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Dong Xu

Dong Xu

Professor

Phone: 573-882-2299
xudong@missouri.edu
271c Bond Life Sciences Center

As computer researcher with a strong background in molecular biology, Xu practices “bioinformatics.” He uses high-capacity computers to help other researchers analyze huge amounts of data, such as DNA sequences in human and plants. Xu’s lab has developed software programs that assist biological modeling; for example, one of their programs enables scientists to predict how proteins on the cellular level will change, or “fold,” when subjected to certain conditions.

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News about Dong Xu

Research Topics

2022

Neural relational inference to learn long-range allosteric interactions in proteins from molecular dynamics simulations. Zhu J, Wang J, Han W, Xu D. Nature Communications; Volume 13, Issue 1.

Date published: March 29, 2022
Featured in this article: Juexin Wang, Dong Xu.

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RNALocate v2.0: An updated resource for RNA subcellular localization with increased coverage and annotation. Cui T., Dou Y, Tan P, Ni Z. , Liu T, Wang D, Huang Y. , Cai K,, Zhao X, Xu D., Li H, Wang D. Nucleic Acids Research; Volume 50, Issue D1, Pages D333 - D339.

Date published: February 7, 2022
Featured in this article: Dong Xu, Duolin Wang.

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An Improved Topology Prediction of Alpha-Helical Transmembrane Protein Based on Deep Multi-Scale Convolutional Neural Network. Yang Y., Yu J, Liu Z, Wang X, Wang H, Ma Z, Xu D.. IEEE/ACM Transactions on Computational Biology and Bioinformatics; Volume 19, Issue 1, Pages 295 - 304.

Date published: January 1, 2022
Featured in this article: Dong Xu, Yang Wang.

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Assessing deep learning methods in cis-regulatory motif finding based on genomic sequencing data. Briefings in Bioinformatics. Volume 23, Issue 1; Zhang S., Ma A. , Zhao J, Xu D. , Ma Q, Wang Y, .

Date published: January 1, 2022
Featured in this article: Yang Wang, Dong Xu.

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2021

Identifying Genes and Their Interactions from Pathway Figures and Text in Biomedical Articles. He F. , Thompson J. , Mao Z. , Ren Y., Nussbaum Y. , Kholod O. , Shin D. , Hannink M., Popescu M., Xu D.. Proceedings - 2021 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2021; Pages 398-405 .

Date published: December 9, 2021
Featured in this article: Mark Hannink, Dong Xu.

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Genetic variation among 481 diverse soybean accessions, inferred from genomic re-sequencing. Valliyodan B, Brown AV, Wang J, Patil G, Liu Y, Otyama PI, Nelson RT, Vuong T, Song Q, Musket TA, Wagner R, Marri P, Reddy S, Sessions A, Wu X, Grant D, Bayer PE, Roorkiwal M, Varshney RK, Liu X, Edwards D, Xu D, Joshi T, Cannon SB, Nguyen HT. Scientific Data; 8(1):50.

Date published: December 1, 2021
Featured in this article: Dong Xu, Trupti Joshi.

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New genotypes of Helicobacter Pylori VacA d-region identified from global strains. Soyfoo DM, Doomah YH, Xu D, Zhang C, Sang H-M, Liu Y-Y, Zhang G-X, Jiang J-X, Xu S-F. BMC Molecular and Cell Biology; 22(1):4.

Date published: December 1, 2021
Featured in this article: Dong Xu.

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DeePaN: deep patient graph convolutional network integrating clinico-genomic evidence to stratify lung cancers for immunotherapy. Fang C, Xu D, Su J, Dry JR, Linghu B. npj Digital Medicine; 4(1):14.

Date published: December 1, 2021
Featured in this article: Dong Xu.

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scGNN is a novel graph neural network framework for single-cell RNA-Seq analyses. Wang J, Ma A, Chang Y, Gong J, Jiang Y, Qi R, Wang C, Fu H, Ma Q, Xu D. Nature Communications; 12(1):1882.

Date published: December 1, 2021
Featured in this article: Dong Xu.

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Deep learning analysis and age prediction from shoeprints. Hassan M, Wang Y, Wang D, Li D, Liang Y, Zhou Y, Xu D. Forensic Science International; 327:110987.

Date published: October 1, 2021
Featured in this article: Dong Xu.

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Variation in gene expression between two sorghum bicolor lines differing in innate immunity response. Cui Y, Chen D, Jiang Y, Xu D, Balint-Kurti P, Stacey G. Plant; 10(8):1536.

Date published: August 1, 2021
Featured in this article: Dong Xu, Gary Stacey.

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Genetic mosaicism, intrafamilial phenotypic heterogeneity, and molecular defects of a novel missense SLC6A1 mutation associated with epilepsy and ADHD. Poliquin S, Hughes I, Shen W, Mermer F, Wang J, Mack T, Xu D, Kang J-Q. Experimental Neurology; 342:113723.

Date published: August 1, 2021
Featured in this article: Dong Xu.

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Editorial: Computational Resources for Understanding Biomacromolecular Covalent Modifications. Xue Y, Huang H-D, Song J, Ren J, Xu D. Frontiers in Cell and Developmental Biology; 9:728127.

Date published: July 14, 2021
Featured in this article: Dong Xu.

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G2PDeep: A web-based deep-learning framework for quantitative phenotype prediction and discovery of genomic markers. Zeng S, Mao Z, Ren Y, Wang D, Xu D, Joshi T. Nucleic Acids Research; 49(W1):W228-W236.

Date published: July 2, 2021
Featured in this article: Dong Xu, Trupti Joshi.

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Domain-specific Topic Model for Knowledge Discovery in Computational and Data-Intensive Scientific Communities. Zhang Y, Calyam P, Joshi T, Nair S, Xu D. IEEE Transactions on Knowledge and Data Engineering; 1-19.

Date published: July 1, 2021
Featured in this article: Trupti Joshi, Dong Xu.

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DM3Loc: Multi-label mRNA subcellular localization prediction and analysis based on multi-head self-attention mechanism. Wang D, Zhang Z, Jiang Y, Mao Z, Wang D, Lin H, Xu D. Nucleic Acids Research; 49(8):E46.

Date published: May 7, 2021
Featured in this article: Dong Xu.

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Multi-Cloud Performance and Security Driven Federated Workflow Management. Dickinson M, Debroy S, Calyam P, Valluripally S, Zhang Y, Antequera RB, Joshi T, White T, Xu D. IEEE Transactions on Cloud Computing; 9(1):240-257.

Date published: January 1, 2021
Featured in this article: Trupti Joshi, Dong Xu.

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MusiteDeep: A deep-learning based webserver for protein post-translational modification site prediction and visualization. Wang D, Liu D, Yuchi J, He F, Jiang Y, Cai S, Li J, Xu D. Nucleic Acids Research; 48(W1):W140-W146.

Date published: January 1, 2021
Featured in this article: Dong Xu.

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Overlapping community detection based on membership degree propagation. Gao R, Li S, Shi X, Liang Y, Xu D. Entropy; 23(1):1-35.

Date published: January 1, 2021
Featured in this article: Dong Xu.

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[Deep Neural Architecture Search: A Survey] [深度神经架构搜索综述]. Meng Z, Gu X, Liang Y, Xu D, Wu C. Jisuanji Yanjiu yu Fazhan/Computer Research and Development; 58(1):22-33.

Date published: January 1, 2021
Featured in this article: Dong Xu.

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MULocDeep: A deep-learning framework for protein subcellular and suborganellar localization prediction with residue-level interpretation. Jiang Y, Wang D, Yao Y, Eubel H, Künzler P, Møller IM, Xu D. Computational and Structural Biotechnology Journal; 19:4825-4839.

Date published: January 1, 2021
Featured in this article: Dong Xu.

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Computational methods for protein localization prediction. Jiang Y, Wang D, Wang W, Xu D. Computational and Structural Biotechnology Journal; 19:5834-5844.

Date published: January 1, 2021
Featured in this article: Dong Xu.

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2020

Genome-wide identification of the expansin gene family and its potential association with drought stress in moso bamboo. Jin K-M, Zhuo R-Y, Xu D, Wang Y-J, Fan H-J, Huang B-Y, Qiao G-R. International Journal of Molecular Sciences; 21(24):1-21.

Date published: December 2, 2020
Featured in this article: Dong Xu.

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Single-Cell Techniques and Deep Learning in Predicting Drug Response. Wu Z, Lawrence PJ, Ma A, Zhu J, Xu D, Ma Q. Trends in Pharmacological Sciences; 41(12):1050-1065.

Date published: December 1, 2020
Featured in this article: Dong Xu.

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Deep Learning Detection of Inaccurate Smart Electricity Meters: A Case Study. Liu M, Liu D, Sun G, Zhao Y, Wang D, Liu F, Fang X, He Q, Xu D. IEEE Industrial Electronics Magazine; 14(4):79-90.

Date published: December 1, 2020
Featured in this article: Dong Xu.

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Recommender-as-a-service with chatbot guided domain-science knowledge discovery in a science gateway. Vekaria K, Calyam P, Sivarathri SS, Wang S, Zhang Y, Pandey A, Chen C, Xu D, Joshi T, Nair S. Concurrency Computation; 33:e6080.

Date published: November 11, 2020
Featured in this article: Dong Xu, Trupti Joshi.

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Leveraging systematic functional analysis to benchmark an in silico framework distinguishes driver from passenger MEK mutants in cancer. Hanrahan AJ, Sylvester BE, Chang MT, Elzein A, Gao J, Han W, Liu Y, Xu D, Gao SP, Gorelick AN, Jones AM, Kiliti AJ, Nissan MH, Nimura CA, Poteshman AN, Yao Z, Gao Y, Hu W, Wise HC, Gavrila EI, Shoushtari AN, Tiwari S, Viale A, Abdel-Wahab O, Merghoub T, Berger MF, Rosen N, Taylor BS, Solit DB. Cancer Research; 80(19):4233-4243.

Date published: October 1, 2020
Featured in this article: Dong Xu.

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How oncogenic mutations activate human MAP kinase 1 (MEK1): a molecular dynamics simulation study. Liu Y, Zhu J, Guo X, Huang T, Han J, Gao J, Xu D, Han W. Journal of Biomolecular Structure and Dynamics; 38(13):3942-3958.

Date published: September 1, 2020
Featured in this article: Dong Xu.

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Metabolomic profiling of wild-type and mutant soybean root nodules using laser-ablation electrospray ionization mass spectrometry reveals altered metabolism. Agtuca BJ, Stopka SA, Evans S, Samarah L, Liu Y, Xu D, Stacey MG, Koppenaal DW, Paša-Tolić L, Anderton CR, Vertes A, Stacey G. Plant Journal; 103(5):1937-1958.

Date published: August 1, 2020
Featured in this article: Dong Xu, Minviluz (Bing) Stacey, Gary Stacey.

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Proteomic and bioinformatic profiling of transporters in higher plant mitochondria. Møller IM, Shyama Prasad Rao R, Jiang Y, Thelen JJ, Xu D. Biomolecules; 10(8):1-13.

Date published: August 1, 2020
Featured in this article: Jay Thelen, Dong Xu.

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Two New Heuristic Methods for Protein Model Quality Assessment. Wang W, Wang J, Xu D, Shang Y. IEEE/ACM Transactions on Computational Biology and Bioinformatics; 17(4):1430-1439.

Date published: July 1, 2020
Featured in this article: Dong Xu.

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Overcoming Wnt–β-catenin dependent anticancer therapy resistance in leukaemia stem cells. Perry JM, Tao F, Roy A, Lin T, He XC, Chen S, Lu X, Nemechek J, Ruan L, Yu X, Dukes D, Moran A, Pace J, Schroeder K, Zhao M, Venkatraman A, Qian P, Li Z, Hembree M, Paulson A, He Z, Xu D, Tran T-H, Deshmukh P, Nguyen CT, Kasi RM, Ryan R, Broward M, Ding S, Guest E, August K, Gamis AS, Godwin A, Sittampalam GS, Weir SJ, Li L. Nature Cell Biology; 22(6):689-700.

Date published: June 1, 2020
Featured in this article: Dong Xu.

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Endoplasmic reticulum retention and degradation of a mutation in SLC6A1 associated with epilepsy and autism. Wang J, Poliquin S, Mermer F, Eissman J, Delpire E, Wang J, Shen W, Cai K, Li B-M, Li Z-Y, Xu D, Nwosu G, Flamm C, Liao W-P, Shi Y-W, Kang J-Q. Molecular Brain; 13(1):76.

Date published: May 12, 2020
Featured in this article: Dong Xu.

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Detecting Cancer Survival Related Gene Markers Based on Rectified Factor Network. Su L, Liu G, Wang J, Gao J, Xu D. Frontiers in Bioengineering and Biotechnology; 8:349.

Date published: April 23, 2020
Featured in this article: Dong Xu.

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Correction: Evidence for plant-derived xenomiRs based on a large-scale analysis of public small RNA sequencing data from human samples (PLOS ONE (2019) 14:10 (e0224537) DOI: 10.1371/journal.pone.0224537). Zhao Q, Liu Y, Zhang N, Hu M, Zhang H, Joshi T, Xu D. PLoS ONE; 15(3):e0230146.

Date published: March 11, 2020
Featured in this article: Trupti Joshi, Dong Xu.

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A self-attention based message passing neural network for predicting molecular lipophilicity and aqueous solubility. Tang B, Kramer ST, Fang M, Qiu Y, Wu Z, Xu D. Journal of Cheminformatics; 12(1):15.

Date published: February 21, 2020
Featured in this article: Dong Xu.

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IMPRes-Pro: A high dimensional multiomics integration method for in silico hypothesis generation. Jiang Y, Wang D, Xu D, Joshi T. Methods; 173:16-23.

Date published: February 15, 2020
Featured in this article: Dong Xu, Trupti Joshi.

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MUFold-SSW: A new web server for predicting protein secondary structures, torsion angles and turns. Fang C, Li Z, Xu D, Shang Y. Bioinformatics; 36(4):1293-1295.

Date published: February 15, 2020
Featured in this article: Dong Xu.

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A dynamic programing approach to integrate gene expression data and network information for pathway model generation. Jiang Y, Liang Y, Wang D, Xu D, Joshi T. Bioinformatics; 36(1):169-176.

Date published: January 1, 2020
Featured in this article: Dong Xu, Trupti Joshi.

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Inductive inference of gene regulatory network using supervised and semi-supervised graph neural networks. Wang J, Ma A, Ma Q, Xu D, Joshi T. Computational and Structural Biotechnology Journal; 18:3335-3343.

Date published: January 1, 2020
Featured in this article: Dong Xu, Trupti Joshi.

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In-situ metabolomic analysis of Setaria viridis roots colonized by beneficial endophytic bacteria. Agtuca BJ, Stopka SA, Tuleski TR, Do Amaral FP, Evan S, Liu Y, Xu D, Monteiro RA, Koppenaal DW, Paša-Tolić L, Anderton CR, Vertes A, Stacey G. Molecular Plant-Microbe Interactions; 33(2):272-283.

Date published: January 1, 2020
Featured in this article: Dong Xu, Gary Stacey.

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A deep dense inception network for protein beta-turn prediction. Fang C, Shang Y, Xu D. Proteins: Structure, Function and Bioinformatics; 88(1):143-151.

Date published: January 1, 2020
Featured in this article: Dong Xu.

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Fuzzified Image Enhancement for Deep Learning in Iris Recognition. Liu M, Zhou Z, Shang P, Xu D. IEEE Transactions on Fuzzy Systems; 28(1):92-99.

Date published: January 1, 2020
Featured in this article: Dong Xu.

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Artificial intelligence-driven structurization of diagnostic information in free-text pathology reports. Giannaris P, Al-Taie Z, Kovalenko M, Thanintorn N, Kholod O, Innokenteva Y, Coberly E, Frazier S, Laziuk K, Popescu M, Shyu C-R, Xu D, Hammer R, Shin D. Journal of Pathology Informatics; 11(1):4.

