A new method for modeling and solving the protein fold recognition problem (extended abstract). - Ying Xu 001; Dong Xu 002; Edward C. Uberbacher (RECOMB, 1998)

An Efficient Computational Method for Globally Optimal Threading. - Ying Xu 001; Dong Xu 002; Edward C. Uberbacher (J. Comput. Biol., 1998)

Protein structure determination using protein threading and sparse NMR data (extended abstract). - Ying Xu 001; Dong Xu 002; Oakley H. Crawford; J. Ralph Einstein; Engin Serpersu (RECOMB, 2000)

Sequence-structure specificity of a knowledge based energy function at the secondary structure level. - Dong Xu 002; Michael A. Unseren; Ying Xu 001; Edward C. Uberbacher (Bioinform., 2000)

Protein domain decomposition using a graph-theoretic approach. - Ying Xu 001; Dong Xu 002; Harold N. Gabow (Bioinform., 2000)

A Computational Method for NMR-Constrained Protein Threading. - Ying Xu 001; Dong Xu 002; Oakley H. Crawford; J. Ralph Einstein (J. Comput. Biol., 2000)

An Efficient Branch-and-Bound Algorithm for the Assignment of Protein Backbone NMR Peaks. - Guo-Hui Lin; Dong Xu 002; Zhi-Zhong Chen; Tao Jiang 001; Jianjun Wen; Ying Xu 001 (CSB, 2002)

Improved Approximation Algorithms for NMR Spectral Peak Assignment. - Zhi-Zhong Chen; Tao Jiang 001; Guo-Hui Lin; Jianjun Wen; Dong Xu 002; Ying Xu 001 (WABI, 2002)

PRIMEGENS: robust and efficient design of gene-specific probes for microarray analysis. - Dong Xu 002; Guangshan Li; Liyou Wu; Jizhong Zhou; Ying Xu 001 (Bioinform., 2002)

Clustering gene expression data using a graph-theoretic approach: an application of minimum spanning trees. - Ying Xu 001; Victor Olman; Dong Xu 002 (Bioinform., 2002)

Automated assignment of backbone NMR peaks using constrained bipartite matching. - Ying Xu 001; Dong Xu 002; Dongsup Kim; Victor Olman; Jane Razumovskaya; Tao Jiang 001 (Comput. Sci. Eng., 2002)

Towards Automated Derivation of Biological Pathways Using High-Throughput Biological Data. - Yu Chen; Trupti Joshi; Ying Xu 001; Dong Xu 002 (BIBE, 2003)

A Computational Method for Assessing Peptide-Identification Reliability in Tandem Mass Spectrometry Analysis with SEQUEST. - Jane Razumovskaya; Victor Olman; Dong Xu 002; Edward C. Uberbacher; Nathan Verberkmoes; Ying Xu 001 (CSB, 2003)

Automated Protein NMR Resonance Assignments. - Xiang Wan; Dong Xu 002; Carolyn M. Slupsky; Guohui Lin (CSB, 2003)

Identification of Regulatory Binding Sites Using Minimum Spanning Trees. - Victor Olman; Dong Xu 002; Ying Xu 001 (Pacific Symposium on Biocomputing, 2003)

A computational pipeline for protein structure prediction and analysis at genome scale. - Manesh J. Shah; Sergei Passovets; Dongsup Kim; Kyle Ellrott; Li Wang 008; Inna Vokler; Philip F. LoCascio; Dong Xu 002; Ying Xu 001 (Bioinform., 2003)

Computational Assignment of Protein Backbone Nmr Peaks Byefficient Bounding and Filtering. - Guohui Lin; Dong Xu 002; Zhi-Zhong Chen; Tao Jiang 001; Jianjun Wen; Ying Xu 001 (J. Bioinform. Comput. Biol., 2003)

Cubic: Identification of Regulatory Binding Sites through Data Clustering. - Victor Olman; Dong Xu 002; Ying Xu 001 (J. Bioinform. Comput. Biol., 2003)

Approximation algorithms for NMR spectral peak assignment. - Zhi-Zhong Chen; Tao Jiang 001; Guo-Hui Lin; Jianjun Wen; Dong Xu 002; Jinbo Xu; Ying Xu 001 (Theor. Comput. Sci., 2003)

PROSPECT-PSPP: an automatic computational pipeline for protein structure prediction. - Jun-tao Guo; Kyle Ellrott; Won Jae Chung; Dong Xu 002; Sergei Passovets; Ying Xu 001 (Nucleic Acids Res., 2004)

ProteinDBS: a real-time retrieval system for protein structure comparison. - Chi-Ren Shyu; Pin-Hao Chi; Grant J. Scott; Dong Xu 002 (Nucleic Acids Res., 2004)

Profiles and fuzzy K-nearest neighbor algorithm for protein secondary structure prediction. - Rajkumar Bondugula; Ognen Duzlevski; Dong Xu 002 (APBC, 2005)

Whole Genome Phylogeny Based on Clustered Signature String Composition. - Xiaomeng Wu; Guohui Lin; Xiu-Feng Wan; Dong Xu 002 (CSB Workshops, 2005)

Cellular function prediction and biological pathway discovery in Arabidopsis thaliana using microarray data. - Trupti Joshi; Yu Chen; Nickolai Alexandrov; Dong Xu 002 (Int. J. Bioinform. Res. Appl., 2005)

