Dong Xu - RankMe

218 papers A 1B 14C 4Misc 7Journal 133Unranked 55

Year	Rank	Type	Title / Venue / Authors
2026	J	`jnl`	Applications of Large Language Models and Prompt Optimization for Knowledge Extraction From Biological Pathway Figures. IEEE J. Biomed. Health Informatics Muhammad Azam, Shuai Zeng, Hasanain Aldihis, Mihail Popescu, Dong Xu
2026	J	`jnl`	TOM: An open-source tongue segmentation method with multi-teacher distillation and task-specific data augmentation. Expert Syst. Appl. Jiacheng Xie, Ziyang Zhang, Biplab Poudel, Congyu Guo, Yang Yu, Guanghui An, Xiaoting Tang, Lening Zhao, Chunhui Xu, Dong Xu
2026	J	`jnl`	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. Sohaib Asif, Fazal Hadi, Qurrat-ul-ain, Yuqi Yan, Vicky Yang Wang, Dong Xu
2025	J	`jnl`	A deep learning based approach for automatic cardiac events identification. Biomed. Signal Process. Control. Yuanshu Li, Kexin Hong, Xiaohu Shi, Wei Pang, Yubin Xiao, Peng Zhao, Dong Xu, Chunli Song, Xu Zhou, You Zhou
2025	J	`jnl`	Agentic RAG-Driven Multi-Omics Analysis for PI3K/AKT Pathway Deregulation in Precision Medicine. Algorithms Micheal Olaolu Arowolo, Sulaiman Olaniyi Abdulsalam, Rafiu Mope Isiaka, Kingsley Theophilus Igulu, Bukola Fatimah Balogun, Mihail Popescu, Dong Xu
2025	J	`jnl`	BenCao: An Instruction-Tuned Large Language Model for Traditional Chinese Medicine. CoRR Jiacheng Xie, Yang Yu, Yibo Chen, Hanyao Zhang, Lening Zhao, Jiaxuan He, Lei Jiang, Xiaoting Tang, Guanghui An, Dong Xu
2025	J	`jnl`	Bridging peptide presentation and T cell recognition with multi-task learning. Nat. Mac. Intell. Li Su, Duolin Wang, Dong Xu
2025	J	`jnl`	Deep learning-driven modality imputation and subregion segmentation to enhance high-grade glioma grading. BMC Medical Informatics Decis. Mak. 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
2025	J	`jnl`	Large Language Models and Prompt-Based Learning: Frontiers and Challenges in Cross-Disciplinary Applications. Int. J. Artif. Intell. Robotics Res. Yibo Chen, Gangqing Hu, Chun Xia, Lihua Yu, Mihail Popescu, Dong Xu
2025	J	`jnl`	Leveraging Group Relative Policy Optimization to Advance Large Language Models in Traditional Chinese Medicine. CoRR Jiacheng Xie, Shuai Zeng, Yang Yu, Xiaoting Tang, Guanghui An, Dong Xu
2025	J	`jnl`	MULoc-target: Targeting peptide classification and detection using a protein language model. Briefings Bioinform. Yuexu Jiang, Duolin Wang, Shuai Zeng, Yichuan Zhang, Lei Jiang, Mahdi Pourmirzaei, Negin Manshour, Farzaneh Esmaili, Weinan Zhang, Ian Max Møller, Dong Xu
2025	J	`jnl`	Reinforcement Learning-Based Nonautoregressive Solver for Traveling Salesman Problems. IEEE Trans. Neural Networks Learn. Syst. Yubin Xiao, Di Wang, Boyang Li, Huanhuan Chen, Wei Pang, Xuan Wu, Hao Li, Dong Xu, Yanchun Liang, You Zhou
2025	J	`jnl`	Relation equivariant graph neural networks to explore the mosaic-like tissue architecture of kidney diseases on spatially resolved transcriptomics. Bioinform. 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
2025	—	`conf`	Synthetic Aperture Radar Change Detection as a Source of Ground-Truth Annotation for Machine Learning Deforestation Detection in the Amazon Using Multispectral Satellite Imagery. AIPR Andrew Kalukin, Joe Soundarajan, Dong Xu, Renaldi Gondosubroto
2025	J	`jnl`	TCM-Ladder: A Benchmark for Multimodal Question Answering on Traditional Chinese Medicine. CoRR Jiacheng Xie, Yang Yu, Ziyang Zhang, Shuai Zeng, Jiaxuan He, Ayush Vasireddy, Xiaoting Tang, Congyu Guo, Lening Zhao, Congcong Jing, Guanghui An, Dong Xu
2025	J	`jnl`	TOM: An Open-Source Tongue Segmentation Method with Multi-Teacher Distillation and Task-Specific Data Augmentation. CoRR Jiacheng Xie, Ziyang Zhang, Biplab Poudel, Congyu Guo, Yang Yu, Guanghui An, Xiaoting Tang, Lening Zhao, Chunhui Xu, Dong Xu
2025	—	`conf`	Tokenizing RNA Structures: A Discrete Generative Approach to Represent the RNA Folding Landscapes. BIBM Hanbo Liu, Hao Zhang, Longyi Li, Xiyuan Mei, Enshuang Zhao, Yuheng Zhu, Yinfei Dai, Jingxun Cao, Dong Xu
2025	J	`jnl`	scBSP: a fast and accurate tool for identifying spatially variable features from high-resolution spatial omics data. Bioinform. Jinpu Li, Mauminah Raina, Yiqing Wang, Chunhui Xu, Li Su, Qi Guo, Ricardo Melo Ferreira, Michael T. Eadon, Qin Ma, Juexin Wang, Dong Xu
2025	J	`jnl`	spaLLM: enhancing spatial domain analysis in multi-omics data through large language model integration. Briefings Bioinform. Longyi Li, Liyan Dong, Hao Zhang, Dong Xu, Yongli Li
2024	J	`jnl`	A comprehensive evaluation of large language models in mining gene relations and pathway knowledge. Quant. Biol. Muhammad Azam, Yibo Chen, Micheal Olaolu Arowolo, Haowang Liu, Mihail Popescu, Dong Xu
2024	J	`jnl`	Bioinformatics and Biomedical Informatics with ChatGPT: Year One Review. CoRR Jinge Wang, Zien Cheng, Qiuming Yao, Li Liu, Dong Xu, Gangqing Hu
2024	J	`jnl`	Bioinformatics and biomedical informatics with ChatGPT: Year one review. Quant. Biol. Jinge Wang, Zien Cheng, Qiuming Yao, Li Liu, Dong Xu, Gangqing Hu
