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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

2021

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: Juexin Wang, Dong Xu, Trupti Joshi.

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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: Yaya Cui, Yuexu Jiang, Dong Xu, Gary Stacey.

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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: Shuai Zeng, Duolin Wang, 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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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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2020

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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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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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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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: Yuexu Jiang, Duolin Wang, Dong Xu, Trupti Joshi.

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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: Yuexu Jiang, Duolin Wang, 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: Juexin Wang, 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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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: Shuai Zeng, Zhen Lyu, 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: Duolin Wang, Juexin Wang, Trupti Joshi, 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) 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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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: Juexin Wang, Zhen Lyu, Gary Stacey, Dong Xu, Trupti Joshi.

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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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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: Shuai Zeng, Zhen Lyu, 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: Yuexu Jiang, Duolin Wang, 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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2018

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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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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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: Duolin Wang, Shuai Zeng, Chunhui Xu, Trupti Joshi, Dong Xu.

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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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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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2016

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: Juexin Wang, 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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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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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, Juexin Wang, 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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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: Juexin Wang, Yuexu Jiang, Duolin Wang, 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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2015

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
Featured in this article: Juexin Wang, Trupti Joshi, Dong Xu.

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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
Featured in this article: Trupti Joshi, Dong Xu.

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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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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
Featured in this article: Trupti Joshi, Dong Xu.

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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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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
Featured in this article: Trupti Joshi, 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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2014

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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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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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: Chunhui Xu, Jay Thelen, 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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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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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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2012

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: Shrikesh C. "Rick" Sachdev, 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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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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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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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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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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2011

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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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: Juexin Wang, 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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2010

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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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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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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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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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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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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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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2009

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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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: Brian Mooney, Trupti Joshi, Ming-Yi Zhou, 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: Shrikesh C. "Rick" Sachdev, Trupti Joshi, Brian Mooney, Dong Xu, Gary Stacey.

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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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2008

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: Jinrong Wan, 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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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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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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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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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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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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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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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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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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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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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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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: Jinrong Wan, Jay Thelen, Brian Mooney, Dong Xu, Gary Stacey.

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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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2004

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, Jinrong Wan, Jay Thelen, Gary Stacey, 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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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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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.

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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2002

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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