More Reliable Protein NMR Peak Assignment via Improved 2-Interval Scheduling. - Zhi-Zhong Chen; Guohui Lin; Romeo Rizzi; Jianjun Wen; Dong Xu 002; Ying Xu 001; Tao Jiang 001 (J. Comput. Biol., 2005)

A Fast Algorithm for Low-Resolution Protein Structure Prediction. - Rajkumar Bondugula; Dong Xu 002; Yi Shang (EMBC, 2006)

Design and Implementation of Probability-Based Scoring Function for Peptide Mass Fingerprinting Protein Identification. - Zhao Song 006; Luonan Chen; Chao Zhang 032; Dong Xu 002 (EMBC, 2006)

Bioinformatics and Fuzzy Logic. - Dong Xu 002; Rajkumar Bondugula; Mihail Popescu; James M. Keller (FUZZ-IEEE, 2006)

DigitalTree: A Tool for Displaying Biological Data in Tree Structure. - Robin Kramer; Victor Olman; Ying Xu 001; Dong Xu 002 (International Conference on Computational Science (2), 2006)

Supervised Inference of Gene Regulatory Networks by Linear Programming. - Yong Wang 001; Trupti Joshi; Dong Xu 002; Xiang-Sun Zhang; Luonan Chen (ICIC (3), 2006)

Inferring gene regulatory networks from multiple microarray datasets. - Yong Wang 001; Trupti Joshi; Xiang-Sun Zhang; Dong Xu 002; Luonan Chen (Bioinform., 2006)

A fast SCOP fold classification system using content-based E-Predict algorithm. - Pin-Hao Chi; Chi-Ren Shyu; Dong Xu 002 (BMC Bioinform., 2006)

Phylogenetic analysis using complete signature information of whole genomes and clustered Neighbour-Joining method. - Xiaomeng Wu; Xiu-Feng Wan; Gang Wu; Dong Xu 002; Guohui Lin (Int. J. Bioinform. Res. Appl., 2006)

CodonO: a new informatics method for measuring synonymous codon usage bias within and across genomes. - X.-F. Wan; J. Zhou; Dong Xu 002 (Int. J. Gen. Syst., 2006)

Rnall: an Efficient Algorithm for Predicting Rna Local Secondary Structural Landscape in Genomes. - Xiu-Feng Wan; Guohui Lin; Dong Xu 002 (J. Bioinform. Comput. Biol., 2006)

GoFuzzKegg: Mapping Genes to KEGG Pathways Using an Ontological Fuzzy Rule System. - Mihail Popescu; Dong Xu 002; Erik Taylor (CIBCB, 2007)

Mapping Genes to Pathways Using Ontological Fuzzy Rule Systems. - Mihail Popescu; Dong Xu 002 (FUZZ-IEEE, 2007)

Applications of Fuzzy Logic in Bioinformatics - Dong Xu 002; James M. Keller; Mihail Popescu; Rajkumar Bondugula (WorldScientific, 2008)

A new clustering-based method for protein structure selection. - Qingguo Wang; Yi Shang; Dong Xu 002 (IJCNN, 2008)

Wanted: unique names for unique atom positions. PDB-wide analysis of diastereotopic atom names of small molecules containing diphosphate. - Christopher A. Bottoms; Dong Xu 002 (BMC Bioinform., 2008)

An integrated probabilistic approach for gene function prediction using multiple sources of high-throughput data. - Chao Zhang 032; Trupti Joshi; Guan Ning Lin; Dong Xu 002 (Int. J. Comput. Biol. Drug Des., 2008)

Projecting Gene Expression Trajectories through Inducing Differential Equations from Microarray Time Series Experiments. - Robin Kramer; Dong Xu 002 (J. Signal Process. Syst., 2008)

Sequence-Based Prediction of Protein Folding Rates Using Contacts, Secondary Structures and Support Vector Machines. - Guan Ning Lin; Zheng Wang 025; Dong Xu 002; Jianlin Cheng (BIBM, 2009)

A New Machine Learning Approach for Protein Phosphorylation Site Prediction in Plants. - Jianjiong Gao; Ganesh Kumar Agrawal; Jay J. Thelen; Zoran Obradovic; A. Keith Dunker; Dong Xu 002 (BICoB, 2009)

ComPhy: prokaryotic composite distance phylogenies inferred from whole-genome gene sets. - Guan Ning Lin; Zhipeng Cai 001; Guohui Lin; Sounak Chakraborty; Dong Xu 002 (BMC Bioinform., 2009)

Mutual understanding between Traditional Chinese Medicine and systems biology: gaps, challenges and opportunities. - Dong Xu 002 (Int. J. Funct. Informatics Pers. Medicine, 2009)

P3DB: a plant protein phosphorylation database. - Jianjiong Gao; Ganesh Kumar Agrawal; Jay J. Thelen; Dong Xu 002 (Nucleic Acids Res., 2009)

Bioinformatics Methods for Protein Identification Using Peptide Mass Fingerprinting. - Zhao Song 006; Luonan Chen; Dong Xu 002 (Proteome Bioinformatics, 2010)

SoyMetDB: The soybean metabolome database. - Trupti Joshi; Qiuming Yao; D. Franklin Levi; Laurent Brechenmacher; Babu Valliyodan; Gary Stacey; Henry T. Nguyen; Dong Xu 002 (BIBM, 2010)