2024	J	`jnl`	Deep learning model for human-intuitive shoeprint reconstruction. Expert Syst. Appl. 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
2024	—	`conf`	Evaluation and Integration of Advanced AI Chatbots for Biological Pathway Curation. BIBM Muhammad Azam, Fei He, Krpns Santosh, Dong Xu, Mihail Popescu
2024	J	`jnl`	FatPlants: a comprehensive information system for lipid-related genes and metabolic pathways in plants. Database J. Biol. Databases Curation 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
2024	J	`jnl`	Iterative Prompt Refinement for Mining Gene Relationships from ChatGPT. Int. J. Artif. Intell. Robotics Res. Yibo Chen, Jeffrey Gao, Marius Petruc, Richard D. Hammer, Mihail Popescu, Dong Xu
2024	—	`conf`	LungX-Net: Lung Cancer Diagnosis from CT and Histopathological Images via Attention Based Multi-Level Feature Fusion Network. BIBM Sohaib Asif, Vicky Yang Wang, Dong Xu
2024	J	`jnl`	MSI-DTI: predicting drug-target interaction based on multi-source information and multi-head self-attention. Briefings Bioinform. Wenchuan Zhao, Yufeng Yu, Guosheng Liu, Yanchun Liang, Dong Xu, Xiaoyue Feng, Renchu Guan
2024	J	`jnl`	Mapping brain development against neurological disorder using contrastive sharing. Expert Syst. Appl. Muhammad Hassan, Jieqiong Lin, Ahmed Ameen Fateh, Yijang Zhuang, Guojun Yun, Adnan Zeb, Dong Xu, Hongwu Zeng
2024	J	`jnl`	NRIMD, a Web Server for Analyzing Protein Allosteric Interactions Based on Molecular Dynamics Simulation. J. Chem. Inf. Model. Yi He, Shuang Wang, Shuai Zeng, Jingxuan Zhu, Dong Xu, Weiwei Han, Juexin Wang
2024	J	`jnl`	Neural Architecture Search for Text Classification With Limited Computing Resources Using Efficient Cartesian Genetic Programming. IEEE Trans. Evol. Comput. Xuan Wu, Di Wang, Huanhuan Chen, Lele Yan, Yubin Xiao, Chunyan Miao, Hongwei Ge, Dong Xu, Yanchun Liang, Kangping Wang, Chunguo Wu, You Zhou
2024	J	`jnl`	On the Responsible Use of Chatbots in Bioinformatics. Genom. Proteom. Bioinform. Gang-Qing Hu, Li Liu, Dong Xu
2024	—	`conf`	PNESR-DDI: An Effective Drug-Drug Interaction Prediction Model Based on Pretraining Method and Enhanced Subgraph Reconstruction. BIBM Ke Chen, Xiaosong Han, Xiaoran Li, Yanchun Liang, Dong Xu, Renchu Guan
2024	—	`conf`	Predicting Gene Relations with a Graph Transformer Network Integrating DNA, Protein, and Descriptive Data. BIBM Yibo Chen, Dong Xu, Richard D. Hammer, Mihail Popescu
2024	B	`conf`	Prompt-Based Learning on Large Protein Language Models Improves Signal Peptide Prediction. RECOMB Shuai Zeng, Duolin Wang, Lei Jiang, Dong Xu
2024	J	`jnl`	SEOE: an option graph based semantically embedding method for prenatal depression detection. Frontiers Comput. Sci. Xiaosong Han, Mengchen Cao, Dong Xu, Xiaoyue Feng, Yanchun Liang, Xiaoduo Lang, Renchu Guan
2024	J	`jnl`	pathCLIP: Detection of Genes and Gene Relations From Biological Pathway Figures Through Image-Text Contrastive Learning. IEEE J. Biomed. Health Informatics Fei He, Kai Liu, Zhiyuan Yang, Yibo Chen, Richard D. Hammer, Dong Xu, Mihail Popescu
2023	J	`jnl`	Adapting Segment Anything Model (SAM) through Prompt-based Learning for Enhanced Protein Identification in Cryo-EM Micrographs. CoRR Fei He, Zhiyuan Yang, Mingyue Gao, Biplab Poudel, Newgin Sam Ebin Sam Dhas, Rajan Gyawali, Ashwin Dhakal, Jianlin Cheng, Dong Xu
2023	J	`jnl`	Contrastive self-supervised learning for diabetic retinopathy early detection. Medical Biol. Eng. Comput. Jihong Ouyang, Dong Mao, Zeqi Guo, Siguang Liu, Dong Xu, Wenting Wang
2023	J	`jnl`	Domain-Specific Topic Model for Knowledge Discovery in Computational and Data-Intensive Scientific Communities. IEEE Trans. Knowl. Data Eng. Yuanxun Zhang, Prasad Calyam, Trupti Joshi, Satish S. Nair, Dong Xu
2023	J	`jnl`	Efficient Self-learning Evolutionary Neural Architecture Search. Appl. Soft Comput. Zhengzhong Qiu, Wei Bi, Dong Xu, Hua Guo, Hongwei Ge, Yanchun Liang, Heow Pueh Lee, Chunguo Wu
2023	J	`jnl`	Large AI Models in Health Informatics: Applications, Challenges, and the Future. CoRR 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
2023	J	`jnl`	Large AI Models in Health Informatics: Applications, Challenges, and the Future. IEEE J. Biomed. Health Informatics 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
2023	J	`jnl`	MULocDeep web service for protein localization prediction and visualization at subcellular and suborganellar levels. Nucleic Acids Res. Yuexu Jiang, Lei Jiang, Chopparapu Sai Akhil, Duolin Wang, Ziyang Zhang, Weinan Zhang, Dong Xu
2023	J	`jnl`	Meta-learning for T cell receptor binding specificity and beyond. Nat. Mac. Intell. Duolin Wang, Fei He, Yang Yu, Dong Xu
2023	J	`jnl`	Reinforcement Learning-based Non-Autoregressive Solver for Traveling Salesman Problems. CoRR Yubin Xiao, Di Wang, Huanhuan Chen, Boyang Li, Wei Pang, Xuan Wu, Hao Li, Dong Xu, Yanchun Liang, You Zhou
2023	J	`jnl`	Semi-supervised active learning hypothesis verification for improved geometric expression in three-dimensional object recognition. Eng. Appl. Artif. Intell. Zhenhao Wang, Rui Xu, Tingyuan Nie, Dong Xu