Date published: January 1, 2020
Featured in this article: Dong Xu.

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An Improved Topology Prediction of Alpha-Helical Transmembrane Protein Based on Deep Multi-Scale Convolutional Neural Network. Yang Y, Yu J, Liu Z, Wang X, Wang H, Ma Z, Xu D. IEEE/ACM Transactions on Computational Biology and Bioinformatics; 1-10.

Date published: January 1, 2020
Featured in this article: Dong Xu.

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Transporters and ascorbate–glutathione metabolism for differential cadmium accumulation and tolerance in two contrasting willow genotypes. Han X, Zhang Y, Yu M, Zhang J, Xu D, Lu Z, Qiao G, Qiu W, Zhuo R. Tree Physiology; 40(8):1126-1142.

Date published: January 1, 2020
Featured in this article: Dong Xu.

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MU-PseUDeep: A deep learning method for prediction of pseudouridine sites. Khan SM, He F, Wang D, Chen Y, Xu D. Computational and Structural Biotechnology Journal; 18:1877-1883.

Date published: January 1, 2020
Featured in this article: Dong Xu.

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2019

Knowledge Base Commons (KBCommons) v1.1: A universal framework for multi-omics data integration and biological discoveries. Zeng S, Lyu Z, Narisetti SRK, Xu D, Joshi T. BMC Genomics; 20:947.

Date published: December 20, 2019
Featured in this article: Dong Xu, Trupti Joshi.

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Phenotype Prediction and Genome-Wide Association Study Using Deep Convolutional Neural Network of Soybean. Liu Y, Wang D, He F, Wang J, Joshi T, Xu D. Frontiers in Genetics; 10:1091.

Date published: November 22, 2019
Featured in this article: Trupti Joshi, Dong Xu.

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ESAE: Evolutionary Strategy-Based Architecture Evolution. Gu X, Meng Z, Liang Y, Xu D, Huang H, Han X, Wu C. Communications in Computer and Information Science; 1159 CCIS:193-208.

Date published: November 22, 2019
Featured in this article: Dong Xu.

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DMCTOP: Topology Prediction of Alpha-Helical Transmembrane Protein Based on Deep Multi-Scale Convolutional Neural Network. Wang H, Yang Y, Yu J, Wang X, Zhao D, Xu D, Sun P. Proceedings - 2019 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2019; 36-43.

Date published: November 18, 2019
Featured in this article: Dong Xu.

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Capsule Network for Predicting Zinc Binding Sites in Metalloproteins. Essien C, Wang D, Xu D. Proceedings - 2019 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2019; 2337-2341.

Date published: November 18, 2019
Featured in this article: Dong Xu.

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Extracting Molecular Entities and Their Interactions from Pathway Figures Based on Deep Learning. He F, Wang D, Innokenteva Y, Kholod O, Shin D, Xu D. Proceedings - 2019 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2019; 1191-1193.

Date published: November 18, 2019
Featured in this article: Dong Xu.

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Protein Ubiquitylation and Sumoylation Site Prediction Based on Ensemble and Transfer Learning. He F, Wang R, Gao Y, Wang D, Yu Y, Xu D, Zhao X. Proceedings - 2019 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2019; 117-123.

Date published: November 1, 2019
Featured in this article: Dong Xu.

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Modeling of contextual information in knowledge graphs of diagnostic reports. Giannaris P, Tang C, Kholod O, Hanson S, Shyu C-R, Hammer R, Xu D, Shin D. CEUR Workshop Proceedings; 2515:20-29.

Date published: October 26, 2019
Featured in this article: Dong Xu.

Correction: Evidence for plant-derived xenomiRs based on a large-scale analysis of public small RNA sequencing data from human samples (PLoS ONE (2019) 13:6 (e0187519) DOI: 10.1371/journal.pone.0187519). Zhao Q, Liu Y, Zhang N, Hu M, Zhang H, Joshi T, Xu D. PLoS ONE; 14(10):e0224537.

Date published: October 1, 2019
Featured in this article: Trupti Joshi, Dong Xu.

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A missense mutation in SLC6A1 associated with Lennox-Gastaut syndrome impairs GABA transporter 1 protein trafficking and function. Cai K, Wang J, Eissman J, Wang J, Nwosu G, Shen W, Liang H-C, Li X-J, Zhu H-X, Yi Y-H, Song J, Xu D, Delpire E, Liao W-P, Shi Y-W, Kang J-Q. Experimental Neurology; 320:112973.

Date published: October 1, 2019
Featured in this article: Dong Xu.

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Extracting molecular entities and their interactions from pathway figures based on deep learning. He F, Wang D, Innokenteva Y, Kholod O, Shin D, Xu D. ACM-BCB 2019 - Proceedings of the 10th ACM International Conference on Bioinformatics, Computational Biology and Health Informatics; 397-404.

Date published: September 7, 2019
Featured in this article: Dong Xu.

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Machine Learning Classifiers for Endometriosis Using Transcriptomics and Methylomics Data. Akter S, Xu D, Nagel SC, Bromfield JJ, Pelch K, Wilshire GB, Joshi T. Frontiers in Genetics; 10:766.

Date published: September 4, 2019
Featured in this article: Dong Xu, Trupti Joshi.

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SoyCSN: Soybean context-specific network analysis and prediction based on tissue-specific transcriptome data. Wang J, Hossain MS, Lyu Z, Schmutz J, Stacey G, Xu D, Joshi T. Plant Direct; 3(9):e00167.

Date published: September 1, 2019
Featured in this article: Gary Stacey, Dong Xu, Trupti Joshi.

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A Fast Projection-Based Algorithm for Clustering Big Data. Wu Y, He Z, Lin H, Zheng Y, Zhang J, Xu D. Interdisciplinary Sciences: Computational Life Sciences; 11(3):360-366.

Date published: September 1, 2019
Featured in this article: Dong Xu.

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A rectified factor network based biclustering method for detecting cancer-related coding genes and miRNAs, and their interactions. Su L, Liu G, Wang J, Xu D. Methods; 166:22-30.

Date published: August 15, 2019
Featured in this article: Dong Xu.

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Capsule network for protein post-translational modification site prediction. Wang D, Liang Y, Xu D. Bioinformatics; 35(14):2386-2394.

Date published: July 15, 2019
Featured in this article: Dong Xu.

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Transcriptome sequencing of active buds from Populus deltoides CL. and Populus × zhaiguanheibaiyang reveals phytohormones involved in branching. Wang J, Tian Y, Li J, Yang K, Xing S, Han X, Xu D, Wang Y. Genomics; 111(4):700-709.

Date published: July 1, 2019
Featured in this article: Dong Xu.

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PSICA: a fast and accurate web service for protein model quality analysis. Wang W, Li Z, Wang J, Xu D, Shang Y. Nucleic Acids Research; 47(W1):W443-W450.

Date published: July 1, 2019
Featured in this article: Dong Xu.

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Prediction of Protein Backbone Torsion Angles Using Deep Residual Inception Neural Networks. Fang C, Shang Y, Xu D. IEEE/ACM Transactions on Computational Biology and Bioinformatics; 16(3):1020-1028.

Date published: May 1, 2019
Featured in this article: Dong Xu.

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The deep learning-based recommender system “pubmender” for choosing a biomedical publication venue: Development and validation study. Feng X, Zhang H, Ren Y, Shang P, Zhu Y, Liang Y, Guan R, Xu D. Journal of Medical Internet Research; 21(5):e12957.

Date published: May 1, 2019
Featured in this article: Dong Xu.

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Identification of new loci for salt tolerance in soybean by high-resolution genome-wide association mapping. Do TD, Vuong TD, Dunn D, Clubb M, Valliyodan B, Patil G, Chen P, Xu D, Nguyen HT, Shannon JG. BMC Genomics; 20(1):318.

Date published: April 25, 2019
Featured in this article: Dong Xu.

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Plant-derived phosphocholine facilitates cellular uptake of anti-pulmonary fibrotic HJT-sRNA-m7. Du J, Liang Z, Xu J, Zhao Y, Li X, Zhang Y, Zhao D, Chen R, Liu Y, Joshi T, Chang J, Wang Z, Zhang Y, Zhu J, Liu Q, Xu D, Jiang C. Science China Life Sciences; 62(3):309-320.

Date published: March 1, 2019
Featured in this article: Trupti Joshi, Dong Xu.

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New deep learning methods for protein loop modeling. Nguyen SP, Li Z, Xu D, Shang Y. IEEE/ACM Transactions on Computational Biology and Bioinformatics; 16(2):596-606.

Date published: March 1, 2019
Featured in this article: Dong Xu.

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Domain-specific Topic Model for Knowledge Discovery through Conversational Agents in Data Intensive Scientific Communities. Zhang Y, Calyam P, Joshi T, Nair S, Xu D. Proceedings - 2018 IEEE International Conference on Big Data, Big Data 2018; 4886-4895.

Date published: January 22, 2019
Featured in this article: Trupti Joshi, Dong Xu.

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Knowledge Base Commons (KBCommons) v1.0: A multi OMICS’ web-based data integration framework for biological discoveries. Zeng S, Lyu Z, Narisetti SRK, Xu D, Joshi T. Proceedings - 2018 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2018; 589-594.

Date published: January 21, 2019
Featured in this article: Dong Xu, Trupti Joshi.

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Integrating Gene Expression Data and Pathway Knowledge for in Silico Hypothesis Generation with IMPRes. Jiang Y, Wang D, Xu D, Joshi T. Proceedings - 2018 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2018; 102-107.

Date published: January 21, 2019
Featured in this article: Dong Xu, Trupti Joshi.

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A Data Mining Approach for Biomarker Discovery Using Transcriptomics in Endometriosis. Akter S, Xu D, Nagel SC, Joshi T. Proceedings - 2018 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2018; 969-972.

Date published: January 21, 2019
Featured in this article: Dong Xu, Trupti Joshi.

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DeepDom: Predicting protein domain boundary from sequence alone using stacked bidirectional LSTM. Jiang Y, Wang D, Xu D. Pacific Symposium on Biocomputing; 24(2019):66-75.

Date published: January 3, 2019
Featured in this article: Dong Xu.

Characterization of select wild soybean accessions in the USDA germplasm collection for seed composition and agronomic traits. La T, Large E, Taliercio E, Song Q, Gillman JD, Xu D, Nguyen HT, Shannon G, Scaboo A. Crop Science; 59(1):233-251.

Date published: January 1, 2019
Featured in this article: Dong Xu.

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Trends in Alzheimer’s disease research based upon machine learning analysis of pubmed abstracts. Guan R, Wen X, Liang Y, Xu D, He B, Feng X. International Journal of Biological Sciences; 15(10):2065-2074.

Date published: January 1, 2019
Featured in this article: Dong Xu.

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Identification and expression analysis of the GDSL esterase/lipase family genes, and the characterization of SaGLIP8 in Sedum alfredii Hance under cadmium Stress. Li H, Han X, Qiu W, Xu D, Wang Y, Yu M, Hu X, Zhuo R. PeerJ; 2019(4):e6741.

Date published: January 1, 2019
Featured in this article: Dong Xu.

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Computational prediction of ubiquitination proteins using evolutionary profiles and functional domain annotation. Qiu W, Xu C, Xiao X, Xu D. Current Genomics; 20(5):389-399.

Date published: January 1, 2019
Featured in this article: Dong Xu.

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Large expert-curated database for benchmarking document similarity detection in biomedical literature search. Brown P, Zhou Y, Tan A-C, El-Esawi MA, Liehr T, Blanck O, Gladue D, Almeida GMF, Cernava T, Sorzano C, Yeung AWK, Engel M, Chandrasekaran A, Muth T, Staege M, Daulatabad S, Widera D, Zhang J, Meule A, Honjo K, Pourret O, Yin C-C, Zhang Z, Cascella M, Flegel WA, Goodyear CS, van Raaij MJ, Bukowy-Bieryllo Z, Campana LG, Kurniawan NA, Lalaouna D, Hüttner FJ, Ammerman BA, Ehret F, Cobine PA, Tan E-C, Han H, Xia W, McCrum C, Dings RPM, Marinello F, Nilsson H, Nixon B, Voskarides K, Yang L, Costa VD, Bengtsson-Palme J, Bradshaw W, Grimm DG, Kumar N, Martis E, Prieto D, Sabnis SC, Amer SEDR, Liew A, Perco P, Rahimi F, Riva G, Zhang C, Devkota HP, Ogami K, Basharat Z, Fierz W, Siebers R, Tan KH, Boehme KA, Brenneisen P, Brown JAL, Dalrymple BP, Harvey DJ, Ng G, Werten S, Bleackley M, Dai Z, Dhariwal R, Gelfer Y, Hartmann MD, Miotla P, Tamaian R, Govender P, Gurney-Champion OJ, Kauppila JH, Zhang X, Echeverría N, Subhash S, Sallmon H, Tofani M, Bae T, Bosch O, Cuív PO, Danchin A, Diouf B, 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Lazo-Langner A, Leclercq G, Li M, Li Q, Li T, Li Y, Liao W-T, Liao Z-Y, Lin J, Lizer J, Lobreglio G, Lowies C, Lu C, Majeed H, Martin A, Martinez-Sobrido L, Meresh E, Middelveen M, Mohebbi A, Mota J, Mozaheb Z, Muyaya L, Nandhakumar A, Ng SHX, Obeidat M, Oh D-H, Owais M, Pace-Asciak P, Panwar A, Park C, Patterson C, Penagos-Tabaree F, Pianosi PT, Pinzi V, Pridans C, Psaroulaki A, Pujala RK, Pulido-Arjona L, Qi P-F, Rahman P, Rai NK, Rassaf T, Refardt J, Ricciardi W, Riess O, Rovas A, Sacks FM, Saleh S, Sampson C, Schmutz A, Sepanski R, Sharma N, Singh M, Spearman P, Subramaniapillai M, Swali R, Tan CM, Tellechea JI, Thomas L-M, Tong X, Vavvas DG, Veys R, Vitriol V, Wang H-D, Wang J, Wang J, Waugh J, Webb SA, Williams BA, Workman AD, Xiang T, Xie L-X, Xu J, Xu T, Yang C, Yoon JG, Yuan CM, Zaritsky A, Zhang Y, Zhao H, Zuckerman H, Lyu R, Pullan W. Database; 2019:1-67.

Date published: January 1, 2019
Featured in this article: Dong Xu.

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2018

An analysis and evaluation of the WeFold collaborative for protein structure prediction and its pipelines in CASP11 and CASP12. Keasar C, McGuffin LJ, Wallner B, Chopra G, Adhikari B, Bhattacharya D, Blake L, Bortot LO, Cao R, Dhanasekaran BK, Dimas I, Faccioli RA, Faraggi E, Ganzynkowicz R, Ghosh S, Ghosh S, Giełdoń A, Golon L, He Y, Heo L, Hou J, Khan M, Khatib F, Khoury GA, Kieslich C, Kim DE, Krupa P, Lee GR, Li H, Li J, Lipska A, Liwo A, Maghrabi AHA, Mirdita M, Mirzaei S, Mozolewska MA, Onel M, Ovchinnikov S, Shah A, Shah U, Sidi T, Sieradzan AK, Ślusarz M, Ślusarz R, Smadbeck J, Tamamis P, Trieber N, Wirecki T, Yin Y, Zhang Y, Bacardit J, Baranowski M, Chapman N, Cooper S, Defelicibus A, Flatten J, Koepnick B, Popović Z, Zaborowski B, Baker D, Cheng J, Czaplewski C, Delbem ACB, Floudas C, Kloczkowski A, Ołdziej S, Levitt M, Scheraga H, Seok C, Söding J, Vishveshwara S, Xu D, Caglar A, Coral A, MacMillan A, Lubow A, Failer B, Kestemont B, Landers CR, Painter CR, Garnier C, Sellin C, Janz D, Wheeler DC, Simon V, Flear DM, Croze E, McIlvaine GV, Beecher G, Lawrie G, Ykman G, Feldmann H, Fuentes HK, Terumasa H, Kovanecz I, Longino JA III, Nijland JH, Diderich JA, Canfield JM, Eriksson J, Slone JD, Appel JG, Mitchell J, Mitch J, Loots-Boiy J, Brownlee JM, Wilson K, Clayton KT, Deford KE, Abbey KJ, Withers L, Wei L, Ives L, Miller LA, Carpenter L, Sharma MG, Ricci M, Binfield MS, Davids MJ, Gaebel M, Cassidy MD, Fagiola M, Pfützenreuter M, Barlow N, Triggiani PJ IV, Innes RBM, Leduc R, Dos Santos Gomes RLC, Morneau RLR, Zaccanelli SJ, Kleinfelter SC, Van Der Laan TJA, Bausewein T, George TJ, Mikhail V, Barmettler W, Crivelli SN. Scientific Reports; 8(1):9939.