Detection and application of CagA sequence markers for assessing risk factor of gastric cancer caused by Helicobacter pylori. - Chao Zhang 032; Shunfu Xu; Dong Xu 002 (BIBM, 2010)

Protein structure selection based on consensus. - Qingguo Wang; Yi Shang; Dong Xu 002 (IEEE Congress on Evolutionary Computation, 2010)

PMirP: A pre-microRNA prediction method based on structure-sequence hybrid features. - Dongyu Zhao; Yan Wang 028; Di Luo; Xiaohu Shi; Liupu Wang; Dong Xu 002; Jun Yu; Yanchun Liang 001 (Artif. Intell. Medicine, 2010)

The Musite open-source framework for phosphorylation-site prediction. - Jianjiong Gao; Dong Xu 002 (BMC Bioinform., 2010)

Prediction of novel miRNAs and associated target genes in Glycine max. - 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 002; Gary Stacey (BMC Bioinform., 2010)

SeqRate: sequence-based protein folding type classification and rates prediction. - Guan Ning Lin; Zheng Wang 025; Dong Xu 002; Jianlin Cheng (BMC Bioinform., 2010)

Identification of transcription factor's targets using tissue-specific transcriptomic data in Arabidopsis thaliana. - Gyan Prakash Srivastava; Ping Li; Jingdong Liu; Dong Xu 002 (BMC Syst. Biol., 2010)

Genome-wide functional annotation by integrating multiple microarray datasets using meta-analysis. - Gyan Prakash Srivastava; Jing Qiu; Dong Xu 002 (Int. J. Data Min. Bioinform., 2010)

ProteinDBS v2.0: a web server for global and local protein structure search. - Chi-Ren Shyu; Bin Pang 001; Pin-Hao Chi; Nan Zhao 002; Dmitry Korkin; Dong Xu 002 (Nucleic Acids Res., 2010)

Identification of Salt Tolerance Genes in Rice from Microarray Data using SVM-RFE. - Juexin Wang; Fan Zhang; Yan Wang 028; Yuan Fu; Dong Xu 002; Yanchun Liang 001 (BICoB, 2011)

A Hybrid Consensus and Clustering Method for Protein Structure Selection. - Qingguo Wang; Yi Shang; Dong Xu 002 (ICTAI, 2011)

Polytomy identification in microbial phylogenetic reconstruction. - Guan Ning Lin; Chao Zhang 032; Dong Xu 002 (BMC Syst. Biol., 2011)

User experience evaluation of Google search for obtaining medical knowledge: a case study. - Liupu Wang; Juexin Wang; Michael Wang; Yanchun Liang 001; Dong Xu 002 (Int. J. Data Min. Bioinform., 2011)

Improving a Consensus Approach for Protein Structure Selection by Removing Redundancy. - Qingguo Wang; Yi Shang; Dong Xu 002 (IEEE ACM Trans. Comput. Biol. Bioinform., 2011)

ZHENG classification in Traditional Chinese Medicine based on modified specular-free tongue images. - Ratchadaporn Kanawong; Tayo Obafemi-Ajayi; Jun Yu; Dong Xu 002; Shao Li; Ye Duan (BIBM Workshops, 2012)

Features for automated tongue image shape classification. - Tayo Obafemi-Ajayi; Ratchadaporn Kanawong; Dong Xu 002; Shao Li; Ye Duan (BIBM Workshops, 2012)

Human encoded miRNAs that regulate the inflenenza virus genome. - Hao Zhang 064; Xin Li; Yuanning Liu; Zhi Li; Minggang Hu; Dong Xu 002 (ISB, 2012)

Protein Structure Prediction and Clustering Using MUFOLD. - Jingfen Zhang; Dong Xu 002 (ISBRA, 2012)

Correlation Between Posttranslational Modification and Intrinsic Disorder in Protein. - Jianjiong Gao; Dong Xu 002 (Pacific Symposium on Biocomputing, 2012)

Mosaic: making biological sense of complex networks. - Chao Zhang 032; Kristina Hanspers; Allan Kuchinsky; Nathan Salomonis; Dong Xu 002; Alexander R. Pico (Bioinform., 2012)

Soybean Knowledge Base (SoyKB): a web resource for soybean translational genomics. - Trupti Joshi; Kapil Patil; Michael R. Fitzpatrick; D. Franklin Levi; Qiuming Yao; Jeffrey R. Cook; Zheng Wang 019; Marc Libault; Laurent Brechenmacher; Babu Valliyodan; Xiaolei Wu; Jianlin Cheng; et al. (BMC Genom., 2012)

Computational Challenges in Characterization of Bacteria and Bacteria-Host Interactions Based on Genomic Data. - Chao Zhang 032; Guolu Zheng; Shunfu Xu; Dong Xu 002 (J. Comput. Sci. Technol., 2012)

Soybean knowledge base (SoyKB): Bridging the gap between soybean translational genomics and breeding. - Trupti Joshi; Michael R. Fitzpatrick; Shiyuan Chen; Yang Liu; Hongxin Zhang; Ryan Z. Endacott; Eric C. Gaudiello; Gary Stacey; Henry T. Nguyen; Dong Xu 002 (BIBM, 2013)

NOA: a cytoscape plugin for network ontology analysis. - Chao Zhang 032; Jiguang Wang; Kristina Hanspers; Dong Xu 002; Luonan Chen; Alexander R. Pico (Bioinform., 2013)

