Publications

  1. Ronny Bazan Antequera, Prasad Calyam, Saptarshi Debroy, Longhai Cui, Sripriya Seetharam, Matthew Dickinson, Trupti Joshi, Dong Xu, Tsegereda Beyene. ADON: Application-Driven Overlay Network-as-a-Service for Data-Intensive Science, IEEE Transactions on Cloud Computing. In press.
  2. Yang Liu, Saad M. Khan, Juexin Wang, Mats Rynge, Yuanxun Zhang, Shuai Zeng, Shiyuan Chen, Joao V. Maldonado dos Santos, Babu Valliyodan, Prasad P. Calyam, Nirav Merchant, Henry T. Nguyen, Dong Xu, Trupti Joshi. PGen: Large-Scale Genomic Variations Analysis Workflow and Browser in SoyKB. BMC Bioinformatics. 201617(Suppl 13):337 DOI: 10.1186/s12859-016-1227-y
  3. Weizhong Lin and Dong Xu. Imbalanced Multi-label Learning for Identifying Antimicrobial Peptides and Their Functional Types. Bioinformatics. Bioinformatics (2016) doi: 10.1093/bioinformatics/btw560
  4. Li Zhang, Han Wang, Lun Yan, Lingtao Su, Dong Xu. OMPcontact: An Outer Membrane Protein Inter-Barrel Residue Contact Prediction Method. Journal of Computational Biology. August 2016. doi:10.1089/cmb.2015.0236.
  5. Matthew J. Salie, Ning Zhang, Veronika Lancikova, Dong Xu, Jay J. Thelen. A Family of Negative Regulators Targets the Committed Step of De novo Fatty Acid Biosynthesis. The Plant Cell August 24, 2016 tpc.00317.2016
  6. Oswaldo Valdes-Lopez, Josef Batek, Nicolas Gomez-Hernandez, Coung T Nguyen, Mariel Carolina Isidra-Arellano, Ning Zhang, Trupti Joshi, Dong Xu, Kim K Hixson, Karl K Weitz, Joshua T Aldrisch, Ljiljana Paša-Tolic, Gary Stacey. Soybean roots grown under heat stress show global changes in their transcriptional and proteomic profiles. Frontiers in Plant Science, Section Plant Physiology.
  7. Yiheng Wang, Tong Liu, Dong Xu, Huidong Shi, Chaoyang Zhang, Yin-Yuan Mo & Zheng Wang. Predicting DNA Methylation State of CpG Dinucleotide Using Genome Topological Features and Deep Networks. Scientific Report. 22;6:19598, 2016.
  8. Hao Zhang, Yanpu Li, Yuanning Liu, Haiming Liu, Hongyu Wang, Wen Jin, Yanmei Zhang, Chao Zhang and Dong Xu. Role of plant MicroRNA in cross-species regulatory networks of humans. BMC Systems Biology 2016, 10:60, DOI: 10.1186/s12918-016-0292-1, 2016.
  9. Cuong The Nguyen, Kiwamu Tanaka, Yangrong Cao, Sung-Hwan Cho, Dong Xu, Gary Stacey. Computational Analysis of the Ligand Binding Site of the Extracellular ATP Receptor, DORN1. PLoS ONE 11(9): e0161894. doi:10.1371/journal.pone.0161894, 2016.
  10. Garima Kushwaha, Mikhail Dozmorov, Jing Qiu, Huidong Shi, Dong Xu. Hypomethylation Coordinates Antagonistically with Hypermethylation in Cancer Development: A Case Study of Leukemia. Human Genomics. 10:18. doi: 10.1186/s40246-016-0071-5, 2016.
  11. Wang-Ren Qiu, Bi-Qian Sun, Xuan Xiao, Dong Xu, Kuo-Chen Chou iPhos-PseEvo: Identifying Human Phosphorylated Proteins by Incorporating Evolutionary Information into General PseAAC via Grey System Theory, Molecular Informatics. 35:1 – 10, DOI: 10.1002/minf.201600010, 2016.
  12. Chuanchao Zhang, Jiguang Wang, Chao Zhang, Juan Liu, Dong Xu and Luonan Chen. Network Stratification Analysis for Identifying Function-specific Network Layers. Mol. BioSyst., 12:1232-1240, DOI: 10.1039/C5MB00782H, 2016.
  13. Chao Wang, Haicang Zhang, Wei-Mou Zheng, Dong Xu, Jianwei Zhu, Bing Wang, Kang Ning, Shiwei Sun, Shuai Cheng Li, and Dongbo Bu. FALCON@home: a high-throughput protein structure prediction server based on remote homologue recognition. Bioinformatics, 32(3):462-464. doi: 10.1093/bioinformatics/btv581, 2016.
  14. Chuanchao Zhang, Wang Jiguang, Zhang chao, Juan Liu, Dong Xu and Luonan Chen. Network Stratification Analysis for Identifying Function-specific Network Layers. Molecular BioSystems, DOI:10.1039/C5MB00782H, 2016.
  15. Henan Wang, Chong He, Garima Kushwaha, Dong Xu and Jing Qiu. A full Bayesian partition model for identifying hypo- and hyper-methylated loci from single nucleotide resolution sequencing data. BMC Bioinformatics, 17(1):7, doi:10.1186/s12859-015-0850-3, 2016.
  16. Hongbo Li, Yanchun Liang, Ning Zhang, Jinsong Guo, Dong Xu, Zhanshan Li. Improving degree-based variable ordering heuristics for solving constraint satisfaction problems. Journal of Heuristics, 22:125–145, DOI:10.1007/s10732-015-9305-2, 2016.
  17. Li Song, Silvas Prince, Babu Valliyodan, Trupti Joshi, Joao V. Maldonado dos Santos, Jiaojiao Wang, Li Lin, Jinrong Wan, Yongqin Wang, Dong Xu and Henry T. Nguyen Genome-wide transcriptome analysis of soybean primary root under varying water-deficit conditions. BMC Genomics. 2016 Jan 15;17(1):57. doi: 10.1186/s12864-016-2378-y.
  18. João Vitor Maldonado dos Santos, Babu Valliyodan, Trupti Joshi, Saad M. Khan, Yang Liu, Juexin Wang, Tri D. Vuong, Marcelo Fernandes de Oliveira, Francismar Corrêa Marcelino-Guimarães,corresponding author Dong Xu, Henry T. Nguyen, and Ricardo Vilela Abdelnoor. Evaluation of genetic variation among Brazilian soybean cultivars through genome resequencing BMC Genomics. 2016 Feb 13. doi: 10.1186/s12864-016-2431-x
  19. Babu Valliyodan, Dan Qiu, Gunvant Patil, Peng Zeng, Jiaying Huang, Lu Dai, Chengxuan Chen, Yanjun Li, Trupti Joshi, Li Song, Tri D. Vuong, Theresa A. Musket, Dong Xu, J. Grover Shannon, Cheng Shifeng, Xin Liu, and Henry T. Nguyenb. Landscape of genomic diversity and trait discovery in soybean BMC Genomics. 2016 Feb 13. doi: 10.1186/s12864-016-2431-x
  20. Oswaldo Valdés-López, Josef Batek, Nicolas Gomez-Hernandez, Cuong T. Nguyen, Mariel C. Isidra-Arellano, Ning Zhang, Trupti Joshi3, Dong Xu, Kim K. Hixson, Karl K. Weitz, Joshua T. Aldrich, Ljiljana Paša-Tolić and Gary Stacey. Soybean roots grown under heat stress show global changes in their transcriptional and proteomic profiles Front. Plant Sci. 7:517. doi: 10.3389/fpls.2016.00517
  21. Juexin Wang, Trupti Joshi, Babu Valliyodan, Haiying Shi, Yanchun Liang, Henry T. Nguyen, Jing Zhang and Dong Xu. A Bayesian model for detection of high-order interactions among genetic variants in genome-wide association studies. BMC Genomics. 2015 Nov 25;16(1):1011. doi: 10.1186/s12864-015-2217-6.
  22. Silvas J Prince, Li Song, Dan Qiu, Joao V Maldonado dos Santos, Chenglin Chai, Trupti Joshi, Gunvant Patil, Babu Valliyodan, Tri D Vuong, Mackensie Murphy, Konstantinos Krampis, Dominic M Tucker, Ruslan Biyashev, Anne E Dorrance, MA Saghai Maroof, Dong Xu, J Grover Shannon and Henry T Nguyen. Genetic variants in root architecture-related genes in a Glycine soja accession, a potential resource to improve cultivated soybean. BMC Genomics. 2015 Feb 25;16:132. doi: 10.1186/s12864-015-1334-6.
  23. Sripriya Seetharam, Prasad Calyam, Tsegereda Beyene. ADON: Application-Driven Overlay Network-as-a-Service for Data-Intensive Science IEEE Transactions on Cloud Computing. 2015. Volume:PP Issue:99. DOI: 10.1109/TCC.2015.2511753
  24. Kiwamu Tanaka, Sung-Hwan Cho, Hyeyoung Lee, An Q. Pham, Josef M. Batek, Shiqi Cui, Jing Qiu, Saad M. Khan, Trupti Joshi, Zhanyuan J. Zhang, Dong Xu, and Gary Stacey. Effect of lipo-chitooligosaccharide on early growth of C4 grass seedlings. J Exp Bot. 2015 Sep; 66(19): 5727–5738. doi: 10.1093/jxb/erv260
  25. Md Shakhawat Hossain, Trupti Joshi, and Gary Stacey. System approaches to study root hairs as a single cell plant model: current status and future perspectives. Front Plant Sci. 2015 May 19;6:363. doi: 10.3389/fpls.2015.00363. eCollection 2015.
  26. Syed NH, Prince SJ, Mutava RN, Patil G, Li S, Chen W, Babu V, Joshi T, Khan S and Nguyen HT. Core clock, SUB1, and ABAR genes mediate flooding and drought responses via alternative splicing in soybean. Journal of Experimental Botany. 2015. doi:10.1093/jxb/erv407.
  27. Truyen N Quach, Hanh TM Nguyen, Babu Valliyodan, Trupti Joshi, Dong Xu, Henry T Nguyen Genome-wide expression analysis of soybean NF-Y genes reveals potential function in development and drought response June 2015, Volume 290, Issue 3, pp 1095-1115 DOI: 10.1007/s00438-014-0978-2
  28. Yongqing Jiao, Tri D Vuong, Yan Liu, Clinton Meinhardt, Yang Liu, Trupti Joshi, Perry B Cregan, Dong Xu, J Grover Shannon, Henry T Nguyen Identification and evaluation of quantitative trait loci underlying resistance to multiple HG types of soybean cyst nematode in soybean PI 437655 January 2015, Volume 128, Issue 1, pp 15-23 DOI: 10.1007/s00122-014-2409-5
  29. Jing-Qiong Kang, Wangzhen Shen, Chengwen Zhou, Dong Xu, Robert L Macdonald The human epilepsy mutation GABRG2 (Q390X) causes chronic subunit accumulation and neurodegeneration Nature Neuroscience 18, 988–996 (2015) doi:10.1038/nn.4024
  30. Sha Lu, Xiaoyan Yin, William Spollen, Ning Zhang, Dong Xu, James Schoelz, Kristin Bilyeu, Zhanyuan J Zhang Analysis of the siRNA-mediated gene silencing process targeting three homologous genes controlling soybean seed oil quality Published: June 10, 2015 DOI: 10.1371/journal.pone.0129010
  31. Daiyong Deng, Ning Zhang, Dong Xu, Mary Reed, Fengjing Liu, Guolu Zheng. Polymorphism of the glucosyltransferase gene (ycjM) in Escherichia coli and its use for tracking human fecal pollution in water Science of The Total Environment. Volume 537, 15 December 2015, Pages 260–267 doi:10.1016/j.scitotenv.2015.08.019
  32. Chengli Xu, Xiangwu Ju, Dandan Song, Fengming Huang, Depei Tang, Zhen Zou, Chao Zhang, Trupti Joshi, Lijuan Jia, Weihai Xu, Kai-Feng Xu, Qian Wang, Yanlei Xiong, Zhenmin Guo, Xiangmei Chen, Fumin Huang, Jiantao Xu, Ying Zhong, Yi Zhu, Yi Peng, Li Wang, Xinyu Zhang, Rui Jiang, Dangsheng Li, Tao Jiang, Dong Xu, Chengyu Jiang. An association analysis between psychophysical characteristics and genome-wide gene expression changes in human adaptation to the extreme climate at the Antarctic Dome Argus. Molecular Psychiatry, 20:536–544; doi:10.1038/mp.2014.72, 2015.