Date published: December 1, 2018
Featured in this article: Dong Xu.

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Improving Protein Gamma-Turn Prediction Using Inception Capsule Networks. Fang C, Shang Y, Xu D. Scientific Reports; 8(1):15741.

Date published: December 1, 2018
Featured in this article: Dong Xu.

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Large-scale prediction of protein ubiquitination sites using a multimodal deep architecture. He F, Wang R, Li J, Bao L, Xu D, Zhao X. BMC Systems Biology; 12:109.

Date published: November 22, 2018
Featured in this article: Dong Xu.

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Genomic analyses based on pulmonary adenocarcinoma in situ reveal early lung cancer signature 11 Medical and Health Sciences 1112 Oncology and Carcinogenesis. Li D, Yang W, Zhang Y, Yang JY, Guan R, Xu D, Yang MQ. BMC Medical Genomics; 11:106.

Date published: November 20, 2018
Featured in this article: Dong Xu.

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A content-based recommender system for computer science publications. Wang D, Liang Y, Xu D, Feng X, Guan R. Knowledge-Based Systems; 157:1-9.

Date published: October 1, 2018
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CarbonylDB: A curated data-resource of protein carbonylation sites. Prasad Rao RS, Zhang N, Xu D, MaxMoøller I. Bioinformatics; 34(14):2518-2520.

Date published: July 15, 2018
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Evidence for plant-derived xenomiRs based on a large-scale analysis of public small RNA sequencing data from human samples. Zhao Q, Liu Y, Zhang N, Hu M, Zhang H, Joshi T, Xu D. PLoS ONE; 13(6):e0187519.

Date published: June 1, 2018
Featured in this article: Trupti Joshi, Dong Xu.

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G2S: A web-service for annotating genomic variants on 3D protein structures. Wang J, Sheridan R, Sumer SO, Schultz N, Xu D, Gao J. Bioinformatics; 34(11):1949-1950.

Date published: June 1, 2018
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MU-LOC: A machine-learning method for predicting mitochondrially localized proteins in plants. Zhang N, Rao RSP, Salvato F, Havelund JF, Møller IM, Thelen JJ, Xu D. Frontiers in Plant Science; 9:634.

Date published: May 23, 2018
Featured in this article: Jay Thelen, Dong Xu.

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MUFOLD-SS: New deep inception-inside-inception networks for protein secondary structure prediction. Fang C, Shang Y, Xu D. Proteins: Structure, Function and Bioinformatics; 86(5):592-598.

Date published: May 1, 2018
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Mapping and confirmation of loci for salt tolerance in a novel soybean germplasm, Fiskeby III. Do TD, Vuong TD, Dunn D, Smothers S, Patil G, Yungbluth DC, Chen P, Scaboo A, Xu D, Carter TE, Nguyen HT, Grover Shannon J. Theoretical and Applied Genetics; 131(3):513-524.

Date published: March 1, 2018
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Whole-exome sequencing and microRNA profiling reveal PI3K/AKT pathway’s involvement in juvenile myelomonocytic leukemia. Khan SM, Denney JE, Wang MX, Xu D. Quantitative Biology; 6(1):85-97.

Date published: March 1, 2018
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Why is a high temperature needed by Thermus thermophilus argonaute during mRNA silencing: A theoretical study. Liu Y, Yu Z, Zhu J, Wang S, Xu D, Han W. Frontiers in Chemistry; 6(JUN):223.

Date published: January 1, 2018
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2017

MusiteDeep: A deep-learning framework for general and kinase-specific phosphorylation site prediction. Wang D, Zeng S, Xu C, Qiu W, Liang Y, Joshi T, Xu D. Bioinformatics; 33(24):3909-3916.

Date published: December 15, 2017
Featured in this article: Trupti Joshi, Dong Xu.

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Understanding the differences of the ligand binding/unbinding pathways between phosphorylated and non-phosphorylated ARH1 using molecular dynamics simulations. Zhu J, Lv Y, Han X, Xu D, Han W. Scientific Reports; 7(1):12439.

Date published: December 1, 2017
Featured in this article: Dong Xu.

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Effects of evolutionary pressure on histone modifications. Khan SM, Conant G, Xu D. Proceedings - 2017 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2017; 2017-January:2267.

Date published: November 13, 2017
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A multimodal deep architecture for large-scale protein ubiquitylation site prediction. He F, Bao L, Wang R, Li J, Xu D, Zhao X. Proceedings - 2017 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2017; 2017-January:108-113.

Date published: November 13, 2017
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Protein loop modeling using deep generative adversarial network. Li Z, Nguyen SP, Xu D, Shang Y. Proceedings - International Conference on Tools with Artificial Intelligence, ICTAI; 2017-November:1085-1091.

Date published: November 6, 2017
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A new deep neighbor residual network for protein secondary structure prediction. Fang C, Shang Y, Xu D. Proceedings - International Conference on Tools with Artificial Intelligence, ICTAI; 2017-November:66-71.

Date published: November 6, 2017
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PzTAC and PzLAZY from a narrow-crown poplar contribute to regulation of branch angles. Xu D, Qi X, Li J, Han X, Wang J, Jiang Y, Tian Y, Wang Y. Plant Physiology and Biochemistry; 118:571.

Date published: September 1, 2017
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BioJava-ModFinder: Identification of protein modifications in 3D structures from the Protein Data Bank. Gao J, Prlić A, Bi C, Bluhm WF, Dlmitropoulos D, Xu D, Bourne PE, Rose PW. Bioinformatics; 33(13):2047-2049.

Date published: July 1, 2017
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Overfitting reduction of text classification based on AdaBELM. Feng X, Liang Y, Shi X, Xu D, Wang X, Guan R. Entropy; 19(7):330.

Date published: July 1, 2017
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iPhos-PseEvo: Identifying Human Phosphorylated Proteins by Incorporating Evolutionary Information into General PseAAC via Grey System Theory. Qiu W-R, Sun B-Q, Xiao X, Xu D, Chou K-C. Molecular Informatics; 36(5):1600010.

Date published: May 1, 2017
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Understanding the Phosphorylation Mechanism by Using Quantum Chemical Calculations and Molecular Dynamics Simulations. Han W, Zhu J, Wang S, Xu D. Journal of Physical Chemistry B; 121(15):3565-3573.

Date published: April 20, 2017
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Divergent cytosine DNA methylation patterns in single-cell, soybean root hairs. Hossain MS, Kawakatsu T, Kim KD, Zhang N, Nguyen CT, Khan SM, Batek JM, Joshi T, Schmutz J, Grimwood J, Schmitz RJ, Xu D, Jackson SA, Ecker JR, Stacey G. New Phytologist; 214(2):808-819.

Date published: April 1, 2017
Featured in this article: Trupti Joshi, Dong Xu, Gary Stacey.

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OMPcontact: An Outer Membrane Protein Inter-Barrel Residue Contact Prediction Method. Zhang L, Wang H, Yan L, Su L, Xu D. Journal of Computational Biology; 24(3):217-228.

Date published: March 1, 2017
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BFDCA: A Comprehensive Tool of Using Bayes Factor for Differential Co-Expression Analysis. Wang D, Wang J, Jiang Y, Liang Y, Xu D. Journal of Molecular Biology; 429(3):446-453.

Date published: February 3, 2017
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End-to-end security formalization and alignment for federated workflow management. Dickinson M, Debroy S, Calyam P, Valluripally S, Zhang Y, Joshi T, Xu D. IEEE International Conference on Cloud Computing, CLOUD; 59-67.

Date published: January 17, 2017
Featured in this article: Trupti Joshi, Dong Xu.

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The evolution of soybean knowledge base (SoyKB). Joshi T, Wang J, Zhang H, Chen S, Zeng S, Xu B, Xu D. Methods in Molecular Biology; 1533:149-159.

Date published: January 1, 2017
Featured in this article: Trupti Joshi, Dong Xu.

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Bioinformatics analysis of protein phosphorylation in plant systems biology using P3DB. Yao Q, Xu D. Methods in Molecular Biology; 1558:127-138.

Date published: January 1, 2017
Featured in this article: Dong Xu.

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Tongue Images Classification Based on Constrained High Dispersal Network. Meng D, Cao G, Duan Y, Zhu M, Tu L, Xu D, Xu J. Evidence-based Complementary and Alternative Medicine; 2017:7452427.

Date published: January 1, 2017
Featured in this article: Dong Xu.

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Tongue image analysis and its mobile app development for health diagnosis. Kanawong R, Obafemi-Ajayi T, Liu D, Zhang M, Xu D, Duan Y. Advances in Experimental Medicine and Biology; 1005:99-121.

Date published: January 1, 2017
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2016

Imbalanced multi-label learning for identifying antimicrobial peptides and their functional types. Lin W, Xu D. Bioinformatics; 32(24):3745-3752.

Date published: December 15, 2016
Featured in this article: Dong Xu.

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A deep tongue image features analysis model for medical application. Meng D, Cao G, Duan Y, Zhu M, Tu L, Xu J, Xu D. Proceedings - 2016 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2016; 1918-1922.

Date published: December 15, 2016
Featured in this article: Dong Xu.

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Classification of tongue images based on doublet and color space dictionary. Cao G, Ding J, Duan Y, Tu L, Xu J, Xu D. Proceedings - 2016 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2016; 1170-1175.

Date published: December 15, 2016
Featured in this article: Dong Xu.

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Exploring human diseases and biological mechanisms by protein structure prediction and modeling. Wang J, Luttrell J IV, Zhang N, Khan S, Shi N, Wang MX, Kang J-Q, Wang Z, Xu D. Advances in Experimental Medicine and Biology; 939:39-61.

Date published: November 1, 2016
Featured in this article: Dong Xu.

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Differential protein structural disturbances and suppression of assembly partners produced by nonsense GABRG2 epilepsy mutations: Implications for disease phenotypic heterogeneity. Wang J, Shen D, Xia G, Shen W, MacDonald RL, Xu D, Kang J-Q. Scientific Reports; 6:35294.

Date published: October 20, 2016
Featured in this article: Dong Xu.

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PGen: Large-scale genomic variations analysis workflow and browser in SoyKB. Liu Y, Khan SM, Wang J, Rynge M, Zhnag Y, Zeng S, Chen S, Maldonado dos Santos JV, Valliyodan B, Calyam PP, Merchant N, Nguyen HT, Xu D, Joshi T. BMC Bioinformatics; 17:337.

Date published: October 6, 2016
Featured in this article: Dong Xu, Trupti Joshi.

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Computational analysis of the ligand binding site of the extracellular ATP receptor, DORN1. Nguyen CT, Tanaka K, Cao Y, Cho S-H, Xu D, Stacey G. PLoS ONE; 11(9):e0161894.

Date published: September 1, 2016
Featured in this article: Dong Xu, Gary Stacey.

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A family of negative regulators targets the committed step of de novo fatty acid biosynthesisopen. Salie MJ, Zhang N, Lancikova V, Xu D, Thelen JJ. Plant Cell; 28(9):2312-2325.

Date published: September 1, 2016
Featured in this article: Dong Xu, Jay Thelen.

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Transcriptome Analysis of Active Axillary Buds from Narrow-crown and Broad-crown Poplars Provides Insight into the Phytohormone Regulatory Network for Branching Angle. Tian Y, Wang J, Guo H, Qu K, Xu D, Hou L, Li J. Plant Molecular Biology Reporter; 39(3):595-606.

Date published: September 1, 2016
Featured in this article: Dong Xu.

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Role of plant MicroRNA in cross-species regulatory networks of humans. Zhang H, Li Y, Liu Y, Liu H, Wang H, Jin W, Zhang Y, Zhang C, Xu D. BMC Systems Biology; 10(1):60.

Date published: August 8, 2016
Featured in this article: Dong Xu.

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Characteristics of staminate catkin development and pollen germination in Populus×liaoningensis. Xu D, Li J, Xie L, Qi X, Wang J, Xing S. Linye Kexue/Scientia Silvae Sinicae; 52(8):38-45.

Date published: August 1, 2016
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Identification and comparative analysis of differential gene expression in soybean leaf tissue under drought and flooding stress revealed by RNA-Seq. Chen W, Yao Q, Patil GB, Agarwal G, Deshmukh RK, Lin L, Wang B, Wang Y, Prince SJ, Song L, Xu D, An YC, Valliyodan B, Varshney RK, Nguyen HT. Frontiers in Plant Science; 7(JULY2016):1044.

Date published: July 19, 2016
Featured in this article: Dong Xu.

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Soybean roots grown under heat stress show global changes in their transcriptional and proteomic profiles. Valdés-López O, Batek J, Gomez-Hernandez N, Nguyen CT, Isidra-Arellano MC, Zhang N, Joshi T, Xu D, Hixson KK, Weitz KK, Alrich JT, Paša-Tolić L, Stacey G. Frontiers in Plant Science; 7(APR2016):517.

Date published: April 25, 2016
Featured in this article: Trupti Joshi, Dong Xu, Gary Stacey.

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Improving degree-based variable ordering heuristics for solving constraint satisfaction problems. Li H, Liang Y, Zhang N, Guo J, Xu D, Li Z. Journal of Heuristics; 22(2):125-145.

Date published: April 1, 2016
Featured in this article: Dong Xu.

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Landscape of genomic diversity and trait discovery in soybean. Valliyodan B, Dan Qiu, Patil G, Zeng P, Huang J, Dai L, Chen C, Li Y, Joshi T, Song L, Vuong TD, Musket TA, Xu D, Shannon JG, Shifeng C, Liu X, Nguyen HT. Scientific Reports; 6:23598.

Date published: March 31, 2016
Featured in this article: Trupti Joshi, Dong Xu.

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Evaluation of genetic variation among Brazilian soybean cultivars through genome resequencing. dos Santos JVM, Valliyodan B, Joshi T, Khan SM, Liu Y, Wang J, Vuong TD, de Oliveira MF, Marcelino-Guimarães FC, Xu D, Nguyen HT, Abdelnoor RV. BMC Genomics; 17(1):110.

Date published: February 13, 2016
Featured in this article: Trupti Joshi, Dong Xu.

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FALCON@home: A high-throughput protein structure prediction server based on remote homologue recognition. Wang C, Zhang H, Zheng W-M, Xu D, Zhu J, Wang B, Ning K, Sun S, Li SC, Bu D. Bioinformatics; 32(3):462-464.

Date published: February 1, 2016
Featured in this article: Dong Xu.

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Predicting DNA Methylation State of CpG Dinucleotide Using Genome Topological Features and Deep Networks. Wang Y, Liu T, Xu D, Shi H, Zhang C, Mo Y-Y, Wang Z. Scientific Reports; 6:19598.

Date published: January 22, 2016
Featured in this article: Dong Xu.

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Genome-wide transcriptome analysis of soybean primary root under varying water-deficit conditions. Song L, Prince S, Valliyodan B, Joshi T, Maldonado dos Santos JV, Wang J, Lin L, Wan J, Wang Y, Xu D, Nugyen HT. BMC Genomics; 17(1):57.

Date published: January 15, 2016
Featured in this article: Trupti Joshi, Dong Xu.

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A full Bayesian partition model for identifying hypo- and hyper-methylated loci from single nucleotide resolution sequencing data. Wang H, He C, Kushwaha G, Xu D, Qiu J. BMC Bioinformatics; 17(1):S7.