Genomic differences between cultivated soybean, G. max and its wild relative G. soja. - Trupti Joshi; Babu Valliyodan; Jeng-Hung Wu; Suk-Ha Lee; Dong Xu 002; Henry T. Nguyen (BMC Genom., 2013)

A computational method for predicting regulation of human microRNAs on the influenza virus genome. - Hao Zhang 064; Zhi Li; Yanpu Li; Yuanning Liu; Junxin Liu; Xin Li; Tingjie Shen; Yunna Duan; Minggang Hu; Dong Xu 002 (BMC Syst. Biol., 2013)

New MDS and Clustering Based Algorithms for protein Model Quality Assessment and Selection. - Qingguo Wang; Charles Shang; Dong Xu 002; Yi Shang (Int. J. Artif. Intell. Tools, 2013)

Optimised design of siRNA based on multi-featured comparison and analysis of H1N1 virus. - Yuanning Liu; Ya-Ping Chang; Dong Xu 002; Zhi Li; Hao Zhang 064; Jie Li; Mingyao Tian (Int. J. Data Min. Bioinform., 2013)

Influence of mRNA Features on siRNA Interference Efficacy. - Yuanning Liu; Yaping Chang; Chao Zhang 032; Qingkai Wei; Jingbo Chen; Hui-Ling Chen 001; Dong Xu 002 (J. Bioinform. Comput. Biol., 2013)

Multi-dimensional scaling and MODELLER-based evolutionary algorithms for protein model refinement. - Yan Chen; Yi Shang; Dong Xu 002 (IEEE Congress on Evolutionary Computation, 2014)

DL-PRO: A novel deep learning method for protein model quality assessment. - Son P. Nguyen; Yi Shang; Dong Xu 002 (IJCNN, 2014)

Identifying critical transitions of complex diseases based on a single sample. - Rui Liu 009; Xiangtian Yu; Xiaoping Liu 002; Dong Xu 002; Kazuyuki Aihara; Luonan Chen (Bioinform., 2014)

BridgeDb app: unifying identifier mapping services for Cytoscape. - Jianjiong Gao; Chao Zhang 032; Martijn P. van Iersel; Li Zhang; Dong Xu 002; Nikolaus Schultz; Alexander R. Pico (F1000Research, 2014)

Virtual physical examination (VPE): a multimedia system for education in 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; et al. (Int. J. Funct. Informatics Pers. Medicine, 2014)

Soybean knowledge base (SoyKB): a web resource for integration of soybean translational genomics and molecular breeding. - Trupti Joshi; Michael R. Fitzpatrick; Shiyuan Chen; Yang Liu; Hongxin Zhang; Ryan Z. Endacott; Eric C. Gaudiello; Gary Stacey; Henry T. Nguyen; Dong Xu 002 (Nucleic Acids Res., 2014)

P3DB 3.0: From plant phosphorylation sites to protein networks. - Qiuming Yao; Huangyi Ge; Shangquan Wu; Ning Zhang 006; Wei Chen; Chunhui Xu; Jianjiong Gao; Jay J. Thelen; Dong Xu 002 (Nucleic Acids Res., 2014)

Guest Editors Introduction to the Special Issue on Software and Databases. - Dong Xu 002; Kun Huang 001; Jeanette Schmidt (IEEE ACM Trans. Comput. Biol. Bioinform., 2015)

End-to-End Security Formalization and Alignment for Federated Workflow Management. - Matthew Dickinson; Saptarshi Debroy; Prasad Calyam; Samaikya Valluripally; Yuanxun Zhang; Trupti Joshi; Dong Xu 002 (CLOUD, 2016)

Complexity Reduction and Visualization of RDF Knowledge Networks for Precision medicine. - Zainab Al-Taie; Nattaphon Thanintorn; Ilker Ersoy; Richard D. Hammer; Dong Xu 002; Trupti Joshi; Dmitriy Shin (AMIA, 2016)

Classification of tongue images based on doublet and color space dictionary. - Guitao Cao; Jie Ding; Ye Duan; Liping Tu; Jiatuo Xu; Dong Xu 002 (BIBM, 2016)

A deep tongue image features analysis model for medical application. - Dan Meng; Guitao Cao; Ye Duan; Minghua Zhu; Liping Tu; Jiatuo Xu; Dong Xu 002 (BIBM, 2016)

RDF Sketch Maps - Knowledge Complexity Reduction for Precision Medicine Analytics. - Nattaphon Thanintorn; Juexin Wang; Ilker Ersoy; Zainab Al-Taie; Yuexu Jiang; Duolin Wang; Megha Verma; Trupti Joshi; Richard D. Hammer; Dong Xu 002; Dmitriy Shin (PSB, 2016)

FALCON@home: a high-throughput protein structure prediction server based on remote homologue recognition. - Chao Wang; Haicang Zhang; Wei-Mou Zheng; Dong Xu 002; Jianwei Zhu; Bing Wang; Kang Ning 001; Shiwei Sun; Shuai Cheng Li 001; Dongbo Bu (Bioinform., 2016)

PGen: large-scale genomic variations analysis workflow and browser in SoyKB. - 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; et al. (BMC Bioinform., 2016)