  33. Silvas J Prince, Li Song, Dan Qiu, Joao V Maldonado dos Santos, Chenglin Chai, Trupti Joshi, Gunvant Patil, Babu Valliyodan, Tri D Vuong, Mackensie Murphy, Konstantinos Krampis, Dominic M Tucker, Ruslan Biyashev, Anne E Dorrance, MA Saghai Maroof, Dong Xu, J Grover Shannon and Henry T Nguyen. Genetic variants in root architecture-related genes in a Glycine soja accession, a potential resource to improve cultivated soybean. BMC Genomics 2015, 16:132 doi:10.1186/s12864-015-1334-6. 2015.
  34. Qiuming Yao, Waltraud X. Schulze, and Dong Xu. Phosphorylation Site Prediction in Plants. In: Plant Phosphoproteomics, edited by Waltraud X. Schulze. Humana Press/Springer, New York, Heidelberg, Dordrecht, London. Chapter 17, 217-228, 2015.
  35. Waltraud X. Schulze, Qiuming Yao, and Dong Xu. Databases for Plant Phosphoproteomics. In: Plant Phosphoproteomics, edited by Waltraud X. Schulze. Humana Press/Springer, New York, Heidelberg, Dordrecht, London. Chapter 16, 207-216, 2015.
  36. Garima Kushwaha, Gyan Prakash Srivastava, and Dong Xu. PRIMEGENSw3: A Web-Based Tool for High-Throughput Primer and Probe Design. 1275:181-99. doi: 10.1007/978-1-4939-2365-6_14. 2015.
  37. Silvas J. Princea, Trupti Joshib, Raymond N. Mutavaa, Naeem Syedc, Maldonado dos Santos Joao Vitora, Gunvant Patila, Li Songa, JiaoJiao Wangb, Li Lina, Wei Chena, J. Grover Shannona, Babu Valliyodana, Dong Xub, c, Henry T. Nguyena. Comparative analysis of the drought-responsive transcriptome in soybean lines contrasting for canopy wilting. Plant Science, Volume 240, Pages 65–78. doi:10.1016/j.plantsci.2015.08.017. November 2015
  38. Chenglin Chai, Yongqin Wang, Trupti Joshi, Babu Valliyodan, Silvas Prince, Lydia Michel, Dong Xu, Henry T Nguyen.Soybean transcription factor ORFeome associated with drought resistance: a valuable resource to accelerate research on abiotic stress resistance. BMC genomics 2015, 16:596
  39. 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 and Nguyen HT. Soybean (Glycine max) SWEET gene family: insights through comparative genomics, transcriptome profiling and whole genome re-sequence analysis. BMC Genomics 2015, 16:520.
  40. Jiao Y, Vuong TD, Liu Y, Li Z, Noe J, Robbins RT, Joshi T, Xu D, Shannon JG, Nguyen HT. Identification of quantitative trait loci underlying resistance to southern root-knot and reniform nematodes in soybean accession PI 567516C. Mol Breed. 2015;35(6):131. Epub 2015 May 23.
  41. Tanaka K, Cho SH, Lee H, Pham AQ, Batek JM, Cui S, Qiu J, Khan SM, Joshi T, Zhang ZJ, Xu D, Stacey G. Effect of lipo-chitooligosaccharide on early growth of C4 grass seedlings. J Exp Bot. 2015 Jun 6. pii: erv260. [Epub ahead of print]
  42. Hossain Md Shakhawat, Joshi Trupti, Stacey Gary. System approaches to study root hairs as a single cell plant model: current status and future perspectives. Front. Plant Sci. 2015. Vol 6. doi: 10.3389/fpls.2015.00363
  43. Yan Zhe, Hossain Md Shakhawat, Valdés-López Oswaldo, Hoang Nhung T, Zhai Jixian, Wang Jun, Libault Marc, Brechenmacher Laurent, Findley Seth, Joshi Trupti, Qi, Lijuan, Sherrier D. Janine, Ji Tieming, Meyers Blake, Xu Dong, Stacey Gary. Identification and functional characterization of soybean root hair microRNAs expressed in response to Bradyrhizobium japonicum infection. Journal of Plant Biotechnology. 2015. Plant Biotechnology Journal (2015), pp. 1–10.
  44. Wan J, Vuong T, Jiao Y, Joshi T, Zhang H, Cui S, Qiu J, Xu D, and Nguyen HT. Whole-genome gene expression profiling revealed genes and pathways potentially involved in regulating the interactions of soybean with cyst nematode (Heterodera glycines Ichinohe). BMC Genomics 2015, 16:148. doi:10.1186/s12864-015-1316-8.
  45. Zhiquan He, Chao Zhang, Yang Xu, Shuai Zeng, Jingfen Zhang, Dong Xu MUFOLD-DB: a processed protein structure database for protein structure prediction and analysis BMC Genomics 2014, 15(Suppl 11):S2 doi:10.1186/1471-2164-15-S11-S2
  46. A new Hidden Markov Model for protein Quality Assessment using compatibility between protein sequence and structure Zhiquan He, Wenji Ma, Jingfen Zhang, Dong Xu Tsinghua Science and Technology (Volume:19 , Issue: 6 ) DOI:10.1109/TST.2014.6961026
  47. DongMei Yu, Chao Zhang, PeiWu Qin, Peter V Cornish, Dong Xu RNA-protein distance patterns in ribosomes reveal the mechanism of translational attenuation November 2014, Volume 57, Issue 11, pp 1131-1139 DOI 10.1007/s11427-014-4753-8
  48. Daiyong Deng, Ning Zhang, Azlin Mustapha, Dong Xu, Tumen Wuliji, Mary Farley, John Yang, Bin Hua, Fengjing Liu, Guolu Zheng Differentiating enteric Escherichia coli from environmental bacteria through the putative glucosyltransferase gene (ycjM) Water Research Volume 61, 15 September 2014, Pages 224–231 doi:10.1016/j.watres.2014.05.015
  49. Ryan McGreevy, Abhishek Singharoy, Qufei Li, Jingfen Zhang, Dong Xu, Eduardo Perozo, Klaus Schulten xMDFF: molecular dynamics flexible fitting of low-resolution X-ray structures Acta Cryst. (2014). D70, 2344-2355 doi:10.1107/S1399004714013856
  50. Zhou Li, Yingfeng Wang, Qiuming Yao, Nicholas B Justice, Tae-Hyuk Ahn, Dong Xu, Robert L Hettich, Jillian F Banfield, Chongle Pan Diverse and divergent protein post-translational modifications in two growth stages of a natural microbial community Nature Communications 5, Article number: 4405 doi:10.1038/ncomms5405
  51. Yan Chen, Yi Shang, Dong Xu Multi-dimensional scaling and MODELLER-based evolutionary algorithms for protein model refinement Evolutionary Computation (CEC), 2014 IEEE Congress on DOI:10.1109/CEC.2014.6900443
  52. Son P Nguyen, Yi Shang, Dong Xu DL-PRO: A novel deep learning method for protein model quality assessment Neural Networks (IJCNN), 2014 International Joint Conference on Page(s): 2071 - 2078. Date of Conference:6-11 July 2014 DOI:10.1109/IJCNN.2014.6889891
  53. Sooyoung Franck, William L Franck, Sean R Birke, Woo-Suk Chang, Dipen P Sangurdekar, Eddie Cytryn, Trupti Joshi, Michael Sadowsky, Gary Stacey, Dong Xu, David W Emerich Comparative transcriptomic analysis of symbiotic Bradyrhizobium japonicum Springer Science Business Media Dordrecht, 2014 DOI 10.1007/s13199-014-0294-y
  54. Rui Liu, Xiangtian Yu, Xiaoping Liu, Dong Xu, Kazuyuki Aihara, Luonan Chen Identifying critical transitions of complex diseases based on a single sample Bioinformatics (2014) 30 (11): 1579-1586. doi: 10.1093/bioinformatics/btu084 First published online: February 10, 2014
  55. Jianjiong Gao, Dong Xu, Grzegorz Sabat, Hector Valdivia, Wei Xu, Nian-Qing Shi Disrupting KATP channels diminishes the estrogen-mediated protection in female mutant mice during ischemia-reperfusion BioMed Central DOI 10.1186/1559-0275-11-19
  56. Tiffany Langewisch, Hongxin Zhang, Ryan Vincent, Trupti Joshi, Dong Xu, Kristin Bilyeu Major Soybean Maturity Gene Haplotypes Revealed by SNPViz Analysis of 72 Sequenced Soybean Genomes Public Library of Science Volume9 Issue4 Pages e94150 Published: April 11, 2014DOI: 10.1371/journal.pone.0094150
  57. Jianjiong Gao, Chao Zhang, Martijn van Iersel, Li Zhang, Dong Xu, Nikolaus Schultz, Alexander R Pico BridgeDb app: unifying identifier mapping services for Cytoscape Version 1. F1000Res. 2014; 3: 148. doi: 10.12688/f1000research.4521.1
  58. Oswaldo Valdes-Lopez, Saad M Khan, Robert J. Schmitz, Shiqi Cui, Jing Qiu, Trupti Joshi, Dong Xu, Brian Diers, Joseph R. Ecker, and Gary Stacey. Genotypic variation of gene expression during the soybean innate immunity response. Plant Genetic Resources: Characterization and Utilization (2014) 12(S1); S27–S30. doi:10.1017/S1479262114000197.
  59. Tiffany Langewisch, Hongxin Zhang, Ryan Vincent, Trupti Joshi, Dong Xu, Kristin Bilyeu. Major soybean maturity gene haplotypes revealed by SNPViz analysis of 72 sequenced soybean genomes. PLoS One. 2014 Apr 11;9(4):e94150. doi: 10.1371/journal.pone.0094150. eCollection 2014.
  60. Trupti Joshi, Robert Williamson, Kapil Patil, Suwit Viyanon, Xiangge Li, Yufu Zhang, Wenchuan Qi, Dong Li, Jeremy Zimmer, Uday Illindala, Shawn Foley, Robert Campbell, Ye Duan, Dong Xu. Virtual physical examination (VPE): a multimedia system for education in medicine. Volume 4, Issue 3-4. DOI: 10.1504/IJFIPM.2014.068176. 2014
  61. Appel, Heidi M., Fescemyer, H., Ehlting, J., Weston, D., Rehrig, E., Joshi, T., Xu, D., Bohlmann, J., and Schultz, Jack. Transcriptional responses of Arabidopsis thaliana to chewing and sucking insect herbivores. Front Plant Sci. 2014 Nov 14;5:565. doi: 10.3389/fpls.2014.00565. eCollection 2014.
  62. Qiuming Yao, Huangyi Ge, Shangquan Wu, Ning Zhang, Wei Chen, Chunhui Xu, Jianjiong Gao, Jay J. Thelen, and Dong Xu. P3DB 3.0: From plant phosphorylation sites to protein networks. Nucleic Acids Research. 1;42(1):D1206-D1213, 2014.
  63. Trupti Joshi, Michael R. Fitzpatrick, Shiyuan Chen, Yang Liu, Hongxin Zhang, Ryan Z. Endacott, Eric C. Gaudiello, Gary Stacey, Henry T. Nguyen, Dong Xu. Soybean Knowledge Base (SoyKB): A web resource for integration of soybean translational genomics and molecular breeding. Nucleic Acids Research. 42(1):D1245-D1252, 2014.
