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Author Details

Dong Xu
University of Missouri
1998
297
60
PMIDPaper TitleJournal TitlePublished Year
37178004MULocDeep web service for protein localization prediction and visualization at subcellular and suborganellar levels.Nucleic Acids Res2023
37789956Applications of cutting-edge artificial intelligence technologies in biomedical literature and document mining.Med Rev (2021)2023
37121210The chemistry and activity-orientedcharacterization of isoflavones difference between roots of Pueraria lobata and P. thomsonii guided by feature-based molecular networking.Food Chem2023
32750879An Improved Topology Prediction of Alpha-Helical Transmembrane Protein Based on Deep Multi-Scale Convolutional Neural Network.IEEE/ACM Trans Comput Biol Bioinform2022
35498680High-Resolution Translatome Analysis Reveals Cortical Cell Programs During Early Soybean Nodulation.Front Plant Sci2022
35463453A Multi-Level Iterative Bi-Clustering Method for Discovering miRNA Co-regulation Network of Abiotic Stress Tolerance in Soybeans.Front Plant Sci2022
35696076A Pretrained ELECTRA Model for Kinase-Specific Phosphorylation Site Prediction.Methods Mol Biol2022
36582438Prediction of protein stability changes upon single-point variant using 3D structure profile.Comput Struct Biotechnol J2022
36570921Identification of genomic regions associated with soybean responses to off-target dicamba exposure.Front Plant Sci2022
35310659Large-Scale Integrative Analysis of Soybean Transcriptome Using an Unsupervised Autoencoder Model.Front Plant Sci2022
34551440RNALocate v2.0: an updated resource for RNA subcellular localization with increased coverage and annotation.Nucleic Acids Res2022
34037802G2PDeep: a web-based deep-learning framework for quantitative phenotype prediction and discovery of genomic markers.Nucleic Acids Res2021
36303780Quality Assessment of Protein Docking Models Based on Graph Neural Network.Front Bioinform2021
33767197scGNN is a novel graph neural network framework for single-cell RNA-Seq analyses.Nat Commun2021
33558550Genetic variation among 481 diverse soybean accessions, inferred from genomic re-sequencing.Sci Data2021
33503258DM3Loc: multi-label mRNA subcellular localization prediction and analysis based on multi-head self-attention mechanism.Nucleic Acids Res2021
34765098Computational methods for protein localization prediction.Comput Struct Biotechnol J2021
34522290MULocDeep: A deep-learning framework for protein subcellular and suborganellar localization prediction with residue-level interpretation.Comput Struct Biotechnol J2021
34451580Variation in Gene Expression between Two <i>Sorghum bicolor</i> Lines Differing in Innate Immunity Response.Plants (Basel)2021
33961861Genetic mosaicism, intrafamilial phenotypic heterogeneity, and molecular defects of a novel missense SLC6A1 mutation associated with epilepsy and ADHD.Exp Neurol2021
30418914Two New Heuristic Methods for Protein Model Quality Assessment.IEEE/ACM Trans Comput Biol Bioinform2020
31658877How oncogenic mutations activate human MAP kinase 1 (MEK1): a molecular dynamics simulation study.J Biomol Struct Dyn2020
33431047A self-attention based message passing neural network for predicting molecular lipophilicity and aqueous solubility.J Cheminform2020
33294129Inductive inference of gene regulatory network using supervised and semi-supervised graph neural networks.Comput Struct Biotechnol J2020
32774783MU-PseUDeep: A deep learning method for prediction of pseudouridine sites.Comput Struct Biotechnol J2020
32824289Proteomic and Bioinformatic Profiling of Transporters in Higher Plant Mitochondria.Biomolecules2020
32477621GenomeForest: An Ensemble Machine Learning Classifier for Endometriosis.AMIA Jt Summits Transl Sci Proc2020
32410239Metabolomic profiling of wild-type and mutant soybean root nodules using laser-ablation electrospray ionization mass spectrometry reveals altered metabolism.Plant J2020
32324217MusiteDeep: a deep-learning based webserver for protein post-translational modification site prediction and visualization.Nucleic Acids Res2020
32166042Artificial Intelligence-Driven Structurization of Diagnostic Information in Free-Text Pathology Reports.J Pathol Inform2020
32426342Detecting Cancer Survival Related Gene Markers Based on Rectified Factor Network.Front Bioeng Biotechnol2020
32511346AI-aided design of novel targeted covalent inhibitors against SARS-CoV-2.bioRxiv2020