Role of plant MicroRNA in cross-species regulatory networks of humans. - Hao Zhang 064; Yanpu Li; Yuanning Liu; Haiming Liu; Hongyu Wang; Wen Jin; Yanmei Zhang; Chao Zhang 032; Dong Xu 002 (BMC Syst. Biol., 2016)

Improving degree-based variable ordering heuristics for solving constraint satisfaction problems. - Hongbo Li 005; Yanchun Liang 001; Ning Zhang 006; Jinsong Guo; Dong Xu 002; Zhanshan Li (J. Heuristics, 2016)

Musite: Tool for Predicting Protein Phosphorylation Sites. - Qiuming Yao; Jianjiong Gao; Dong Xu 002 (Encyclopedia of Algorithms, 2016)

A multimodal deep architecture for large-scale protein ubiquitylation site prediction. - Fei He 003; Lingling Bao; Rui Wang; Jiagen Li; Dong Xu 002; Xiaowei Zhao 004 (BIBM, 2017)

IMPRes: Integrative MultiOmics pathway resolution algorithm and tool. - Yuexu Jiang; Yanchun Liang 001; Duolin Wang; Dong Xu 002; Trupti Joshi (BIBM, 2017)

Effects of evolutionary pressure on histone modifications. - Saad M. Khan; Gavin C. Conant; Dong Xu 002 (BIBM, 2017)

A deep-learning framework for amidation site prediction. - Penghui Shang; Duolin Wang; Dongpeng Liu; Dong Xu 002 (BIBM, 2017)

A new method for disease-related gene prioritization. - Lingtao Su; Dong Xu 002; Guixia Liu (BIBM, 2017)

SoyTSN: A web-based prediction tool for soybean tissue specific network within SoyKB. - Juexin Wang; Zhen Lyu; Shakhawat Hossain; Gary Stacey; Dong Xu 002; Trupti Joshi (BIBM, 2017)

Computational prediction of ubiquitination protein using evolutionary profiles and functional domains. - Chunhui Xu; Wangren Qiu; Xuan Xiao; Dong Xu 002 (BIBM, 2017)

A New Deep Neighbor Residual Network for Protein Secondary Structure Prediction. - Chao Fang; Yi Shang; Dong Xu 002 (ICTAI, 2017)

Protein Loop Modeling Using Deep Generative Adversarial Network. - Zhaoyu Li; Son P. Nguyen; Dong Xu 002; Yi Shang (ICTAI, 2017)

BioJava-ModFinder: identification of protein modifications in 3D structures from the Protein Data Bank. - Jianjiong Gao; Andreas Prlic; Chunxiao Bi; Wolfgang Bluhm; Dimitris Dimitropoulos; Dong Xu 002; Philip E. Bourne; Peter W. Rose (Bioinform., 2017)

MusiteDeep: a deep-learning framework for general and kinase-specific phosphorylation site prediction. - Duolin Wang; Shuai Zeng; Chunhui Xu; Wangren Qiu; Yanchun Liang 001; Trupti Joshi; Dong Xu 002 (Bioinform., 2017)

MUFold-SS: Protein Secondary Structure Prediction Using Deep Inception-Inside-Inception Networks. - Chao Fang; Yi Shang; Dong Xu 002 (CoRR, 2017)

Overfitting Reduction of Text Classification Based on AdaBELM. - Xiaoyue Feng; Yanchun Liang 001; Xiaohu Shi; Dong Xu 002; Xu Wang; Renchu Guan (Entropy, 2017)

OMPcontact: An Outer Membrane Protein Inter-Barrel Residue Contact Prediction Method. - Li Zhang; Han Wang; Lun Yan; Lingtao Su; Dong Xu 002 (J. Comput. Biol., 2017)

A Data Mining Approach for Biomarker Discovery Using Transcriptomics in Endometriosis. - Sadia Akter; Dong Xu 002; Susan C. Nagel; Trupti Joshi (BIBM, 2018)

Integrating Gene Expression Data and Pathway Knowledge for In Silico Hypothesis Generation with IMPRes. - Yuexu Jiang; Duolin Wang; Dong Xu 002; Trupti Joshi (BIBM, 2018)

Knowledge Base Commons (KBCommons) v1.0: A multi OMICS' web-based data integration framework for biological discoveries. - Shuai Zeng; Zhen Lyu; Siva Ratna Kumari Narisetti; Dong Xu 002; Trupti Joshi (BIBM, 2018)

Domain-specific Topic Model for Knowledge Discovery through Conversational Agents in Data Intensive Scientific Communities. - Yuanxun Zhang; Prasad Calyam; Trupti Joshi; Satish S. Nair; Dong Xu 002 (IEEE BigData, 2018)

CarbonylDB: a curated data-resource of protein carbonylation sites. - R. Shyama Prasad Rao; Ning Zhang 006; Dong Xu 002; Ian Max Møller (Bioinform., 2018)

G2S: a web-service for annotating genomic variants on 3D protein structures. - Juexin Wang; Robert Sheridan; Selçuk Onur Sümer; Nikolaus Schultz; Dong Xu 002; Jianjiong Gao (Bioinform., 2018)

A content-based recommender system for computer science publications. - Donghui Wang; Yanchun Liang 001; Dong Xu 002; Xiaoyue Feng; Renchu Guan (Knowl. Based Syst., 2018)

