Jun-tao Guo, Ph.D.

Biography:

Jun-tao Guo is professor and chair of 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 Master’s degree in Computer Science from 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 protein structure prediction, protein-nucleic acids interactions. He is also interested in studying the effect of small indels (insertions/deletions) on protein structure and function.

Selected Publications (* corresponding author):

• Wu, S. and Guo, J-T*. “Improved prediction of DNA and RNA binding proteins with deep learning models”, Briefings In Bioinformatics, 25(4):bbae285, 2024
• Malik, F. and Guo, J-T*. “ComparePD: improving protein-DNA complex model comparison with hydrogen bond energy-based metrics”, Proteins: Structure, Function, and Bioinformatics, 91(8):1077-1088, 2023
• Chen, J. Ni, P. Wu, S. Niu, M. Guo, J-T*. Su, Z*. “Prevalent use and evolution of exonic regulatory sequences in the human genome”, Natural Sciences, 3(2):e20220058, 2023
• Malik, F. and Guo, J-T*. “Insights into protein-DNA interactions from hydrogen bond energy-based comparative protein-ligand analyses”, Proteins: Structure, Function, and Bioinformatics, 90(6):1303-1341, 2022 .
• Chen, J. and Guo, J-T.* “Structural and functional analysis of somatic coding and UTR indels in breast and lung cancer genomes”, Scientific Reports, 11:21178, 2021
• Lin, M. Malik, F. and Guo, J-T.* “A comparative study of protein-ssDNA interactions”, NAR Genomics and Bioinformatics, 3(1):lqab006, 2021
• Chen, J. and Guo, J-T.* “Comparative assessments of indel annotations in healthy and cancer genomes with next-generation sequencing data”, BMC Medical Genomics, 13:170, 2020
• Lin, M. Guo, J-T.* “New insights into protein-DNA binding specificity from hydrogen bond based comparative study”, Nucleic Acids Research, 47(21):11103-11113, 2019
• Corona, RI. Sudarshan, S. Aluru, S. Guo, J-T*. “An SVM-based method for assessment of transcription factor-DNA complex models”, BMC Bioinformatics, 2018, 19(suppl 20):506 (invited journal version)
• 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
• 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, JT.* “Structure-based prediction of transcription factor binding specificity using an integrative energy function”, Bioinformatics, 32: i306-313, 2016.
• 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
• 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
• 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. Jaromczyk, JW. Xu, Y. “Analysis of Chameleon Sequences and Their Implications in Biological Processes”,Proteins: Structure, Function, and Bioinformatics, 67(3):548-58, 2007
• Wang, P. Yan, B. Guo, J-T. Hicks, C. Xu, Y. “Structural genomics analysis of alternative splicing and its application in modeling structures of alternatively spliced variants”, Proc Natl Acad Sci USA, 102(52):18920-18925, 2005
• 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

Education:

• Ph.D. Molecular and Cellular Biochemistry, University of Kentucky
• M.S. Computer Science, University of Kentucky
• B.S./M.S. Biochemistry, Nankai University