2022	J	`jnl`	An Improved Topology Prediction of Alpha-Helical Transmembrane Protein Based on Deep Multi-Scale Convolutional Neural Network. IEEE ACM Trans. Comput. Biol. Bioinform. Yuning Yang, Jiawen Yu, Zhe Liu, Xi Wang, Han Wang, Zhiqiang Ma, Dong Xu
2022	J	`jnl`	Assessing deep learning methods in cis-regulatory motif finding based on genomic sequencing data. Briefings Bioinform. Shuangquan Zhang, Anjun Ma, Jing Zhao, Dong Xu, Qin Ma, Yan Wang
2022	—	`conf`	Comprehensive Assessment of OCR Tools for Gene Name Recognition in Biological Pathway Figures. BIBM Stuart Aldrich, Micheal Olaolu Arowolo, Fei He, Mihail Popescu, Dong Xu
2022	J	`jnl`	Discovering trends and hotspots of biosafety and biosecurity research via machine learning. Briefings Bioinform. Renchu Guan, Haoyu Pang, Yanchun Liang, Zhongjun Shao, Xin Gao, Dong Xu, Xiaoyue Feng
2022	—	`conf`	Evaluating template-based and template-free protein-peptide complex structure prediction using AlphaFold2. BIBM Negin Manshour, Yang Yu, Wenyuan Qin, Fei He, Duolin Wang, Dong Xu
2022	—	`conf`	Extraction of Gene Regulatory Relation Using BioBERT. BIBM Clement Essien, Fei He, Mark Hannink, Mihail Popescu, Dong Xu
2022	J	`jnl`	GUV-Net for high fidelity shoeprint generation. Complex Intell. Syst. Muhammad Hassan, Yan Wang, Wei Pang, Di Wang, Daixi Li, You Zhou, Dong Xu
2022	J	`jnl`	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. Muhammad Hassan, Yan Wang, Wei Pang, Di Wang, Daixi Li, You Zhou, Dong Xu
2022	—	`conf`	Integration of Gene Regulatory Pathways Found in the Literature in a Graph Database. BIBM Yibo Chen, Dong Xu, Mihail Popescu
2022	—	`conf`	Machine learning development environment for single-cell sequencing data analyses. BIBM Lei Jiang, Yuexu Jiang, Cankun Wang, Clement Essien, Juexin Wang, Anjun Ma, Qin Ma, Dong Xu
2022	—	`conf`	New Heuristic Methods for Protein Model Quality Assessment via Two-Stage Machine Learning and Hierarchical Ensemble. CogMI Junlin Wang, Wenbo Wang, Yi Shang, Dong Xu
2022	—	`conf`	Predicting Compound-Protein Interaction by Deepening the Systemic Background via Molecular Network Feature Embedding. BIBM Han Wang, Hangxu Zhu, Wenhao Li, Ming Liu, Li Zhang, Dong Xu
2022	J	`jnl`	RNALocate v2.0: an updated resource for RNA subcellular localization with increased coverage and annotation. Nucleic Acids Res. Tianyu Cui, Yiying Dou, Puwen Tan, Zhen Ni, Tianyuan Liu, Duolin Wang, Yan Huang, Kaican Cai, Xiaoyang Zhao, Dong Xu, Hao Lin, Dong Wang
2022	J	`jnl`	Restorable-inpainting: A novel deep learning approach for shoeprint restoration. Inf. Sci. Muhammad Hassan, Yan Wang, Di Wang, Wei Pang, Kangping Wang, Daixi Li, You Zhou, Dong Xu
2022	J	`jnl`	scGNN 2.0: a graph neural network tool for imputation and clustering of single-cell RNA-Seq data. Bioinform. Haocheng Gu, Hao Cheng, Anjun Ma, Yang Li, Juexin Wang, Dong Xu, Qin Ma
2021	—	`conf`	A Rule-Based Approach for Generating Synthetic Biological Pathways. CIBB Joshua Thompson, Haoyu Dong, Kai Liu, Fei He, Mihail Popescu, Dong Xu
2021	—	`conf`	Acupuncture and Tuina Knowledge Graph for Ancient Literature of Traditional Chinese Medicine. BIBM Xiaosong Han, Xiaoran Li, Yanchun Liang, Xinghao Wang, Dong Xu, Renchu Guan
2021	J	`jnl`	DeePaN: deep patient graph convolutional network integrating clinico-genomic evidence to stratify lung cancers for immunotherapy. npj Digit. Medicine Chao Fang, Dong Xu, Jing Su, Jonathan R. Dry, Bolan Linghu
2021	J	`jnl`	G2PDeep: a web-based deep-learning framework for quantitative phenotype prediction and discovery of genomic markers. Nucleic Acids Res. Shuai Zeng, Ziting Mao, Yijie Ren, Duolin Wang, Dong Xu, Trupti Joshi
2021	—	`conf`	Identifying Genes and Their Interactions from Pathway Figures and Text in Biomedical Articles. BIBM Fei He, Joshua Thompson, Ziting Mao, Yijie Ren, Yulia I. Nussbaum, Olha Kholod, Dmitriy Shin, Mark Hannink, Mihail Popescu, Dong Xu
2021	J	`jnl`	Multi-Cloud Performance and Security Driven Federated Workflow Management. IEEE Trans. Cloud Comput. Matthew Dickinson, Saptarshi Debroy, Prasad Calyam, Samaikya Valluripally, Yuanxun Zhang, Ronny Bazan Antequera, Trupti Joshi, Tommi A. White, Dong Xu
2021	J	`jnl`	Overlapping Community Detection Based on Membership Degree Propagation. Entropy Rui Gao, Shoufeng Li, Xiaohu Shi, Yanchun Liang, Dong Xu
2021	J	`jnl`	Quality Assessment of Protein Docking Models Based on Graph Neural Network. Frontiers Bioinform. Ye Han, Fei He, Yongbing Chen, Wenyuan Qin, Helong Yu, Dong Xu
2021	J	`jnl`	Recommender-as-a-service with chatbot guided domain-science knowledge discovery in a science gateway. Concurr. Comput. Pract. Exp. Komal Vekaria, Prasad Calyam, Sai Swathi Sivarathri, Songjie Wang, Yuanxun Zhang, Ashish Pandey, Cong Chen, Dong Xu, Trupti Joshi, Satish S. Nair
2021	—	`conf`	Text Mining Enhancements for Image Recognition of Gene Names and Gene Relations. CIBB Yijie Ren, Fei He, Jing Qu, Yifan Li, Joshua Thompson, Mark Hannink, Mihail Popescu, Dong Xu
