Publication Page - Digital Biology Laboratory

134. 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. In press.

133. Dong Xu, James Keller, Mihail Popescu, and Rajkumar Bondugula. "Application of Fuzzy Logic in Bioinformatics", Imperial College Press, London, UK. In press.

132. 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 "Advance in Computational Intelligence". Ed: Xin Yao. University of Science and Technology of China Press, 2008.

131. L Pena-Castillo, M Tasan, CL Myers, H Lee, T Joshi, C Zhang, Y Guan, M Leone, A Pagnani, WK Kim, C Krumpelman, W Tian, G Obozinski, Y Qi, S Mostafavi, Guan N. Lin, G Berriz, F Gibbons, G Lanckriet, J Qiu, C Grant, Z Barutcuoglu, DP Hill, D Warde-Farely, C Grouios, D Ray, JA Blake, M Deng, M Jordan, WS Noble, Q Morris, J Klein-Seetharaman, Z Bar-Joseph, T Chen, F Sun, OG Troyanskaya, EM Marcotte, D Xu, TR Hughes and FP Roth. "A critical assessment of M. musculus gene function prediction using integrated genomic evidence." Genome Biology. In press.

130. 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. In press.

129. 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. In press.

2008-

128. 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.

127. 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.

2007-

126. 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.

125. 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.

124. 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.

123. 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, 2007.

122. Trupti Joshi and Dong Xu. Quantitative assessment of relationship between sequence similarity and function similarity. BMC Genomics, Vol. 8(1):222, 2007.

121. 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.

120. 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.

119.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.

118. 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.

117. 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.

116. 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, 2007.

115. 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, 2007.

114. 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, 2007.

113. 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, 2007.

112. 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, 2007.

2006-

111. Ying Xu, Dong Xu, and Jie Liang eds. "Computational Methods for Protein Structure Prediction and Modeling", I, II, Springer-Verlag. 2006.

110. 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.

109. 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.

108. 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.

107. 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.

106.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.

105. 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).

104. Yong Wang, Trupti Joshi, Xiang-Sun Zhang, Dong Xu, Luonan Chen. Inferring Gene Regulatory Networks from Multiple Microarray Datasets. Bioinformatics. 22:2413-2420, 2006.

103. Pin-Hao Chi, Heather Nelson, Jeff Reneker, Christopher Topinka, Dong Xu, Chi-Ren Shyu. ProteinDBS v2.0: Real-Time Protein Tertiary Structure Retrievals and SCOP Fold Classifications. BMC Bioinformatics. 7:362, 2006.

102. 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.

101. 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.

100. Seung Yon Rhee, Julie Dickerson, and Dong Xu. Bioinformatics and Its Applications in Plant Biology. Annual Review of Plant Biology. 57:335-360. 2006

99. 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. International Journal of Bioinformatics Research and Applications. 2:219-248, 2006.

98. 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

97. 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.

2005-

96. 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.

92. Jianjun Wen, Zhi-Zhong Chen, Romeo Rizzi, Dong Xu, Guohui Lin, Ying Xu, Tao Jiang. An improved approximation algorithm for 2-interval scheduling and NMR spectral peak assignment. Journal of Computational Biology. 12 (2):129-146, 2005.

91. 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.

90. 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.

89. 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.

88. Yu Chen and Dong Xu. Genome-Scale Understanding Protein Dispensability through Machine-Learning Analysis of High-Throughput Data. Bioinformatics. 21:575-581, 2005.

85. 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.

84. 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.

83. 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

82. 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.

81. 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

77. 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.

76. 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.

75. 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.

72. 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.

71. 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.

2003-
70. 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.

69. 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.

68. 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.

67. 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.

66. 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.

65. 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.

64. 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.

63. Yu Chen and Dong Xu. Computational Analyses of High-Throughput Protein-Protein Interaction Data. Current Protein and Peptide Science. 4:159-181. 2003.

62. 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.

61. 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.

60. 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.

59. 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.

58. 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.

57. 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.

56. 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.

55. 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.

54. 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.

53. 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.

52. 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.

2002- Top
51. 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.

50. 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.

49. 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.

48. 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.

47. 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.

46. 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.

45. 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.

44. 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.

43. 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.

42. 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.

41. 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.

40. 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.

2001-
39. 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.

38. 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.

37. 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.

2000- Top
36. 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.

35. 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.

34. 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.

33. 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.

32. Dong Xu, Ying Xu, and Edward C. Uberbacher. Computational tools for protein modeling. Current Protein and Peptide Science. 1:1-21. 2000.

31. 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.

30. Ying Xu and Dong Xu. Protein threading using PROSPECT: Design and evaluation.Proteins: Structure, Function, and Genetics. 40:343-354. 2000.

29. 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.

28. Ying Xu, Dong Xu, and Harold N. Gabow. Protein Domain Decomposition using a Graph-Theoretic Approach. Bioinformatics. 16:1091-1104. 2000.

1999-
27. 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.

26. 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.

1998- Top
25. 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).

24. 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.

23. 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.

22. Chung-Jung Tsai, Dong Xu, and Ruth Nussinov. Protein folding via binding, and vice versa (Review). Folding & Design, 3:R71-R80, 1998.

21. 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.

20. Ying Xu, Dong Xu, and Edward C. Uberbacher. An efficient computational method for globally optimal threading. Journal of Computational Biology. 5:597-614, 1998.

1997-
19. 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.

18. 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.

17. 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.

16. 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.

15. . Dong Xu, Chung-Jung Tsai, and Ruth Nussinov. Hydrogen bonds and salt bridges across protein-protein interfaces. Protein Engineering, 10:999-1012, 1997.

14. Dong Xu and Ruth Nussinov. Favorable Domain Size in Proteins. Folding & Design, 3:11-17, 1997.

1996-
13. 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.

12. 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.

11. 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.

10. 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.

1995- Top
9. Dong Xu, Klaus Schulten, Oren M. Becker, and Martin Karplus. Temperature quench echoes in proteins. Journal of Chemical Physics, 103:3112-3123, 1995.

8. Dong Xu and Klaus Schulten. Velocity reassignment echoes in proteins. Journal of Chemical Physics, 103:3124-3139, 1995.

7. Dong Xu, Mordechai Sheves, and Klaus Schulten. Molecular dynamics study of the M412 intermediate of bacteriorhodopsin. Biophysical Journal, 69:2745-2760, 1995.

6. 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.

5. 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.

4. 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.

1994-
3. 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.

1992- Top
2. 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.

1. 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.