Jun-tao Guo

Presonal Webpage: http://guolab.charlottewp.psapp.dev/directory/jun-tao-guo-phd Degree Institution: University of Kentucky
Degree: Ph.D. Molecular and Cellular Biochemistry
Year Graduated: 2001 Jun-tao Guo is a professor in the Department of Bioinformatics and Genomics, College of Computing and Informatics, University of North Carolina at Charlotte. Before joining UNC Charlotte in August 2007, he was an assistant research scientist in the Department of Biochemistry and Molecular Biology and an associate member of the Institute of Bioinformatics at the University of Georgia. He received his Ph.D. degree in Molecular and Cellular Biochemistry and a Master’s degree in Computer Science from the University of Kentucky in 2001 and 2002 respectively. He started his bioinformatics career at Oak Ridge National Laboratory (ORNL) as a postdoctoral research associate. His research interests are in the broad area of structural bioinformatics. Specifically, he is interested in proteins structure prediction, protein-DNA interactions and their applications in deciphering biological regulatory networks through an integrated methodology of computational prediction and wet-lab experiment. He is also interested in the evolution of regulatory pathways.

Publications:

• Corona, RI. Sudarshan, S. Aluru, S. Guo, J-T*. “Confidence assessment of protein-DNA complex models”, 2017 IEEE International Conference on Bioinformatics and Biomedicine (BIBM 2017), (19% acceptance rate), 9-15, 2017
• Lin, M. Whitmire, S. Chen, J. Farrel, A. Shi, X. Guo, J-T*. “Effects of short indels on protein structure and function in human genomes”, Scientific Reports, 7:9313, 2017
• Farrel, A. Guo, J-T.*. “An efficient algorithm for improving structure-based prediction of transcription factor binding sites”, BMC Bioinformatics, 18:342, 2017
• Schneider, A. Malone, RW. Guo, J-T. Homan, J. Linchangco, G. Witter, ZL. Vinesett, D. Damodaran L. and Janies, DA. “Molecular evolution of Zika virus as it crossed the Pacific to the Americas”, Cladistics, 33(1), 1-20, 2017
• Corona, RI. Guo, J-T.* “Statistical analysis of structural determinants for protein-DNA binding specificity”, Proteins: Structure, Function, and Bioinformatics, 84(8):1147-1161, 2016.
• Farrel, A. Murphy, J.- Guo, J-T.* “Structure-based prediction of transcription factor binding specificity using an integrative energy function”, Bioinformatics, 32: i306-313, 2016.
• Wang, Y. Cheung, AC. Guo, J-T. Feng, B. “Genome-wide massive sequencing in embryonic stem cell biology: recent insights and challenges”, J Stem Cell Res Ther, 5(296), 2, 2015.
• Song, W. and Guo, J-T.* “Investigation of Arc repressor DNA binding specificity by comparative molecular dynamics simulations”, Journal of Biomolecular Structure & Dynamics, 33(10):2083-2093, 2015.
• Guo, J-T.* Lofgren, S. Farrel, A. “Structure-based prediction of transcription factor binding sites”, Tsinghua Science and Technology, 19(6): 568-577, 2014.
• Hu, J. Lei, Y. Wong, W. Liu, S. Kee, K-C. He, X. You, W. Zhou, R. Guo, J-T. Chen, X. Peng, X. Sun, H. Huang, H. Zhao, H. Feng, B. “Direct activation of human and mouse Oct4 genes using engineered TALE and Cas9 transcription factors”, Nucleic Acids Research, 42(7):4375-90, 2014.
• Verma, D. Guo, J-T. Jacobs, D. and Livesay, DR. “Towards comprehensive analysis of protein family quantitative stability/flexibility relationships using homology models”, Methods in Molecular Biology, 1084:239-254, 2014.
• Takeda, T. Corona, RI. Guo, J-T. “A knowledge-based orientation potential for transcription factor-DNA docking”, Bioinformatics, 29(3):322-30, 2013
• Liao, H. Guo, J-T. Lange, MD. Fan, R. Zemlin, M. Su, K. Guan, Y. and Zhang, Z. “Contribution of VH replacement products to the generation of anti-HIV antibodies”,Clinical Immunology, 146:46-55, 2013
• Turner, D. Kim, R. Guo, J-T. “TFinDit: transcription factor-DNA interaction data depository”, BMC Bioinformatics,13:220, 2012
• Wu, J. Hong, B. Takeda, T. Guo, J-T. “High performance transcription factor-DNA docking with GPU computing”, Proteome Science, 10 (Suppl 1):S17, 2012 (Extended journal version)
• Kim, R., Corona, R., Hong, B., and Guo, J-T. “Benchmarks for flexible and rigid transcription factor-DNA docking”, BMC Structural Biology, 11:45, 2011
• Hong, B., Wu, J., and Guo, J-T. “Improving prediction accuracy of protein-DNA docking with GPU computing”, 2011 IEEE International Conference on Bioinformatics and Biomedicine (BIBM 2011), (19.4% acceptance rate), 482-487, 2011, Best Paper Award
• Li, T., Bonkovsky, HL., and Guo, J-T. ” Structural analysis of heme proteins: implications for design and prediction”, BMC Structural Biology, 11:13, 2011
• Kim, R. and Guo, J-T. “Systematic analysis of short internal indels and their impact on protein folding”, BMC Structural Biology, 10:24, 2010
• 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
• 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
• Guo, J-T. Xu, Y. “Toward Modeling of Amyloid Fibril Structures” Frontiers in Bioscience, 13:4039-4050, 2008
• Guo, J-T. Ellrott, K. Xu, Y. “A historical perspective of template-based protein structure prediction”, Methods Mol Biol., 413:3-42, 2008
• 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
• 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.
• 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.
• 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.
• 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