2020	J	`jnl`	A dynamic programing approach to integrate gene expression data and network information for pathway model generation. Bioinform. Yuexu Jiang, Yanchun Liang, Duolin Wang, Dong Xu, Trupti Joshi
2020	J	`jnl`	A self-attention based message passing neural network for predicting molecular lipophilicity and aqueous solubility. J. Cheminformatics Bowen Tang, Skyler T. Kramer, Meijuan Fang, Yingkun Qiu, Zhen Wu, Dong Xu
2020	J	`jnl`	Deep Learning Analysis and Age Prediction from Shoeprints. CoRR Muhammad Hassan, Yan Wang, Di Wang, Daixi Li, Yanchun Liang, You Zhou, Dong Xu
2020	J	`jnl`	Fuzzified Image Enhancement for Deep Learning in Iris Recognition. IEEE Trans. Fuzzy Syst. Ming Liu, Zhiqian Zhou, Penghui Shang, Dong Xu
2020	J	`jnl`	MUFold-SSW: a new web server for predicting protein secondary structures, torsion angles and turns. Bioinform. Chao Fang, Zhaoyu Li, Dong Xu, Yi Shang
2020	J	`jnl`	MusiteDeep: a deep-learning based webserver for protein post-translational modification site prediction and visualization. Nucleic Acids Res. Duolin Wang, Dongpeng Liu, Jiakang Yuchi, Fei He, Yuexu Jiang, Siteng Cai, Jingyi Li, Dong Xu
2020	J	`jnl`	Two New Heuristic Methods for Protein Model Quality Assessment. IEEE ACM Trans. Comput. Biol. Bioinform. Wenbo Wang, Junlin Wang, Dong Xu, Yi Shang
2019	Misc	`conf`	An Informatics Framework for Knowledge Representation and Reconciliation of Disease Pathways. AMIA Yulia Innokenteva, Olha Kholod, Fei He, Duolin Wang, Richard D. Hammer, Dong Xu, Dmitriy Shin
2019	—	`conf`	Capsule Network for Predicting Zinc Binding Sites in Metalloproteins. BIBM Clement Essien, Duolin Wang, Dong Xu
2019	J	`jnl`	Capsule network for protein post-translational modification site prediction. Bioinform. Duolin Wang, Yanchun Liang, Dong Xu
2019	—	`conf`	DMCTOP: Topology Prediction of Alpha-Helical Transmembrane Protein Based on Deep Multi-Scale Convolutional Neural Network. BIBM Han Wang, Yuning Yang, Jiawen Yu, Xi Wang, Dawei Zhao, Dong Xu, Pingping Sun
2019	Misc	`conf`	DeepDom: Predicting protein domain boundary from sequence alone using stacked bidirectional. PSB Yuexu Jiang, Duolin Wang, Dong Xu
2019	J	`jnl`	Detection of Malfunctioning Smart Electricity Meter. CoRR Ming Liu, Dongpeng Liu, Guangyu Sun, Yi Zhao, Duolin Wang, Fangxing Liu, Xiang Fang, Qing He, Dong Xu
2019	—	`conf`	ESAE: Evolutionary Strategy-Based Architecture Evolution. BIC-TA (1) Xue Gu, Ziyao Meng, Yanchun Liang, Dong Xu, Han Huang, Xiaosong Han, Chunguo Wu
2019	—	`conf`	Extracting Molecular Entities and Their Interactions from Pathway Figures Based on Deep Learning. BCB Fei He, Duolin Wang, Yulia Innokenteva, Olha Kholod, Dmitriy Shin, Dong Xu
2019	—	`conf`	Extracting Molecular Entities and Their Interactions from Pathway Figures Based on Deep Learning. BIBM Fei He, Duolin Wang, Yulia Innokenteva, Olha Kholod, Dmitriy Shin, Dong Xu
2019	—	`conf`	Modeling of Contextual Information in Knowledge Graphs of Diagnostic Reports. SWH@ISWC Pericles S. Giannaris, Cynthia Tang, Olha Kholod, Steve Hanson, Chi-Ren Shyu, Richard D. Hammer, Dong Xu, Dmitriy Shin
2019	J	`jnl`	New Deep Learning Methods for Protein Loop Modeling. IEEE ACM Trans. Comput. Biol. Bioinform. Son P. Nguyen, Zhaoyu Li, Dong Xu, Yi Shang
2019	J	`jnl`	PSICA: a fast and accurate web service for protein model quality analysis. Nucleic Acids Res. Wenbo Wang, Zhaoyu Li, Junlin Wang, Dong Xu, Yi Shang
2019	J	`jnl`	Prediction of Protein Backbone Torsion Angles Using Deep Residual Inception Neural Networks. IEEE ACM Trans. Comput. Biol. Bioinform. Chao Fang, Yi Shang, Dong Xu
2019	—	`conf`	Protein Ubiquitylation and Sumoylation Site Prediction Based on Ensemble and Transfer Learning. BIBM Fei He, Rui Wang, Yanxin Gao, Duolin Wang, Yang Yu, Dong Xu, Xiaowei Zhao
2019	J	`jnl`	Sliding mode control with PI-based saturation for nano-positioning. Int. J. Wirel. Mob. Comput. Liu Yang, Dong Xu
2018	—	`conf`	A Data Mining Approach for Biomarker Discovery Using Transcriptomics in Endometriosis. BIBM Sadia Akter, Dong Xu, Susan C. Nagel, Trupti Joshi
2018	J	`jnl`	A content-based recommender system for computer science publications. Knowl. Based Syst. Donghui Wang, Yanchun Liang, Dong Xu, Xiaoyue Feng, Renchu Guan
2018	J	`jnl`	ADON: Application-Driven Overlay Network-as-a-Service for Data-Intensive Science. IEEE Trans. Cloud Comput. Ronny Bazan Antequera, Prasad Calyam, Saptarshi Debroy, Longhai Cui, Sripriya Seetharam, Matthew Dickinson, Trupti Joshi, Dong Xu, Tsegereda Beyene
2018	J	`jnl`	CarbonylDB: a curated data-resource of protein carbonylation sites. Bioinform. R. Shyama Prasad Rao, Ning Zhang, Dong Xu, Ian Max Møller
2018	—	`conf`	Domain-specific Topic Model for Knowledge Discovery through Conversational Agents in Data Intensive Scientific Communities. IEEE BigData Yuanxun Zhang, Prasad Calyam, Trupti Joshi, Satish S. Nair, Dong Xu
2018	J	`jnl`	G2S: a web-service for annotating genomic variants on 3D protein structures. Bioinform. Juexin Wang, Robert Sheridan, Selçuk Onur Sümer, Nikolaus Schultz, Dong Xu, Jianjiong Gao