  64. Jianjiong Gao, Qiuming Yao, CURTIS HARRISON BOLLINGER, DONG XU Analysis and Prediction of Protein Posttranslational Modification Sites Publisher : Wiley-IEEE Press Edition : 1 Pages : 536 Copyright Year : 2014 ISBN : 9781118567869
  65. R SP Rao, Dong Xu, Jay J Thelen, Ján A Miernyk Circles within circles: crosstalk between protein Ser/Thr/Tyr-phosphorylation and Met oxidation BMC Bioinformatics201314(Suppl 14):S14 DOI: 10.1186/1471-2105-14-S14-S14© Prasad Rao et al.; licensee BioMed Central Ltd. 2013 Published: 9 October 2013
  66. Qingguo Wang, Charles Shang, Dong Xu, Yi Shang. New MDS and Clustering Based Algorithms for Protein Model Quality Assessment and Selection. International Journal on Artificial Intelligence Tools. 22:1360006 (19 pages), 2013.
  67. Han Wang, Zhiquan He, Chao Zhang, Li Zhang, Dong Xu. Transmembrane Protein Alignment and Fold Recognition Based on Predicted Topology. PLoS ONE 8(7): e69744. doi:10.1371/journal.pone.0069744. 2013.
  68. Schmitz RJ1, He Y, Valdés-López O, Khan SM, Joshi T, Urich MA, Nery JR, Diers B, Xu D, Stacey G, Ecker JR. Epigenome-wide inheritance of cytosine methylation variants in a recombinant inbred population. Genome Res. 2013 Oct;23(10):1663-74. doi: 10.1101/gr.152538.112. Epub 2013 Jun 5.
  69. Juexin Wang, Liang Chen, Yan Wang, Jingfen Zhang, Yanchun Liang, Dong Xu. A Computational Systems Biology Study for Understanding Salt Tolerance Mechanism in Rice. PLoS ONE 8(6): e64929. doi:10.1371/journal.pone.0064929, 2013.
  70. Hao Zhang, Zhi Li, Yanpu Li, Yuanning Liu, Junxin Liu, Xin Li, Tingjie Shen, Yunna Duan, Minggang Hu, Dong Xu. A computational method for predicting regulation of human microRNAs on the influenza virus genome. BMC Systems Biology. 7(Suppl 2):S3 doi:10.1186/1752-0509-7-S2-S3, 2013.
  71. Yuanning Liu, Yaping Chang, Chao Zhang, Qingkai Wei, Jingbo Chen, Huiling Chen, Dong Xu. Influence of mRNA features on siRNA interference efficacy. Journal of Bioinformatics and Computational Biology. 11(3):1341004. doi: 10.1142/S0219720013410047, 2013.
  72. Yuanning Liu, Yaping Chang, Dong Xu, Zhi Li, Hao Zhang, Jie Li, Mingyao Tian. Optimized Design of siRNA Based on Multi-featured Comparison and Analysis of H1N1 Virus. International Journal of Data Mining and Bioinformatics. 7(4):345-57, 2013.
  73. Zhiquan He, Meshari Alazmi, Jingfen Zhang, Dong Xu. Protein structural model selection by combining consensus and single scoring methods. PLoS One. 8(9):e74006. doi: 10.1371/journal.pone.0074006. 2013.
  74. Chao Zhang, Jiguang Wang, Kristina Hanspers, Dong Xu, Luonan Chen, Alexander R. Pico. NOA: a cytoscape plugin for network ontology analysis. Bioinformatics. 29(16):2066-2067, 2013.
  75. Jingfen Zhang, Dong Xu: Fast algorithm for population-based protein structural model analysis. Proteomics, 13:221-229, 2013.
  76. Nagib Ahsan, Yadong Huang, Alejandro Tovar-Mendez, Kirby N Swatek, Jingfen Zhang, Ján A. Miernyk, Dong Xu, and Jay J Thelen. A versatile mass spectrometry-based method to both identify kinase client-relationships and characterize signaling network topology. Journal of Proteome Research. 12:937-948, 2013.
  77. Trupti Joshi, Babu Valliyodan, Jeng-Hung Wu, Suk-Ha Lee, Dong Xu, Henry T. Nguyen. Genomic differences between cultivated soybean, G. max and its wild relative G. soja. BMC Genomics. 14 Suppl 1:S5. doi: 10.1186/1471-2164-14-S1-S5. 2013.
  78. Trupti Joshi, Kapil Patil, Michael R Fitzpatrick, Levi D Franklin, Qiuming Yao, Jeffrey R Cook, Zheng Wang, Marc Libault, Laurent Brechenmacher, Babu Valliyodan, Xiaolei Wu, Jianlin Cheng, Gary Stacey, Henry T Nguyen and Dong Xu. Soybean Knowledge Base (SoyKB): a web resource for soybean translational genomics. BMC Genomics, 13(Suppl 1):S15. doi:10.1186/1471-2164-13-S1-S15, 2012.
  79. Chao Zhang, Guolu Zheng, Shun-Fu Xu, and Dong Xu. Computational challenges in characterization of bacteria and bacteria-host interactions based on genomic data. Journal of Computer Science and Technology, 27(2): 225-239, 2012.
  80. Chao Zhang, Shun-Fu Xu, and Dong Xu. Risk Assessment of Gastric Cancer Caused by Helicobacter pylori Using CagA Sequence Markers. PLoS ONE. 7(5): e36844. doi:10.1371/journal.pone.0036844, 2012.
  81. Chao Zhang, Kristina Hanspers, Allan Kuchinsky, Nathan Salomonis, Dong Xu, Alexander R Pico. Mosiac: Making Biological Sense of Complex Networks. Bioinformatics. 28:1943–1944, 2012.
  82. Liupu Wang, Juexin Wang, Michael Wang, Yong Li, Yanchun Liang, Dong Xu. Using internet search engines to obtain medical information: a comparative study. J Med Internet Res 14(3):e74, 2012.
  83. Tran Hong Nha Nguyen, Laurent Brechenmacher, Joshua Aldrich, Therese Clauss, Marina Gritsenko, Kim Hixson, Marc Libault, Kiwamu Tanaka, Feng Yang, Qiuming Yao, Ljiljana Pasa-Tolic, Dong Xu, Henry T. Nguyen, and Gary Stacey. Quantitative Phosphoproteomic Analysis of Soybean Root Hairs Inoculated with Bradyrhizobium japonicum. Mol Cell Proteomics, 10.1074/mcp.M112.018028, 2012.
  84. Qiuming Yao, Curtis Bollinger, Jianjiong Gao, Dong Xu, and Jay J. Thelen. P3DB: an integrated database for plant protein phosphorylation. Front. Plant Sci. 3:206. doi: 10.3389/fpls.2012.00206. 2012.
  85. Qiuming Yao, Jianjiong Gao, Curtis Bollinger, Jay J. Thelen, and Dong Xu. Predicting and analyzing protein phosphorylation sites in plants using Musite. Front. Plant Sci. 3:186. doi: 10.3389/fpls.2012.00186. 2012.
  86. Mingzhu Zhu, Xin Deng, Trupti Joshi, Dong Xu, Gary Stacey, Jianlin Cheng. Reconstructing differentially co-expressed gene modules and regulatory networks of soybean cells. BMC Genomics. 13:437. doi: 10.1186/1471-2164-13-437, 2012.
  87. David A. Roeseler, Shrikesh Sachdev, Desire M. Buckley, Trupti Joshi, Doris K. Wu, Dong Xu, Mark Hannink and Samuel T. Waters. Elongation Factor 1 alpha1 and genes associated with Usher syndromes are down-stream targets of GBX2. Plos One. 7:e47366. doi:10.1371/journal.pone.0047366, 2012.
  88. Allison N. Tegge, Charles W. Caldwell, Dong Xu. Pathway correlation profile of gene-gene co-expression for identifying pathway perturbation. PLoS One. 7:e52127. doi: 10.1371/journal.pone.0052127. 2012.
  89. Nagib Ahsan, Kirby N Swatek, Jingfen Zhang, Ján A. Miernyk, Dong Xu, and Jay J Thelen. Scanning mutagenesis" of the amino acid sequences flanking phosphorylation site 1 of the mitochondrial pyruvate dehydrogenase complex. Front Plant Sci. 3:153. doi: 10.3389/fpls.2012.00153, 2012.
  90. Xue-Cheng Zhang, Zheng Wang, Xinyan Zhang, Mi Ha Le, Jianguo Sun, Dong Xu, Jianlin Cheng, Gary Stacey. Evolutionary dynamics of protein domain architecture in plants. BMC Evol Biol. 12:6. doi: 10.1186/1471-2148-12-6, 2012.
  91. Ratchadaporn Kanawong, Wentao Xu, Dong Xu, Shao Li, Tao Ma, Ye Duan: An automatic tongue detection and segmentation framework for computer-aided tongue image analysis. I. J. Functional Informatics and Personalised Medicine. 4:56-68, 2012.
  92. Ratchadaporn Kanawong, Tayo Obafemi-Ajayi, Tao Ma, Dong Xu, Shao Li, and Ye Duan. Automated Tongue Feature Extraction for ZHENG Classification in Traditional Chinese Medicine. Evidence-Based Complementary and Alternative Medicine, doi:10.1155/2012/912852, 2012.
  93. Louis J. Meyer, Jianjiong Gao, Dong Xu, and Jay J. Thelen. Phosphoproteomic analysis of seed maturation in arabidopsis, rapeseed, and soybean. Plant Physiology. 159:517-528, 2012.
  94. Jingfen Zhang, Zhiquan He, Qingguo Wang, Bogdan Barz, Ioan Kosztin, Yi Shang, and Dong Xu. Prediction of protein tertiary structures using MUFOLD. Methods Mol Biol. 815:3-13, 2012.
  95. Dong Xu. Protein Databases on the Internet. In: Current Protocols in Protein Science, edited by J. E. Coligan, B. M. Dunn, H. L. Ploegh, D. W. Speicher, and P. T. Wingfield. John Wiley & Sons, New York. Chapter 2:Unit2.6. doi: 10.1002/0471140864.ps0206s70, 2012.
  96. Jianjiong Gao, Dong Xu. Correlation between posttranslational modification and intrinsic disorder in protein. Pac Symp Biocomput. 94-103, 2012.
  97. Zhiquan He, Jingfen Zhang, Yang Xu, and Yi Shang, Dong Xu. Protein structural model selection based on protein-dependent scoring function. Statistics and its Interface. 5:109-115, 2012.
  98. Chao Zhang, Kristina Hanspers, Allan Kuchinsky, Nathan Salomonis, Dong Xu and Alexander R. Pico. Mosaic: making biological sense of complex networks. Bioinformatics. 28 (14):1943-1944, 2012.
  99. Louis J. Meyer, Jianjiong Gao, Dong Xu, and Jay J. Thelen. Phosphoproteomic analysis of seed maturation in arabidopsis, rapeseed, and soybean. Plant Physiology. 159:517-528, 2012.
  100. Zheng Wang, Xuecheng Zhang, Mi Ha Le, Dong Xu, Gary Stacey, Jianlin Cheng. A protein domain co-occurrence network approach for predicting protein function and inferring species phylogeny. PLoS ONE. 6(3):e17906, 2011.
  101. Gyan Prakash Srivastava, Mamatha Hanumappa, Garima Kushwaha, Henry T. Nguyen and Dong Xu. PRIMEGENS-v2: Homolog-specific PCR primer design for profiling splice variants. Nucleic Acid Research. 39(10):e69, 2011.
  102. Yanchun Liang, Fan Zhang, Juexin Wang, Trupti Joshi, Yan Wang, Dong Xu. Prediction of drought-resistant genes in Arabidopsis thaliana using SVM-RFE. PLoS ONE. 6(7):e21750. doi:10.1371/journal.pone.0021750, 2011.
  103. Marc Libault, Manjula Govindarajulu, R. Howard Berg, Yee Tsuey Ong, Kari Puricelli, Christopher G. Taylor, Dong Xu, and Gary Stacey. A Dual-Targeted Soybean Protein Is Involved in Bradyrhizobium japonicum Infection of Soybean Root Hair and Cortical Cells. Mol Plant Microbe Interact. 24:1051- 1060, 2011.