Date published: January 11, 2016
Featured in this article: Dong Xu.

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RDF Sketch Maps – Knowledge complexity reduction for precision medicine analytics. Thanintorn N, Wang J, Ersoy I, Al-Taie Z, Jiang Y, Wang D, Verma M, Joshi T, Hammer R, Xu D, Shin D. Pacific Symposium on Biocomputing; 417-428.

Date published: January 4, 2016
Featured in this article: Trupti Joshi, Dong Xu.

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Identification and functional characterization of soybean root hair microRNAs expressed in response to Bradyrhizobium japonicum infection. Yan Z, Hossain MS, Valdés-López O, Hoang NT, Zhai J, Wang J, Liabault M, Brechenmacher L, Findley S, Joshi T, Qiu L, Sherrier DJ, Ji T, Meyers BC, Xu D, Stacey G. Plant Biotechnology Journal; 14(1):332-341.

Date published: January 1, 2016
Featured in this article: Trupti Joshi, Dong Xu, Gary Stacey.

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Network stratification analysis for identifying function-specific network layers. Zhang C, Wang J, Zhang C, Liu J, Xu D, Chen L. Molecular BioSystems; 12(4):1232-1240.

Date published: January 1, 2016
Featured in this article: Dong Xu.

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Hypomethylation coordinates antagonistically with hypermethylation in cancer development: A case study of leukemia. Kushwaha G, Dozmorov M, Wren JD, Qiu J, Shi H, Xu D. Human Genomics; 10:18.

Date published: January 1, 2016
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2015

Polymorphism of the glucosyltransferase gene (ycjM) in Escherichia coli and its use for tracking human fecal pollution in water. Deng D, Zhang N, Xu D, Reed M, Liu F, Zheng G. Science of the Total Environment; 537:260-267.

Date published: December 15, 2015
Featured in this article: Dong Xu.

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Whole-genome gene expression profiling revealed genes and pathways potentially involved in regulating interactions of soybean with cyst nematode (Heterodera glycines Ichinohe). Wan J, Vuong T, Jiao Y, Joshi T, Zhang H, Xu D, Nguyen HT. BMC Genomics; 16(1):148.

Date published: December 12, 2015
Featured in this article: Trupti Joshi, Dong Xu.

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A Bayesian model for detection of high-order interactions among genetic variants in genome-wide association studies. Wang J, Joshi T, Valliyodan B, Shi H, Liang Y, Nguyen HT, Zhang J, Xu D. BMC Genomics; 16(1):1011.

Date published: November 25, 2015
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Comparative analysis of the drought-responsive transcriptome in soybean lines contrasting for canopy wilting. Prince SJ, Joshi T, Mutava RN, Syed N, Joao Vitor MDS, Patil G, Song L, Wang J, Lin L, Chen W, Shannon JG, Valliyodan B, Xu D, Nguyen HT. Plant Science; 240:65-78.

Date published: November 1, 2015
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Identification of Soybean Proteins and Genes Differentially Regulated in Near Isogenic Lines Differing in Resistance to Aphid Infestation. Brechenmacher L, Nguyen THN, Zhang N, Jun T-H, Xu D, Mian MAR, Stacey G. Journal of Proteome Research; 14(10):4137-4146.

Date published: October 2, 2015
Featured in this article: Dong Xu, Gary Stacey.

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Selective refinement and selection of near-native models in protein structure prediction. Zhang J, Barz B, Zhang J, Xu D, Kosztin I. Proteins: Structure, Function and Bioinformatics; 83(10):1823-1835.

Date published: October 1, 2015
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Effect of lipo-chitooligosaccharide on early growth of C4 grass seedlings. Tanaka K, Cho S-H, Lee H, Pham AQ, Batek JM, Cui S, Qiu J, Khan SM, Joshi T, Zhang ZT, Xu D, Stacey G. Journal of Experimental Botany; 66(19):5727-5738.

Date published: September 1, 2015
Featured in this article: Trupti Joshi, Dong Xu, Gary Stacey.

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Soybean transcription factor ORFeome associated with drought resistance: A valuable resource to accelerate research on abiotic stress resistance. Chai C, Wang Y, Joshi T, Valliyodan B, Prince S, Michel L, Xu D, Nguyen HT. BMC Genomics; 16(1):596.

Date published: August 13, 2015
Featured in this article: Trupti Joshi, Dong Xu.

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Soybean (Glycine max) SWEET gene family: Insights through comparative genomics, transcriptome profiling and whole genome re-sequence analysis. Patil G, Valliyodan B, Deshmukh R, Prince S, Nicander B, Zhao M, Sonah H, Song L, Lin L, Chaudhary J, Liu Y, Joshi T, Xu D, Nguyen HT. BMC Genomics; 16(1):520.

Date published: July 11, 2015
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Guest Editors Introduction to the Special Issue on Software and Databases. Xu D, Huang K, Schmidt J. IEEE/ACM Transactions on Computational Biology and Bioinformatics; 12(4):793-794.

Date published: July 1, 2015
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Identification of quantitative trait loci underlying resistance to southern root-knot and reniform nematodes in soybean accession PI 567516C. Jiao Y, Vuong TD, Liu Y, Li Z, Noe J, Robbins RT, Joshi T, Xu D, Shannon JG, Nguyen HT. Molecular Breeding; 35(6):131.

Date published: June 26, 2015
Featured in this article: Trupti Joshi, Dong Xu.

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The human epilepsy mutation GABRG2(Q390X) causes chronic subunit accumulation and neurodegeneration. Kang J-Q, Shen W, Zhou C, Xu D, Macdonald RL. Nature Neuroscience; 18(7):988-996.

Date published: June 25, 2015
Featured in this article: Dong Xu.

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Genome-wide expression analysis of soybean NF-Y genes reveals potential function in development and drought response. Quach TN, Nguyen HTM, Valliyodan B, Joshi T, Xu D, Nguyen HT. Molecular Genetics and Genomics; 290(3):1095-1115.

Date published: June 23, 2015
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Analysis of the siRNA-mediated gene silencing process targeting three homologous genes controlling soybean seed oil quality. Lu S, Yin X, Spollen W, Zhang N, Xu D, Schoelz J, Bilyeu K, Zhang ZJ. PLoS ONE; 10(6):e0129010.

Date published: June 10, 2015
Featured in this article: Dong Xu.

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Phosphorylation site prediction in plants. Yao Q, Schulze WX, Xu D. Plant Phosphoproteomics: Methods and Protocols; 217-228.

Date published: April 30, 2015
Featured in this article: Dong Xu.

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Genetic stability analysis in somatic embryo regeneration of erica carnea by RAPD and ISSR markers. Wang J-N, Li J-H, Qi X, Yao P-J, Xu D. Zhiwu Shengli Xuebao/Plant Physiology Journal; 51(4):448-494.

Date published: April 20, 2015
Featured in this article: Dong Xu.

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An association analysis between psychophysical characteristics and genome-wide gene expression changes in human adaptation to the extreme climate at the Antarctic Dome Argus. Xu C, Ju X, Song D, Huang F, Tang D, Zou Z, Zhang C, Joshi T, Jia L, Xu W, Xu K-F, Wang Q, Xiong Y, Guo Z, Chen X, Huang F, Xu J, Zhong Y, Zhu Y, Peng Y, Wang L, Zhang X, Jiang R, Li D, Jiang T, Xu D, Jiang C. Molecular Psychiatry; 20(4):536-544.

Date published: April 2, 2015
Featured in this article: Trupti Joshi, Dong Xu.

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Genetic variants in root architecture-related genes in a Glycine soja accession, a potential resource to improve cultivated soybean. Prince SJ, Song L, Qiu D, Maldonado dos Santos JV, Chai C, Joshi T, Patil G, Valliyodan B, Vuong TD, Murphy M, Krampis K, Tucker DM, Biyashev R, Dorrance AE, Maroof MAS, Xu D, Shannon JG, Nguyen HT. BMC Genomics; 16(1):132.

Date published: February 25, 2015
Featured in this article: Trupti Joshi, Dong Xu.

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Identification and evaluation of quantitative trait loci underlying resistance to multiple HG types of soybean cyst nematode in soybean PI 437655. Jiao Y, Vuong TD, Liu Y, Meinhardt C, Liu Y, Joshi T, Cregan PB, Xu D, Shannon JG, Nguyen HT. Theoretical and Applied Genetics; 128(1):15-23.

Date published: January 17, 2015
Featured in this article: Trupti Joshi, Dong Xu.

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PRIMEGENSw3: A web-based tool for high-throughput primer and probe design. Kushwaha G, Srivastava GP, Xu D. Methods in Molecular Biology; 1275:181-199.

Date published: January 1, 2015
Featured in this article: Dong Xu.

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Databases for plant phosphoproteomics. Schulze WX, Yao Q, Xu D. Methods in Molecular Biology; 1306:207-216.

Date published: January 1, 2015
Featured in this article: Dong Xu.

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Phosphorylation site prediction in plants. Yao Q, Schulze WX, Xu X. Methods in Molecular Biology; 1306:217-228.

Date published: January 1, 2015
Featured in this article: Dong Xu.

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2014

Advances in translational bioinformatics facilitate revealing the landscape of complex disease mechanisms. Yang JY, Dunker AK, Liu JS, Qin X, Arabnia HR, Yang W, Niemierko A, Chen Z, Luo Z, Wang L, Liu Y, Xu D, Deng Y, Tong W, Yang MQ. BMC Bioinformatics; 15(17):I1.

Date published: December 16, 2014
Featured in this article: Dong Xu.

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Identification of genes and pathways involved in kidney renal clear cell carcinoma. Yang W, Yoshigoe K, Qin X, Liu JS, Yang JY, Niemierko A, Deng Y, Liu Y, Dunker AK, Chen Z, Wang L, Xu D, Arabnia HR, Tong W, Yang MQ. BMC Bioinformatics; 15(17):S2.

Date published: December 16, 2014
Featured in this article: Dong Xu.

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A new Hidden Markov Model for protein quality assessment using compatibility between protein sequence and structure. He Z, Ma W, Zhang J, Xu D. Tsinghua Science and Technology; 19(6):559-567.

Date published: December 1, 2014
Featured in this article: Dong Xu.

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Transcriptional responses of Arabidopsis thaliana to chewing and sucking insect herbivores. Appel HM, Fescemyer H, Ehlting J, Weston D, Rehrig E, Joshi T, Xu D, Bohlmann J, Schultz J. Frontiers in Plant Science; 5(November):1-20.

Date published: November 14, 2014
Featured in this article: Trupti Joshi, Dong Xu.

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RNA-protein distance patterns in ribosomes reveal the mechanism of translational attenuation. Yu DM, Zhang C, Qin PW, Cornish PV, Xu D. Science China Life Sciences; 57(11):1131-1139.

Date published: November 1, 2014
Featured in this article: Dong Xu.

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Flower-visiting insects and their potential impact on transgene flow in rice. Pu D-Q, Shi M, Wu Q, Gao M-Q, Liu J-F, Ren S-P, Yang F, Tang P, Ye G-Y, Shen Z-C, He J-H, Yang D, Bu W-J, Zhang C-T, Song Q, Xu D, Strand MR, Chen X-X. Journal of Applied Ecology; 51(5):1357-1365.

Date published: October 1, 2014
Featured in this article: Dong Xu.

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Differentiating enteric Escherichia coli from environmental bacteria through the putative glucosyltransferase gene (ycjM). Deng D, Zhang L, Mustapha A, Xu D, Wuliji T, Farley M, Yang J, Hua B, Liu F, Zheng G. Water Research; 61:224-231.

Date published: September 15, 2014
Featured in this article: Dong Xu.

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XMDFF: Molecular dynamics flexible fitting of low-resolution X-ray structures. Mcgreevy R, Singharoy A, Li Q, Zhang J, Xu D, Perozo E, Schulten K. Acta Crystallographica Section D: Biological Crystallography; 70(9):2344-2355.

Date published: August 26, 2014
Featured in this article: Dong Xu.

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Diverse and divergent protein post-translational modifications in two growth stages of a natural microbial community. Li Z, Wang Y, Yao Q, Justice NB, Ahn T-H, Xu D, Hettich RL, Banfield JF, Pan C. Nature Communications; 5:4405.

Date published: July 25, 2014
Featured in this article: Dong Xu.

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DL-PRO: A novel deep learning method for protein model quality assessment. Nguyen SP, Shang Y, Xu D. Proceedings of the International Joint Conference on Neural Networks; 2071-2078.

Date published: July 6, 2014
Featured in this article: Dong Xu.

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Multi-dimensional scaling and MODELLER-based evolutionary algorithms for protein model refinement. Chen Y, Shang Y, Xu D. Proceedings of the 2014 IEEE Congress on Evolutionary Computation, CEC 2014; 1038-1045.

Date published: July 6, 2014
Featured in this article: Dong Xu.

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Genotypic variation of gene expression during the soybean innate immunity response. Valdés-López O, Khan SM, Schmitz RJ, Cui S, Qiu J, Joshi T, Xu D, Diers B, Ecker JR, Stacey G. Plant Genetic Resources: Characterisation and Utilisation; 12(SUPPL.1):S27-S30.

Date published: July 1, 2014
Featured in this article: Trupti Joshi, Dong Xu, Gary Stacey.

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Comparative transcriptomic analysis of symbiotic Bradyrhizobium japonicum. Franck S, Franck WL, Birke SR, Chang W-S, Sangurdekar DP, Cytryn E, Joshi T, Sadowsky M, Stacey G, Xu D, Emerich DW. Symbiosis; 63(3):123-135.

Date published: July 1, 2014
Featured in this article: Trupti Joshi, Gary Stacey, Dong Xu.

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BridgeDb app: Unifying identifier mapping services for cytoscape. Gao J, Zhang C, van Iersel M, Zhang L, Xu D, Schultz N, R Pico A. F1000Research; 3:4521.1.

Date published: July 1, 2014
Featured in this article: Dong Xu.

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Identifying critical transitions of complex diseases based on a single sample. Liu R, Yu X, Liu X, Xu D, Aihara K, Chen L. Bioinformatics; 30(11):1579-1586.

Date published: June 1, 2014
Featured in this article: Dong Xu.

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Major soybean maturity gene haplotypes revealed by SNPViz analysis of 72 sequenced soybean genomes. Langewisch T, Zhang H, Vincent R, Joshi T, Xu D, Bilyeu K. PLoS ONE; 9(4):e94150.

Date published: April 11, 2014
Featured in this article: Trupti Joshi, Dong Xu.

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Soybean knowledge base (SoyKB): A web resource for integration of soybean translational genomics and molecular breeding. Joshi T, Fitzpatrick MR, Chen S, Liu Y, Zhang H, Endacott RZ, Gaudiello EC, Stacey G, Nguyen HT, Xu D. Nucleic Acids Research; 42(D1):D1245-D1252.

Date published: January 1, 2014
Featured in this article: Trupti Joshi, Gary Stacey, Dong Xu.

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Virtual physical examination (VPE): A multimedia system for education in medicine. Joshi T, Williamson R, Patil K, Viyanon S, Li X, Zhang Y, Qi W, Li D, Zimmer J, Illindala U, Foley S, Campbell R, Duan Y, Xu D. International Journal of Functional Informatics and Personalised Medicine; 4(3-4):181-197.

Date published: January 1, 2014
Featured in this article: Trupti Joshi, Dong Xu.

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P³DB 3.0: From plant phosphorylation sites to protein networks. Yao Q, Ge H, Wu S, Zhang N, Chen W, Xu C, Gao J, Thelen JJ, Xu D. Nucleic Acids Research; 42(D1):D1206-D1213.

Date published: January 1, 2014
Featured in this article: Jay Thelen, Dong Xu.

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Disrupting KATP channels diminishes the estrogen-mediated protection in female mutant mice during ischemia-reperfusion. Gao J, Xu D, Sabat G, Valdivia H, Xu W, Shi N-Q. Clinical Proteomics; 11(1):19.