2018	—	`conf`	Integrating Gene Expression Data and Pathway Knowledge for In Silico Hypothesis Generation with IMPRes. BIBM Yuexu Jiang, Duolin Wang, Dong Xu, Trupti Joshi
2018	—	`conf`	Knowledge Base Commons (KBCommons) v1.0: A multi OMICS' web-based data integration framework for biological discoveries. BIBM Shuai Zeng, Zhen Lyu, Siva Ratna Kumari Narisetti, Dong Xu, Trupti Joshi
2018	J	`jnl`	Whole-exome sequencing and microRNA profiling reveal PI3K/AKT pathway's involvement in juvenile myelomonocytic leukemia. Quant. Biol. Saad M. Khan, Jason E. Denney, Michael X. Wang, Dong Xu
2017	B	`conf`	A New Deep Neighbor Residual Network for Protein Secondary Structure Prediction. ICTAI Chao Fang, Yi Shang, Dong Xu
2017	—	`conf`	A deep-learning framework for amidation site prediction. BIBM Penghui Shang, Duolin Wang, Dongpeng Liu, Dong Xu
2017	—	`conf`	A multimodal deep architecture for large-scale protein ubiquitylation site prediction. BIBM Fei He, Lingling Bao, Rui Wang, Jiagen Li, Dong Xu, Xiaowei Zhao
2017	—	`conf`	A new method for disease-related gene prioritization. BIBM Lingtao Su, Dong Xu, Guixia Liu
2017	J	`jnl`	BioJava-ModFinder: identification of protein modifications in 3D structures from the Protein Data Bank. Bioinform. Jianjiong Gao, Andreas Prlic, Chunxiao Bi, Wolfgang Bluhm, Dimitris Dimitropoulos, Dong Xu, Philip E. Bourne, Peter W. Rose
2017	—	`conf`	Computational prediction of ubiquitination protein using evolutionary profiles and functional domains. BIBM Chunhui Xu, Wangren Qiu, Xuan Xiao, Dong Xu
2017	—	`conf`	Effects of evolutionary pressure on histone modifications. BIBM Saad M. Khan, Gavin C. Conant, Dong Xu
2017	—	`conf`	IMPRes: Integrative MultiOmics pathway resolution algorithm and tool. BIBM Yuexu Jiang, Yanchun Liang, Duolin Wang, Dong Xu, Trupti Joshi
2017	J	`jnl`	MUFold-SS: Protein Secondary Structure Prediction Using Deep Inception-Inside-Inception Networks. CoRR Chao Fang, Yi Shang, Dong Xu
2017	J	`jnl`	MusiteDeep: a deep-learning framework for general and kinase-specific phosphorylation site prediction. Bioinform. Duolin Wang, Shuai Zeng, Chunhui Xu, Wangren Qiu, Yanchun Liang, Trupti Joshi, Dong Xu
2017	J	`jnl`	OMPcontact: An Outer Membrane Protein Inter-Barrel Residue Contact Prediction Method. J. Comput. Biol. Li Zhang, Han Wang, Lun Yan, Lingtao Su, Dong Xu
2017	J	`jnl`	Overfitting Reduction of Text Classification Based on AdaBELM. Entropy Xiaoyue Feng, Yanchun Liang, Xiaohu Shi, Dong Xu, Xu Wang, Renchu Guan
2017	B	`conf`	Protein Loop Modeling Using Deep Generative Adversarial Network. ICTAI Zhaoyu Li, Son P. Nguyen, Dong Xu, Yi Shang
2017	—	`conf`	SoyTSN: A web-based prediction tool for soybean tissue specific network within SoyKB. BIBM Juexin Wang, Zhen Lyu, Shakhawat Hossain, Gary Stacey, Dong Xu, Trupti Joshi
2016	—	`conf`	A deep tongue image features analysis model for medical application. BIBM Dan Meng, Guitao Cao, Ye Duan, Minghua Zhu, Liping Tu, Jiatuo Xu, Dong Xu
2016	—	`conf`	Classification of tongue images based on doublet and color space dictionary. BIBM Guitao Cao, Jie Ding, Ye Duan, Liping Tu, Jiatuo Xu, Dong Xu
2016	Misc	`conf`	Complexity Reduction and Visualization of RDF Knowledge Networks for Precision medicine. AMIA Zainab Al-Taie, Nattaphon Thanintorn, Ilker Ersoy, Richard D. Hammer, Dong Xu, Trupti Joshi, Dmitriy Shin
2016	B	`conf`	End-to-End Security Formalization and Alignment for Federated Workflow Management. CLOUD Matthew Dickinson, Saptarshi Debroy, Prasad Calyam, Samaikya Valluripally, Yuanxun Zhang, Trupti Joshi, Dong Xu
2016	J	`jnl`	FALCON@home: a high-throughput protein structure prediction server based on remote homologue recognition. Bioinform. Chao Wang, Haicang Zhang, Wei-Mou Zheng, Dong Xu, Jianwei Zhu, Bing Wang, Kang Ning, Shiwei Sun, Shuai Cheng Li, Dongbo Bu
2016	J	`jnl`	Improving degree-based variable ordering heuristics for solving constraint satisfaction problems. J. Heuristics Hongbo Li, Yanchun Liang, Ning Zhang, Jinsong Guo, Dong Xu, Zhanshan Li
2016	—	`ch.`	Musite: Tool for Predicting Protein Phosphorylation Sites. Encyclopedia of Algorithms Qiuming Yao, Jianjiong Gao, Dong Xu
2016	J	`jnl`	PGen: large-scale genomic variations analysis workflow and browser in SoyKB. BMC Bioinform. 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
2016	Misc	`conf`	RDF Sketch Maps - Knowledge Complexity Reduction for Precision Medicine Analytics. PSB Nattaphon Thanintorn, Juexin Wang, Ilker Ersoy, Zainab Al-Taie, Yuexu Jiang, Duolin Wang, Megha Verma, Trupti Joshi, Richard D. Hammer, Dong Xu, Dmitriy Shin
2016	J	`jnl`	Role of plant MicroRNA in cross-species regulatory networks of humans. BMC Syst. Biol. Hao Zhang, Yanpu Li, Yuanning Liu, Haiming Liu, Hongyu Wang, Wen Jin, Yanmei Zhang, Chao Zhang, Dong Xu
2015	J	`jnl`	Guest Editors Introduction to the Special Issue on Software and Databases. IEEE ACM Trans. Comput. Biol. Bioinform. Dong Xu, Kun Huang, Jeanette Schmidt
2014	J	`jnl`	BridgeDb app: unifying identifier mapping services for Cytoscape. F1000Research Jianjiong Gao, Chao Zhang, Martijn P. van Iersel, Li Zhang, Dong Xu, Nikolaus Schultz, Alexander R. Pico
