web-Server-Issue):522-525 (2004)
• 
  [j12]
  Chi-Ren Shyu,Pin-Hao Chi,Grant J. Scott,Dong Xu:
  ProteinDBS: a real-time retrieval system for protein structure comparison.Nucleic Acids Res.32(Web-Server-Issue):572-575 (2004)
• 2003
• 
  [j11]
  Manesh J. Shah,Sergei Passovets,Dongsup Kim,Kyle Ellrott,Li Wang,Inna Vokler,Philip F. LoCascio,Dong Xu,Ying Xu:
  A computational pipeline for protein structure prediction and analysis at genome scale.Bioinform.19(15):1985-1996 (2003)
• 
  [j10]
  Victor Olman,Dong Xu,Ying Xu:
  Cubic: Identification of Regulatory Binding Sites through Data Clustering.J. Bioinform. Comput. Biol.1(1):21-40 (2003)
• 
  [j9]
  Guohui Lin,Dong Xu,Zhi-Zhong Chen,Tao Jiang,Jianjun Wen,Ying Xu:
  Computational Assignment of Protein Backbone Nmr Peaks Byefficient Bounding and Filtering.J. Bioinform. Comput. Biol.1(2):387-410 (2003)
• 
  [j8]
  Zhi-Zhong Chen,Tao Jiang,Guo-Hui Lin,Jianjun Wen,Dong Xu,Jinbo Xu,Ying Xu:
  Approximation algorithms for NMR spectral peak assignment.Theor. Comput. Sci.299(1-3):211-229 (2003)
• 
  [c11]
  Manesh J. Shah,Sergei Passovets,Dongsup Kim,Kyle Ellrott,Li Wang,Inna Vokler,Philip F. LoCascio,Dong Xu,Ying Xu:
  A Computational Pipeline for Protein Structure Prediction and Analysis at Genome Scale.BIBE2003:3-10
• 
  [c10]
  Yu Chen,Trupti Joshi,Ying Xu,Dong Xu:
  Towards Automated Derivation of Biological Pathways Using High-Throughput Biological Data.BIBE2003:18-25
• 
  [c9]
  Xiang Wan,Dong Xu,Carolyn M. Slupsky,Guohui Lin:
  Automated Protein NMR Resonance Assignments.CSB2003:197-208
• 
  [c8]
  Jane Razumovskaya,Victor Olman,Dong Xu,Edward C. Uberbacher,Nathan Verberkmoes,Ying Xu:
  A Computational Method for Assessing Peptide-Identification Reliability in Tandem Mass Spectrometry Analysis with SEQUEST.CSB2003:421-423
• 
  [c7]
  Victor Olman,Dong Xu,Ying Xu:
  CUBIC: Identification of Regulatory Binding Sites Through Data Clustering.CSB2003:448-449
• 
  [c6]
  Zhi-Zhong Chen,Tao Jiang,Guohui Lin,Romeo Rizzi,Jianjun Wen,Dong Xu,Ying Xu:
  More Reliable Protein NMR Peak Assignment via Improved 2-Interval Scheduling.ESA2003:580-592
• 
  [c5]
  Victor Olman,Dong Xu,Ying Xu:
  Identification of Regulatory Binding Sites Using Minimum Spanning Trees.Pacific Symposium on Biocomputing2003:327-338
• 2002
• 
  [j7]
  Ying Xu,Victor Olman,Dong Xu:
  Clustering gene expression data using a graph-theoretic approach: an application of minimum spanning trees.Bioinform.18(4):536-545 (2002)
• 
  [j6]
  Dong Xu,Guangshan Li,Liyou Wu,Jizhong Zhou,Ying Xu:
  PRIMEGENS: robust and efficient design of gene-specific probes for microarray analysis.Bioinform.18(11):1432-1437 (2002)
• 
  [j5]
  Ying Xu,Dong Xu,Dongsup Kim,Victor Olman,Jane Razumovskaya,Tao Jiang:
  Automated assignment of backbone NMR peaks using constrained bipartite matching.Comput. Sci. Eng.4(1):50-62 (2002)
• 
  [c4]
  Guo-Hui Lin,Dong Xu,Zhi-Zhong Chen,Tao Jiang,Jianjun Wen,Ying Xu:
  An Efficient Branch-and-Bound Algorithm for the Assignment of Protein Backbone NMR Peaks.CSB2002:165-174
• 
  [c3]
  Zhi-Zhong Chen,Tao Jiang,Guo-Hui Lin,Jianjun Wen,Dong Xu,Ying Xu:
  Improved Approximation Algorithms for NMR Spectral Peak Assignment.WABI2002:82-96
• 2000
• 
  [j4]
  Dong Xu,Michael A. Unseren,Ying Xu,Edward C. Uberbacher:
  Sequence-structure specificity of a knowledge based energy function at the secondary structure level.Bioinform.16(3):269-285 (2000)
• 
  [j3]
  Ying Xu,Dong Xu,Harold N. Gabow:
  Protein domain decomposition using a graph-theoretic approach.Bioinform.16(12):1091-1104 (2000)
• 
  [j2]
  Ying Xu,Dong Xu,Oakley H. Crawford,J. Ralph Einstein:
  A Computational Method for NMR-Constrained Protein Threading.J. Comput. Biol.7(3-4):449-467 (2000)
• 
  [c2]
  Ying Xu,Dong Xu,Oakley H. Crawford,J. Ralph Einstein,Engin Serpersu:
  Protein structure determination using protein threading and sparse NMR data (extended abstract).RECOMB2000:299-307

• 1998
• 
  [j1]
  Ying Xu,Dong Xu,Edward C. Uberbacher:
  An Efficient Computational Method for Globally Optimal Threading.J. Comput. Biol.5(3):597-614 (1998)
• 
  [c1]
  Ying Xu,Dong Xu,Edward C. Uberbacher:
  A new method for modeling and solving the protein fold recognition problem (extended abstract).RECOMB1998:285-292