Date published: January 1, 2014
Featured in this article: Dong Xu.

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MUFOLD-DB: A processed protein structure database for protein structure prediction and analysis. He Z, Zhang C, Xu Y, Zeng S, Zhang J, Xu D. BMC Genomics; 15:S2.

Date published: January 1, 2014
Featured in this article: Dong Xu.

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2013

Soybean knowledge base (SoyKB): Bridging the gap between soybean translational genomics and breeding. Joshi T, Fitzpatrick MR, Chen S, Liu Y, Zhang H, Endacott RZ, Gaudiello EC, Stacey G, Nguyen HT, Xu D. Proceedings - 2013 IEEE International Conference on Bioinformatics and Biomedicine, IEEE BIBM 2013; 42-44.

Date published: December 18, 2013
Featured in this article: Trupti Joshi, Gary Stacey, Dong Xu.

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Using an intervening sequence of Faecalibacterium 16S rDNA to identify poultry feces. Shen Z, Duan C, Zhang C, Carson A, Xu D, Zheng G. Water Research; 47(16):6415-6422.

Date published: October 15, 2013
Featured in this article: Dong Xu.

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Circles within circles: Crosstalk between protein Ser/Thr/Tyr-phosphorylation and Met oxidation. Rao RSP, Xu D, Thelen JJ, Miernyk JA. BMC Bioinformatics; 14(SUPPL.14):S14.

Date published: October 9, 2013
Featured in this article: Dong Xu, Jay Thelen.

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Epigenome-wide inheritance of cytosine methylation variants in a recombinant inbred population. Schmitz RJ, He Y, Valdés-López O, Khan SM, Joshi T, Urich MA, Nery JR, Diers B, Xu D, Stacey G, Ecker JR. Genome Research; 23(10):1663-1674.

Date published: October 1, 2013
Featured in this article: Trupti Joshi, Dong Xu, Gary Stacey.

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New MDS and clustering based algorithms for protein model quality assessment and selection. Wang Q, Shang C, Xu D, Shang Y. International Journal on Artificial Intelligence Tools; 22(5):1360006.

Date published: October 1, 2013
Featured in this article: Dong Xu.

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NOA: A cytoscape plugin for network ontology analysis. Zhang C, Wang J, Hanspers K, Xu D, Chen L, Pico AR. Bioinformatics; 29(16):2066-2067.

Date published: August 15, 2013
Featured in this article: Dong Xu.

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Transmembrane Protein Alignment and Fold Recognition Based on Predicted Topology. Wang H, He Z, Zhang C, Zhang L, Xu D. PLoS ONE; 8(7):e69744.

Date published: July 19, 2013
Featured in this article: Dong Xu.

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A Computational Systems Biology Study for Understanding Salt Tolerance Mechanism in Rice. Wang J, Chen L, Wang Y, Zhang J, Liang Y, Xu D. PLoS ONE; 8(6):e64929.

Date published: June 7, 2013
Featured in this article: Dong Xu.

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Influence of mRNA features on siRNA interference efficacy. Liu Y, Chang Y, Zhang C, Wei Q, Chen J, Chen H, Xu D. Journal of Bioinformatics and Computational Biology; 11(3):1341004.

Date published: June 1, 2013
Featured in this article: Dong Xu.

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A versatile mass spectrometry-based method to both identify kinase client-relationships and characterize signaling network topology. Ahsan N, Huang Y, Tovar-Mendez A, Swatek KN, Zhang J, Miernyk JA, Xu D, Thelen JJ. Journal of Proteome Research; 12(2):937-948.

Date published: February 1, 2013
Featured in this article: Dong Xu, Jay Thelen.

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Genomic differences between cultivated soybean, G. max and its wild relative G. soja. Joshi T, Valliyodan B, Wu J-H, Lee S-H, Xu D, Nguyen HT. BMC Genomics; 14:S5.

Date published: January 21, 2013
Featured in this article: Trupti Joshi, Dong Xu.

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Fast algorithm for population-based protein structural model analysis. Zhang J, Xu D. Proteomics; 13(2):221-229.

Date published: January 1, 2013
Featured in this article: Dong Xu.

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Optimised design of siRNA based on multi-featured comparison and analysis of H1N1 virus. Liu Y, Chang Y, Xu D, Li Z, Zhang H, Li J, Tian M. International Journal of Data Mining and Bioinformatics; 7(4):345-357.

Date published: January 1, 2013
Featured in this article: Dong Xu.

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Protein structural model selection by combining consensus and single scoring methods. He Z, Alazmi M, Zhang J, Xu D. PLoS ONE; 8(9):e74006.

Date published: January 1, 2013
Featured in this article: Dong Xu.

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A computational method for predicting regulation of human microRNAs on the influenza virus genome. Zhang H, Li Z, Li Y, Liu Y, Liu J, Li X, Shen T, Duan Y, Hu M, Xu D. BMC Systems Biology; 7:S3.

Date published: January 1, 2013
Featured in this article: Dong Xu.

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Analysis and prediction of protein posttranslational modification sites. Gao J, Yao Q, Bollinger CH, Xu D. Algorithmic and Artificial Intelligence Methods for Protein Bioinformatics; 91-106.

Date published: January 1, 2013
Featured in this article: Dong Xu.

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2012

Pathway Correlation Profile of Gene-Gene Co-Expression for Identifying Pathway Perturbation. Tegge AN, Caldwell CW, Xu D. PLoS ONE; 7(12):e52127.

Date published: December 20, 2012
Featured in this article: Dong Xu.

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RNA secondary structure comparison based on dynamic programming. Zhang H, Li Z, Liu Y, Li Y, Duan Y, Xu D. Proceedings - 2012 7th International Conference on Computing and Convergence Technology (ICCIT, ICEI and ICACT), ICCCT 2012; 1364-1368.

Date published: December 3, 2012
Featured in this article: Dong Xu.

Elongation Factor 1 alpha1 and Genes Associated with Usher Syndromes Are Downstream Targets of GBX2. Roeseler DA, Sachdev S, Buckley DM, Joshi T, Wu DK, Xu D, Hannink M, Waters ST. PLoS ONE; 7(11):e47366.

Date published: November 8, 2012
Featured in this article: Trupti Joshi, Dong Xu, Mark Hannink.

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Quantitative phosphoproteomic analysis of soybean root hairs inoculated with Bradyrhizobium japonicum. Nguyen THN, Brechenmacher L, Aldrich JT, Clauss TR, Gritsenko MA, Hixson KK, Libault M, Tanaka K, Yang F, Yao Q, Paša-Tolić L, Xu D, Nguyen HT, Stacey G. Molecular and Cellular Proteomics; 11(11):1140-1155.

Date published: November 1, 2012
Featured in this article: Dong Xu, Gary Stacey.

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Protein databases on the internet. Xu D. Current protocols in protein science; 2:Unit2.6.

Date published: November 1, 2012
Featured in this article: Dong Xu.

Protein databases on the internet. Xu D. Current Protocols in Protein Science; 1(SUPPL.70):2.6.

Date published: November 1, 2012
Featured in this article: Dong Xu.

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Features for automated tongue image shape classification. Obafemi-Ajayi T, Kanawong R, Xu D, Li S, Duan Y. Proceedings - 2012 IEEE International Conference on Bioinformatics and Biomedicine Workshops, BIBMW 2012; 273-279.

Date published: October 4, 2012
Featured in this article: Dong Xu.

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ZHENG classification in Traditional Chinese Medicine based on modified specular-free tongue images. Obafemi-Ajayi T, Kanawong R, Yu J, Xu D, Li S, Duan Y. Proceedings - 2012 IEEE International Conference on Bioinformatics and Biomedicine Workshops, BIBMW 2012; 288-294.

Date published: October 4, 2012
Featured in this article: Dong Xu.

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P³DB: An integrated database for plant protein phosphorylation. Yao Q, Bollinger C, Gao J, Xu D, Thelen JJ. Frontiers in Plant Science; 3(SEP):206.

Date published: September 7, 2012
Featured in this article: Dong Xu, Jay Thelen.

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Reconstructing differentially co-expressed gene modules and regulatory networks of soybean cells. Zhu M, Deng X, Joshi T, Xu D, Stacey G, Cheng J. BMC Genomics; 13(1):437.

Date published: August 31, 2012
Featured in this article: Trupti Joshi, Dong Xu, Gary Stacey.

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Predicting and analyzing protein phosphorylation sites in plants using Musite. Yao Q, Gao J, Bollinger C, Thelen JJ, Xu D. Frontiers in Plant Science; 3(AUG):186.

Date published: August 21, 2012
Featured in this article: Jay Thelen, Dong Xu.

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“Scanning mutagenesis” of the amino acid sequences flanking phosphorylation site 1 of the mitochondrial pyruvate dehydrogenase complex. Ahsan N, Swatek KN, Zhang J, Miernyk JA, Xu D, Thelen JJ. Frontiers in Plant Science; 3(JUL):153.

Date published: July 16, 2012
Featured in this article: Dong Xu, Jay Thelen.

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Protein structure prediction and clustering using MUFOLD. Zhang J, Xu D. Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); 7292 LNBI:328-329.

Date published: May 21, 2012
Featured in this article: Dong Xu.

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Phosphoproteomic analysis of seed maturation in arabidopsis, rapeseed, and soybean. Meyer LJ, Gao J, Xu D, Thelen JJ. Plant Physiology; 159(1):517-528.

Date published: May 1, 2012
Featured in this article: Dong Xu, Jay Thelen.

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Using internet search engines to obtain medical information: A comparative study. Wang L, Wang J, Wang M, Li Y, Liang Y, Xu D. Journal of Medical Internet Research; 14(3):E74.

Date published: May 1, 2012
Featured in this article: Dong Xu.

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Computational challenges in characterization of bacteria and bacteria-host interactions based on genomic data. Zhang C, Zheng G, Xu S-F, Xu D. Journal of Computer Science and Technology; 27(2):225-239.

Date published: March 1, 2012
Featured in this article: Dong Xu.

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Soybean knowledge base (SoyKB): A web resource for soybean translational genomics. Joshi T, Patil K, Fitzpatrick MR, Franklin LD, Yao Q, Cook JR, Wang Z, Libault M, Brechenmacher L, Valliyodan B, Wu X, Cheng J, Stacey G, Nguyen HT, Xu D. Series on Advances in Bioinformatics and Computational Biology; 13:S15.

Date published: January 17, 2012
Featured in this article: Trupti Joshi, Gary Stacey, Dong Xu.

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Correlation between posttranslational modification and intrinsic disorder in Protein. Gao J, Xu D. Pacific Symposium on Biocomputing; 94-103.

Date published: January 3, 2012
Featured in this article: Dong Xu.

Evolutionary dynamics of protein domain architecture in plants. Zhang X-C, Wang Z, Zhang X, Le MH, Sun J, Xu D, Cheng J, Stacey G. BMC Evolutionary Biology; 12(1):6.

Date published: January 1, 2012
Featured in this article: Dong Xu, Gary Stacey.

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Protein structural model selection based on protein-dependent scoring function. He Z, Zhang J, Xu Y, Shang Y, Xu D. Statistics and its Interface; 5(1):109-117.

Date published: January 1, 2012
Featured in this article: Dong Xu.

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An automatic tongue detection and segmentation framework for computer-aided tongue image analysis. Kanawong R, Xu W, Xu D, Li S, Ma T, Duan Y. International Journal of Functional Informatics and Personalised Medicine; 4(1):56-68.

Date published: January 1, 2012
Featured in this article: Dong Xu.

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Prediction of protein tertiary structures using MUFOLD. Zhang J, He Z, Wang Q, Barz B, Kosztin I, Shang Y, Xu D. Methods in Molecular Biology; 815:3-13.

Date published: January 1, 2012
Featured in this article: Dong Xu.

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Automated tongue feature extraction for ZHENG classification in Traditional Chinese Medicine. Kanawong R, Obafemi-Ajayi T, Ma T, Xu D, Li S, Duan Y. Evidence-based Complementary and Alternative Medicine; 2012:912852.

Date published: January 1, 2012
Featured in this article: Dong Xu.

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2011

Polytomy identification in microbial phylogenetic reconstruction. Lin GN, Zhang C, Xu D. BMC Systems Biology; 5(SUPPL. 3):S2.

Date published: December 23, 2011
Featured in this article: Dong Xu.

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Fast algorithm for clustering a large number of protein structural decoys. Zhang J, Xu D. Proceedings - 2011 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2011; 30-36.

Date published: November 12, 2011
Featured in this article: Dong Xu.

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PRIMEGENSw3: A web-based tool for high-throughput primer and probe design. Kushwaha G, Srivastava GP, Xu D. Proceedings - 2011 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2011; 345-351.

Date published: November 12, 2011
Featured in this article: Dong Xu.

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A hybrid consensus and clustering method for protein structure selection. Wang Q, Shang Y, Xu D. Proceedings - International Conference on Tools with Artificial Intelligence, ICTAI; 1-8.

Date published: November 7, 2011
Featured in this article: Dong Xu.

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Targeted bisulfite sequencing by solution hybrid selection and massively parallel sequencing. Lee E-J, Pei L, Srivastava G, Joshi T, Kushwaha G, Choi J-H, Robertson KD, Wang X, Colbourne JK, Zhang L, Schroth GP, Xu D, Zhang K, Shi H. Nucleic Acids Research; 39(19).

Date published: October 1, 2011
Featured in this article: Trupti Joshi, Dong Xu.

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A Dual-targeted soybean protein is involved in Bradyrhizobium japonicum infection of soybean root hair and cortical cells. Libault M, Govindarajulu M, Berg RH, Ong YT, Puricelli K, Taylor CG, Xu D, Stacey G. Molecular Plant-Microbe Interactions; 24(9):1051-1060.

Date published: September 1, 2011
Featured in this article: Dong Xu, Gary Stacey.

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A sampling-based method for ranking protein structural models by integrating multiple scores and features. Shi X, Zhang J, He Z, Shang Y, Xu D. Current Protein and Peptide Science; 12(6):540-548.

Date published: September 1, 2011
Featured in this article: Dong Xu.

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Homolog-specific PCR primer design for profiling splice variants. Srivastava GP, Hanumappa M, Kushwaha G, Nguyen HT, Xu D. Nucleic Acids Research; 39(10):e69.

Date published: May 1, 2011
Featured in this article: Dong Xu.

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Identification of salt tolerance genes in rice from microarray data using SVM-RFE. Wang J, Zhang F, Wang Y, Fu Y, Xu D, Liang Y. 3rd International Conference on Bioinformatics and Computational Biology 2011, BICoB 2011; 30-35.

Date published: March 23, 2011
Featured in this article: Dong Xu.

Prediction of Drought-Resistant genes in Arabidopsis thaliana using SVM-RFE. Liang Y, Zhang F, Wang J, Joshi T, Wang Y, Xu D. PLoS ONE; 6(7):e21750.

Date published: January 1, 2011
Featured in this article: Trupti Joshi, Dong Xu.

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A protein domain Co-occurrence network approach for predicting protein function and inferring species phylogeny. Wang Z, Zhang X-C, Le MH, Xu D, Stacey G, Cheng J. PLoS ONE; 6(3):e17906.

Date published: January 1, 2011
Featured in this article: Dong Xu, Gary Stacey.

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Improving a consensus approach for protein structure selection by removing redundancy. Wang Q, Shang Y, Xu D. IEEE/ACM Transactions on Computational Biology and Bioinformatics; 8(6):1708-1715.

Date published: January 1, 2011
Featured in this article: Dong Xu.

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A multilayer evaluation approach for protein structure prediction and model quality assessment. Zhang J, Wang Q, Vantasin K, Zhang J, He Z, Kosztin I, Shang Y, Xu D. Proteins: Structure, Function and Bioinformatics; 79(SUPPL. 10):172-184.

Date published: January 1, 2011
Featured in this article: Dong Xu.

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2010

The Musite open-source framework for phosphorylation-site prediction. Gao J, Xu D. BMC Bioinformatics; 11(SUPPL. 12):S9.