2014	B	`conf`	DL-PRO: A novel deep learning method for protein model quality assessment. IJCNN Son P. Nguyen, Yi Shang, Dong Xu
2014	J	`jnl`	Identifying critical transitions of complex diseases based on a single sample. Bioinform. Rui Liu, Xiangtian Yu, Xiaoping Liu, Dong Xu, Kazuyuki Aihara, Luonan Chen
2014	B	`conf`	Multi-dimensional scaling and MODELLER-based evolutionary algorithms for protein model refinement. IEEE Congress on Evolutionary Computation Yan Chen, Yi Shang, Dong Xu
2014	J	`jnl`	P Nucleic Acids Res. Qiuming Yao, Huangyi Ge, Shangquan Wu, Ning Zhang, Wei Chen, Chunhui Xu, Jianjiong Gao, Jay J. Thelen, Dong Xu
2014	J	`jnl`	Soybean knowledge base (SoyKB): a web resource for integration of soybean translational genomics and molecular breeding. Nucleic Acids Res. Trupti Joshi, Michael R. Fitzpatrick, Shiyuan Chen, Yang Liu, Hongxin Zhang, Ryan Z. Endacott, Eric C. Gaudiello, Gary Stacey, Henry T. Nguyen, Dong Xu
2014	J	`jnl`	Virtual physical examination (VPE): a multimedia system for education in medicine. Int. J. Funct. Informatics Pers. Medicine 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
2013	J	`jnl`	A computational method for predicting regulation of human microRNAs on the influenza virus genome. BMC Syst. Biol. Hao Zhang, Zhi Li, Yanpu Li, Yuanning Liu, Junxin Liu, Xin Li, Tingjie Shen, Yunna Duan, Minggang Hu, Dong Xu
2013	J	`jnl`	Genomic differences between cultivated soybean, G. max and its wild relative G. soja. BMC Genom. Trupti Joshi, Babu Valliyodan, Jeng-Hung Wu, Suk-Ha Lee, Dong Xu, Henry T. Nguyen
2013	J	`jnl`	Influence of mRNA Features on siRNA Interference Efficacy. J. Bioinform. Comput. Biol. Yuanning Liu, Yaping Chang, Chao Zhang, Qingkai Wei, Jingbo Chen, Hui-Ling Chen, Dong Xu
2013	J	`jnl`	NOA: a cytoscape plugin for network ontology analysis. Bioinform. Chao Zhang, Jiguang Wang, Kristina Hanspers, Dong Xu, Luonan Chen, Alexander R. Pico
2013	J	`jnl`	New MDS and Clustering Based Algorithms for protein Model Quality Assessment and Selection. Int. J. Artif. Intell. Tools Qingguo Wang, Charles Shang, Dong Xu, Yi Shang
2013	J	`jnl`	Optimised design of siRNA based on multi-featured comparison and analysis of H1N1 virus. Int. J. Data Min. Bioinform. Yuanning Liu, Ya-Ping Chang, Dong Xu, Zhi Li, Hao Zhang, Jie Li, Mingyao Tian
2013	—	`conf`	Soybean knowledge base (SoyKB): Bridging the gap between soybean translational genomics and breeding. BIBM Trupti Joshi, Michael R. Fitzpatrick, Shiyuan Chen, Yang Liu, Hongxin Zhang, Ryan Z. Endacott, Eric C. Gaudiello, Gary Stacey, Henry T. Nguyen, Dong Xu
2012	J	`jnl`	An automatic tongue detection and segmentation framework for computer-aided tongue image analysis. Int. J. Funct. Informatics Pers. Medicine Ratchadaporn Kanawong, Wentao Xu, Dong Xu, Shao Li, Tao Ma, Ye Duan
2012	J	`jnl`	Computational Challenges in Characterization of Bacteria and Bacteria-Host Interactions Based on Genomic Data. J. Comput. Sci. Technol. Chao Zhang, Guolu Zheng, Shunfu Xu, Dong Xu
2012	Misc	`conf`	Correlation Between Posttranslational Modification and Intrinsic Disorder in Protein. Pacific Symposium on Biocomputing Jianjiong Gao, Dong Xu
2012	—	`conf`	Features for automated tongue image shape classification. BIBM Workshops Tayo Obafemi-Ajayi, Ratchadaporn Kanawong, Dong Xu, Shao Li, Ye Duan
2012	—	`conf`	Human encoded miRNAs that regulate the inflenenza virus genome. ISB Hao Zhang, Xin Li, Yuanning Liu, Zhi Li, Minggang Hu, Dong Xu
2012	J	`jnl`	Mosaic: making biological sense of complex networks. Bioinform. Chao Zhang, Kristina Hanspers, Allan Kuchinsky, Nathan Salomonis, Dong Xu, Alexander R. Pico
2012	—	`conf`	Protein Structure Prediction and Clustering Using MUFOLD. ISBRA Jingfen Zhang, Dong Xu
2012	J	`jnl`	Soybean Knowledge Base (SoyKB): a web resource for soybean translational genomics. BMC Genom. 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
2012	—	`conf`	ZHENG classification in Traditional Chinese Medicine based on modified specular-free tongue images. BIBM Workshops Ratchadaporn Kanawong, Tayo Obafemi-Ajayi, Jun Yu, Dong Xu, Shao Li, Ye Duan
2011	B	`conf`	A Hybrid Consensus and Clustering Method for Protein Structure Selection. ICTAI Qingguo Wang, Yi Shang, Dong Xu
2011	—	`conf`	Identification of Salt Tolerance Genes in Rice from Microarray Data using SVM-RFE. BICoB Juexin Wang, Fan Zhang, Yan Wang, Yuan Fu, Dong Xu, Yanchun Liang
2011	J	`jnl`	Improving a Consensus Approach for Protein Structure Selection by Removing Redundancy. IEEE ACM Trans. Comput. Biol. Bioinform. Qingguo Wang, Yi Shang, Dong Xu
2011	J	`jnl`	Polytomy identification in microbial phylogenetic reconstruction. BMC Syst. Biol. Guan Ning Lin, Chao Zhang, Dong Xu
2011	J	`jnl`	User experience evaluation of Google search for obtaining medical knowledge: a case study. Int. J. Data Min. Bioinform. Liupu Wang, Juexin Wang, Michael Wang, Yanchun Liang, Dong Xu
2010	—	`ch.`	Bioinformatics Methods for Protein Identification Using Peptide Mass Fingerprinting. Proteome Bioinformatics Zhao Song, Luonan Chen, Dong Xu
