Dong Xu
Orcid: 0000-0002-4809-0514Affiliations:
- University of Missouri, Department of Computer Science / C.S. Bond Life Sciences Center, Columbia, MO, USA
- Jilin University, College of Computer Science and Technology, Changchun, China (former)
- Oak Ridge National Laboratory, Life Sciences Division, Protein Informatics Group, Oak Ridge, TN, USA (former)
- University of Illinois at Urbana-Champaign, IL, USA (PhD 1995)
According to our database1,
Dong Xu
authored at least 173 papers
between 1998 and 2023.
Collaborative distances:
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Bibliography
2023
IEEE J. Biomed. Health Informatics, December, 2023
Appl. Soft Comput., October, 2023
Medical Biol. Eng. Comput., September, 2023
MULocDeep web service for protein localization prediction and visualization at subcellular and suborganellar levels.
Nucleic Acids Res., July, 2023
Nat. Mac. Intell., April, 2023
Semi-supervised active learning hypothesis verification for improved geometric expression in three-dimensional object recognition.
Eng. Appl. Artif. Intell., April, 2023
Domain-Specific Topic Model for Knowledge Discovery in Computational and Data-Intensive Scientific Communities.
IEEE Trans. Knowl. Data Eng., 2023
Adapting Segment Anything Model (SAM) through Prompt-based Learning for Enhanced Protein Identification in Cryo-EM Micrographs.
CoRR, 2023
Reinforcement Learning-based Non-Autoregressive Solver for Traveling Salesman Problems.
CoRR, 2023
2022
scGNN 2.0: a graph neural network tool for imputation and clustering of single-cell RNA-Seq data.
Bioinform., November, 2022
An Improved Topology Prediction of Alpha-Helical Transmembrane Protein Based on Deep Multi-Scale Convolutional Neural Network.
IEEE ACM Trans. Comput. Biol. Bioinform., 2022
RNALocate v2.0: an updated resource for RNA subcellular localization with increased coverage and annotation.
Nucleic Acids Res., 2022
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., 2022
Inf. Sci., 2022
Assessing deep learning methods in cis-regulatory motif finding based on genomic sequencing data.
Briefings Bioinform., 2022
Discovering trends and hotspots of biosafety and biosecurity research via machine learning.
Briefings Bioinform., 2022
New Heuristic Methods for Protein Model Quality Assessment via Two-Stage Machine Learning and Hierarchical Ensemble.
Proceedings of the 4th IEEE International Conference on Cognitive Machine Intelligence, 2022
Predicting Compound-Protein Interaction by Deepening the Systemic Background via Molecular Network Feature Embedding.
Proceedings of the IEEE International Conference on Bioinformatics and Biomedicine, 2022
Evaluating template-based and template-free protein-peptide complex structure prediction using AlphaFold2.
Proceedings of the IEEE International Conference on Bioinformatics and Biomedicine, 2022
Proceedings of the IEEE International Conference on Bioinformatics and Biomedicine, 2022
Proceedings of the IEEE International Conference on Bioinformatics and Biomedicine, 2022
Proceedings of the IEEE International Conference on Bioinformatics and Biomedicine, 2022
Comprehensive Assessment of OCR Tools for Gene Name Recognition in Biological Pathway Figures.
Proceedings of the IEEE International Conference on Bioinformatics and Biomedicine, 2022
2021
IEEE Trans. Cloud Comput., 2021
DeePaN: deep patient graph convolutional network integrating clinico-genomic evidence to stratify lung cancers for immunotherapy.
npj Digit. Medicine, 2021
G2PDeep: a web-based deep-learning framework for quantitative phenotype prediction and discovery of genomic markers.
Nucleic Acids Res., 2021
Frontiers Bioinform., 2021
Entropy, 2021
Recommender-as-a-service with chatbot guided domain-science knowledge discovery in a science gateway.
Concurr. Comput. Pract. Exp., 2021
Proceedings of the Computational Intelligence Methods for Bioinformatics and Biostatistics, 2021
Proceedings of the Computational Intelligence Methods for Bioinformatics and Biostatistics, 2021
Acupuncture and Tuina Knowledge Graph for Ancient Literature of Traditional Chinese Medicine.
Proceedings of the IEEE International Conference on Bioinformatics and Biomedicine, 2021
Identifying Genes and Their Interactions from Pathway Figures and Text in Biomedical Articles.
Proceedings of the IEEE International Conference on Bioinformatics and Biomedicine, 2021
2020
IEEE Trans. Fuzzy Syst., 2020
IEEE ACM Trans. Comput. Biol. Bioinform., 2020
MusiteDeep: a deep-learning based webserver for protein post-translational modification site prediction and visualization.