Date published: December 21, 2010
Featured in this article: Dong Xu.

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SoyMetDB: The Soybean Metabolome Database. Joshi T, Yao Q, Franklin LD, Brechenmacher L, Valliyodan B, Stacey G, Nguyen H, Xu D. Proceedings - 2010 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2010; 203-208.

Date published: December 18, 2010
Featured in this article: Trupti Joshi, Gary Stacey, Dong Xu.

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Detection and application of CagA sequence markers for assessing risk factor of gastric cancer caused by Helicobacter pylori. Zhang C, Xu S, Xu D. Proceedings - 2010 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2010; 485-488.

Date published: December 18, 2010
Featured in this article: Dong Xu.

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Musite, a tool for global prediction of general and kinase-specific phosphorylation sites. Gao J, Thelen JJ, Dunker AK, Xu D. Molecular and Cellular Proteomics; 9(12):2586-2600.

Date published: December 1, 2010
Featured in this article: Jay Thelen, Dong Xu.

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Effector prediction in host-pathogen interaction based on a Markov model of a ubiquitous EPIYA motif. Xu S, Zhang C, Miao Y, Gao J, Xu D. BMC Genomics; 11(SUPPL. 3):S1.

Date published: December 1, 2010
Featured in this article: Dong Xu.

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2K09 and thereafter: The coming era of integrative bioinformatics, systems biology and intelligent computing for functional genomics and personalized medicine research. Yang JY, Niemierko A, Bajcsy R, Xu D, Athey BD, Zhang A, Ersoy OK, Li G-Z, Borodovsky M, Zhang JC, Arabnia HR, Deng Y, Dunker AK, Liu Y, Ghafoor A. BMC Genomics; 11(SUPPL. 3):I1.

Date published: November 29, 2010
Featured in this article: Dong Xu.

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Whole genome co-expression analysis of soybean cytochrome P450 genes identifies nodulation-specific P450 monooxygenases. Guttikonda SK, Trupti J, Bisht NC, Chen H, An Y-QC, Pandey S, Xu D, Yu O. BMC Plant Biology; 10:243.

Date published: November 9, 2010
Featured in this article: Trupti Joshi, Dong Xu.

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Root hair systems biology. Libault M, Brechenmacher L, Cheng J, Xu D, Stacey G. Trends in Plant Science; 15(11):641-650.

Date published: November 1, 2010
Featured in this article: Dong Xu, Gary Stacey.

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Identification of transcription factor’s targets using tissue-specific transcriptomic data in Arabidopsis thaliana. Srivastava CP, Li P, Liu J, Xu D. BMC Systems Biology; 4(SUPPL. 2):2.

Date published: September 13, 2010
Featured in this article: Dong Xu.

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SNP discovery by high-throughput sequencing in soybean. Wu X, Ren C, Joshi T, Vuong T, Xu D, Nguyen HT. BMC Genomics; 11(1):469.

Date published: August 11, 2010
Featured in this article: Trupti Joshi, Dong Xu.

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Protein structure selection based on consensus. Wang Q, Shang Y, Xu D. 2010 IEEE World Congress on Computational Intelligence, WCCI 2010 - 2010 IEEE Congress on Evolutionary Computation, CEC 2010; 5585949.

Date published: July 18, 2010
Featured in this article: Dong Xu.

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An integrated transcriptome atlas of the crop model Glycine max, and its use in comparative analyses in plants. Libault M, Farmer A, Joshi T, Takahashi K, Langley RJ, Franklin LD, He J, Xu D, May G, Stacey G. Plant Journal; 63(1):86-99.

Date published: July 1, 2010
Featured in this article: Trupti Joshi, Dong Xu, Gary Stacey.

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Genome-wide functional annotation by integrating multiple microarray datasets using meta-analysis. Srivastava CP, Qiu J, Xu D. International Journal of Data Mining and Bioinformatics; 4(4):357-376.

Date published: July 1, 2010
Featured in this article: Dong Xu.

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ProteinDBS v2.0: A web server for global and local protein structure search. Shyu C-R, Pang B, Chi P-H, Zhao N, Korkin D, Xu D. Nucleic Acids Research; 38(SUPPL. 2):W53-W58.

Date published: June 10, 2010
Featured in this article: Dong Xu.

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PMirP: A pre-microRNA prediction method based on structure-sequence hybrid features. Zhao D, Wang Y, Luo D, Shi X, Wang L, Xu D, Yu J, Liang Y. Artificial Intelligence in Medicine; 49(2):127-132.

Date published: June 1, 2010
Featured in this article: Dong Xu.

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Erratum: Genome sequence of the palaeopolyploid soybean (Nature (2010) 463 (178-183)). Schmutz J, Cannon SB, Schlueter J, Ma J, Mitros T, Nelson W, Hyten DL, Song Q, Thelen JJ, Cheng J, Xu D, Hellsten U, May GD, Yu Y, Skaurai T, Umezawa T, Bhattacharyya MK, Sandhu D, Valliyodan B, Lindquist E, Peto M, Grant D, Shu S, Goodstein D, Barry K, Futrell-Griggs M, Abernathy B, Du J, Tian Z, Zhu L, Gill N, Joshi T, Libault M, Sethuraman A, Zhang X-C, Shinozaki K, Nguyen HT, Wing RA, Cregan P, Specht J, Grimwood J, Rokhsar D, Stacey G, Shoemaker RC, Jackson SA. Nature; 465(7294):120.

Date published: May 6, 2010
Featured in this article: Jay Thelen, Dong Xu, Trupti Joshi, Gary Stacey.

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SeqRate: Sequence-based protein folding type classification and rates prediction. Lin GN, Wang Z, Xu D, Cheng J. BMC Bioinformatics; 11(SUPPL. 3):S1.

Date published: April 29, 2010
Featured in this article: Dong Xu.

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Systems analysis of seed filling in Arabidopsis: Using general linear modeling to assess concordance of transcript and protein expression. Hajduch M, Hearne LB, Miernyk JA, Casteel JE, Joshi T, Agrawal GK, Song Z, Zhou M, Xu D, Thelen JJ. Plant Physiology; 152(4):2078-2087.

Date published: April 1, 2010
Featured in this article: Trupti Joshi, Dong Xu, Jay Thelen.

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Prediction of novel miRNAs and associated target genes in Glycine max. Joshi T, Yan Z, Libault M, Jeong D-H, Park S, Green PJ, Sherrier DJ, Farmer A, May G, Meyers BC, Xu D, Stacey G. BMC Bioinformatics; 11(SUPPLL.1):S14.

Date published: January 18, 2010
Featured in this article: Trupti Joshi, Dong Xu, Gary Stacey.

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SoyDB: A knowledge database of soybean transcription factors. Wang Z, Libault M, Joshi T, Valliyodan B, Nguyen HT, Xu D, Stacey G, Cheng J. BMC Plant Biology; 10:14.

Date published: January 18, 2010
Featured in this article: Trupti Joshi, Dong Xu, Gary Stacey.

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Genome sequence of the palaeopolyploid soybean. Schmutz J, Cannon SB, Schlueter J, Ma J, Mitros T, Nelson W, Hyten DL, Song Q, Thelen JJ, Cheng J, Xu D, Hellsten U, May GD, Yu Y, Skaurai T, Umezawa T, Bhattacharyya MK, Sandhu D, Valliyodan B, Lindquist E, Peto M, Grant D, Shu S, Goodstein D, Barry K, Futrell-Griggs M, Abernathy B, Du J, Tian Z, Zhu L, Gill N, Joshi T, Libault M, Sethuraman A, Zhang X-C, Shinozaki K, Nguyen HT, Wing RA, Cregan P, Specht J, Grimwood J, Rokhsar D, Stacey G, Shoemaker RC, Jackson SA. Nature; 463(7278):178-183.

Date published: January 14, 2010
Featured in this article: Jay Thelen, Dong Xu, Trupti Joshi, Gary Stacey.

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Bioinformatics methods for protein identification using Peptide mass fingerprinting. Song Z, Chen L, Xu D. Methods in molecular biology (Clifton, N.J.); 604:7-22.

Date published: January 1, 2010
Featured in this article: Dong Xu.

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MUFOLD: A new solution for protein 3D structure prediction. Zhang J, Wang Q, Barz B, He Z, Kosztin L, Shang Y, Xu D. Proteins: Structure, Function and Bioinformatics; 78(5):1137-1152.

Date published: January 1, 2010
Featured in this article: Dong Xu.

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2009

Isotope pattern vector based tandem mass spectral data calibration for improved peptide and protein identification. Zhang J, Xu D, Gao W, Lin G, He S. Rapid Communications in Mass Spectrometry; 23(21):3448-3456.

Date published: November 15, 2009
Featured in this article: Dong Xu.

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Legume transcription factor genes: What makes legumes so special?. Libault M, Joshi T, Benedito VA, Xu D, Udvardi MK, Stacey G. Plant Physiology; 151(3):991-1001.

Date published: November 1, 2009
Featured in this article: Trupti Joshi, Dong Xu, Gary Stacey.

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Large-scale analysis of putative soybean regulatory gene expression identifies a Myb gene involved in soybean nodule development. Libault M, Joshi T, Takahashi K, Hurley-Sommer A, Puricelli K, Blake S, Finger RE, Taylor CS, Xu D, Nguyen HT, Stacey G. Plant Physiology; 151(3):1207-1220.

Date published: November 1, 2009
Featured in this article: Trupti Joshi, Dong Xu, Gary Stacey.

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Evolution analysis of the matrix (M) protein genes of 17 H9N2 chicken influenza viruses isolated in northern China during 1998-2008. Huang Y, Hu B, Wen X, Cao S, Xu D, Zhang X, Khan MI. Virus Genes; 38(3):398-403.

Date published: June 1, 2009
Featured in this article: Dong Xu.

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Confidence assessment for protein identification by using peptide-mass fingerprinting data. Song Z, Chen L, Xu D. Proteomics; 9(11):3090-3099.

Date published: June 1, 2009
Featured in this article: Dong Xu.

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System analysis of an arabidopsis mutant altered in de novo fatty acid synthesis reveals diverse changes in seed composition and metabolism. Chen M, Mooney BP, Hajduch M, Joshi T, Zhou M, Xu D, Thelen JJ. Plant Physiology; 150(1):27-41.

Date published: May 1, 2009
Featured in this article: Trupti Joshi, Dong Xu, Jay Thelen.

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A new machine learning approach for protein phosphorylation site prediction in plants. Gao J, Agrawal GK, Thelen JJ, Obradovic Z, Dunker AK, Xu D. Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); 5462 LNBI:18-29.

Date published: April 8, 2009
Featured in this article: Jay Thelen, Dong Xu.

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Establishment of a protein reference map for soybean root hair cells. Brechenmacher L, Lee J, Sachdev S, Song Z, Nguyen THN, Joshi T, Oehrle N, Libault M, Mooney B, Xu D, Cooper B, Stacey G. Plant Physiology; 149(2):670-682.

Date published: February 1, 2009
Featured in this article: Trupti Joshi, Dong Xu, Gary Stacey.

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ComPhy: Prokaryotic composite distance phylogenies inferred from whole-genome gene sets. Lin GN, Cai Z, Lin G, Chakraborty S, Xu D. BMC Bioinformatics; 10(SUPPL. 1):S5.

Date published: January 30, 2009
Featured in this article: Dong Xu.

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Generation of Phaseolus vulgaris ESTs and investigation of their regulation upon Uromyces appendiculatus infection. Thibivilliers S, Joshi T, Campbell KB, Scheffler B, Xu D, Cooper B, Nguyen HT, Stacey G. BMC Plant Biology; 9:46.

Date published: January 1, 2009
Featured in this article: Trupti Joshi, Dong Xu, Gary Stacey.

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A linear programming framework for inferring gene regulatory networks by integrating heterogeneous data. Wang Y, Wang R-S, Joshi T, Xu D, Zhang X-S, Chen L, Xia Y. Handbook of Research on Computational Methodologies in Gene Regulatory Networks; 450-475.

Date published: January 1, 2009
Featured in this article: Trupti Joshi, Dong Xu.

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P³DB: A plant protein phosphorylation database. Gao J, Agrawal GK, Thelen JJ, Xu D. Nucleic Acids Research; 37(SUPPL. 1):D960-D962.

Date published: January 1, 2009
Featured in this article: Jay Thelen, Dong Xu.

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Mutual understanding between Traditional Chinese Medicine and systems biology: gaps, challenges and opportunities. Xu D. International Journal of Functional Informatics and Personalised Medicine; 2(3):248-260.

Date published: January 1, 2009
Featured in this article: Dong Xu.

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Computational methods for protein sequence comparison and search. Xu D. Current Protocols in Protein Science; SUPPL. 56:2.1.1-2.1.27.

Date published: January 1, 2009
Featured in this article: Dong Xu.

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Sequence-based prediction of protein folding rates using contacts, secondary structures and support vector machines. Lin GN, Wang Z, Xu D, Cheng J. 2009 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2009; 3-8.

Date published: January 1, 2009
Featured in this article: Dong Xu.

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2008

Functional annotation from meta-analysis of microarray datasets. Srivastava CP, Qiu J, Xu D. Proceedings - IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2008; 367-371.

Date published: November 3, 2008
Featured in this article: Dong Xu.

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Predicting Functional Modules Using Microarray and Protein Interaction Data. Chen Y, Xu D. Analysis of Microarray Data: A Network-Based Approach; 307-329.

Date published: September 16, 2008
Featured in this article: Dong Xu.

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PRIMEGENS-v2: Genome-wide primer design for analyzing DNA methylation patterns of CpG islands. Srivastava CP, Guo J, Shi H, Xu D. Bioinformatics; 24(17):1837-1842.

Date published: September 1, 2008
Featured in this article: Dong Xu.

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A link between SIN1 (MAPKAP1) and poly(rC) binding protein 2 (PCBP2) in counteracting environmental stress. Ghosh D, Srivastava GP, Xu D, Schulz LC, Roberts RM. Proceedings of the National Academy of Sciences of the United States of America; 105(33):11673-11678.

Date published: August 19, 2008
Featured in this article: Dong Xu, Michael Roberts.

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Wanted: Unique names for unique atom positions. PDB-wide analysis of diastereotopic atom names of small molecules containing diphosphate. Bottoms CA, Xu D. BMC Bioinformatics; 9(SUPPL. 9):S16.

Date published: August 12, 2008
Featured in this article: Dong Xu.

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A lectin receptor-like kinase is required for pollen development in Arabidopsis. Wan J, Patel A, Mathieu M, Kim S-Y, Xu D, Stacey G. Plant Molecular Biology; 67(5):469-482.

Date published: July 1, 2008
Featured in this article: Dong Xu, Gary Stacey.

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A critical assessment of Mus musculus gene function prediction using integrated genomic evidence. Peña-Castillo L, Tasan M, Myers CL, Lee H, Joshi T, Zhang C, Guan Y, Leone M, Pagnani A, Kim WK, Krumpelman C, Tian W, Obozinski G, Qi Y, Mostafavi S, Lin GN, Berriz GF, Gibbons FD, Lanckriet G, Qiu J, Grant C, Barutcuoglu Z, Hill DP, Warde-Farley D, Grouios C, Ray D, Blake JA, Deng M, Jordan MI, Noble WS, Morris Q, Klein-Seetharaman J, Bar-Joseph Z, Chen T, Sun F, Troyanskaya OG, Marcotte EM, Xu D, Highes TR, Roth FP. Genome Biology; 9(SUPPL. 1):S2.

Date published: June 27, 2008
Featured in this article: Trupti Joshi, Dong Xu.

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A new clustering-based method for protein structure selection. Wang Q, Shang Y, Xu D. Proceedings of the International Joint Conference on Neural Networks; 2891-2898.

Date published: June 1, 2008
Featured in this article: Dong Xu.

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Transcription profiling of soybean nodulation by Bradyrhizobium japonicum. Brechenmacher L, Kim M-Y, Benitez M, Li M, Joshi T, Calla B, Mei PL, Libault M, Vodkin LO, Xu D, Lee S-H, Clough SJ, Stacey G. Molecular Plant-Microbe Interactions; 21(5):631-645.