2010	—	`conf`	Detection and application of CagA sequence markers for assessing risk factor of gastric cancer caused by Helicobacter pylori. BIBM Chao Zhang, Shunfu Xu, Dong Xu
2010	J	`jnl`	Genome-wide functional annotation by integrating multiple microarray datasets using meta-analysis. Int. J. Data Min. Bioinform. Gyan Prakash Srivastava, Jing Qiu, Dong Xu
2010	J	`jnl`	Identification of transcription factor's targets using tissue-specific transcriptomic data in Arabidopsis thaliana. BMC Syst. Biol. Gyan Prakash Srivastava, Ping Li, Jingdong Liu, Dong Xu
2010	J	`jnl`	PMirP: A pre-microRNA prediction method based on structure-sequence hybrid features. Artif. Intell. Medicine Dongyu Zhao, Yan Wang, Di Luo, Xiaohu Shi, Liupu Wang, Dong Xu, Jun Yu, Yanchun Liang
2010	J	`jnl`	Prediction of novel miRNAs and associated target genes in BMC Bioinform. 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
2010	B	`conf`	Protein structure selection based on consensus. IEEE Congress on Evolutionary Computation Qingguo Wang, Yi Shang, Dong Xu
2010	J	`jnl`	ProteinDBS v2.0: a web server for global and local protein structure search. Nucleic Acids Res. Chi-Ren Shyu, Bin Pang, Pin-Hao Chi, Nan Zhao, Dmitry Korkin, Dong Xu
2010	J	`jnl`	SeqRate: sequence-based protein folding type classification and rates prediction. BMC Bioinform. Guan Ning Lin, Zheng Wang, Dong Xu, Jianlin Cheng
2010	—	`conf`	SoyMetDB: The soybean metabolome database. BIBM Trupti Joshi, Qiuming Yao, D. Franklin Levi, Laurent Brechenmacher, Babu Valliyodan, Gary Stacey, Henry T. Nguyen, Dong Xu
2010	J	`jnl`	The Musite open-source framework for phosphorylation-site prediction. BMC Bioinform. Jianjiong Gao, Dong Xu
2009	—	`conf`	A New Machine Learning Approach for Protein Phosphorylation Site Prediction in Plants. BICoB Jianjiong Gao, Ganesh Kumar Agrawal, Jay J. Thelen, Zoran Obradovic, A. Keith Dunker, Dong Xu
2009	J	`jnl`	ComPhy: prokaryotic composite distance phylogenies inferred from whole-genome gene sets. BMC Bioinform. Guan Ning Lin, Zhipeng Cai, Guohui Lin, Sounak Chakraborty, Dong Xu
2009	J	`jnl`	Mutual understanding between Traditional Chinese Medicine and systems biology: gaps, challenges and opportunities. Int. J. Funct. Informatics Pers. Medicine Dong Xu
2009	J	`jnl`	P Nucleic Acids Res. Jianjiong Gao, Ganesh Kumar Agrawal, Jay J. Thelen, Dong Xu
2009	—	`book`	Semantic Mining Technologies for Multimedia Databases. Dacheng Tao, Dong Xu, Xuelong Li
2009	—	`conf`	Sequence-Based Prediction of Protein Folding Rates Using Contacts, Secondary Structures and Support Vector Machines. BIBM Guan Ning Lin, Zheng Wang, Dong Xu, Jianlin Cheng
2008	B	`conf`	A new clustering-based method for protein structure selection. IJCNN Qingguo Wang, Yi Shang, Dong Xu
2008	J	`jnl`	An integrated probabilistic approach for gene function prediction using multiple sources of high-throughput data. Int. J. Comput. Biol. Drug Des. Chao Zhang, Trupti Joshi, Guan Ning Lin, Dong Xu
2008	—	`book`	Applications of Fuzzy Logic in Bioinformatics Dong Xu, James M. Keller, Mihail Popescu, Rajkumar Bondugula
2008	J	`jnl`	Projecting Gene Expression Trajectories through Inducing Differential Equations from Microarray Time Series Experiments. J. Signal Process. Syst. Robin Kramer, Dong Xu
2008	J	`jnl`	Wanted: unique names for unique atom positions. PDB-wide analysis of diastereotopic atom names of small molecules containing diphosphate. BMC Bioinform. Christopher A. Bottoms, Dong Xu
2007	C	`conf`	GoFuzzKegg: Mapping Genes to KEGG Pathways Using an Ontological Fuzzy Rule System. CIBCB Mihail Popescu, Dong Xu, Erik Taylor
2007	B	`conf`	Mapping Genes to Pathways Using Ontological Fuzzy Rule Systems. FUZZ-IEEE Mihail Popescu, Dong Xu
2006	—	`conf`	A Fast Algorithm for Low-Resolution Protein Structure Prediction. EMBC Rajkumar Bondugula, Dong Xu, Yi Shang
2006	J	`jnl`	A fast SCOP fold classification system using content-based E-Predict algorithm. BMC Bioinform. Pin-Hao Chi, Chi-Ren Shyu, Dong Xu
2006	B	`conf`	Bioinformatics and Fuzzy Logic. FUZZ-IEEE Dong Xu, Rajkumar Bondugula, Mihail Popescu, James M. Keller
2006	J	`jnl`	CodonO: a new informatics method for measuring synonymous codon usage bias within and across genomes. Int. J. Gen. Syst. X.-F. Wan, J. Zhou, Dong Xu
2006	—	`conf`	Design and Implementation of Probability-Based Scoring Function for Peptide Mass Fingerprinting Protein Identification. EMBC Zhao Song, Luonan Chen, Chao Zhang, Dong Xu
2006	Misc	`conf`	DigitalTree: A Tool for Displaying Biological Data in Tree Structure. International Conference on Computational Science (2) Robin Kramer, Victor Olman, Ying Xu, Dong Xu
2006	J	`jnl`	Inferring gene regulatory networks from multiple microarray datasets. Bioinform. Yong Wang, Trupti Joshi, Xiang-Sun Zhang, Dong Xu, Luonan Chen
2006	J	`jnl`	Phylogenetic analysis using complete signature information of whole genomes and clustered Neighbour-Joining method. Int. J. Bioinform. Res. Appl. Xiaomeng Wu, Xiu-Feng Wan, Gang Wu, Dong Xu, Guohui Lin