  104. Jingfen Zhang, Qingguo Wang, Kittinun Vantasin, Jiong Zhang, Zhiquan He, Ioan Kosztin, Yi Shang, and Dong Xu. A multilayer evaluation approach for protein structure prediction and model quality assessment. Proteins: Structure, Function, and Bioinformatics, 79 (S10):172–184, 2011.
  105. Qingguo Wang, Kittinun Vantasin, Dong Xu, Yi Shang. MUFOLD-WQA: A new selective consensus method for quality assessment in protein structure prediction. Proteins: Structure, Function, and Bioinformatics, 79 (S10):185-195, 2011.
  106. Liupu Wang, Juexin Wang, Michael Wang, Yanchun Liang, and Dong Xu. User experience evaluation of Google search for obtaining medical knowledge: a case study. International Journal of Data Mining and Bioinformatics. 5:626 – 639, 2011.
  107. Xiaohu Shi, Jingfen Zhang, Zhiquan He, Yi Shang, and Dong Xu. A sampling-based method for ranking protein structural models by integrating multiple scores and features. Current Protein and Peptide Science. 12(6):540-8, 2011.
  108. Qingguo Wang, Yi Shang, and Dong Xu. Improving Consensus Approach for Protein Structure Selection by Removing Redundancy. IEEE/ACM Transactions on Computational Biology and Bioinformatics. 8: 1708-1715, 2011.
  109. Eun-Joon Lee, Lirong Pei, Gyan Srivastava, Trupti Joshi, Garima Kushwaha, Jeong-Hyeon Choi, Keith D. Robertson, Xinguo Wang, John K. Colbourne, Lu Zhang, Gary P. Schroth, Dong Xu, Kun Zhang, Huidong Shi. Targeted bisulfite sequencing by solution hybrid selection and massively parallel sequencing. Nucleic Acids Research. doi: 10.1093/nar/gkr598, 2011.
  110. Guan Ning Lin, Chao Zhang, Dong Xu. Polytomy identification in microbial phylogenetic reconstruction. BMC Genomics. 5(Suppl 3):S2 doi:10.1186/1752-0509-5-S3-S2, 2011.
  111. Juexin Wang, Fan Zhang, Yan Wang, Yuan Fu, Dong Xu, and Yanchun Liang. Identification of salt tolerance genes in rice from microarray data using SVM-RFE. Proceeding of the International Conference on Bioinformatics and Computational Biology (BICoB-2011), March 2011, New Orleans, USA, pp. 30-35.
  112. Wentao Xu, Ratchadaporn Kanawong, Dong Xu, Shao Li, Tao Ma, Guixu Zhang, Ye Duan. An automatic tongue detection and segmentation framework for computer-aided tongue image analysis. 13th IEEE International Conference on e-Health Networking Applications and Services (Healthcom), 2011.
  113. Jingfen Zhang and Dong Xu. Fast Algorithm for Clustering a Large Number of Protein Structural Decoys. Proceedings of IEEE International Conference on Bioinformatics & Biomedicine (BIBM 2011), Atlanta, USA, pp 30-36, November 2011.
  114. Libault M, Farmer A, Joshi T, Takahashi K, Langley RJ, Franklin LD, He J, Xu D, May G, Stacey G. An integrated transcriptome atlas of the crop model Glycine max, and its use in comparative analyses in plants. Plant J. 2010 Jul 1;63(1):86-99.
  115. Trupti Joshi, Qiuming Yao, Levi D. Franklin, Laurent Brechenmacher, Babu Valliyodan, Gary Stacey, Henry Nguyen, and Dong Xu. SoyMetDB: The Soybean Metabolome Database. Proceedings of IEEE International Conference on Bioinformatics & Biomedicine (BIBM 2010), Hong Kong, pp 203-208, December 2010.
  116. Chao Zhang, Shunfu Xu, and Dong Xu. Detection and application of CagA sequence markers for assessing risk factor of gastric cancer caused by Helicobacter pylori. Proceedings of IEEE International Conference on Bioinformatics & Biomedicine (BIBM 2010), Hong Kong, pp 485-488, December 2010.
  117. Wu X, Ren C, Joshi T, Vuong T, Xu D, Nguyen HT. SNP discovery by high-throughput sequencing in soybean. BMC Genomics. 2010 Aug 11;11:469.
  118. Martin Hajduch, Ganesh Kumar Agrawal, Jill E. Casteel, Trupti Joshi, Zhao Song, Mingyi Zhou, Huachun Wang, Dong Xu, Jay J. Thelen. Systems Analysis of Seed Filling in Arabidopsis: Using General Linear Modeling to Assess Concordance of Transcript and Protein Expression. Plant Physiology, April 2010, Vol. 152, pp. 1-10.
  119. Trupti Joshi, Zhe Yan, Marc Libault, Dong-Hoon Jeong, Sunhee Park, Pamela J Green, D Janine Sherrier, Andrew Farmer, Greg May, Blake C Meyers, Dong Xu and Gary Stacey. Prediction of novel miRNAs and associated target genes in Glycine max. BMC Bioinformatics, 11(Suppl 1):S14, 2010.
  120. Zheng Wang, Marc Libault, Trupti Joshi, Babu Valliyodan, Henry Nguyen, Dong Xu, Gary Stacey, and Jianlin Cheng. SoyDB: A Knowledge Database of Soybean Transcription Factors, BMC: Plant Biology 2010, 10:14.
  121. Jeremy Schmutz, Steven B. Cannon, Jessica Schlueter, Jianxin Ma, Therese Mitros, William Nelson, David L. Hyten, Qijian Song, Jay J. Thelen, Jianlin Cheng, Dong Xu, Uffe Hellsten, Gregory D. May, Yeisoo Yu, Tetsuya Sakurai, Taishi Umezawa, Madan K. Bhattacharyya, Devinder Sandhu, Babu Valliyodan, Erika Lindquist, Myron Peto, David Grant, Shengqiang Shu, David Goodstein, Kerrie Barry, Montona Futrell-Griggs, Brian Abernathy, Jianchang Du, Zhixi Tian, Liucun Zhu, Navdeep Gill, Trupti Joshi, Marc Libault, Anand Sethuraman, Xue-Cheng Zhang, Kazuo Shinozaki, Henry T. Nguyen, Rod A. Wing, Perry Cregan, James Specht, Jane Grimwood, Dan Rokhsar, Gary Stacey, Randy C. Shoemaker and Scott A. Jackson. Genome Sequence of the Palaeopolyploid Soybean . Nature. 463:178-83, 2010.
  122. Jingfen Zhang, Qingguo Wang, Bogdan Barz, Zhiquan He, Ioan Kosztin, Yi Shang, and Dong Xu. MUFOLD: A New Solution for Protein 3D Structure Prediction. Proteins: Structure, Function, and Bioinformatics, 78:1137-1152, 2010.
  123. Dongyu Zhao, Yan Wang, Di Luo, Xiaohu Shi, Liupu Wang, Dong Xu, Jun Yu, Yanchun Liang. PMirP: A pre-microRNA prediction method based on structure-sequence hybrid features. Artificial Intelligence in Medicine. 49(2):127-132. 2010.
  124. Gyan Prakash Srivastava, Ping Li, Jingdong Liu, and Dong Xu. Identification of Transcription Factor's Targets Using Tissue-specific Transcriptomic Data in Arabidopsis thaliana. BMC Systems Biology. 4(Suppl 2):S2. 2010.
  125. Guan Ning Lin, Zheng Wang, Dong Xu, and Jianlin Cheng. SeqRate: sequence-based protein folding type classification and rates prediction. BMC Bioinformatics. 11(S-3): 1. 2010.
  126. Gyan Prakash Srivastava, Jing Qiu, and Dong Xu. Genome-wide functional annotation by integrating multiple microarray datasets using meta-analysis. International Journal of Data Mining and Bioinformatics. 4(4):357-376. 2010.
  127. Shunfu Xu, Chao Zhang, Yi Miao, Jianjiong Gao, Dong Xu. Effector prediction in host-pathogen interaction based on a Markov model of a ubiquitous EPIYA motif. BMC Genomics. 11(Suppl 3):S1. 2010.
  128. Jianjiong Gao, Jay J. Thelen, A. Keith Dunker, and Dong Xu. Musite: a Tool for Global Prediction of General and Kinase-Specific Phosphorylation Sites. Molecular & Cellular Proteomics. 9(12):2586-600. 2010.
  129. Jeong-Hyeon Choi, Yajun Li, Juyuan Guo, Lirong Pei, Tibor Rauch, Robin S. Kramer, Simone Macmil, Graham Wiley, Lynda B. Bennett, Jennifer L. Schnabel, Kristen H. Taylor, Sun Kim, Dong Xu, Arun Sreekumar, Gerd P. Pfeifer, Bruce Roe, Charles W. Caldwell, Kapil N. Bhalla and Huidong Shi. Genome-wide DNA methylation maps in follicular lymphoma cells determined by methylation-enriched bisulfite sequencing. PLoS ONE. 5:9. 2010.
  130. Satish K. Guttikonda, Trupti Joshi, Naveen Bisht, Hui Chen, Charles An, Sona Pandey, Dong Xu and Oliver Yu. Whole Genome Co-expression Analysis of Soybean Cytochrome P450 Genes Identifies Nodulation-Specific P450 Monooxygenases. BMC Plant Biology. 10:243. 2010.
  131. Jianjiong Gao and Dong Xu. The Musite open-source framework for phosphorylation-site prediction. BMC Bioinformatics. 11(Suppl 12):S9. 2010.
  132. Marc Libault, Laurent Brechenmacher, Jianlin Cheng, Dong Xu and Gary Stacey. Root Hair Systems Biology. Trends in Plant Science. 15:641-650, 2010.
  133. Chi-Ren Shyu, Bin Pang, Pin-Hao Chi, Nan Zhao, Dmitry Korkin1, and Dong Xu. ProteinDBS v2.0: A web server for global and local protein structure search. Nucleic Acids Research; 38(SUPPL. 2):W53-W58. 2010.
  134. Jack Y Yang, Andrzej Niemierko, Ruzena Bajcsy, Dong Xu, Brian D Athey, Aidong Zhang, Okan K Ersoy, Guo-zheng Li, Mark Borodovsky, Joe C Zhang, Hamid R Arabnia, Youping Deng, A Keith Dunker, Yunlong Liu, and Arif Ghafoor. 2K09 and thereafter : the coming era of integrative bioinformatics, systems biology and intelligent computing for functional genomics and personalized medicine research. BMC Genomics. 11 Suppl 3:I1, 2010.
  135. Gyan Prakash Srivastava, Garima Kushwaha, Huidong Shi, and Dong Xu. High-throughput Primer and Probe Design for Genome-Wide DNA Methylation Study Using PRIMEGENS. In "A Practical Guide to Bioinformatics Analysis". iConcept Press Ltd. 151-171, 2010.
  136. Huan Yang, Yan Wang, Trupti Joshi, Dong Xu, Shoupeng Yu, and Yanchun Liang. MicroRNA Precursor Prediction Using SVM with RNA Pairing Continuity Feature. In "Interdisciplinary Research and Applications in Bioinformatics, Computational Biology, and Environmental Sciences". Limin Angela Liu, Dong-Qing Wei and Yixue Li eds. Medical Information Science Reference, Hershey-New York. Chapter 7, 73-82. 2010.
  137. Chao Zhang Shunfu Xu Dong Xu. Detection and application of CagA sequence markers for assessing risk factor of gastric cancer caused by Helicobacter pylori. Proceedings of IEEE International Conference on Bioinformatics & Biomedicine (BIBM 2010), Hong Kong, pp 485-488, December 2010.
  138. Jingfen Zhang, Dong Xu, Wen Gao, Guohui Lin, Simin He. Isotope pattern vector based tandem mass spectral data calibration for improved peptide and protein identification, Rapid Communications in Mass Spectrometry, 23(21):3448-3456, 2009.
  139. Yi Shang, Qingguo Wang, Jingfen Zhang, Bogdan Barz, Rajkumar Bondugula, Ioan Kosztin, and Dong Xu. A New Computational Intelligent Approach to Protein Tertiary Structure Prediction, in “Computational Intelligence and Its Applications”. Ed: Xin Yao, Xuelong Li, Dacheng Tao. University of Science and Technology of China Press, 2009. ISBN 978-7-312-02218-0.