32160248Correction: Evidence for plant-derived xenomiRs based on a large-scale analysis of public small RNA sequencing data from human samples.PLoS One2020
31532508MUFold-SSW: a new web server for predicting protein secondary structures, torsion angles and turns.Bioinformatics2020
31294886A deep dense inception network for protein beta-turn prediction.Proteins2020
31544655In-Situ Metabolomic Analysis of <i>Setaria viridis</i> Roots Colonized by Beneficial Endophytic Bacteria.Mol Plant Microbe Interact2020
31220603IMPRes-Pro: A high dimensional multiomics integration method for in silico hypothesis generation.Methods2020
31168616A dynamic programing approach to integrate gene expression data and network information for pathway model generation.Bioinformatics2020
30520972Capsule network for protein post-translational modification site prediction.Bioinformatics2019
31856718Knowledge Base Commons (KBCommons) v1.1: a universal framework for multi-omics data integration and biological discoveries.BMC Genomics2019
31824557Phenotype Prediction and Genome-Wide Association Study Using Deep Convolutional Neural Network of Soybean.Front Genet2019
31648238Correction: Evidence for plant-derived xenomiRs based on a large-scale analysis of public small RNA sequencing data from human samples.PLoS One2019
32476995Computational Prediction of Ubiquitination Proteins Using Evolutionary Profiles and Functional Domain Annotation.Curr Genomics2019
29990046New Deep Learning Methods for Protein Loop Modeling.IEEE/ACM Trans Comput Biol Bioinform2019
29882026A Fast Projection-Based Algorithm for Clustering Big Data.Interdiscip Sci2019
31552087Machine Learning Classifiers for Endometriosis Using Transcriptomics and Methylomics Data.Front Genet2019
31176687A missense mutation in SLC6A1 associated with Lennox-Gastaut syndrome impairs GABA transporter 1 protein trafficking and function.Exp Neurol2019
31549018SoyCSN: Soybean context-specific network analysis and prediction based on tissue-specific transcriptome data.Plant Direct2019
31127307PSICA: a fast and accurate web service for protein model quality analysis.Nucleic Acids Res2019
30864311DeepDom: Predicting protein domain boundary from sequence alone using stacked bidirectional LSTM.Pac Symp Biocomput2019
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Collaborators

Ying Xu
Oak Ridge National Laboratory
Co-authored papers 26
Yang Zhang
University of Michigan ann arbor
Co-authored papers 14
Jianjiong Gao
Memorial Sloan Kettering Cancer Center
Co-authored papers 13
Jianlin Cheng
University of Missouri
Co-authored papers 9
Gyan P Srivastava
Foundational Neuroscience Center, Inc.
Co-authored papers 8
Victor Olman
University of Georgia
Co-authored papers 7
Zheng Wang
University of Miami
Co-authored papers 7
Jizhong Zhou
Institute for Environmental Genomics, University of Oklahoma
Co-authored papers 5
Dongsup Kim
Korea Advanced Institute of Science and Technology
Co-authored papers 4
Jack Y Yang
Massachusetts General Hospital and Harvard Medical School
Co-authored papers 4
Ljiljana Pa??a-Toli??
Pacific Northwest National Laboratory
Co-authored papers 4
James Andrew McCammon
Co-authored papers 4
Hongxin Zhang
Memorial Sloan Kettering Cancer Center
Co-authored papers 4
Alan Keith Dunker
Center for Computational Biology, Indiana University School of Medicine
Co-authored papers 4
Rommie E Amaro
University of California
Co-authored papers 4
Lukasz Jaroszewski
University of California Riverside School of Medicine
Co-authored papers 3
Adam Godzik
University of California Riverside
Co-authored papers 3
Youping Deng
John A. Burns School of Medicine, University of Hawaii at Manoa
Co-authored papers 3
Hamid R Arabnia
University of Georgia
Co-authored papers 3
Sergei Passovets
Co-authored papers 3
Liyou Wu
Institute for Environmental Genomics, University of Oklahoma
Co-authored papers 3
Tao Jiang
University of California riverside
Co-authored papers 3
Kyle Ellrott
Oregon Health & Science University
Co-authored papers 3
Yunlong Liu
The First Affiliated Hospital of Zhengzhou University
Co-authored papers 3
Andrzej Niemierko
Massachusetts General Hospital
Co-authored papers 3
Jeong-Hyeon Choi
National Marine Biodiversity Institute of Korea
Co-authored papers 3
Philip F LoCascio
University of Oxford
Co-authored papers 3
Jun-Tao Guo
University of North Carolina at Charlotte
Co-authored papers 3
Ying Xu
The China-Japan Union Hospital, Jilin University
Co-authored papers 3
Manesh Shah
University of Tennessee Knoxville
Co-authored papers 3
Release 1.2