Date published: May 1, 2008
Featured in this article: Trupti Joshi, Dong Xu, Gary Stacey.

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Projecting gene expression trajectories through inducing differential equations from microarray time series experiments. Kramer R, Xu D. Journal of Signal Processing Systems; 50(3):321-329.

Date published: March 1, 2008
Featured in this article: Dong Xu.

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An integrated probabilistic approach for gene function prediction using multiple sources of high-throughput data. Zhang C, Joshi T, Lin GN, Xu D. International Journal of Computational Biology and Drug Design; 1(3):254-274.

Date published: January 1, 2008
Featured in this article: Trupti Joshi, Dong Xu.

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GeneFAS: A tool for prediction of gene function using multiple sources of data. Joshi T, Zhang C, Lin GN, Song Z, Xu D. Methods in Molecular Biology; 439:369-386.

Date published: January 1, 2008
Featured in this article: Trupti Joshi, Dong Xu.

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Combining sequence and structural profiles for protein solvent accessibility prediction. Bondugula R, Xu D. Computational systems bioinformatics / Life Sciences Society. Computational Systems Bioinformatics Conference; 7:195-202.

Date published: January 1, 2008
Featured in this article: Dong Xu.

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Predicting DNA methylation susceptibility using CpG flanking sequences. Kim S, Li M, Pair H, Nephew K, Shi H, Kramer R, Xu D, Huang T-H. Pacific Symposium on Biocomputing 2008, PSB 2008; 315-326.

Date published: January 1, 2008
Featured in this article: Dong Xu.

2007

Transcriptional and physiological responses of Bradyrhizobium japonicum to desiccation-induced stress (Journal of Bacteriology (2007) 189, 19, (6751-6752)). Cytryn EJ, Sangurdekar DP, Streeter JG, Frank WL, Chang W-S, Stacey G, Emerich DW, Joshi T, Xu D, Sadowsky MJ. Journal of Bacteriology; 189(24):9150.

Date published: December 1, 2007
Featured in this article: Gary Stacey, Trupti Joshi, Dong Xu.

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An oligonucleotide microarray resource for transcriptional profiling of bradyrhizobium japonicum. Chang W-S, Frank WL, Cytryn E, Jeong S, Joshi T, Emerich DW, Sadowsky MJ, Xu D, Stacey G. Molecular Plant-Microbe Interactions; 20(10):1298-1307.

Date published: October 1, 2007
Featured in this article: Trupti Joshi, Dong Xu, Gary Stacey.

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Transcriptional and physiological responses of Bradyrhizobium japonicum to desiccation-induced stress. Cytryn EJ, Sangurdekar DP, Streeter JG, Frank WL, Chang W-S, Stacey G, Emerich DW, Joshi T, Xu D, Sadowsky MJ. Journal of Bacteriology; 189(19):6751-6762.

Date published: October 1, 2007
Featured in this article: Gary Stacey, Trupti Joshi, Dong Xu.

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Comparisons among two fertile and three male-sterile mitochondrial genomes of maize. Allen JO, Fauron CM, Minx P, Roark L, Oddiraju S, Guan NL, Meyer L, Sun H, Kim K, Wang C, Du F, Xu D, Gibson M, Cifrese J, Clifton SW, Newton KJ. Genetics; 177(2):1173-1192.

Date published: October 1, 2007
Featured in this article: Dong Xu.

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Ultradeep bisulfite sequencing analysis of DNA methylation patterns in multiple gene promoters by 454 sequencing. Taylor KH, Kramer RS, Davis JW, Guo J, Duff DJ, Xu D, Caldwell CW, Shi H. Cancer Research; 67(18):8511-8518.

Date published: September 15, 2007
Featured in this article: Dong Xu.

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Genome-scale probe and primer design with PRIMEGENS. Srivastava CP, Xu D. Methods in Molecular Biology; 402:159-175.

Date published: August 2, 2007
Featured in this article: Dong Xu.

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Mapping genes to pathways using ontological fuzzy rule systems. Popescu M, Xu D. IEEE International Conference on Fuzzy Systems; 4295549.

Date published: July 23, 2007
Featured in this article: Dong Xu.

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Quantitative assessment of relationship between sequence similarity and function similarity. Joshi T, Xu D. BMC Genomics; 8:222.

Date published: July 9, 2007
Featured in this article: Trupti Joshi, Dong Xu.

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A new method for protein tertiary structure prediction. Shang Y, Bondugula R, Xu D, Wang Q. Proceedings of the 3rd IASTED International Conference on Computational Intelligence, CI 2007; 13-18.

Date published: July 2, 2007
Featured in this article: Dong Xu.

Bioinformatics Analyses of Arabidopsis thaliana Tiling Array Expression Data. Joshi T, Wan J, Palm CJ, Juneau K, Davis R, Southwick A, Ramonell KM, Stacey G, Xu D. Knowledge Discovery in Bioinformatics: Techniques, Methods, and Applications; 57-70.

Date published: May 23, 2007
Featured in this article: Trupti Joshi, Gary Stacey, Dong Xu.

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GoFuzzKegg: Mapping genes to KEGG pathways using an ontological fuzzy rule system. Popescu M, Xu D, Taylor E. 2007 IEEE Symposium on Computational Intelligence and Bioinformatics and Computational Biology, CIBCB 2007; 298-303.

Date published: April 1, 2007
Featured in this article: Dong Xu.

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Single feature polymorphism discovery in rice. Kumar R, Qiu J, Joshi T, Valliyodan B, Xu D, Nguyen HT. PLoS ONE; 2(3):e284.

Date published: March 14, 2007
Featured in this article: Trupti Joshi, Dong Xu.

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Development and assessment of scoring functions for protein identification using PMF data. Zhao S, Chen L, Ganapathy A, Wan X-F, Brechenmacher L, Tao N, Emerich D, Stacey G, Xu D. Electrophoresis; 28(5):864-870.

Date published: March 1, 2007
Featured in this article: XiuFeng “Henry” Wan, Gary Stacey, Dong Xu.

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MUPRED: A tool for bridging the gap between template based methods and sequence profile based methods for protein secondary structure prediction. Bondugula R, Xu D. Proteins: Structure, Function and Genetics; 66(3):664-670.

Date published: February 15, 2007
Featured in this article: Dong Xu.

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2006

Inferring gene regulatory networks from multiple microarray datasets. Wang Y, Joshi T, Zhang X-S, Xu D, Chen L. Bioinformatics; 22(19):2413-2420.

Date published: October 1, 2006
Featured in this article: Trupti Joshi, Dong Xu.

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Rnall: An efficient algorithm for predicting RNA local secondary structural landscape in genomes. Wan X-F, Lin G, Xu D. Journal of Bioinformatics and Computational Biology; 4(5):1015-1031.

Date published: October 1, 2006
Featured in this article: XiuFeng “Henry” Wan, Dong Xu.

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Design and implementation of probability-based scoring function for peptide mass fingerprinting protein identification. Song Z, Chen L, Zhang C, Xu D. Annual International Conference of the IEEE Engineering in Medicine and Biology - Proceedings; 4556-4559.

Date published: August 30, 2006
Featured in this article: Dong Xu.

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Supervised inference of gene regulatory networks by linear programming. Wang Y, Joshi T, Xu D, Zhang X-S, Chen L. Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); 4115 LNBI-III:551-561.

Date published: August 16, 2006
Featured in this article: Trupti Joshi, Dong Xu.

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A fast SCOP fold classification system using content-based E-Predict algorithm. Chi P-H, Shyu C-R, Xu D. BMC Bioinformatics; 7:362.

Date published: July 26, 2006
Featured in this article: Dong Xu.

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DigitalTree: A tool for displaying biological data in tree structure. Kramer R, Olman V, Xu Y, Xu D. Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); 3992 LNCS - II:855-862.

Date published: May 28, 2006
Featured in this article: Dong Xu.

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The ribosomal shunt translation strategy of Cauliflower mosaic virus has evolved from ancient long terminal repeats. Shababi M, Bourque J, Palanichelvam K, Cole A, Xu D, Wan X-F, Schoelz J. Journal of Virology; 80(8):3811-3822.

Date published: April 1, 2006
Featured in this article: Dong Xu, XiuFeng “Henry” Wan.

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CodonO: A new informatics method for measuring synonymous codon usage bias within and across genomes. Wan X-F, Zhou J, Xu D. International Journal of General Systems; 35(1):109-125.

Date published: February 1, 2006
Featured in this article: XiuFeng “Henry” Wan, Dong Xu.

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Survey sequencing of soybean elucidates the genome structure, composition and identifies novel repeats. Nunberg A, Bedell JA, Budiman MA, Citek RW, Clifton SW, Fulton L, Pape D, Cai Z, Joshi T, Nguyen H, Xu D, Stacey G. Functional Plant Biology; 33(8):765-773.

Date published: January 1, 2006
Featured in this article: Trupti Joshi, Dong Xu, Gary Stacey.

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Phylogenetic analysis using complete signature information of whole genomes and clustered Neighbour-Joining method. Wu X, Wan X-F, Wu G, Xu D, Lin G. International Journal of Bioinformatics Research and Applications; 2(3):219-248.

Date published: January 1, 2006
Featured in this article: XiuFeng “Henry” Wan, Dong Xu.

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Bioinformatics and its applications in plant biology. Rhee SY, Dickerson J, Xu D. Annual Review of Plant Biology; 57:335-360.

Date published: January 1, 2006
Featured in this article: Dong Xu.

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2005

Computational methods for remote homolog identification. Wan X-F, Xu D. Current Protein and Peptide Science; 6(6):527-546.

Date published: December 1, 2005
Featured in this article: XiuFeng “Henry” Wan, Dong Xu.

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Whole genome phylogeny based on clustered signature string composition. Wu X, Lin G, Wan X-F, Xu D. 2005 IEEE Computational Systems Bioinformatics Conference, Workshops and Poster Abstracts; 53-54.

Date published: August 8, 2005
Featured in this article: XiuFeng “Henry” Wan, Dong Xu.

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Intrinsic terminator prediction and its application in synechococcus sp. WH8102. Wan X-F, Xu D. Journal of Computer Science and Technology; 20(4):465-482.

Date published: July 1, 2005
Featured in this article: XiuFeng “Henry” Wan, Dong Xu.

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Toward electronic conductance characterization of DNA nucleotide bases. Krstić PS, Wells JC, Fuentes-Cabrera M, Xu D, Lee JW. Solid State Phenomena; 121-123(PART 2):1387-1390.

Date published: June 9, 2005
Featured in this article: Dong Xu.

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Genetic characterization of H5N1 avian influenza viruses isolated in southern China during the 2003-04 avian influenza outbreaks: Brief report. Wan X-F, Ren T, Luo K-J, Liao M, Zhang G-H, Chen J-D, Cao W-S, Li Y, Jin N-Y, Xu D, Xin C-A. Archives of Virology; 150(6):1257-1266.

Date published: June 1, 2005
Featured in this article: XiuFeng “Henry” Wan, Dong Xu.

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Proteomic analysis of soybean root hairs after infection by Bradyrhizobium japonicum. Wan J, Torres M, Ganapathy A, Thelen J, DaGue BB, Mooney B, Xu D, Stacey G. Molecular Plant-Microbe Interactions; 18(5):458-467.

Date published: May 1, 2005
Featured in this article: Jay Thelen, Dong Xu, Gary Stacey.

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Understanding protein dispensability through machine-learning analysis of high-throughput data. Chen Y, Xu D. Bioinformatics; 21(5):575-581.

Date published: March 1, 2005
Featured in this article: Dong Xu.

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Profiles and Fuzzy K-Nearest Neighbor Algorithm for protein secondary structure prediction. Bondugula R, Duzlevski O, Xu D. Series on Advances in Bioinformatics and Computational Biology; 1:85-94.

Date published: January 17, 2005
Featured in this article: Dong Xu.

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Genome-scale protein function prediction in yeast saccharomyces cerevisiae through integrating multiple sources of high- Throughput data. Chen Y, Xu D. Proceedings of the Pacific Symposium on Biocomputing 2005, PSB 2005; 471-482.

Date published: January 4, 2005
Featured in this article: Dong Xu.

Cellular function prediction and biological pathway discovery in Arabidopsis thaliana using microarray data. Joshi T, Chen Y, Alexandrov NN, Xu D. International Journal of Bioinformatics Research and Applications; 1(3):335-350.

Date published: January 1, 2005
Featured in this article: Trupti Joshi, Dong Xu.

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More reliable protein NMR peak assignment via improved 2-interval scheduling. Chen Z-Z, Lin G, Rizzi R, Wen J, Xu D, Xu Y, Jiang T. Journal of Computational Biology; 12(2):129-146.

Date published: January 1, 2005
Featured in this article: Dong Xu.

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2004

Protein databases on the internet. Xu D, Xu Y. Current protocols in molecular biology; 19:Unit 19.4.

Date published: November 4, 2004
Featured in this article: Dong Xu.

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Cellular function prediction and biological pathway discovery in arabidopsis thaliana using microarray data. Joshi T, Chen Y, Alexandrov N, Xu D. Annual International Conference of the IEEE Engineering in Medicine and Biology - Proceedings; 26(IV):2881-2884.

Date published: September 1, 2004
Featured in this article: Trupti Joshi, Dong Xu.

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Statistical assessment for mass-spec protein identification using peptide fingerprinting approach. Ganapathy A, Wan X-F, Wan J, Thelen J, Emerich DW, Stacey G, Xu D. Annual International Conference of the IEEE Engineering in Medicine and Biology - Proceedings; 26 IV:3051-3054.

Date published: September 1, 2004
Featured in this article: XiuFeng “Henry” Wan, Jay Thelen, Gary Stacey, Dong Xu.

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Framework for developing a hierarchical model of reward focusing on the nucleus accumbens. Smith W, Nair SS, Xu D, Nair J, Beitman B. Annual International Conference of the IEEE Engineering in Medicine and Biology - Proceedings; 26 I:133-136.

Date published: September 1, 2004
Featured in this article: Dong Xu.

Modeling obsessive compulsive disorder. Clinch CH, Nair SS, Xu D, Nair J, Beitman B. Annual International Conference of the IEEE Engineering in Medicine and Biology - Proceedings; 26 II:890-892.

Date published: September 1, 2004
Featured in this article: Dong Xu.

Computational modeling of hysterical paralysis. Iyoho A, Nair SS, Xu D, Nair J, Beitman B. Annual International Conference of the IEEE Engineering in Medicine and Biology - Proceedings; 26 II:894-897.

Date published: September 1, 2004
Featured in this article: Dong Xu.

PROSPECT-PSPP: An automatic computational pipeline for protein structure prediction. Guo J-T, Ellrott K, Chung WJ, Xu D, Passovets S, Xu Y. Nucleic Acids Research; 32(WEB SERVER ISS.):W522-W525.

Date published: July 1, 2004
Featured in this article: Dong Xu.

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ProteinDBS: A real-time retrieval system for protein structure comparison. Shyu C-R, Chi P-H, Scott G, Xu D. Nucleic Acids Research; 32(WEB SERVER ISS.):W527-W575.

Date published: July 1, 2004
Featured in this article: Dong Xu.

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Quantitative relationship between synonymous codon usage bias and GC composition across unicellular genomes. Wan X-F, Xu D, Kleinhofs A, Zhou J. BMC Evolutionary Biology; 4:19.

Date published: June 28, 2004
Featured in this article: XiuFeng “Henry” Wan, Dong Xu.

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Evaluation of 50-mer oligonucleotide arrays for detecting microbial populations in environmental samples. Tiquia SM, Wu L, Chong SC, Passovets S, Xu D, Xu Y, Zhou J. BioTechniques; 36(4):644-675.

Date published: April 1, 2004
Featured in this article: Dong Xu.

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A computational method for assessing peptide-identification reliability in tandem mass spectrometry analysis with SEQUEST. Razumovskaya J, Olman V, Xu D, Uberbacher EC, VerBerkmoes NC, Hettich RL, Xu Y. Proteomics; 4(4):961-969.

