Publications

2009

  • Kim R. McCafferty, J. and Guo, J-T. "A systematic study of homologous protein structures with insertions/deletions", Comput Syst Bioinformatics Conf., 103-113, 2009
  • Kim R. and Guo, J-T. "PDA: an automatic and comprehensive analysis program for protein-DNA complex structures", BMC Genomics, 10(Supple 1):S13, 2009

2008

  • Liu, Z.* Guo, J-T.* Li, T. Xu, Y. "Structure-based recognition of binding sites of transcription factors using an efficient protein-DNA docking approach", Proteins: Structure, Function, and Bioinformatics, 72(4), 1114-1124, 2008. *equal contribution
  • Ellrott, K. Guo, J-T. Olman, V. Xu, Y. "Improving the performance of protein threading using Insertion/Deletion Frequency Arrays", Journal of Bioinformatics and Computational Biology (By invitation), 6(3):585-602, 2008
  • Guo, J-T.* Xu, Y. "Toward Modeling of Amyloid Fibril Structures", Frontiers in Bioscience, 13:4039-4050, 2008, *corresponding author
  • Guo, J-T. Ellrott, K. Xu, Y. "A historical perspective of template-based protein structure prediction", Methods Mol Biol., 413:3-42, 2008

2007

  • Ellrott, K. Guo, J-T. Olman, V. Xu, Y. "Improvment in Protein Sequence Structure Alignment using Insertion/Deletion Frequency Array", Comput Syst Bioinformatics Conf., 6:335-342, 2007 (referred conference paper)
  • Guo, J-T. Jaromczyk, JW. Xu, Y. "Analysis of Chameleon Sequences and Their Implications in Biological Processes", Proteins: Structure, Function, and Bioinformatics, 67(3):548-58, 2007
  • Li, G. Liu, Z. Guo,J-T. Xu, Y. "An Algorithm for Simultaneous Backbone Threading and Side-Chain Packing", Algorithmica, 48(4):329-342, 2007.

2006

  • Ellrott, K. Guo, J-T. Olman, V. and Xu, Y. "A Generalized Threading Model using Integer Programming with Secondary Structure Element Deletion", Genome Informatics, 17(2):248-258, 2006 (referred conference paper)
  • Guo,J-T. Hall, C. Xu, Y. and Wetzel, R. "Modeling Protein Aggregate Assembly and Structure", Computational Methods for Protein Structure Prediction and Modeling, 279-317, 2006
  • Guo, J-T. and Xu, Y. "Computational approaches to amyloid beta fibril core structures", Methods in Enzymology, 412:300-314, 2006.

2005

  • Wang, P. Yan, B. Guo, J-T. Hicks, C. Xu, Y. "Structural genomics analysis of alternative splicing and its application in modeling structures ofalternatively spliced variants", Proc Natl Acad Sci USA, 102(52):18920-18925, 2005.
  • Sharp, JS. Guo, J-T. Uchiki, T. Xu, Y. Dealwis, C. Hettich, R. "Application of Photochemical Surface Mapping of C14S Sml1p to Constrained Computational Modeling", Analytical Biochemistry, 340(2):201-212, 2005.
  • Liu, Z. Mao, F. Guo, J-T. Yan, B. Wang, P. Qu, Y. Xu, Y. "Quantitative Validation of Protein-DNA Interaction using an Optimized Knowlege-based Potential", Nucleic Acids Research, 2005, 33(2):546-558.

2004

  • Gupta, V. Peterson, C.B. Dice, L. Uchiki, T. Guo, J-T. Xu, Y. Hettich, R. Dealwis, C. "Sml1p Protein is a Dimer in Solution: Characterization of Denaturation and Renaturationof Recombinant Sml1p", Biochemistry, 2004, 43(26):8568-8578.
  • Guo, J-T. Ellrott, K. Chung, WJ. Xu, D. Passovets, S. Xu, Y. "PROSPECT-PSPP: An Automatic Computational Pipeline for Protein Structure Prediction", Nucleic Acids Res., 2004, 32:W522-5.
  • Guo, J-T. Wetzel, R. Xu, Y. "Molecular Modeling of the Core of Abeta Amyloid Fibrils", Proteins: Structure, Function, and Bioinformatics, 57(2):357-364, 2004.
  • Williams, A. Portelius, E. Kheterpal, I. Guo, J-T. Cook, K. Xu, Y. and Wetzel, R. "Mapping Abeta Amyloid Fibril Secondary Structure Using Scanning proline Mutagenesis", J Mol Biol, 2004, 335, 833-842.
  • Qu, Y. Guo, J-T. Olman, V. and Xu, Y. "Protein Structure Prediction Using Sparse Dipolar Coupling Data", Nucleic Acids Res., 32(2):551-561, 2004.
  • Qu, Y. Guo,J-T. Olman, V. and Xu, Y. "Protein Fold Recognition Through Application of Residual Dipolar Coupling Data", Proceedings of the 9th Pacific Symposium on Biocomputing (PSB), 9:459-470, 2004. (referred conference paper)

2003

  • Kim, D. Xu, D. Guo, J-T. Ellrott, K. Xu, Y. "PROSPECT II: Protein Structure Prediction Program for the Genome-scale Application". Protein Eng. 16(9), 641-650, 2003
  • Guo, J-T. Xu, D. Kim, D. Xu, Y. "Improving the Performance of DomainParser for Structural Domain Partition Using Neural Network". Nucleic Acids Res. 31(3), 944-952, 2003.

Earlier Publications

  • Guo, J-T. Yu, J. Grass, D. de beer, F.C. Kindy, M.S. "Inflammation Dependent Cerebral Deposition of Serum Amyloid A Protein in a Mouse Model of Amyloidosis". J. Neurosci. 2002, July 15, 22(14) 5900-5909
  • Xie, C. Lovell, M. Xiong, S. Kindy, M.S. Guo, J-T. Xie, J. Amaranth, V. Montine, T.J. Marksbery, W. "Expression of Glutathione-S-transferase isozyme in the SY5Y Neuroblastoma Cell Line Increases Resistance to Oxidative Stress". Free Radical Biology and Medicine, 2001, Jul, 31(1):73-81
  • Yu, J. Zhu, H. Guo, J-T. de Beer, FC. Kindy, M.S. "Expression of mouse apolipoprotein SAA1.1 in CE/J mice: isoform-specific effects on amyloidogenesis". Lab Invest, 2000 Dec; 80(12):1797-806.
  • De villiers, W.J.S Varilek, G.W. de beer, M.C. Guo, J-T. Kindy, M.S. "Increased Serum Amyloid A Levels Reflect Colitis severity and Precede Amyloid Formation in IL-2 Deficient Mice". Cytokine, 2000,12(9):1337-1347
  • Yu, J. Guo,J-T. Zhu, H. Kindy, M.S. "Amyloid Formation in the Rat:Adenoviral Expression of Mouse Serum Amyloid A Proteins". Amyloid, 2000 Mar 7(1):32-40
  • Kindy, M.S. Yu, J. Guo, J-T. Zhu, H. "Apolipoprotein Serum Amyloid A in Alzheimer's Disease". J. Alzheimer's Disease, 1999, 1:155-167