  140. Yong Wang, Rui-Sheng Wang, Trupti Joshi, Dong Xu, Xiang-Sun Zhang, Luonan Chen, Yu Xia. A Linear Programming Framework for Inferring Gene Regulatory Networks by Integrating Heterogeneous Data. In " Handbook of Research on Computational Methodologies in Gene Regulatory Networks". Sanjoy Das, Doina Caragea, Stephen M. Welch, William H. Hsu eds. Medical Information Science Reference, Hershey-New York. Chapter 19, 450-474, 2009.
  141. Guan Ning Lin, Zheng Wang, Dong Xu, and Jianlin Cheng. Sequence-based prediction of protein folding rates using contacts, secondary structures and support vector machines. Proceeding of IEEE International Conference on Bioinformatics and Biomedicine (BIBM 2009), Washington DC, USA, pp. 3-8, 2009.
  142. Jianjiong Gao, Ganesh Kumar Agrawal, Jay J. Thelen, and Dong Xu. P3DB: a plant protein phosphorylation database. Nucleic Acids Research, 37 (Database issue):D960-962, Epub 2009.
  143. Marc Libault , Trupti Joshi , Vagner A. Benedito , Dong Xu , Michael K. Udvardi , and Gary Stacey. Legume transcription factor genes; what makes legumes so special?. Plant Physiology 151:991-1001, 2009.
  144. Marc Libault, Trupti Joshi, Kaori Takahashi, Andrea Hurley-Sommer, Kari Puricelli, Sean Blake, Richard E. Finger, Christopher G. Taylor, Dong Xu, Henry Nguyen, Gary Stacey. Large scale analysis of soybean regulatory gene expression identifies a Myb gene involved in soybean nodule development. Plant Physiology 151:1207-1220, 2009.
  145. Gyan Prakash Srivastava, Trupti Joshi, Zhao Song, Chao Zhang, Guan Ning Lin, Ping Li, Andy Ross, Mihail Popescu, Jingdong Liu, Jing Qiu, and Dong Xu, "GO-based Gene Function and Network Characterization", in, "Ontology-Based Data Mining in Biomedical Research", Mihail Popescu and Dong Xu eds. Artech House, Norwood, MA, USA. 83-111, 2009.
  146. Mihail Popescu and Dong Xu, "Mapping Genes to Biological Pathways Using Ontological Fuzzy Rule Systems", Mihail Popescu and Dong Xu eds. Artech House, Norwood, MA, USA. 113-132, 2009.
  147. Dong Xu. Computational Methods for Protein Sequence Comparison and Search. In: Current Protocols in Protein Science, edited by J. E. Coligan, B. M. Dunn, H. L. Ploegh, D. W. Speicher, and P. T. Wingfield. John Wiley & Sons, New York. 56:2.1.1-2.1.27, UNIT 2.1, 2009.
  148. Zhao Song, Luonan Chen, and Dong Xu. Confidence Assessment for Protein Identification by Using Peptide-Mass Fingerprinting Data. Proteomics, 9(11):3090-3099, 2009.
  149. Jianjiong Gao, Ganesh Kumar Agrawal, Jay J. Thelen, Zoran Obradovic, A. Keith Dunker, and Dong Xu. A New Machine Learning Approach for Protein Phosphorylation Site Prediction in Plants. Lecture Notes in Bioinformatics (LNBI 5462): Proceeding of the First International Conference on Bioinformatics and Computational Biology (BICoB), April 2009, New Orleans, USA, pp. 18-29.
  150. Guan Ning Lin, Zhipeng Cai, Guohui Lin, Sounak Chakraborty, and Dong Xu, ComPhy: Prokaryotic Composite Distance Phylogenies Inferred from Whole-Genome Gene Sets. BMC Bioinformatics, 2009, 10(Suppl 1):S5.
  151. Mingjie Chen, Brian P. Mooney, Martin Hajduch, Jill E. Casteel, Trupti Joshi, Mingyi Zhou, Dong Xu, Jay J. Thelen. System Analysis of An Arabidopsis Mutant Altered in de novo Fatty Acid Synthesis Reveals Diverse Changes in Seed Composition and Metabolic Regulation. Plant Physiology. 150:27-41, 2009.
  152. Sandra Thibivilliers, Trupti Joshi, Kimberly B. Campbell, Brian Scheffler, Dong Xu, Bret Cooper, Henry T. Nguyen and Gary Stacey. Generation of Phaseolus vulgaris ESTs and investigation of their regulation upon Uromyces appendiculatus infection. BMC Plant Biology 2009, 9:46 (27 Apr 2009)
  153. Laurent Brechenmacher, Joohyun Lee, Sherri Sachdev, Zhao Song, Tran Hong Nha Nguyen; Joshi Trupti, Beverly Dague, Nathan Oehrle, Marc Libault, Brian Mooney, Dong Xu, Bret Cooper, and Gary Stacey. Establishment of a Protein Reference Map for Soybean Root Hair Cells.Plant Physiology, February 2009, Vol. 149, pp. 670-682.
  154. Guan Ning Lin, Zhipeng Cai, Guohui Lin, Sounak Chakraborty, and Dong Xu. Using genome-scale-gene-based composite distance to infer prokaryotic phylogenies. Proceeding of 7th APBC (Asian Pacific Bioinformatics Conference), Beijing, China, pp. 40-52, 2009.
  155. Dong Xu. Mutual understanding between Traditional Chinese Medicine and systems biology: gaps, challenges and opportunities, International Journal of Functional Informatics and Personalised Medicine, 2:248-260, 2009.
  156. Chao Zhang, Trupti Joshi, Guan Ning Lin, Dong Xu. An integrated probabilistic approach for gene function prediction using multiple sources of high-throughput data. International Journal of Computational Biology and Drug Design, Volume 1, Number 3, 26 November 2008 , pp. 254-274(21).
  157. Christopher A. Bottoms and Dong Xu "Wanted: Unique Names for Unique Atom Positions. PDB-Wide Analysis of Diastereotopic Atom Names of Small Molecules Containing Diphosphate", BMC Bioinformatics, 9 Suppl 9:S16, 2008.
  158. Gyan P Srivastava, Juyuan Guo, Huidong Shi, and Dong Xu. PRIMEGENS-v2: Genome-wide primer design for analyzing DNA methylation patterns of CpG islands. Bioinformatics, 24(17):1837-42, 2008.
  159. Robin Kramer and Dong Xu. Projecting Gene Expression Trajectories through Inducing Differential Equations from Microarray Time Series Experiments. Journal of VLSI Signal Processing Systems. 50(3):321-329, 2008.
  160. Jianjiong Gao, Ganesh Kumar Agrawal, Jay J. Thelen, and Dong Xu. P3DB: a plant protein phosphorylation database. Nucleic Acids Research, Advance Access published online on October 17, 2008.
  161. Rajkumar Bondugula and Dong Xu. Combining Sequence and Structural Profiles for Protein Solvent Accessibility Prediction, Proceeding of the 7th Annual International Conference on Computational Systems Bioinformatics (CSB 2008), Stanford University, California, USA, pp. 195-200, 2008.
  162. Gyan P. Srivastava, Jing Qiu, Dong Xu. Functional Annotation from Meta-Analysis of Microarray Datasets, Proceeding of IEEE International Conference on Bioinformatics and Biomedicine (BIBM 2008), Philadelphia, Pennsylvania, USA, pp. 367-271, November 2008.
  163. Debjani Ghosh, Gyan P Srivastava, Dong Xu, and R. Michael Roberts. The Interaction between Stress-Activated Protein Kinase Interacting Protein 1 (SIN1/MAKPAP1) and poly(RC) Binding Protein-2(PCBP2): Potential Involvement In Counteracting Environmental Stress. Proceedings of National Academy of Sciences. 105 (33):11673-11678, 2008.
  164. Dong Xu, James Keller, Mihail Popescu, and Rajkumar Bondugula. "Application of Fuzzy Logic in Bioinformatics", Imperial College Press, London, UK. 2008.
  165. Lourdes Pena-Castillo, Murat Tasan, Chad L Myers, Hyunju Lee, Trupti Joshi, Chao Zhang, Yuanfang Guan, Michele Leone, Andrea Pagnani, Wan Kyu Kim, Chase Krumpelman, Weidong Tian, Guillaume Obozinski, Yanjun Qi, Sara Mostafavi, Guan Ning Lin, Gabriel F Berriz, Francis D Gibbons, Gert Lanckriet, Jian Qiu, Charles Grant, Zafer Barutcuoglu, David P Hill, David Warde-Farley, Chris Grouios, Debajyoti Ray, Judith A Blake, Minghua Deng, Michael I Jordan, William S Noble, Quaid Morris, Judith Klein-Seetharaman, Ziv Bar-Joseph, Ting Chen, Fengzhu Sun, Olga G Troyanskaya, Edward M Marcotte, Dong Xu, Timothy R Hughes, Frederick P Roth. A critical assessment of Mus musculus gene function prediction using integrated genomic evidence, Genome Biology. 9(Suppl 1):S2 (27 June 2008).
  166. Laurent Brechenmacher, Moon-Young Kim, Marisol Benitez, Min Li, Trupti Joshi, Bernarda Calla, Mei Phing Lee, Marc Libault, Lila O. Vodkin, Dong Xu, Suk-Ha Lee, Steven J. Clough, and Gary Stacey. Transcription profiling of soybean nodulation by Bradyrhizobium japonicum. Molecular Plant-Microbe Interactions. Vol.21, No. 5, 631-645, 2008.
  167. Trupti Joshi, Chao Zhang, Guan Ning Lin, Zhao Song, Dong Xu. GeneFAS: A tool for prediction of gene function using multiple sources of data. In "Genomics Protocols" volume of "Methods in Molecular Biology", the second edition, edited by Ramnath Elaswarapu and Michael P. Starkey. Humana Press, Totowa, New Jersey. Vol.439, 369-386, 2008.
  168. Yu Chen and Dong Xu. Predicting Functional Modules Using Microarray and Protein Interaction Data. In: Analysis of Microarray Data, A Network-Based Approach, edited by F. Emmert-Streib and M. Dehmer. VILEY_VCH Verlag GmbH &Co. KGaA, Weinheim. 307-329, 2008.
  169. Sum Kim, Meng Li, Henry H. Paik, Kenneth P. Nephew, Huidong Shi, Robin Kramer, Dong Xu, Tim H.-M. Huang. Predicting DNA Methylation Susceptibility Using CpG Flanking Sequences. Pacific Symposium on Biocomputing, the Big Island of Hawaii, 13:315-326, January, 2008.
  170. Qingguo Wang, Yi Shang, Dong Xu. A New Clustering-Based Method for Protein Structure Selection, Proceeding of the IEEE World Congress on Computational Intelligence, pp. 2891-2898, June 2008.
  171. Trupti Joshi, Jinrong Wan, Curtis J. Palm, Kara Juneau, Ron Davis, Audrey Southwick, Katrina M. Ramonell, Gary Stacey, Dong Xu. Bioinformatics Analyses of Arabidopsis thaliana Tiling Array Expression Data In "Knowledge Discovery in Bioinformatics: Techniques, Methods and Application" edited by Yi Pan and Xiaohua (Tony) Hu, John Wiley and Sons, New York. Pages 57-70, 2007.
  172. Kristen H. Taylor, Robin S. Kramer, J. Wade Davis, Dong Xu, Charles W. Caldwell, and Huidong Shi. Ultra-Deep Bisulfite Sequencing Analysis of DNA Methylation Patterns in Multiple Gene Promoters by 454-Sequencing. Cancer Research. 67(18):8511-8518, 2007.
  173. James O. Allen, Christiane M. Fauron, Patrick Minx, Leah Westgate, Swetha Oddiraju, Guan Ning Lin, Louis Meyer, Hui Sun, Kyung Kim, Chunyan Wang, Feiyu Du, Dong Xu, Michael Gibson, Jill Cifrese, Sandra W. Clifton and Kathleen J. Newton. Comparisons Among Two Fertile and Three Male-Sterile Mitochondrial Genomes of Maize. Genetics, Vol. 177, 1173-1192. 2007.