Date published: April 1, 2004
Featured in this article: Dong Xu.

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Computational and experimental studies on Human Misshapen/NIK-related kinase MINK-1. Qu K, Lu Y, Lin N, Singh R, Xu X, Payan DG, Xu D. Current Medicinal Chemistry; 11(5):569-582.

Date published: March 1, 2004
Featured in this article: Dong Xu.

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Genome-scale gene function prediction using multiple sources of high-throughput data in yeast Saccharomyces cerevisiae. Joshi T, Chen Y, Becker JM, Alexandrov N, Xu D. OMICS A Journal of Integrative Biology; 8(4):322-333.

Date published: January 1, 2004
Featured in this article: Trupti Joshi, Dong Xu.

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Global protein function annotation through mining genome-scale data in yeast Saccharomyces cerevisiae. Chen Y, Xu D. Nucleic Acids Research; 32(21):6414-6424.

Date published: January 1, 2004
Featured in this article: Dong Xu.

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2003

A new informatics method for measuring synonymous codon usage bias. Wan X, Zhou J, Xu D. Intelligent Engineering Systems Through Artificial Neural Networks; 13:1011-1018.

Date published: November 2, 2003
Featured in this article: XiuFeng “Henry” Wan, Dong Xu.

A computational pipeline for protein structure prediction and analysis at genome scale. Shah M, Passovets S, Kim D, Ellrott K, Wang L, Vokler I, LoCascio P, Xu D, Xu Y. Bioinformatics; 19(15):1985-1996.

Date published: October 12, 2003
Featured in this article: Dong Xu.

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EXCAVATOR: A computer program for efficiently mining gene expression data. Xu D, Olman V, Wang L, Xu Y. Nucleic Acids Research; 31(19):5582-5589.

Date published: October 1, 2003
Featured in this article: Dong Xu.

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PROSPECT II: Protein structure prediction program for genome-scale applications. Kim D, Xu D, Guo J-T, Ellrott K, Xu Y. Protein Engineering; 16(9):641-650.

Date published: September 1, 2003
Featured in this article: Dong Xu.

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Automated protein NMR resonance assignments. Wan X, Xu D, Slupsky CM, Lin G. Proceedings of the 2003 IEEE Bioinformatics Conference, CSB 2003; 197-208.

Date published: August 11, 2003
Featured in this article: Dong Xu.

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Probability profiles-novel approach in tandem mass spectrometry De Novo sequencing. Fridman T, Day R, Razumovskaya J, Xu D, Gorin A. Proceedings of the 2003 IEEE Bioinformatics Conference, CSB 2003; 415-418.

Date published: August 11, 2003
Featured in this article: Dong Xu.

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Computational assignment of protein backbone NMR peaks by efficient bounding and filtering. Lin G, Xu D, Chen ZZ, Jiang T, Wen J, Xu Y. Journal of Bioinformatics and Computational Biology; 1(2):387-409.

Date published: July 1, 2003
Featured in this article: Dong Xu.

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Computational analyses of high-throughput protein-protein interaction data. Chen Y, Xu D. Current Protein and Peptide Science; 4(3):159-181.

Date published: June 1, 2003
Featured in this article: Dong Xu.

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Approximation algorithms for NMR spectral peak assignment. Chen Z-Z, Jiang T, Lin G, Wen J, Xu D, Xu J, Xu Y. Theoretical Computer Science; 299(1-3):211-229.

Date published: April 18, 2003
Featured in this article: Dong Xu.

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CUBIC: identification of regulatory binding sites through data clustering. Olman V, Xu D, Xu Y. Journal of Bioinformatics and Computational Biology; 1(1):21-40.

Date published: April 1, 2003
Featured in this article: Dong Xu.

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Transcriptome dynamics of deinococcus radiodurans recovering from ionizing radiation. Liu Y, Zhou J, Omelchenko MV, Beliaev AS, Venkateswaran A, Stair J, Wu L, Thompson DK, Xu D, Rogozin IB, Gaidamakova EK, Zhai M, Makarova KS, Koonin EV, Daly MJ. Proceedings of the National Academy of Sciences of the United States of America; 100(7):4191-4196.

Date published: April 1, 2003
Featured in this article: Dong Xu.

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Towards automated derivation of biological pathways using high-throughput biological data. Chen Y, Joshi T, Xu Y, Xu D. Proceedings - 3rd IEEE Symposium on BioInformatics and BioEngineering, BIBE 2003; 18-25.

Date published: March 10, 2003
Featured in this article: Trupti Joshi, Dong Xu.

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A computational pipeline for protein structure prediction and analysis at genome scale. Shah M, Passovets S, Kim D, Ellrott K, Wang L, Vokler I, LoCascio P, Xu D, Xu Y. Proceedings - 3rd IEEE Symposium on BioInformatics and BioEngineering, BIBE 2003; 3-10.

Date published: March 10, 2003
Featured in this article: Dong Xu.

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Improving the performance of DomainParser for structural domain partition using neural network. Guo J-T, Xu D, Kim D, Xu Y. Nucleic Acids Research; 31(3):944-952.

Date published: February 1, 2003
Featured in this article: Dong Xu.

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A computational study of Shewanella oneidensis MR-1: Structural prediction and functional inference of hypothetical proteins. Yost C, Hauser L, Larimer F, Thompson D, Beliaev A, Zhou J, Xu Y, Xu D. OMICS A Journal of Integrative Biology; 7(2):177-191.

Date published: January 1, 2003
Featured in this article: Dong Xu.

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Identification of regulatory binding sites using minimum spanning trees. Olman V, Xu D, Xu Y. Pacific Symposium on Biocomputing; 327-338.

Date published: January 1, 2003
Featured in this article: Dong Xu.

More reliable protein NMR peak assignment via improved 2-interval scheduling. Chen Z-Z, Jiang T, Lin G, Rizzi R, Wen J, Xu D, Xu Y. Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); 2832:580-592.

Date published: January 1, 2003
Featured in this article: Dong Xu.

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Characterization of protein structure and function at genome scale with a computational prediction pipeline. Xu D, Kim D, Dam P, Shah M, Uberbacher EC, Xu Y. Genetic Engineering; 25:269-293.

Date published: January 1, 2003
Featured in this article: Dong Xu.

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Solving data clustering problem as a string search problem. Olman V, Xu D, Xu Y. Statistical Data Mining and Knowledge Discovery; 415-432.

Date published: January 1, 2003
Featured in this article: Dong Xu.

2002

PRIMEGENS: Robust and efficient design of gene-specific probes for microarray analysis. Xu D, Li G, Wu L, Zhou J, Xu Y. Bioinformatics; 18(11):1432-1437.

Date published: November 1, 2002
Featured in this article: Dong Xu.

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Improved approximation algorithms for NMR spectral peak assignment. Chen Z-Z, Jiang T, Lin G, Wen J, Xu D, Xu Y. Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); 2452:82-96.

Date published: September 17, 2002
Featured in this article: Dong Xu.

Microarray analysis of chitin elicitation in Arabidopsis thaliana. Ramonell KM, Zhang B, Ewing RM, Chen Y, Xu D, Stacey G, Somerville S. Molecular Plant Pathology; 3(5):301-311.

Date published: September 1, 2002
Featured in this article: Dong Xu, Gary Stacey.

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Residues in the first extracellular loop of a G protein-coupled receptor play a role in signal transduction. Akal-Strader A, Khare S, Xu D, Naider F, Becker JM. Journal of Biological Chemistry; 277(34):30581-30590.

Date published: August 23, 2002
Featured in this article: Dong Xu.

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Clustering gene expression data using a graph-theoretic approach: An application of minimum spanning trees. Xu Y, Olman V, Xu D. Bioinformatics; 18(4):536-545.

Date published: January 1, 2002
Featured in this article: Dong Xu.

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A practical method for interpretation of threading scores: An application of neural network. Xu Y, Xu D, Olman V. Statistica Sinica; 12(1):159-177.

Date published: January 1, 2002
Featured in this article: Dong Xu.

Automated assignment of backbone NMR peaks using constrained bipartite matching. Xu Y, Xu D, Kim D, Olman V, Razumovskaya J, Jiang T. Computing In Science and Engineering; 4(1):50-62.

Date published: January 1, 2002
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Carbon sequestration in Synechococcus Sp.: From molecular machines to hierarchical modeling. Heffelfinger GS, Martino A, Gorin A, Xu Y, Rintoul MD III, Geist A, Hashimi HA, Davidson GS, Faulon JL, Frink LJ, Haaland DM, Hart WE, Jakobsson E, Lane T, Li M, Locascio P, Olken F, Olman V, Palenik B, Plimpton SJ, Roe DC, Samatova NF, Shah M, Shoshoni A, Strauss CM, Thomas EV, Timlin JA, Xu D. OMICS A Journal of Integrative Biology; 6(4):305-330.

Date published: January 1, 2002
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An efficient branch-and-bound algorithm for the assignment of protein backbone NMR peaks. Lin G, Xu d, Chen Z-Z, Jiang T, Wen J, Xu Y. Proceedings - IEEE Computer Society Bioinformatics Conference, CSB 2002; 165-174.

Date published: January 1, 2002
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2001

Model for the three-dimensional structure of vitronectin: Predictions for the multi-domain protein from threading and docking. Xu D, Baburaj K, Peterson CB, Xu Y. Proteins: Structure, Function and Genetics; 44(3):312-320.

Date published: August 15, 2001
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Protein tertiary structure prediction. Xu D, Xu Y. Current Protocols in Protein Science; 2:Unit2.7.

Date published: May 1, 2001
Featured in this article: Dong Xu.

Minimum spanning trees for gene expression data clustering. Xu Y, Olman V, Xu D. Genome informatics. International Conference on Genome Informatics; 12:24-33.

Date published: January 1, 2001
Featured in this article: Dong Xu.

Application of PROSPECT in CASP4: Characterizing protein structures with new folds. Xu D, Crawford OH, Locascio PF, Xu Y. Proteins: Structure, Function and Genetics; 45(SUPPL. 5):140-148.

Date published: January 1, 2001
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2000

Protein threading using PROSPECT: Design and evaluation. Xu Y, Xu D. Proteins: Structure, Function and Genetics; 40(3):343-354.

Date published: August 15, 2000
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Computational Tools for Protein Modeling. Xu Y, Xu D, Uberbacher EC. Current Protein and Peptide Science; 1(1):1-21.

Date published: July 1, 2000
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Protein structure determination using protein threading and sparse NMR data. Xu Ying, Xu Dong, Crawford Oakley H, Einstein J Ralph, Sepersu Engin. Proceedings of the Annual International Conference on Computational Molecular Biology, RECOMB; 299-307.

Date published: April 8, 2000
Featured in this article: Dong Xu.

Sequence-structure specificity of a knowledge based energy function at the secondary structure level. Xu D, Unseren MA, Xu Y, Uberbacher EC. Bioinformatics; 3/1/2000.

Date published: March 1, 2000
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Protein domain decomposition using a graph-theoretic approach. Xu Y, Xu D, Gabow HN. Bioinformatics; 16(12):1091-1104.

Date published: January 1, 2000
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A computational method for NMR-constrained protein threading. Xu Y, Xu D, Crawford OH, Einstein JR. Journal of Computational Biology; 7(3-4):449-467.

Date published: January 1, 2000
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1999

Protein threading by PROSPECT: A prediction experiment in CASP3. Xu Y, Xu D, Crawford OH, Einstein JR, Larimer F, Uberbacher E, Unseren MA, Zhang G. Protein Engineering; 12(11):899-907.

Date published: January 1, 1999
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Protein structure prediction in a 210-type lattice model: Parameter optimization in the genetic algorithm using orthogonal array. Sun Z, Xia X, Guo Q, Xu D. Journal of Protein Chemistry; 18(1):39-46.

Date published: January 1, 1999
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1998

Electrostatics, allostery, and activity of the yeast chorismate mutase. Lin SL, Xu D, Li A, Nussinov R. Proteins: Structure, Function and Genetics; 31(4):445-452.

Date published: June 1, 1998
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New method for modeling and solving the protein fold recognition problem. Xu Ying, Xu Dong, Uberbacher Edward C. Proceedings of the Annual International Conference on Computational Molecular Biology, RECOMB; 285-292.

Date published: March 22, 1998
Featured in this article: Dong Xu.

Mechanism and evolution of protein dimerization. Xu D, Tsai C-J, Nussinov R. Protein Science; 7(3):533-544.

Date published: March 1, 1998
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An efficient computational method for globally optimal threading. Xu Y, Xu D, Uberbacher EC. Journal of Computational Biology; 5(3):597-614.

Date published: January 1, 1998
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Protein folding via binding and vice versa. Tsai C-J, Xu D, Nussinov R. Folding and Design; 3(4):R71-R80.

Date published: January 1, 1998
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Favorable domain size in proteins. Xu D, Nussinov R. Folding and Design; 3(1):11-17.

Date published: January 1, 1998
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1997

Investigation of the enzymatic mechanism of the yeast chorismate mutase by docking a transition state analog. Lin SL, Xu D, Li A, Rosen M, Wolfson HJ, Nussinov R. Journal of Molecular Biology; 271(5):838-845.

Date published: September 5, 1997
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Structural motifs at protein-protein interfaces: Protein cores versus two-state and three-state model complexes. Tsai C-J, Xu D, Nussinov R. Protein Science; 6(9):1793-1805.

Date published: September 1, 1997
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Prediction of protein supersecondary structures based on the artificial neural network method. Sun Z, Rao X, Peng L, Xu D. Protein Engineering; 10(7):763-769.

Date published: July 1, 1997
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Protein binding versus protein folding: The role of hydrophilic bridges in protein associations. Xu D, Lin SL, Nussinov R. Journal of Molecular Biology; 265(1):68-84.

Date published: January 10, 1997
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Hydrogen bonds and salt bridges across protein-protein interfaces. Xu D, Tsai C-J, Nussinov R. Protein Engineering; 10(9):999-1012.

Date published: January 1, 1997
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1996

Protein response to external electric fields: Relaxation, hysteresis, and echo. Xu D, Phillips JC, Schulten K. Journal of Physical Chemistry; 100(29):12108-12121.

Date published: July 18, 1996
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Molecular dynamics study of early picosecond events in the bacteriorhodopsin photocycle: Dielectric response, vibrational cooling and the J, K intermediates. Xu D, Martin C, Schulten K. Biophysical Journal; 70(1):453-460.

Date published: January 1, 1996
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1995

Predicting the structure of the light‐harvesting complex II of rhodospirillum molischianum. Hu X, Xu D, Hamer K, Schulten K, Koepke J, Michel H. Protein Science; 4(9):1670-1682.

Date published: September 1, 1995
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Molecular dynamics study of the early intermediates in the bacteriorhodopsin photocycle. Humphrey W, Xu D, Sheves M, Schulten K. Journal of Physical Chemistry; 99(39):14549-14560.

Date published: January 1, 1995
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Temperature quench echoes in proteins. Xu D, Schulten K, Becker OM, Karplus M. The Journal of Chemical Physics; 103(8):3112-3123.

Date published: January 1, 1995
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Velocity reassignment echoes in proteins. Xu D, Schulten K. The Journal of Chemical Physics; 103(8):3124-3139.

Date published: January 1, 1995
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Molecular dynamics study of the M412 intermediate of bacteriorhodopsin. Xu D, Sheves M, Schulten K. Biophysical Journal; 69(6):2745-2760.

Date published: January 1, 1995
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Molecular Dynamics Studies of Bacteriorhodopsin’s Photocycles. Schulten K, Humphrey W, Logunov I, Sheves M, Xu D. Israel Journal of Chemistry; 35(3-4):447-464.

Date published: January 1, 1995
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1994

Coupling of protein motion to electron transfer in a photosynthetic reaction center: investigating the low temperature behavior in the framework of the spin-boson model. Xu D, Schulten K. Chemical Physics; 182(2-3):91-117.

Date published: May 1, 1994
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