2006	J	`jnl`	Rnall: an Efficient Algorithm for Predicting Rna Local Secondary Structural Landscape in Genomes. J. Bioinform. Comput. Biol. Xiu-Feng Wan, Guohui Lin, Dong Xu
2006	—	`conf`	Supervised Inference of Gene Regulatory Networks by Linear Programming. ICIC (3) Yong Wang, Trupti Joshi, Dong Xu, Xiang-Sun Zhang, Luonan Chen
2005	J	`jnl`	Cellular function prediction and biological pathway discovery in Arabidopsis thaliana using microarray data. Int. J. Bioinform. Res. Appl. Trupti Joshi, Yu Chen, Nickolai Alexandrov, Dong Xu
2005	J	`jnl`	More Reliable Protein NMR Peak Assignment via Improved 2-Interval Scheduling. J. Comput. Biol. Zhi-Zhong Chen, Guohui Lin, Romeo Rizzi, Jianjun Wen, Dong Xu, Ying Xu, Tao Jiang
2005	B	`conf`	Profiles and fuzzy K-nearest neighbor algorithm for protein secondary structure prediction. APBC Rajkumar Bondugula, Ognen Duzlevski, Dong Xu
2005	—	`conf`	Whole Genome Phylogeny Based on Clustered Signature String Composition. CSB Workshops Xiaomeng Wu, Guohui Lin, Xiu-Feng Wan, Dong Xu
2004	J	`jnl`	PROSPECT-PSPP: an automatic computational pipeline for protein structure prediction. Nucleic Acids Res. Jun-tao Guo, Kyle Ellrott, Won Jae Chung, Dong Xu, Sergei Passovets, Ying Xu
2004	J	`jnl`	ProteinDBS: a real-time retrieval system for protein structure comparison. Nucleic Acids Res. Chi-Ren Shyu, Pin-Hao Chi, Grant J. Scott, Dong Xu
2003	—	`conf`	A Computational Method for Assessing Peptide-Identification Reliability in Tandem Mass Spectrometry Analysis with SEQUEST. CSB Jane Razumovskaya, Victor Olman, Dong Xu, Edward C. Uberbacher, Nathan Verberkmoes, Ying Xu
2003	C	`conf`	A Computational Pipeline for Protein Structure Prediction and Analysis at Genome Scale. BIBE Manesh J. Shah, Sergei Passovets, Dongsup Kim, Kyle Ellrott, Li Wang, Inna Vokler, Philip F. LoCascio, Dong Xu, Ying Xu
2003	J	`jnl`	A computational pipeline for protein structure prediction and analysis at genome scale. Bioinform. Manesh J. Shah, Sergei Passovets, Dongsup Kim, Kyle Ellrott, Li Wang, Inna Vokler, Philip F. LoCascio, Dong Xu, Ying Xu
2003	J	`jnl`	Approximation algorithms for NMR spectral peak assignment. Theor. Comput. Sci. Zhi-Zhong Chen, Tao Jiang, Guo-Hui Lin, Jianjun Wen, Dong Xu, Jinbo Xu, Ying Xu
2003	—	`conf`	Automated Protein NMR Resonance Assignments. CSB Xiang Wan, Dong Xu, Carolyn M. Slupsky, Guohui Lin
2003	—	`conf`	CUBIC: Identification of Regulatory Binding Sites Through Data Clustering. CSB Victor Olman, Dong Xu, Ying Xu
2003	J	`jnl`	Computational Assignment of Protein Backbone Nmr Peaks Byefficient Bounding and Filtering. J. Bioinform. Comput. Biol. Guohui Lin, Dong Xu, Zhi-Zhong Chen, Tao Jiang, Jianjun Wen, Ying Xu
2003	J	`jnl`	Cubic: Identification of Regulatory Binding Sites through Data Clustering. J. Bioinform. Comput. Biol. Victor Olman, Dong Xu, Ying Xu
2003	Misc	`conf`	Identification of Regulatory Binding Sites Using Minimum Spanning Trees. Pacific Symposium on Biocomputing Victor Olman, Dong Xu, Ying Xu
2003	A	`conf`	More Reliable Protein NMR Peak Assignment via Improved 2-Interval Scheduling. ESA Zhi-Zhong Chen, Tao Jiang, Guohui Lin, Romeo Rizzi, Jianjun Wen, Dong Xu, Ying Xu
2003	C	`conf`	Towards Automated Derivation of Biological Pathways Using High-Throughput Biological Data. BIBE Yu Chen, Trupti Joshi, Ying Xu, Dong Xu
2002	—	`conf`	An Efficient Branch-and-Bound Algorithm for the Assignment of Protein Backbone NMR Peaks. CSB Guo-Hui Lin, Dong Xu, Zhi-Zhong Chen, Tao Jiang, Jianjun Wen, Ying Xu
2002	J	`jnl`	Automated assignment of backbone NMR peaks using constrained bipartite matching. Comput. Sci. Eng. Ying Xu, Dong Xu, Dongsup Kim, Victor Olman, Jane Razumovskaya, Tao Jiang
2002	J	`jnl`	Clustering gene expression data using a graph-theoretic approach: an application of minimum spanning trees. Bioinform. Ying Xu, Victor Olman, Dong Xu
2002	C	`conf`	Improved Approximation Algorithms for NMR Spectral Peak Assignment. WABI Zhi-Zhong Chen, Tao Jiang, Guo-Hui Lin, Jianjun Wen, Dong Xu, Ying Xu
2002	J	`jnl`	PRIMEGENS: robust and efficient design of gene-specific probes for microarray analysis. Bioinform. Dong Xu, Guangshan Li, Liyou Wu, Jizhong Zhou, Ying Xu
2000	J	`jnl`	A Computational Method for NMR-Constrained Protein Threading. J. Comput. Biol. Ying Xu, Dong Xu, Oakley H. Crawford, J. Ralph Einstein
2000	J	`jnl`	Protein domain decomposition using a graph-theoretic approach. Bioinform. Ying Xu, Dong Xu, Harold N. Gabow
2000	B	`conf`	Protein structure determination using protein threading and sparse NMR data (extended abstract). RECOMB Ying Xu, Dong Xu, Oakley H. Crawford, J. Ralph Einstein, Engin Serpersu
2000	J	`jnl`	Sequence-structure specificity of a knowledge based energy function at the secondary structure level. Bioinform. Dong Xu, Michael A. Unseren, Ying Xu, Edward C. Uberbacher
1998	B	`conf`	A new method for modeling and solving the protein fold recognition problem (extended abstract). RECOMB Ying Xu, Dong Xu, Edward C. Uberbacher
1998	J	`jnl`	An Efficient Computational Method for Globally Optimal Threading. J. Comput. Biol. Ying Xu, Dong Xu, Edward C. Uberbacher