  174. Woo-Suk Chang, William L. Franck, Eddie Cytryn, Sooyoung Jeong, Trupti Joshi, David W. Emerich, Michael J. Sadowsky, Dong Xu, and Gary Stacey. An Oligonucleotide Microarray Resource for Transcriptional Profiling of Bradyrhizobium japonicum. Molecular Plant-Microbe Interactions Vol. 20, No. 10, 1298-1307. 2007.
  175. Trupti Joshi and Dong Xu. Quantitative assessment of relationship between sequence similarity and function similarity. BMC Genomics, Vol. 8(1):222, 2007.
  176. Mihail Popescu, Dong Xu, Erik Taylor. GoFuzzKegg: Mapping Genes to KEGG Pathways Using an Ontological Fuzzy Rule System. Proc. of the 2007 IEEE Symposium on Comp. Intell. in Bioinf. and Comp. Biology (CIBCB 2007), Hawaii, USA, pp. 298-303, 2007.
  177. Rajesh Kumar, Jing Qiu, Trupti Joshi, Babu Valliyodan, Dong Xu, Henry T. Nguyen. Single Feature Polymorphism Discovery in Rice. PLoS ONE 2(3): e284. doi:10.1371/journal.pone.0000284, 2007.
  178. Predrag S Krstic, Jack C. Wells, Miguel Fuentes-Cabrera, Dong Xu, and James W. Lee. Toward electronic conductance characterization of DNA nucleotide bases. Solid State Phenomena. Vols 121-123, pages 1387-1390, 2007.
  179. Zhao Song, Luonan Chen, Ashwin Ganapathy, Xiu-Feng Wan, Laurent Brechenmacher, Nengbing Tao, David Emerich, Gary Stacey, Dong Xu. Development and Assessment of Scoring Functions for Protein Identification Using Peptide Mass Fingerprinting Data. Electrophoresis. 28:864-870, 2007.
  180. Rajkumar Bondugula and Dong Xu. MUPRED: A Tool for Bridging the Gap between Template Based Methods and Sequence Profile Based Methods for Protein Secondary Structure Prediction. Proteins. 66(3):664-670, 2007.
  181. Mihail Popescu, Dong Xu. Mapping Genes to Pathways Using Ontological Fuzzy Rule Systems. Fuzzy Systems Conference, FUZZIEEE2007, London, UK, July 23-26, pp. 1-6, 2007.
  182. Yi Shang, Rajkumar Bondugula, Dong Xu, and Qingguo Wang. "A New Method for Protein Tertiary Structure Prediction," in Proc. IASTED Int'l Conf. on Computational Intelligence, Banff, Canada, July, 2007.
  183. Ying Xu, Dong Xu, and Jie Liang eds. "Computational Methods for Protein Structure Prediction and Modeling", I, II, Springer-Verlag. 2006.
  184. Dong Xu and Ying Xu. Protein Structure Prediction as a Systems Problem. In “Computational Methods for Protein Structure Prediction and Modeling”, edited by Ying Xu, Dong Xu, and Jie Liang. Springer-Verlag. Vol. 2. Pages 177-206, 2006.
  185. Guohui Lin, Dong Xu, Ying Xu. Computer Science for Structural Bioinformatics. In “Computational Methods for Protein Structure Prediction and Modeling”, edited by Ying Xu, Dong Xu, and Jie Liang. Springer-Verlag. Vol. 2. Pages 241-266, 2006.
  186. Gyan Prakash Srivastava and Dong Xu. Genome-Scale Probe and Primer Design with PRIMEGENS. In “Methods in Molecular Biology”, vol 402: PCR Primer Design”, edited by Anton Yuryev, Humana Press, Totowa, New Jersey. Pages 159-175, 2006.
  187. Hui Lu, Ognjen Perisic, and Dong Xu. Physical and Chemical Basis for Structural Bioinformatics. In “Computational Methods for Protein Structure Prediction and Modeling”, edited by Ying Xu, Dong Xu, and Jie Liang. Springer-Verlag. Vol. 2. Pages 267-297, 2006.
  188. Ying Xu, Zhijie Liu, Liming Cai, Dong Xu. Protein Structure Prediction by Protein Threading. In “Computational Methods for Protein Structure Prediction and Modeling”, edited by Ying Xu, Dong Xu, and Jie Liang. Springer-Verlag. Vol. 2. Pages 1-42, 2006.
  189. Dong Xu, Jie Liang, and Ying Xu. Resources and Infrastructure for Structural Bioinformatics. In “Computational Methods for Protein Structure Prediction and Modeling”, edited by Ying Xu, Dong Xu, and Jie Liang. Springer-Verlag. Vol. 2. Pages 207-227, 2006.
  190. Xiufeng Wan, Guohui Lin and Dong Xu. Rnall: An Efficient Algorithm for Predicting RNA Local Secondary Structural Landscape in Genomes. Journal of Bioinformatics and Computational Biology. 4:1015-1031, 2006.
  191. Andrew Nunberg, Joseph A. Bedell, Mohammad A. Budiman, Robert W. Citek, Sandra W. Clifton, Lucinda Fulton, Deana Pape, Zheng Cai, Trupti Joshi, Henry Nguyen, Dong Xu and Gary Stacey. Survey sequencing of soybean elucidates the genome structure and composition. Functional Plant Biology. Vol. 33(8) 765-773, 2006.
  192. Dong Xu, Rajkumar Bondugula, Mihail Popescu, James M Keller. "Bioinformatics and Fuzzy Logic". Proceeding of Fuzz-IEEE 2006 (IEEE International Conference on Fuzzy Systems), Vancouver, BC, Canada, July 2006.
  193. Rajkumar Bondugula, Dong Xu, and Yi Shang. "A Fast Algorithm for Low-Resolution Protein Structure Prediction". Proceeding of the 28th International Conference of the IEEE Engineering in Medicine and Biology Society, New York. 2006.
  194. Zhao Song, Luonan Chen, Chao Zhang, Dong Xu. "Design and Implementation of Probability-Based Scoring Function for Peptide Mass Fingerprinting Protein Identification". Proceeding of the 28th International Conference of the IEEE Engineering in Medicine and Biology Society, New York. 2006. In press.
  195. Yong Wang, Trupti Joshi, Dong Xu, Xiang-Sun Zhang, and Luonan Chen. "Supervised Inference of Gene Regulatory Networks by Linear Programming". Lecture Notes in Computer Science, 4115, 551-561, 2006. (Also in Proceeding of the 2006 International Conference on Intelligent Computing (ICIC 2006), Kunming, China).
  196. Yong Wang, Trupti Joshi, Xiang-Sun Zhang, Dong Xu, Luonan Chen. Inferring Gene Regulatory Networks from Multiple Microarray Datasets. Bioinformatics. 22:2413-2420, 2006.
  197. Pin-Hao Chi, Chi-Ren Shyu, Dong Xu. A fast SCOP fold classification system using content-based E-Predict algorithm. BMC Bioinformatics. 7:362, 2006.
  198. Robin Kramer, Victor Olman, Ying Xu, and Dong Xu, DigitalTree: A Tool for Displaying Biological Data in Tree Structure. Lecture Notes in Computer Science, 3992, 855-862. (Also in Proceeding of International Conference on Computational Science 2006 (ICCS 2006), University of Reading, UK.
  199. Monir Shababi, Karuppaiah Palanichelvam, Anthony B. Cole, Dong Xu, Xiu-Feng Wan, and James E. Schoelz. The ribosomal shunt translation strategy of Cauliflower mosaic virus has evolved from ancient long terminal repeats. Journal of Virology. 80:3811-3822, 2006.
  200. Seung Yon Rhee, Julie Dickerson, and Dong Xu. Bioinformatics and Its Applications in Plant Biology. Annual Review of Plant Biology. 57:335-360. 2006.
  201. Xiaomeng Wu, Xiu-Feng Wan, Gang Wu, Dong Xu, and Guohui Lin. Phylogenetic Analysis Using Complete Signature Information of Whole Genomes and Clustered Neighbor-Joining Method. Journal of Bioinformatics Research and Applications. 2:219-248, 2006.
  202. Xiu-Feng Wan, Jizhong Zhou, and Dong Xu. CodonO: A new informatics method measuring synonymous codon usage bias. International Journal of General Systems. 35:109-125, 2006
  203. Dong Xu, Ognen Duzlevski, and Xiu-Feng Wan. In search of remote homolog. In Handbook of Computational Molecular Biology, edited by Srinivas Aluru, CRC Press. 33:1-33:27, 2006.
  204. Yu Chen and Dong Xu. Bioinformatics Analysis for Interactive Proteomics. In Current Protocols in Protein Science, edited by J. E. Coligan, B. M. Dunn, H. L. Ploegh, D. W. Speicher, and P. T. Wingfield. John Wiley & Sons, New York. 25.1.1-25.1.14, 2005.
  205. Xiu-Feng Wan and Dong Xu. Computational Methods for Remote Homlog Identification. Current Protein and Peptide Science. Vol 6:527-546, 2005.
  206. Jinrong Wan, Michael Torres, Ashwin Ganapathy, Jay Thelen, Beverly B. DaGue, Brian Mooney, Dong Xu, and Gary Stacey. Proteomic analysis of soybean root hairs after infection by Bradyrhizobium japonicum. Mol. Plant-Microbe Int. 18:458-467, 2005.
  207. Trupti Joshi, Yu Chen, Nickolai Alexandrov, Dong Xu. Cellular Function Prediction and Biological Pathway Discovery in Arabidopsis thaliana Using Microarray Data. International Journal of Bioinformatics Research and Applications. Vol 1:335-350, 2005.
  208. Zhi-Zhong Chen, Guohui Lin, Romeo Rizzi, Jianjun Wen, Dong Xu, Ying Xu, Tao Jiang: More Reliable Protein NMR Peak Assignment via Improved 2-Interval Scheduling. Journal of Computational Biology. 12 (2): 129-146, 2005.
  209. Xiu-Feng Wan, Tao Ren, Kai-Jian Luo, Ming Liao, Gui-Hong Zhang, Jin-Ding Chen, Wei-Sheng Cao, Ye Li, Ning-Yi Jin, Dong Xu and Chao-An Xin. Genetic characterization of H5N1 Avian Influenza Viruses isolated in Southern China during the 2003-04 avian influenza breakouts. Archives of Virology. 150 (6):1257-1266, 2005.
  210. Xiu-Feng Wan, Demet Ataman, Dong Xu.Application of computational biology in understanding emerging infectious diseases: inferring the biological function for S-M complex of SARS-CoV. In "Bioinformatics:New Research", Edited by Nova Science Publishers, Inc. New York. Pages 55-80. 2005.
  211. Xiu-Feng Wan and Dong Xu. Intrinsic terminator prediction and its application in Synechococcus sp. WH8102. Journal of Computer and Science Technology. 20:465-482, 2005.
  212. Yu Chen and Dong Xu. Genome-Scale Understanding Protein Dispensability through Machine-Learning Analysis of High-Throughput Data. Bioinformatics. 21:575-581, 2005.
  213. Rajkumar Bondugula, Ognen Duzlevski, Dong Xu. Profiles and fuzzy K-nearest neighbor algorithm for protein secondary structure prediction. Pages 85-94. Yi-Ping Phoebe Chen and Limsoon Wong, editors. Proceedings of 3rd Asia-Pacific Bioinformatics Conference, 17-21 January 2005, Singapore. Imperial College Press, London.
  214. Yu Chen and Dong Xu. Genome-Scale Protein Function Prediction in Yeast Saccharomyces Cerevisiae Through Integrating Multiple Sources Of High-Throughput Data. Proceedings of the 2005 Pacific Symposium on Biocomputing (PSB), 471-482.
  215. Trupti Joshi, Yu Chen, Jeffrey M. Becker, Nickolai Alexandrov, Dong Xu. Genome-Scale Gene Function Prediction Using Multiple Sources of High-Throughput Data in Yeast Saccharomyces cerevisiae. OMICS: A Journal of Integrative Biology Dec 2004, Vol. 8, No. 4: 322-333.