Whole-exome sequencing and microRNA profiling reveal PI3K/AKT pathway's involvement in juvenile myelomonocytic leukemia. - Saad M. Khan; Jason E. Denney; Michael X. Wang; Dong Xu 002 (Quant. Biol., 2018)

ADON: Application-Driven Overlay Network-as-a-Service for Data-Intensive Science. - Ronny Bazan Antequera; Prasad Calyam; Saptarshi Debroy; Longhai Cui; Sripriya Seetharam; Matthew Dickinson; Trupti Joshi; Dong Xu 002; Tsegereda Beyene (IEEE Trans. Cloud Comput., 2018)

An Informatics Framework for Knowledge Representation and Reconciliation of Disease Pathways. - Yulia Innokenteva; Olha Kholod; Fei He 005; Duolin Wang; Richard D. Hammer; Dong Xu 002; Dmitriy Shin (AMIA, 2019)

Capsule Network for Predicting Zinc Binding Sites in Metalloproteins. - Clement Essien; Duolin Wang; Dong Xu 002 (BIBM, 2019)

Protein Ubiquitylation and Sumoylation Site Prediction Based on Ensemble and Transfer Learning. - Fei He 003; Rui Wang; Yanxin Gao; Duolin Wang; Yang Yu; Dong Xu 002; Xiaowei Zhao 004 (BIBM, 2019)

Extracting Molecular Entities and Their Interactions from Pathway Figures Based on Deep Learning. - Fei He 005; Duolin Wang; Yulia Innokenteva; Olha Kholod; Dmitriy Shin; Dong Xu 002 (BIBM, 2019)

DMCTOP: Topology Prediction of Alpha-Helical Transmembrane Protein Based on Deep Multi-Scale Convolutional Neural Network. - Han Wang; Yuning Yang; Jiawen Yu; Xi Wang; Dawei Zhao; Dong Xu 002; Pingping Sun (BIBM, 2019)

ESAE: Evolutionary Strategy-Based Architecture Evolution. - Xue Gu; Ziyao Meng; Yanchun Liang 001; Dong Xu 002; Han Huang; Xiaosong Han; Chunguo Wu (BIC-TA (1), 2019)

DeepDom: Predicting protein domain boundary from sequence alone using stacked bidirectional. - Yuexu Jiang; Duolin Wang; Dong Xu 002 (PSB, 2019)

Modeling of Contextual Information in Knowledge Graphs of Diagnostic Reports. - Pericles S. Giannaris; Cynthia Tang; Olha Kholod; Steve Hanson; Chi-Ren Shyu; Richard D. Hammer; Dong Xu 002; Dmitriy Shin (SWH@ISWC, 2019)

Capsule network for protein post-translational modification site prediction. - Duolin Wang; Yanchun Liang 001; Dong Xu 002 (Bioinform., 2019)

Detection of Malfunctioning Smart Electricity Meter. - Ming Liu 024; Dongpeng Liu; Guangyu Sun; Yi Zhao; Duolin Wang; Fangxing Liu; Xiang Fang; Qing He; Dong Xu 002 (CoRR, 2019)

Sliding mode control with PI-based saturation for nano-positioning. - Liu Yang; Dong Xu 002 (Int. J. Wirel. Mob. Comput., 2019)

PSICA: a fast and accurate web service for protein model quality analysis. - Wenbo Wang; Zhaoyu Li; Junlin Wang; Dong Xu 002; Yi Shang (Nucleic Acids Res., 2019)

Prediction of Protein Backbone Torsion Angles Using Deep Residual Inception Neural Networks. - Chao Fang; Yi Shang; Dong Xu 002 (IEEE ACM Trans. Comput. Biol. Bioinform., 2019)

New Deep Learning Methods for Protein Loop Modeling. - Son P. Nguyen; Zhaoyu Li; Dong Xu 002; Yi Shang (IEEE ACM Trans. Comput. Biol. Bioinform., 2019)

MUFold-SSW: a new web server for predicting protein secondary structures, torsion angles and turns. - Chao Fang; Zhaoyu Li; Dong Xu 002; Yi Shang (Bioinform., 2020)

A dynamic programing approach to integrate gene expression data and network information for pathway model generation. - Yuexu Jiang; Yanchun Liang 001; Duolin Wang; Dong Xu 002; Trupti Joshi (Bioinform., 2020)

Deep Learning Analysis and Age Prediction from Shoeprints. - Muhammad Hassan; Yan Wang 028; Di Wang 004; Daixi Li; Yanchun Liang 001; You Zhou 008; Dong Xu 002 (CoRR, 2020)

A self-attention based message passing neural network for predicting molecular lipophilicity and aqueous solubility. - Bowen Tang; Skyler T. Kramer; Meijuan Fang; Yingkun Qiu; Zhen Wu; Dong Xu 002 (J. Cheminformatics, 2020)

MusiteDeep: a deep-learning based webserver for protein post-translational modification site prediction and visualization. - Duolin Wang; Dongpeng Liu; Jiakang Yuchi; Fei He 005; Yuexu Jiang; Siteng Cai; Jingyi Li; Dong Xu 002 (Nucleic Acids Res., 2020)

Two New Heuristic Methods for Protein Model Quality Assessment. - Wenbo Wang; Junlin Wang; Dong Xu 002; Yi Shang (IEEE ACM Trans. Comput. Biol. Bioinform., 2020)