Nucleic Acids Res., 2020
A self-attention based message passing neural network for predicting molecular lipophilicity and aqueous solubility.
J. Cheminformatics, 2020
A dynamic programing approach to integrate gene expression data and network information for pathway model generation.
Bioinform., 2020
MUFold-SSW: a new web server for predicting protein secondary structures, torsion angles and turns.
Bioinform., 2020
2019
IEEE ACM Trans. Comput. Biol. Bioinform., 2019
Prediction of Protein Backbone Torsion Angles Using Deep Residual Inception Neural Networks.
IEEE ACM Trans. Comput. Biol. Bioinform., 2019
Nucleic Acids Res., 2019
Int. J. Wirel. Mob. Comput., 2019
Bioinform., 2019
Proceedings of the Second International Workshop on Semantic Web Meets Health Data Management (SWH 2019) co-located with the 18th International Semantic Web Conference (ISWC 2019), 2019
DeepDom: Predicting protein domain boundary from sequence alone using stacked bidirectional.
Proceedings of the Biocomputing 2019: Proceedings of the Pacific Symposium, 2019
Proceedings of the Bio-inspired Computing: Theories and Applications, 2019
DMCTOP: Topology Prediction of Alpha-Helical Transmembrane Protein Based on Deep Multi-Scale Convolutional Neural Network.
Proceedings of the 2019 IEEE International Conference on Bioinformatics and Biomedicine, 2019
Extracting Molecular Entities and Their Interactions from Pathway Figures Based on Deep Learning.
Proceedings of the 2019 IEEE International Conference on Bioinformatics and Biomedicine, 2019
Protein Ubiquitylation and Sumoylation Site Prediction Based on Ensemble and Transfer Learning.
Proceedings of the 2019 IEEE International Conference on Bioinformatics and Biomedicine, 2019
Proceedings of the 2019 IEEE International Conference on Bioinformatics and Biomedicine, 2019
An Informatics Framework for Knowledge Representation and Reconciliation of Disease Pathways.
Proceedings of the AMIA 2019, 2019
2018
IEEE Trans. Cloud Comput., 2018
Whole-exome sequencing and microRNA profiling reveal PI3K/AKT pathway's involvement in juvenile myelomonocytic leukemia.
Quant. Biol., 2018
Knowl. Based Syst., 2018
Bioinform., 2018
Domain-specific Topic Model for Knowledge Discovery through Conversational Agents in Data Intensive Scientific Communities.
Proceedings of the IEEE International Conference on Big Data (IEEE BigData 2018), 2018
Knowledge Base Commons (KBCommons) v1.0: A multi OMICS' web-based data integration framework for biological discoveries.
Proceedings of the IEEE International Conference on Bioinformatics and Biomedicine, 2018
Integrating Gene Expression Data and Pathway Knowledge for In Silico Hypothesis Generation with IMPRes.
Proceedings of the IEEE International Conference on Bioinformatics and Biomedicine, 2018
A Data Mining Approach for Biomarker Discovery Using Transcriptomics in Endometriosis.
Proceedings of the IEEE International Conference on Bioinformatics and Biomedicine, 2018
2017
OMPcontact: An Outer Membrane Protein Inter-Barrel Residue Contact Prediction Method.
J. Comput. Biol., 2017
MUFold-SS: Protein Secondary Structure Prediction Using Deep Inception-Inside-Inception Networks.
CoRR, 2017
MusiteDeep: a deep-learning framework for general and kinase-specific phosphorylation site prediction.
Bioinform., 2017
BioJava-ModFinder: identification of protein modifications in 3D structures from the Protein Data Bank.
Bioinform., 2017
Proceedings of the 29th IEEE International Conference on Tools with Artificial Intelligence, 2017
Proceedings of the 29th IEEE International Conference on Tools with Artificial Intelligence, 2017
Computational prediction of ubiquitination protein using evolutionary profiles and functional domains.
Proceedings of the 2017 IEEE International Conference on Bioinformatics and Biomedicine, 2017
SoyTSN: A web-based prediction tool for soybean tissue specific network within SoyKB.
Proceedings of the 2017 IEEE International Conference on Bioinformatics and Biomedicine, 2017
Proceedings of the 2017 IEEE International Conference on Bioinformatics and Biomedicine, 2017
Proceedings of the 2017 IEEE International Conference on Bioinformatics and Biomedicine, 2017
Proceedings of the 2017 IEEE International Conference on Bioinformatics and Biomedicine, 2017
Proceedings of the 2017 IEEE International Conference on Bioinformatics and Biomedicine, 2017
A multimodal deep architecture for large-scale protein ubiquitylation site prediction.
