Publications

2008-present (*corresponding author)

  • Ranjan, V. Leighton, G. Yan, C. Arango M. Lustig, J.  Corona, RI. Guo, J-T. Nesmelov, Y. Ivics, Z. Nesmelova, IV. “DNA binding and transposition activity of the Sleeping Beauty transposase: role of structural stability of the primary DNA-binding domain”, Nucleic Acids Research, in press
  • Wu, S. Xu, J. and Guo, J-T*. “Prediction of single-stranded DNA binding proteins with protein language model”, 2024 IEEE International Conference on Bioinformatics and Biomedicine (BIBM2024), 257-262, 2024 (21% acceptance rate)  
  • 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
  • Guo, J-T. * and Malik, F. “Single-stranded DNA binding proteins and their identification using machine learning-based approaches”, Biomolecules, 12(9), 1187, 2022
  • 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):1303-1314, 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)
  • 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
  • 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.
  • Bonkovsky, H. L., Guo, J.-T., Hou, W., Li, T., Narang, T. and Thapar, M. “Porphyrin and heme metabolism and the porphyrias”. Comprehensive Physiology. 365–401, 2013.
  • Turner, D. Kim, R. Guo, J-T.* “TFinDit: transcription factor-DNA interaction data depository”, BMC Bioinformatics,13:220, 2012. Highly accessed
  • 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. Highly accessed
  • Kim, R. and Guo, J-T.* “Systematic analysis of short internal indels and their impact on protein folding”, BMC Structural Biology, 10:24, 2010. (Extended journal version)
  • 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(Suppl 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
  • 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.

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2003-2007

  • 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.
  • 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.
  • 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.
  • 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, 33(2):546-558, 2005.
  • 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, 43(26):8568-8578, 2004.
  • 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., 32:W522-5, 2004.
  • 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, 335:833-842, 2004.
  • 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)
  • 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.

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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. 22(14):5900-5909, 2002.
  • 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, 31(1):73-81, 2001.
  • 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, 80(12):1797-806, 2000
  • 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, 12(9):1337-1347, 2000.
  • Yu, J. Guo,J-T. Zhu, H. Kindy, M.S. “Amyloid formation in the rat: adenoviral expression of mouse serum amyloid A proteins”. Amyloid, 7(1):32-40, 2000.
  • Kindy, M.S. Yu, J. Guo, J-T. Zhu, H. “Apolipoprotein serum amyloid A in Alzheimer’s disease”. J. Alzheimer’s Disease, 1:155-167, 1999.

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