Fuzzified Image Enhancement for Deep Learning in Iris Recognition. - Ming Liu 024; Zhiqian Zhou; Penghui Shang; Dong Xu 002 (IEEE Trans. Fuzzy Syst., 2020)

Identifying Genes and Their Interactions from Pathway Figures and Text in Biomedical Articles. - Fei He 005; Joshua Thompson; Ziting Mao; Yijie Ren; Yulia I. Nussbaum; Olha Kholod; Dmitriy Shin; Mark Hannink; Mihail Popescu; Dong Xu 002 (BIBM, 2021)

Acupuncture and Tuina Knowledge Graph for Ancient Literature of Traditional Chinese Medicine. - Xiaosong Han; Xiaoran Li; Yanchun Liang 001; Xinghao Wang; Dong Xu 002; Renchu Guan (BIBM, 2021)

Text Mining Enhancements for Image Recognition of Gene Names and Gene Relations. - Yijie Ren; Fei He 005; Jing Qu; Yifan Li; Joshua Thompson; Mark Hannink; Mihail Popescu; Dong Xu 002 (CIBB, 2021)

A Rule-Based Approach for Generating Synthetic Biological Pathways. - Joshua Thompson; Haoyu Dong; Kai Liu; Fei He 005; Mihail Popescu; Dong Xu 002 (CIBB, 2021)

Recommender-as-a-service with chatbot guided domain-science knowledge discovery in a science gateway. - Komal Vekaria; Prasad Calyam; Sai Swathi Sivarathri; Songjie Wang; Yuanxun Zhang; Ashish Pandey; Cong Chen; Dong Xu 002; Trupti Joshi; Satish S. Nair (Concurr. Comput. Pract. Exp., 2021)

Overlapping Community Detection Based on Membership Degree Propagation. - Rui Gao; Shoufeng Li; Xiaohu Shi; Yanchun Liang 001; Dong Xu 002 (Entropy, 2021)

Quality Assessment of Protein Docking Models Based on Graph Neural Network. - Ye Han; Fei He 003; Yongbing Chen; Wenyuan Qin; Helong Yu; Dong Xu 002 (Frontiers Bioinform., 2021)

G2PDeep: a web-based deep-learning framework for quantitative phenotype prediction and discovery of genomic markers. - Shuai Zeng; Ziting Mao; Yijie Ren; Duolin Wang; Dong Xu 002; Trupti Joshi (Nucleic Acids Res., 2021)

DeePaN: deep patient graph convolutional network integrating clinico-genomic evidence to stratify lung cancers for immunotherapy. - Chao Fang; Dong Xu 002; Jing Su; Jonathan R. Dry; Bolan Linghu (npj Digit. Medicine, 2021)

Multi-Cloud Performance and Security Driven Federated Workflow Management. - Matthew Dickinson; Saptarshi Debroy; Prasad Calyam; Samaikya Valluripally; Yuanxun Zhang; Ronny Bazan Antequera; Trupti Joshi; Tommi A. White; Dong Xu 002 (IEEE Trans. Cloud Comput., 2021)

Comprehensive Assessment of OCR Tools for Gene Name Recognition in Biological Pathway Figures. - Stuart Aldrich; Micheal Olaolu Arowolo; Fei He 003; Mihail Popescu; Dong Xu 002 (BIBM, 2022)

Integration of Gene Regulatory Pathways Found in the Literature in a Graph Database. - Yibo Chen; Dong Xu 002; Mihail Popescu (BIBM, 2022)

Extraction of Gene Regulatory Relation Using BioBERT. - Clement Essien; Fei He 003; Mark Hannink; Mihail Popescu; Dong Xu 002 (BIBM, 2022)

Machine learning development environment for single-cell sequencing data analyses. - Lei Jiang; Yuexu Jiang; Cankun Wang; Clement Essien; Juexin Wang; Anjun Ma; Qin Ma 003; Dong Xu 002 (BIBM, 2022)

Evaluating template-based and template-free protein-peptide complex structure prediction using AlphaFold2. - Negin Manshour; Yang Yu; Wenyuan Qin; Fei He 003; Duolin Wang; Dong Xu 002 (BIBM, 2022)

Predicting Compound-Protein Interaction by Deepening the Systemic Background via Molecular Network Feature Embedding. - Han Wang; Hangxu Zhu; Wenhao Li; Ming Liu 024; Li Zhang; Dong Xu 002 (BIBM, 2022)

New Heuristic Methods for Protein Model Quality Assessment via Two-Stage Machine Learning and Hierarchical Ensemble. - Junlin Wang; Wenbo Wang; Yi Shang; Dong Xu 002 (CogMI, 2022)

Discovering trends and hotspots of biosafety and biosecurity research via machine learning. - Renchu Guan; Haoyu Pang; Yanchun Liang 001; Zhongjun Shao; Xin Gao 001; Dong Xu 002; Xiaoyue Feng (Briefings Bioinform., 2022)

Assessing deep learning methods in cis-regulatory motif finding based on genomic sequencing data. - Shuangquan Zhang; Anjun Ma; Jing Zhao; Dong Xu 002; Qin Ma 003; Yan Wang 028 (Briefings Bioinform., 2022)

Restorable-inpainting: A novel deep learning approach for shoeprint restoration. - Muhammad Hassan; Yan Wang 028; Di Wang 004; Wei Pang 001; Kangping Wang; Daixi Li; You Zhou 008; Dong Xu 002 (Inf. Sci., 2022)