Proceedings of the 2017 IEEE International Conference on Bioinformatics and Biomedicine, 2017
2016
Encyclopedia of Algorithms, 2016
Improving degree-based variable ordering heuristics for solving constraint satisfaction problems.
J. Heuristics, 2016
BMC Syst. Biol., 2016
BMC Bioinform., 2016
FALCON@home: a high-throughput protein structure prediction server based on remote homologue recognition.
Bioinform., 2016
Proceedings of the Biocomputing 2016: Proceedings of the Pacific Symposium, 2016
Proceedings of the IEEE International Conference on Bioinformatics and Biomedicine, 2016
Proceedings of the IEEE International Conference on Bioinformatics and Biomedicine, 2016
Complexity Reduction and Visualization of RDF Knowledge Networks for Precision medicine.
Proceedings of the AMIA 2016, 2016
Proceedings of the 9th IEEE International Conference on Cloud Computing, 2016
2015
IEEE ACM Trans. Comput. Biol. Bioinform., 2015
2014
Nucleic Acids Res., 2014
Soybean knowledge base (SoyKB): a web resource for integration of soybean translational genomics and molecular breeding.
Nucleic Acids Res., 2014
Int. J. Funct. Informatics Pers. Medicine, 2014
F1000Research, 2014
Bioinform., 2014
Proceedings of the 2014 International Joint Conference on Neural Networks, 2014
Multi-dimensional scaling and MODELLER-based evolutionary algorithms for protein model refinement.
Proceedings of the IEEE Congress on Evolutionary Computation, 2014
2013
J. Bioinform. Comput. Biol., 2013
Optimised design of siRNA based on multi-featured comparison and analysis of H1N1 virus.
Int. J. Data Min. Bioinform., 2013
New MDS and Clustering Based Algorithms for protein Model Quality Assessment and Selection.
Int. J. Artif. Intell. Tools, 2013
A computational method for predicting regulation of human microRNAs on the influenza virus genome.
BMC Syst. Biol., 2013
Genomic differences between cultivated soybean, G. max and its wild relative G. soja.
BMC Genom., 2013
Soybean knowledge base (SoyKB): Bridging the gap between soybean translational genomics and breeding.
Proceedings of the 2013 IEEE International Conference on Bioinformatics and Biomedicine, 2013
2012
Computational Challenges in Characterization of Bacteria and Bacteria-Host Interactions Based on Genomic Data.
J. Comput. Sci. Technol., 2012
BMC Genom., 2012
Correlation Between Posttranslational Modification and Intrinsic Disorder in Protein.
Proceedings of the Biocomputing 2012: Proceedings of the Pacific Symposium, 2012
Proceedings of the Bioinformatics Research and Applications - 8th International Symposium, 2012
Proceedings of the 6th IEEE International Conference on Systems Biology, 2012
Proceedings of the 2012 IEEE International Conference on Bioinformatics and Biomedicine Workshops, 2012
ZHENG classification in Traditional Chinese Medicine based on modified specular-free tongue images.
Proceedings of the 2012 IEEE International Conference on Bioinformatics and Biomedicine Workshops, 2012
2011
Improving a Consensus Approach for Protein Structure Selection by Removing Redundancy.
IEEE ACM Trans. Comput. Biol. Bioinform., 2011
User experience evaluation of Google search for obtaining medical knowledge: a case study.
Int. J. Data Min. Bioinform., 2011
BMC Syst. Biol., 2011
Proceedings of the IEEE 23rd International Conference on Tools with Artificial Intelligence, 2011
Identification of Salt Tolerance Genes in Rice from Microarray Data using SVM-RFE.
Proceedings of the ISCA 3rd International Conference on Bioinformatics and Computational Biology, 2011
2010
Nucleic Acids Res., 2010
Genome-wide functional annotation by integrating multiple microarray datasets using meta-analysis.
Int. J. Data Min. Bioinform., 2010
Identification of transcription factor's targets using tissue-specific transcriptomic data in Arabidopsis thaliana.
BMC Syst. Biol., 2010
BMC Bioinform., 2010
BMC Bioinform., 2010
BMC Bioinform., 2010
Artif. Intell. Medicine, 2010
Proceedings of the IEEE Congress on Evolutionary Computation, 2010
Detection and application of CagA sequence markers for assessing risk factor of gastric cancer caused by Helicobacter pylori.
Proceedings of the 2010 IEEE International Conference on Bioinformatics and Biomedicine, 2010
Proceedings of the 2010 IEEE International Conference on Bioinformatics and Biomedicine, 2010
Proceedings of the Proteome Bioinformatics, 2010
2009
Mutual understanding between Traditional Chinese Medicine and systems biology: gaps, challenges and opportunities.
Int. J. Funct. Informatics Pers. Medicine, 2009
ComPhy: prokaryotic composite distance phylogenies inferred from whole-genome gene sets.