  216. Yu Chen and Dong Xu. Global Protein Function Annotation through Mining Genome-Scale Data in Yeast Saccharomyces cerevisiae. Nucleic Acid Research. 32:6414-6424, 2004.
  217. Wes G. Smith, Satish S. Nair, Dong Xu, Jyotsna Nair, and Bernard D. Beitman. “Framework for Developing a Hierarchical Model for Reward Focusing on the Nucleus Accumbens,” 26th International Conference of the IEEE Engineering in Medicine and Biology Society, Sept 2004, San Francisco, CA, USA. September 1-5, 2004.133-136
  218. Cline, C. H., Satish S. Nair, Dong Xu, Jyotsna Nair, and Bernard D. Beitman. “Modeling Obsessive Compulsive Disorder,” 26th International Conference of the IEEE Engineering in Medicine and Biology Society, Sept 2004, San Francisco, CA, USA. September 1-5, 2004.890-893.
  219. Iyoho, A., Satish S. Nair, Dong Xu, Jyotsna Nair, and Bernard D. Beitman. “Computational Modeling of Hysterical Paralysis,” 26th International Conference of the IEEE Engineering in Medicine and Biology Society, Sept 2004, San Francisco, CA, USA. September 1-5, 2004.894-897
  220. Trupti Joshi, Yu Chen, Nickolai Alexandrov, Dong Xu. Cellular Function Prediction and Biological Pathway Discovery in Arabidopsis thaliana Using Microarray Data. Proceedings of the 26th Annual International Conference of the IEEE EMBS San Francisco, CA, USA. September 1-5, 2004. 2881-2884.
  221. Ashwin Ganapathy, Xiu-Feng Wan, Jinrong Wan, Jay Thelen, David W. Emerich, Gary Stacey, and Dong Xu. "Statistical Assessment for Mass-spec Protein Identification Using Peptide Fingerprinting Approach". Preceedings of the 26th International Conference of the IEEE Engineering in Medicine and Biology Society, pp. 3051-3054. Sept 1-5, 2004, San Francisco, CA.
  222. Xiu-Feng Wan, Dong Xu, Andris Kleinhofs, and Jizhong Zhou. Quantitative relationship between codon usage bias and GC composition across the unicellular genomes. BMC Evolutionary Biology. BMC Evolutionary Biology 2004, 4:19, 2004.
  223. Yu Chen and Dong Xu. Prediction of Protein dispensability through integrated analysis of multi-source high-throughput data. In Proceeding of the 5th International Conference on Software Engineering, Artificial Intelligence, Networking and Parallel/Distributed Computing (SNPD 2004), pp 158-166. June 30 - July 2, 2004. Beijing, China.
  224. Chi-Ren Shyu, Pin-Hao Chi, Grant Scott, Dong Xu. ProteinDBS: A real-time retrieval system for protein structure comparison. Nucleic Acid Research. 32 (Web Server issue): W572 - CW575, 2004.
  225. Jun-tao Guo, Kyle Ellrott, Won Jae Chung, Dong Xu, Serguei Passovets, Ying Xu. PROSPECT-PSPP: An Automatic Computational Pipeline for Protein Structure Prediction. Nucleic Acid Research. 32 (Web Server issue): W522 - CW525, 2004.
  226. Joshi, Trupti; Chen, Yu; Becker, Jeffrey; Alexandrov, Nickolai; Xu, Dong. Function Prediction for Hypothetical Proteins in Yeast Saccharomyces cerevisiae Using Multiple Sources of High-Throughput Data. Proceeding of the 8th World Multi-Conference on Systemics, Cybernetics and Informatics (2004). Vol. IX, 17-20.
  227. Kunbin Qu, Yanmei Lu, Nan Lin, Rajinder Singh, Donald G. Payan, Dong Xu. Computational and Experimental Studies on Human Misshapen/NIK-Related Kinase MINK-1. Current Medicinal Chemistry. 11:569-582, 2004.
  228. Jane Razumovskaya, Victor Olman, Dong Xu, Ed Uberbacher, Nathan C. VerBerkmoes, Robert L. Hettich, and Ying Xu, A Computational Method for Assessing Peptide-Identification Reliability in Tandem Mass Spectrometry Analysis with SEQUEST, Proteomics. 4:961-969, 2004.
  229. Sonia M. Tiquia, Liyou Wu, Song C. Chong, Sergei Passovets, Dong Xu, Ying Xu, and Jizhong Zhou. Evaluation of 50-mer oligonucleotide arrays for detecting microbial populations in environmental samples. BioTechniques. 36:664-670, 2004.
  230. Xiufeng Wan, Dong Xu, and Jizhong Zhou. A new informatics method measuring synonymous codon usage bias. In Intelligent engineering systems through artificial neural networks, vol 13, eds. Dagli et al., 1101-1018. New York, NY: ASME Press.
  231. Victor Olman, Dong Xu, and Ying Xu. Solving data clustering problem as a string search problem. Proceedings of Conference on Statistical Data Mining and Knowledge Discovery (ed by Hamparsum Bozdogan), Chapman & Hall/CRC, 417-434, 2003.
  232. Zhi-Zhong Chen, Tao Jiang, Guohui Lin, Jianjun Wen, Dong Xu, Jinbo Xu, and Ying Xu. Approximation algorithms for NMR spectral peak assignment. Theoretical Computer Science, 1-3(299):211-229. 2003.
  233. Victor Olman, Dong Xu, and Ying Xu. Identifications of Regulatory Binding Sites Using Minimum Spanning Trees. In Proceedings of the 2003 Pacific Symposium on Biocomputing (PSB). Pages 327-338. 2003.
  234. Yu Chen, Trupti Joshi, Ying Xu, and Dong Xu. Towards Automated Derivation of Biological Pathways Using High-Throughput Biological Data. Proceeding of the 3rd IEEE Symposium on Bioinformatics and Bioengineering (2003). 18-25, IEEE/CS Press.
  235. Manesh Shah, Sergei Passovets, Dongsup Kim, Kyle Ellrott, Li Wang, Inna Vokler, Philip LoCascio, Dong Xu, and Ying Xu. A Computational Pipeline for Protein Structure Prediction and Analysis at Genome Scale. Proceeding of the 3rd IEEE Symposium on Bioinformatics and Bioengineering (2003). 3-10, IEEE/CS Press.
  236. Guohui Lin, Dong Xu, Zhi-zhong Chen, Tao Jiang, Jianjun Wen, and Ying Xu, Computational assignments of protein backbone NMR peaks by efficient bounding and filtering, Journal of Bioinformatics and Computational Biology. 31:944-52. 2003.
  237. Yu Chen and Dong Xu. Computational Analyses of High-Throughput Protein-Protein Interaction Data. Current Protein and Peptide Science. 4:159-181. 2003.
  238. Dong Xu, Dongsup Kim, Phuongan Dam, Manesh Shah, Edward C. Uberbacher, and Ying Xu. Characterization of Protein Structure and Function at Genome Scale Using a Computational Prediction Pipeline. In "Genetic Engineering, Principles and Methods", edited by Jane K. Setlow. Kluwer Academic / Plenum Publishers, New York. 269-293. 2003.
  239. Yongqing Liu, Jizhong Zhou, Marina V. Omelchenko, Alex S. Beliaev, Amudhan Venkateswaran, Julia Stair, Liyou Wu, Dorothea K. Thompson, Dong Xu, Igor B. Rogozin, Elena K. Gaidamakova, Min Zhai, Kira S. Makarova, Eugene V. Koonin, and Michael J. Daly. Transcriptome dynamics of Deinococcus radiodurans recovering from ionizing radiation. Proceedings of National Academy of Sciences. 100: 4191-4196. 2003.
  240. Christal Yost, Loren Hauser, Frank Larimer, Dorothea Thompson, Alexander Beliaev, Jizhong Zhou, Ying Xu, and Dong Xu. A computational study of Shewanella oneidensis MR-1: Structural prediction and functional inference of hypothetical proteins. OMICS. 7:177-192. 2003.
  241. Victor Olman, Dong Xu, and Ying Xu. CUBIC: Identifications of Regulatory Binding Sites through Data Clustering. Journal of Bioinformatics and Computational Biology. 1:21-40. 2003.
  242. Yu Chen, Yutao Liu, Keith M. Goldstein, Jeffrey M. Becker, Ying Xu, and Dong Xu. A Computational Study on the Signal Transduction Pathway for Amino Acid and Peptide Transport in Yeast: Bridging the Gap between High-Throughput Data and Traditional Biology. Applied Genomics and Proteomics. 2:43-50. 2003.
  243. Dong Xu, Victor Olman, Li Wang, and Ying Xu. EXCAVATOR: a computer program for gene expression data analysis. Nucleic Acid Research. 31: 5582-5589. 2003.
  244. Manesh Shah, Sergei Passovets, Dongsup Kim, Kyle Ellrott, Li Wang, Inna Vokler, Philip LoCascio, Dong Xu, and Ying Xu. A Computational Pipeline for Protein Structure Prediction and Analysis at Genome Scale. Bioinformatics. 19:1985-1996. 2003.
  245. Zhi-Zhong Chen, Tao Jiang, Guohui Lin, Romeo Rizzi, Jianjun Wen, Dong Xu, Ying Xu. More reliable protein NMR peak assignment via improved 2-interval scheduling. Proceedings of 11th European Symposium on Algorithms (ESA2003). 580-592, 2003.
  246. Xiang Wan, Dong Xu, Carolyn M. Slupsky, Guohui Lin. Automated Protein NMR Resonance Assignments. In Computational Systems Bioinformatics (CSB2003). IEEE Computer Society, Los Alamitos, California. Pages 197-207. 2003.
  247. Tema Fridman, Robert Day, Jane Razumovskaya, Dong Xu, Andrey Gorin. Probability Profiles - Novel Approach in Tendem Mass Spectrometry De Novo Sequencing. In Computational Systems Bioinformatics (CSB2003). IEEE Computer Society, Los Alamitos, California. Pages 415-418. 2003.
  248. Dongsup Kim, Dong Xu, Juntao Guo, Kyle Ellrott, Ying Xu, PROSPECT II: protein structure prediction program for genome-scale application. Protein Engineering, 16(9), 641-650, 2003.
  249. Ying Xu and Dong Xu. Protein Structure Prediction by Protein Threading and Partial Experimental Data. In: Current topics in computational biology, edited by Tao Jiang, Ying Xu, and Michael Q. Zhang. The MIT press. Cambridge, Massachusetts. Pages 467-502. 2002.
  250. Ying Xu, Dong Xu, and Victor Olman. A Practical Method for Interpretation of Threading Scores: An Application of Neural Network. Statistica Sinica (special issue in bioinformatics). 12:159-177. 2002.
  251. Dong Xu and Ying Xu. Computational Studies of Protein Structure and Function Using Threading Program PROSPECT. In Protein Structure Prediction: Bioinformatic Approach, edited by Igor Tsigelny. International University Line publishers (IUL), La Jolla, CA. Pages 5-41. 2002.
  252. Ying Xu, Victor Olman, and Dong Xu. Clustering Gene Expression Data Using a Graph-Theoretic Approach: An Application of Minimum Spanning Trees. Bioinformatics. 18:526-535, 2002.
  253. Ying Xu, Dong Xu, Dongsup Kim, Victor Olman, Jane Razumovskaya, and Tao Jiang Automated Assignment of Backbone NMR Peaks Using Constrained Bipartite Matching. Computing in Science and Engineering. Jan/Feb: 50-62. 2002.
  254. Dong Xu, Guangshan Li, Liyou Wu, Jizhong Zhou, and Ying Xu. PRIMEGENS: A Computer Program for Robust and Efficient Design of Gene-Specific Probes for Microarray Analysis. Bioinformatics. 18:1432-1437. 2002.
  255. Katrina M. Ramonell, Bing Zhang, Rob M. Ewing, Yu Chen, Dong Xu, Gary Stacey, and Shauna Somerville. Microarray analysis of chitin elicitation in Arabidopsis thaliana. Molecular Plant Pathology. 3:301-311. 2002.
