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ORCIDDong Xu 0002
Person information
- 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
Other persons with the same name
- Dong Xu — disambiguation page
- Dong Xu 0001
![[0000-0003-2775-9730]](https://dblp1.uni-trier.de/img/orcid-mark.12x12.png "0000-0003-2775-9730")
— University of Hong Kong, Department of Computer Science, Hong Kong (and 4 more) - Dong Xu 0003 — Shanghai Normal University, Shanghai, China
- Dong Xu 0004 — Tsinghua University, Department of Precision Instrument, Beijing, China
- Dong Xu 0005 — Beihang University, School of Automation Science and Electrical Engineering, Beijing, China (and 1 more)
- Dong Xu 0006 — Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Hangzhou, China (and 1 more)
- Dong Xu 0007 — University of Arizona, Department of Systems and Industrial Engineering, Tucson, AZ, USA
- Dong Xu 0008 — Sanford-Burnham Medical Research Institute, San Diego, CA, USA (and 2 more)
- Dong Xu 0009 — East China Normal University, School of Geographic Sciences, Key Laboratory of Geographic Information Science, Shanghai, China
- Dong Xu 0010 — Harbin Engineering University, College of Computer Science and Technology, Harbin, China
- Dong Xu 0011 — Wuhan University, State Key Laboratory of Information Engineering in Surveying Mapping and Remote Sensing, Wuhan, China
- Dong Xu 0012 — University of Duisburg-Essen, Department of Communication Technology, Duisburg, Germany
- Dong Xu 0013 — University of Science and Technology Beijing, National Engineering Research Center for Advanced Rolling and Intelligent Manufacturing, Beijing, China (and 1 more)
- Dong Xu 0014 — Anhui University of Technology, Engineering Research Institute, Ma'anshan, China
- Dong Xu 0015 — ZTE Corporation, Shanghai, China
- Dong Xu 0016 — Chang Gung University, Taoyuan, Taiwan
- Dong Xu 0017 — Beijing Normal University, Faculty of Geographical Science, State Key Laboratory of Remote Sensing Science, Beijing, China (and 2 more)
- Dong Xu 0018 — Tongji University, School of Mechanical Engineering, Tongji, China (and 1 more)
- Dong Xu 0019 — Northeastern University, College of Information Science and Engineering, Shenyang, China
- Dong Xu 0020 — East China Jiaotong University, Department of Internet of Things, NanChang, China
- Dong Xu 0021 — University of Virginia, Charlottesville, VA, USA
- Dong Xu 0022 — Idaho State University, College of Pharmacy, Department of Biomedical and Pharmaceutical Sciences, Meridian, ID, USA
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2020 – today
- 2023
[j94]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)- [j93]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) - [j92]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) - [j91]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) - [j90]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) - [j89]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 Informatics 27(12): 6074-6087 (2023) - [j88]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) - [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. CoRR abs/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. CoRR abs/2311.16140 (2023) - 2022
- [j87]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) - [j86]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) - [j85]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) - [j84]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) - [j83]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) - [j82]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) - [j81]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. BIBM 2022: 346-353 - [c73]Clement Essien, Fei He, Mark Hannink, Mihail Popescu, Dong Xu:
Extraction of Gene Regulatory Relation Using BioBERT. BIBM 2022: 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. BIBM 2022: 3574-3579 - [c71]Yibo Chen, Dong Xu, Mihail Popescu:
Integration of Gene Regulatory Pathways Found in the Literature in a Graph Database. BIBM 2022: 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. BIBM 2022: 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. BIBM 2022: 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. CogMI 2022: 84-90 - 2021
- [j80]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) - [j79]Rui Gao, Shoufeng Li, Xiaohu Shi, Yanchun Liang, Dong Xu:
Overlapping Community Detection Based on Membership Degree Propagation. Entropy 23(1): 15 (2021) - [j78]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) - [j77]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) - [j76]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. Medicine 4 (2021) - [j75]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 Nussbaum, Olha Kholod, Dmitriy Shin, Mark Hannink, Mihail Popescu, Dong Xu:
Identifying Genes and Their Interactions from Pathway Figures and Text in Biomedical Articles. BIBM 2021: 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. BIBM 2021: 674-677 - [c65]Joshua Thompson, Haoyu Dong, Kai Liu, Fei He, Mihail Popescu, Dong Xu:
A Rule-Based Approach for Generating Synthetic Biological Pathways. CIBB 2021: 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. CIBB 2021: 132-142 - 2020
- [j74]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) - [j73]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) - [j72]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. Cheminformatics 12(1): 15 (2020) - [j71]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) - [j70]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) - [j69]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. CoRR abs/2011.03794 (2020)
2010 – 2019
- 2019
- [j68]Duolin Wang, Yanchun Liang, Dong Xu:
Capsule network for protein post-translational modification site prediction. Bioinform. 35(14): 2386-2394 (2019) - [j67]Liu Yang, Dong Xu:
Sliding mode control with PI-based saturation for nano-positioning. Int. J. Wirel. Mob. Comput. 16(3): 204-210 (2019) - [j66]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) - [j65]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) - [j64]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. AMIA 2019 - [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. BCB 2019: 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. BIBM 2019: 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. BIBM 2019: 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. BIBM 2019: 1191-1193 - [c58]Clement Essien, Duolin Wang, Dong Xu:
Capsule Network for Predicting Zinc Binding Sites in Metalloproteins. BIBM 2019: 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. PSB 2019: 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@ISWC 2019: 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. CoRR abs/1907.11377 (2019) - 2018
- [j63]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) - [j62]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) - [j61]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) - [j60]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) - [j59]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. BIBM 2018: 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. BIBM 2018: 589-594 - [c52]Sadia Akter, Dong Xu, Susan C. Nagel, Trupti Joshi:
A Data Mining Approach for Biomarker Discovery Using Transcriptomics in Endometriosis. BIBM 2018: 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 BigData 2018: 4886-4895 - 2017
- [j58]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) - [j57]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) - [j56]Xiaoyue Feng, Yanchun Liang, Xiaohu Shi, Dong Xu, Xu Wang, Renchu Guan:
Overfitting Reduction of Text Classification Based on AdaBELM. Entropy 19(7): 330 (2017) - [j55]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. BIBM 2017: 108-113 - [c49]Yuexu Jiang, Yanchun Liang, Duolin Wang, Dong Xu, Trupti Joshi:
IMPRes: Integrative MultiOmics pathway resolution algorithm and tool. BIBM 2017: 2260 - [c48]Saad M. Khan, Gavin C. Conant, Dong Xu:
Effects of evolutionary pressure on histone modifications. BIBM 2017: 2267 - [c47]Chunhui Xu, Wangren Qiu, Xuan Xiao, Dong Xu:
Computational prediction of ubiquitination protein using evolutionary profiles and functional domains. BIBM 2017: 2296 - [c46]Penghui Shang, Duolin Wang, Dongpeng Liu, Dong Xu:
A deep-learning framework for amidation site prediction. BIBM 2017: 2302 - [c45]Lingtao Su, Dong Xu, Guixia Liu:
A new method for disease-related gene prioritization. BIBM 2017: 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. BIBM 2017: 2326 - [c43]Chao Fang, Yi Shang, Dong Xu:
A New Deep Neighbor Residual Network for Protein Secondary Structure Prediction. ICTAI 2017: 66-71 - [c42]Zhaoyu Li, Son P. Nguyen, Dong Xu, Yi Shang:
Protein Loop Modeling Using Deep Generative Adversarial Network. ICTAI 2017: 1085-1091 - [i2]Chao Fang, Yi Shang, Dong Xu:
MUFold-SS: Protein Secondary Structure Prediction Using Deep Inception-Inside-Inception Networks. CoRR abs/1709.06165 (2017) - 2016
- [j54]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) - [j53]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) - [j52]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) - [j51]Hongbo Li, Yanchun Liang, Ning Zhang, Jinsong Guo, Dong Xu, Zhanshan Li:
Improving degree-based variable ordering heuristics for solving constraint satisfaction problems. J. Heuristics 22(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. CLOUD 2016: 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. AMIA 2016 - [c39]Guitao Cao, Jie Ding, Ye Duan, Liping Tu, Jiatuo Xu, Dong Xu:
Classification of tongue images based on doublet and color space dictionary. BIBM 2016: 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. BIBM 2016: 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. PSB 2016: 417-428 - [r1]Qiuming Yao, Jianjiong Gao, Dong Xu:
Musite: Tool for Predicting Protein Phosphorylation Sites. Encyclopedia of Algorithms 2016: 1393-1397 - 2015