BMC Bioinform., 2009
A New Machine Learning Approach for Protein Phosphorylation Site Prediction in Plants.
Proceedings of the Bioinformatics and Computational Biology, 2009
Sequence-Based Prediction of Protein Folding Rates Using Contacts, Secondary Structures and Support Vector Machines.
Proceedings of the 2009 IEEE International Conference on Bioinformatics and Biomedicine, 2009
2008
Projecting Gene Expression Trajectories through Inducing Differential Equations from Microarray Time Series Experiments.
J. Signal Process. Syst., 2008
An integrated probabilistic approach for gene function prediction using multiple sources of high-throughput data.
Int. J. Comput. Biol. Drug Des., 2008
Wanted: unique names for unique atom positions. PDB-wide analysis of diastereotopic atom names of small molecules containing diphosphate.
BMC Bioinform., 2008
Proceedings of the International Joint Conference on Neural Networks, 2008
Series on Advances in Bioinformatics and Computational Biology 9, WorldScientific, ISBN: 978-1-908978-71-4, 2008
2007
Proceedings of the FUZZ-IEEE 2007, 2007
Proceedings of the 2007 IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology, 2007
2006
Rnall: an Efficient Algorithm for Predicting Rna Local Secondary Structural Landscape in Genomes.
J. Bioinform. Comput. Biol., 2006
CodonO: a new informatics method for measuring synonymous codon usage bias within and across genomes.
Int. J. Gen. Syst., 2006
Phylogenetic analysis using complete signature information of whole genomes and clustered Neighbour-Joining method.
Int. J. Bioinform. Res. Appl., 2006
BMC Bioinform., 2006
Bioinform., 2006
Proceedings of the Computational Intelligence and Bioinformatics, 2006
Proceedings of the Computational Science, 2006
Proceedings of the IEEE International Conference on Fuzzy Systems, 2006
Design and Implementation of Probability-Based Scoring Function for Peptide Mass Fingerprinting Protein Identification.
Proceedings of the 28th International Conference of the IEEE Engineering in Medicine and Biology Society, 2006
Proceedings of the 28th International Conference of the IEEE Engineering in Medicine and Biology Society, 2006
2005
J. Comput. Biol., 2005
Cellular function prediction and biological pathway discovery in Arabidopsis thaliana using microarray data.
Int. J. Bioinform. Res. Appl., 2005
Proceedings of the Fourth International IEEE Computer Society Computational Systems Bioinformatics Conference Workshops & Poster Abstracts, 2005
Profiles and fuzzy K-nearest neighbor algorithm for protein secondary structure prediction.
Proceedings of 3rd Asia-Pacific Bioinformatics Conference, 17-21 January 2005, Singapore, 2005
2004
Nucleic Acids Res., 2004
Nucleic Acids Res., 2004
2003
J. Bioinform. Comput. Biol., 2003
Computational Assignment of Protein Backbone Nmr Peaks Byefficient Bounding and Filtering.
J. Bioinform. Comput. Biol., 2003
A computational pipeline for protein structure prediction and analysis at genome scale.
Bioinform., 2003
Proceedings of the 8th Pacific Symposium on Biocomputing, 2003
Proceedings of the 2nd IEEE Computer Society Bioinformatics Conference, 2003
A Computational Method for Assessing Peptide-Identification Reliability in Tandem Mass Spectrometry Analysis with SEQUEST.
Proceedings of the 2nd IEEE Computer Society Bioinformatics Conference, 2003
Towards Automated Derivation of Biological Pathways Using High-Throughput Biological Data.
Proceedings of the 3rd IEEE International Symposium on BioInformatics and BioEngineering (BIBE 2003), 2003
2002
Comput. Sci. Eng., 2002
Clustering gene expression data using a graph-theoretic approach: an application of minimum spanning trees.
Bioinform., 2002
PRIMEGENS: robust and efficient design of gene-specific probes for microarray analysis.
Bioinform., 2002
Proceedings of the Algorithms in Bioinformatics, Second International Workshop, 2002
An Efficient Branch-and-Bound Algorithm for the Assignment of Protein Backbone NMR Peaks.
Proceedings of the 1st IEEE Computer Society Bioinformatics Conference, 2002
2000
Sequence-structure specificity of a knowledge based energy function at the secondary structure level.
Bioinform., 2000
Protein structure determination using protein threading and sparse NMR data (extended abstract).
Proceedings of the Fourth Annual International Conference on Computational Molecular Biology, 2000
1998
J. Comput. Biol., 1998
A new method for modeling and solving the protein fold recognition problem (extended abstract).
Proceedings of the Second Annual International Conference on Research in Computational Molecular Biology, 1998