  256. Guohui Lin, Dong Xu, Zhi-Zhong Chen, Tao Jiang, and Ying Xu. An Efficient Branch-and-Bound Algorithm for the Assignment of Protein Backbone NMR Peaks. In Proceedings of the IEEE Computer Society Bioinformatics Conference (CSB2002). IEEE Computer Society, Los Alamitos, California. Pages 165-174. 2002.
  257. Ayca Akal-Strader, Sanjay Khare, Dong Xu, Fred Naider, Jeff M. Becker. Residues in the first extracellular loop of a G protein-coupled receptor play a role in signal transduction. Journal of Biological Chemistry. 277:30581-30590. 2002.
  258. Zhi-Zhong Chen, Tao Jiang, Guohui Lin, Jianjun Wen, Dong Xu, Ying Xu. Improved Approximation algorithms for NMR spectral peak assignment In Proceedings of the 2002 Workshop on Algorithms in BioInformatics (WABI 2002). 82-96. 2002.
  259. Grant S. Heffelfinger, Anthony Martino, Andrey Gorin, Ying Xu, Mark D. Rintoul III, Al Geist, Hashimi M. Al-Hashimi, George S. Davidson, Jean Loup Faulon, Laurie J. Frink, David M. Haaland, William E. Hart, Erik Jakobsson, Todd Lane, Ming Li, Phil Locascio, Frank Olken, Victor Olman,Brian Palenik, Steven J. Plimpton, Diana C. Roe, Nagiza F. Samatova, Manesh Shah, Arie Shoshoni, Charlie E. M. Strauss, Edward V.Thomas, Jerilyn A. Timlin, and Dong Xu. Carbon Sequestration in Synechococcus Sp.: From Molecular Machines to Hierarchical Modeling. OMICS. 6: 305-329. 2002.
  260. Juntao Guo, Dongsup Kim, Dong Xu, and Ying Xu, Improving the Performance of DomainParser for Structural Domain Partition using Neural Network, Nucleic Acids Research. 31:1-9, 2002.
  261. Dong Xu, Kunnumal Baburaj, Cynthia B. Peterson, and Ying Xu. A Model for the Three-Dimensional Structure of Vitronectin: Predictions for the Multi-Domain Protein from Threading and Docking. Proteins: Structure, Function, and Genetics. 44:312-320. 2001.
  262. Dong Xu, Oakley H. Crawford, Philip F. LoCascio, and Ying Xu. Application of PROSPECT in CASP4: Characterizing Protein Structures with New Folds.Proteins: Structure, Function, and Genetics (CASP4 Special Issue). 46:140-148. 2001.
  263. Ying Xu, Victor Olman, and Dong Xu. Minimum Spanning Trees for Gene Expression Data Clustering. In Proceedings of the 12th International Conference on Genome Informatics (GIW), edited by S. Miyano, R. Shamir and T. Takagi. Universal Academy Press, Tokyo. Pages 24-33. 2001.
  264. Dong Xu, Michael A. Unseren, Ying Xu, and Edward C. Uberbacher. Sequence-structure specificity of a knowledge based energy function at the secondary structure level. Bioinformatics. 16:257-68, 2000.
  265. Ying Xu, Dong Xu, Oakley H. Crawford, J. Ralph Einstein, and Engin Serpersu. Protein structure determination using protein threading and sparse NMR data. In: The Fourth Annual International Conference on Computational Molecular Biology, edited by R. Shamir, S. Miyano, S. Istrail, P. Pevzner, and M. Waterman. Pages 299-307, ACM, Tokyo, Japan. 2000.
  266. Dong Xu and Ying Xu. Protein Databases on the Internet. In: Current Protocols in Protein Science, edited by J. E. Coligan, B. M. Dunn, H. L. Ploegh, D. W. Speicher, and P. T. Wingfield. John Wiley & Sons, New York. Volume 1, pages 2.6.1-2.6.15. 2000.
  267. Dong Xu and Ying Xu. Protein tertiary structure prediction. In: Current Protocols in Protein Science, edited by J. E. Coligan, B. M. Dunn, H. L. Ploegh, D. W. Speicher, and P. T. Wingfield. John Wiley & Sons, New York. Volume 1, pages 2.7.1-2.7.17. 2000.
  268. Dong Xu, Ying Xu, and Edward C. Uberbacher. Computational tools for protein modeling. Current Protein and Peptide Science. 1:1-21. 2000.
  269. Dong Xu, Ying Xu, Gary Li, and Jizhong Zhou. A Computer Program for Generating Gene-Specific Fragments for Microarrays. In Currents in Computational Molecular Biology, edited by S. Miyano, R. Shamir and T. Takagi. Universal Academy Press, Inc. Tokyo, Japan. Pages 3-4. 2000.
  270. Ying Xu and Dong Xu. Protein threading using PROSPECT: Design and evaluation.Proteins: Structure, Function, and Genetics. 40:343-354. 2000.
  271. Ying Xu, Dong Xu. Oakley H. Crawford, and J. Ralph Einstein. "A computational method for NMR-constrained protein threading." Journal of Computational Biology. 7:449-467. 2000.
  272. Ying Xu, Dong Xu, and Harold N. Gabow. Protein Domain Decomposition using a Graph-Theoretic Approach. Bioinformatics. 16:1091-1104. 2000.
  273. Zhirong Sun, Xiaofeng Xia, Qing Guo, and Dong Xu. Protein structure prediction in a 210-type lattice model: parameter optimization in the genetic algorithm using orthogonal array. Journal of Protein Chemistry. 18:39-46, 1999.
  274. Ying Xu, Dong Xu, Oakley H. Crawford, J. Ralph Einstein, Frank Larimer, Edward C. Uberbacher, Michael A. Unseren, and Ge Zhang. Protein threading by PROSPECT: a prediction experiment in CASP3. Protein Engineering. 12:899-907, 1999.
  275. Dong Xu, Chung-Jung Tsai, and Ruth Nussinov. Mechanism and Evolution of Protein Dimerization Protein Science. 7:533-544, 1998 (with a picture selected on the cover of the issue).
  276. Raquel Norel, Shuo L. Lin, Dong Xu, Haim J. Wolfson, and Ruth Nussinov. Molecular surface variability and induced conformational changes upon protein-protein associations. In: Structure, Motion, Interaction and Expression of Biological Macromolecules (Sarma, R. H. and Sarma, M. H. Eds.), Vol. 2, pp. 33-52, 1998, (also in The Proceedings of the 10th Conversation) Adenine Press, Albany, NY.
  277. Shuo L. Lin, Dong Xu, Aijun Li, Maria Roiterst, Haim J. Wolfson, and Ruth Nussinov. Electrostatics, allostericity and activity of the yeast chorismate mutate. Proteins: Structure, Function, and Genetics. 31:445-452, 1998.
  278. Chung-Jung Tsai, Dong Xu, and Ruth Nussinov. Protein folding via binding, and vice versa (Review). Folding & Design, 3:R71-R80, 1998.
  279. Ying Xu, Dong Xu, and Edward C. Uberbacher. A new method for modeling and solving the protein fold recognition problem. In: The Second Annual International Conference on Computational Molecular Biology, (Istrail, S, Pevzner, P, Waterman, M, eds) pp. 285-292. ACM New York, 1998.
  280. Ying Xu, Dong Xu, and Edward C. Uberbacher. An efficient computational method for globally optimal threading. Journal of Computational Biology. 5:597-614, 1998.
  281. Dong Xu, Shuo L. Lin, and Ruth Nussinov. Protein Binding versus Protein Folding: The Role of Hydrophilic Bridges in Protein Associations. Journal of Molecular Biology, 265:68-84, 1997.
  282. Zhirong Sun, Xiaoqian Rao, Liwei Peng, and Dong Xu. Prediction of protein supersecondary structures based on the artificial neural network method. Protein Engineering, 10:763-769, 1997.
  283. Shuo L. Lin, Dong Xu, Aijun Li, Maria Rosen, Haim J. Wolfson, and Ruth Nussinov. Investigation of the enzymatic mechanism of the yeast chorismate mutase by docking a transition state analog. Journal of Molecular Biology, 271:838-845 1997.
  284. Chung-Jung Tsai, Dong Xu, and Ruth Nussinov. Structural motifs at protein-protein interfaces: Protein cores versus two-state and three-state model complexes. Protein Science, 6:1793-1805, 1997.
  285. Dong Xu, Chung-Jung Tsai, and Ruth Nussinov. Hydrogen bonds and salt bridges across protein-protein interfaces. Protein Engineering, 10:999-1012, 1997.
  286. Dong Xu and Ruth Nussinov. Favorable Domain Size in Proteins. Folding & Design, 3:11-17, 1997.
  287. Xiche Hu, Dong Xu, Kenneth Hamer, Klaus Schulten, Jurgen Kopke, and Hartmut Michel. Knowledge based structure prediction of the light-harvesting complex II of rhodospirillum molischianum. In P.M. Pardalos, D. Shalloway, and G. Xue, editors, Global Minimization of Nonconvex Energy Functions: Molecular Conformation and Protein Folding. American Mathematical Society. 97-122, 1996.
  288. Dong Xu, Charles Martin, and Klaus Schulten. Molecular dynamics study of early picosecond events in the bacteriorhodopsin photocycle: Dielectric response, vibrational cooling and the J, K intermediates. Biophysical Journal, 70:453-460, 1996.
  289. Xiche Hu, Dong Xu, Kenneth Hamer, Klaus Schulten, Jurgen Kopke, and Hartmut Michel. Prediction of the structure of an integral membrane protein-the light-harvesting complex II of rhodospirillum molischianum. In K.M. Merz and B. Roux, editors, Biological Membranes: A Molecular Perspective from Computation and Experiment, pages 503-533. Birkhauser, Cambridge, MA. 1996.
  290. Dong Xu, James Christopher Phillips, and Klaus Schulten. Protein response to external electric fields: Relaxation, hysteresis, echo. Journal of Physical Chemistry, 100:12108-12121, 1996.
  291. Dong Xu, Klaus Schulten, Oren M. Becker, and Martin Karplus. Temperature quench echoes in proteins. Journal of Chemical Physics, 103:3112-3123, 1995.
  292. Dong Xu and Klaus Schulten. Velocity reassignment echoes in proteins. Journal of Chemical Physics, 103:3124-3139, 1995.
  293. Dong Xu, Mordechai Sheves, and Klaus Schulten. Molecular dynamics study of the M412 intermediate of bacteriorhodopsin. Biophysical Journal, 69:2745-2760, 1995.
  294. Xiche Hu, Dong Xu, Kenneth Hamer, Klaus Schulten, Jurgen Kopke, and Hartmut Michel. Predicting the structure of the light-harvesting complex II of rhodospirillum molischianum. Protein Science, 4:1670-1682, 1995.
  295. William Humphrey, Dong Xu, Klaus Schulten, and Mordechai Sheves. Molecular dynamics study of the early intermediates in the bacteriorhodopsin photocycle. Journal of Physical Chemistry, 99:14549-14560, 1995.
  296. Klaus Schulten, William Humphrey, Ilya Logunov, Mordechai Sheves, and Dong Xu. Molecular dynamics and quantum chemistry studies of bacteriorhodopsin. Israel Journal of Chemistry, 99:14549-14560, 1995.
  297. Dong Xu and Klaus Schulten. Coupling of protein motion to electron transfer in a photosynthetic reaction center: Investigating the low temperature behaviour in the framework of the spin-boson model. Chemical Physics, 182:91-117, 1994.
  298. Wensheng Zhou and Dong Xu. Microwave magnetic resonance in reentrant spin glass spinel CoxZn1-xFe 2yCr1-2y O4 , Acta Physica Sinica, 41(12):2043-2048, 1992.
  299. Dong Xu and Klaus Schulten. Multi-mode coupling of protein motion to electron transfer in the photosynthetic reaction center: Spin-boson theory based on a classical molecular dynamics simulation. In The Photosynthetic Bacterial Reaction Center: II. Structure, Spectroscopy and Dynamics, NATO ASI Series A: Life Sciences (J. Breton and A. Vermeglio, editors), pages 301-312. Plenum Press, New York, 1992.