IPAS-Net: A deep-learning model for generating high-fidelity shoeprints from low-quality images with no natural references. - Muhammad Hassan; Yan Wang 028; Wei Pang 001; Di Wang 004; Daixi Li; You Zhou 008; Dong Xu 002 (J. King Saud Univ. Comput. Inf. Sci., 2022)

RNALocate v2.0: an updated resource for RNA subcellular localization with increased coverage and annotation. - Tianyu Cui; Yiying Dou; Puwen Tan; Zhen Ni; Tianyuan Liu; Duolin Wang; Yan Huang; Kaican Cai; Xiaoyang Zhao; Dong Xu 002; Hao Lin 001; Dong Wang 011 (Nucleic Acids Res., 2022)

An Improved Topology Prediction of Alpha-Helical Transmembrane Protein Based on Deep Multi-Scale Convolutional Neural Network. - Yuning Yang; Jiawen Yu; Zhe Liu 030; Xi Wang; Han Wang; Zhiqiang Ma 003; Dong Xu 002 (IEEE ACM Trans. Comput. Biol. Bioinform., 2022)

scGNN 2.0: a graph neural network tool for imputation and clustering of single-cell RNA-Seq data. - Haocheng Gu; Hao Cheng; Anjun Ma; Yang Li 089; Juexin Wang; Dong Xu 002; Qin Ma 003 (Bioinform., 2022)

Reinforcement Learning-based Non-Autoregressive Solver for Traveling Salesman Problems. - Yubin Xiao; Di Wang 004; Huanhuan Chen; Boyang Li; Wei Pang 001; Xuan Wu; Hao Li; Dong Xu 002; Yanchun Liang 001; You Zhou 008 (CoRR, 2023)

Adapting Segment Anything Model (SAM) through Prompt-based Learning for Enhanced Protein Identification in Cryo-EM Micrographs. - Fei He; Zhiyuan Yang; Mingyue Gao; Biplab Poudel; Newgin Sam Ebin Sam Dhas; Rajan Gyawali; Ashwin Dhakal; Jianlin Cheng; Dong Xu 002 (CoRR, 2023)

Domain-Specific Topic Model for Knowledge Discovery in Computational and Data-Intensive Scientific Communities. - Yuanxun Zhang; Prasad Calyam; Trupti Joshi; Satish S. Nair; Dong Xu 002 (IEEE Trans. Knowl. Data Eng., 2023)

Semi-supervised active learning hypothesis verification for improved geometric expression in three-dimensional object recognition. - Zhenhao Wang; Rui Xu; Tingyuan Nie; Dong Xu 002 (Eng. Appl. Artif. Intell., 2023)

Meta-learning for T cell receptor binding specificity and beyond. - Duolin Wang; Fei He 003; Yang Yu; Dong Xu 002 (Nat. Mac. Intell., 2023)

MULocDeep web service for protein localization prediction and visualization at subcellular and suborganellar levels. - Yuexu Jiang; Lei Jiang; Chopparapu Sai Akhil; Duolin Wang; Ziyang Zhang; Weinan Zhang 002; Dong Xu 002 (Nucleic Acids Res., 2023)

Contrastive self-supervised learning for diabetic retinopathy early detection. - Jihong Ouyang; Dong Mao; Zeqi Guo; Siguang Liu; Dong Xu 002; Wenting Wang (Medical Biol. Eng. Comput., 2023)

Efficient Self-learning Evolutionary Neural Architecture Search. - Zhengzhong Qiu; Wei Bi; Dong Xu 002; Hua Guo; Hongwei Ge; Yanchun Liang 001; Heow Pueh Lee; Chunguo Wu (Appl. Soft Comput., 2023)

Large AI Models in Health Informatics: Applications, Challenges, and the Future. - Jianing Qiu; Lin Li; Jiankai Sun; Jiachuan Peng; Peilun Shi; Ruiyang Zhang; Yinzhao Dong; Kyle Lam; Frank P.-W. Lo; Bo Xiao 002; Wu Yuan 001; Ningli Wang; et al. (IEEE J. Biomed. Health Informatics, 2023)

Prompt-Based Learning on Large Protein Language Models Improves Signal Peptide Prediction. - Shuai Zeng; Duolin Wang; Lei Jiang; Dong Xu 002 (RECOMB, 2024)

Deep learning model for human-intuitive shoeprint reconstruction. - Muhammad Hassan; Yan Wang 028; Di Wang 004; Wei Pang 001; Daixi Li; You Zhou 008; Dong Xu 002; Sami Ur Rahman; Amin ur Rahman; Ahmed Fateh Ameen; Peiwu Qin (Expert Syst. Appl., 2024)

On the Responsible Use of Chatbots in Bioinformatics. - Gang-Qing Hu; Li Liu 035; Dong Xu 002 (Genom. Proteom. Bioinform., 2024)

Neural Architecture Search for Text Classification With Limited Computing Resources Using Efficient Cartesian Genetic Programming. - Xuan Wu; Di Wang 004; Huanhuan Chen; Lele Yan; Yubin Xiao; Chunyan Miao; Hongwei Ge; Dong Xu 002; Yanchun Liang 001; Kangping Wang; Chunguo Wu; You Zhou 008 (IEEE Trans. Evol. Comput., 2024)