- [j50]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
- [j49]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) - [j48]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. Medicine 4(3/4): 181-197 (2014) - [j47]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) - [j46]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 Computation 2014: 1038-1045 - [c35]Son P. Nguyen, Yi Shang, Dong Xu:
DL-PRO: A novel deep learning method for protein model quality assessment. IJCNN 2014: 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. F1000Research 3: 148 (2014) - 2013
- [j45]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) - [j44]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) - [j43]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) - [j42]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. Tools 22(5) (2013) - [j41]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) - [j40]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. BIBM 2013: 42-44 - 2012
- [j39]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) - [j38]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) - [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 Workshops 2012: 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 Workshops 2012: 288-294 - [c31]Hao Zhang, Xin Li, Yuanning Liu, Zhi Li, Minggang Hu, Dong Xu:
Human encoded miRNAs that regulate the inflenenza virus genome. ISB 2012: 22-25 - [c30]Jingfen Zhang, Dong Xu:
Protein Structure Prediction and Clustering Using MUFOLD. ISBRA 2012: 328-329 - [c29]Jianjiong Gao, Dong Xu:
Correlation Between Posttranslational Modification and Intrinsic Disorder in Protein. Pacific Symposium on Biocomputing 2012: 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. BICoB 2011: 30-35 - [c27]Qingguo Wang, Yi Shang, Dong Xu:
A Hybrid Consensus and Clustering Method for Protein Structure Selection. ICTAI 2011: 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. Medicine 49(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 in Glycine 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. BIBM 2010: 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. BIBM 2010: 485-488 - [c24]Qingguo Wang, Yi Shang, Dong Xu:
Protein structure selection based on consensus. IEEE Congress on Evolutionary Computation 2010: 1-7 - [p1]Zhao Song, Luonan Chen, Dong Xu:
Bioinformatics Methods for Protein Identification Using Peptide Mass Fingerprinting. Proteome Bioinformatics 2010: 7-22
2000 – 2009
- 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. Medicine 2(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. BIBM 2009: 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. BICoB 2009: 18-29 - [e1]Dacheng Tao, Dong Xu, Xuelong Li:
Semantic Mining Technologies for Multimedia Databases. IGI Global 2009, ISBN 978-1-60566-188-9 [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, WorldScientific 2008, ISBN 978-1-84816-258-7, 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. IJCNN 2008: 2891-2898 - 2007
- [c20]Mihail Popescu, Dong Xu, Erik Taylor:
GoFuzzKegg: Mapping Genes to KEGG Pathways Using an Ontological Fuzzy Rule System. CIBCB 2007: 298-303 - [c19]Mihail Popescu, Dong Xu:
Mapping Genes to Pathways Using Ontological Fuzzy Rule Systems. FUZZ-IEEE 2007: 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. EMBC 2006: 4556-4559 - [c17]Rajkumar Bondugula, Dong Xu, Yi Shang:
A Fast Algorithm for Low-Resolution Protein Structure Prediction. EMBC 2006: 5826-5829 - [c16]Dong Xu, Rajkumar Bondugula, Mihail Popescu, James M. Keller:
Bioinformatics and Fuzzy Logic. FUZZ-IEEE 2006: 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. APBC 2005: 85-94 - [c12]Xiaomeng Wu, Guohui Lin, Xiu-Feng Wan, Dong Xu:
Whole Genome Phylogeny Based on Clustered Signature String Composition. CSB Workshops 2005: 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. BIBE 2003: 3-10 - [c10]Yu Chen, Trupti Joshi, Ying Xu, Dong Xu:
Towards Automated Derivation of Biological Pathways Using High-Throughput Biological Data. BIBE 2003: 18-25 - [c9]Xiang Wan, Dong Xu, Carolyn M. Slupsky, Guohui Lin:
Automated Protein NMR Resonance Assignments. CSB 2003: 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. CSB 2003: 421-423 - [c7]Victor Olman, Dong Xu, Ying Xu:
CUBIC: Identification of Regulatory Binding Sites Through Data Clustering. CSB 2003: 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. ESA 2003: 580-592 - [c5]Victor Olman, Dong Xu, Ying Xu:
Identification of Regulatory Binding Sites Using Minimum Spanning Trees. Pacific Symposium on Biocomputing 2003: 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. CSB 2002: 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. WABI 2002: 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). RECOMB 2000: 299-307
1990 – 1999
- 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). RECOMB 1998: 285-292
Coauthor Index
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