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2022 Book Chapter Using the evolutionary history of proteins to engineer insertion-deletion mutants from robust, ancestral templates using Graphical Representation of Ancestral Sequence Predictions (GRASP)Ross, Connie M., Foley, Gabriel, Boden, Mikael and Gillam, Elizabeth M. J. (2022). Using the evolutionary history of proteins to engineer insertion-deletion mutants from robust, ancestral templates using Graphical Representation of Ancestral Sequence Predictions (GRASP). Enzyme engineering. (pp. 85-110) edited by Francesca Magnani, Chiara Marabelli and Francesca Paradisi. New York, NY, United States: Humana Press. doi: 10.1007/978-1-0716-1826-4_6 |
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2024 Journal Article Optimal phylogenetic reconstruction of insertion and deletion eventsTule, Sanjana, Foley, Gabriel, Zhao, Chongting, Forbes, Michael and Bodén, Mikael (2024). Optimal phylogenetic reconstruction of insertion and deletion events. Bioinformatics, 40 (s1), i277-i286. doi: 10.1093/bioinformatics/btae254 |
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2024 Journal Article Engineering Biocatalysts for the C−H Activation of Fatty Acids by Ancestral Sequence Reconstruction**Jones, Bethan S., Ross, Connie M., Foley, Gabriel, Pozhydaieva, Nadiia, Sharratt, Joseph W., Kress, Nico, Seibt, Lisa S., Thomson, Raine E. S., Gumulya, Yosephine, Hayes, Martin A., Gillam, Elizabeth M. J. and Flitsch, Sabine L. (2024). Engineering Biocatalysts for the C−H Activation of Fatty Acids by Ancestral Sequence Reconstruction**. Angewandte Chemie, 136 (18). doi: 10.1002/ange.202314869 |
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2024 Journal Article Engineering Biocatalysts for the C‐H Activation of Fatty Acids by Ancestral Sequence ReconstructionJones, Bethan S., Ross, Connie M., Foley, Gabriel, Pozhydaieva, Nadiia, Sharratt, Joseph W., Kress, Nico, Seibt, Lisa S., Thomson, Raine E. S., Gumulya, Yosephine, Hayes, Martin A., Gillam, Elizabeth M. J. and Flitsch, Sabine (2024). Engineering Biocatalysts for the C‐H Activation of Fatty Acids by Ancestral Sequence Reconstruction. Angewandte Chemie International Edition, 63 (18) e202314869, 1-10. doi: 10.1002/anie.202314869 |
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2022 Journal Article Engineering indel and substitution variants of diverse and ancient enzymes using Graphical Representation of Ancestral Sequence Predictions (GRASP)Foley, Gabriel, Mora, Ariane, Ross, Connie M., Bottoms, Scott, Sützl, Leander, Lamprecht, Marnie L., Zaugg, Julian, Essebier, Alexandra, Balderson, Brad, Newell, Rhys, Thomson, Raine E. S., Kobe, Bostjan, Barnard, Ross T., Guddat, Luke, Schenk, Gerhard, Carsten, Jörg, Gumulya, Yosephine, Rost, Burkhard, Haltrich, Dietmar, Sieber, Volker, Gillam, Elizabeth M. J. and Bodén, Mikael (2022). Engineering indel and substitution variants of diverse and ancient enzymes using Graphical Representation of Ancestral Sequence Predictions (GRASP). PL o S Computational Biology, 18 (10) e1010633, e1010633. doi: 10.1371/journal.pcbi.1010633 |
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2022 Journal Article Ancestral sequence reconstruction of a cytochrome P450 family involved in chemical defense reveals the functional evolution of a promiscuous, xenobiotic-metabolizing enzyme in vertebratesHarris, Kurt L., Thomson, Raine E.S., Gumulya, Yosephine, Foley, Gabriel, Carrera-Pacheco, Saskya E., Syed, Parnayan, Janosik, Tomasz, Sandinge, Ann-Sofie, Andersson, Shalini, Jurva, Ulrik, Bodén, Mikael and Gillam, Elizabeth M.J. (2022). Ancestral sequence reconstruction of a cytochrome P450 family involved in chemical defense reveals the functional evolution of a promiscuous, xenobiotic-metabolizing enzyme in vertebrates. Molecular Biology and Evolution, 39 (6) msac116. doi: 10.1093/molbev/msac116 |
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2022 Other Outputs Methods for ancestral sequence reconstruction of large and complex protein familiesFoley, Gabriel (2022). Methods for ancestral sequence reconstruction of large and complex protein families. PhD Thesis, School of Chemistry and Molecular Biosciences, The University of Queensland. doi: 10.14264/04aa4aa |
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2019 Journal Article NAD+ cleavage activity by animal and plant TIR domains in cell death pathwaysHorsefield, Shane, Burdett, Hayden, Zhang, Xiaoxiao, Manik, Mohammad K., Shi, Yun, Chen, Jian, Qi, Tiancong, Gilley, Jonathan, Lai, Jhih-Siang, Rank, Maxwell X., Casey, Lachlan W., Gu, Weixi, Ericsson, Daniel J., Foley, Gabriel, Hughes, Robert O., Bosanac, Todd, von Itzstein, Mark, Rathjen, John P., Nanson, Jeffrey D., Boden, Mikael, Dry, Ian B., Williams, Simon J., Staskawicz, Brian J., Coleman, Michael P., Ve, Thomas, Dodds, Peter N. and Kobe, Bostjan (2019). NAD+ cleavage activity by animal and plant TIR domains in cell death pathways. Science, 365 (6455), 793-799. doi: 10.1126/science.aax1911 |
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2019 Journal Article SeqScrub: a web tool for automatic cleaning and annotation of FASTA file headers for bioinformatic applicationsFoley, Gabriel, Sützl, Leander, D'Cunha, Stephlina A., Gillam, Elizabeth M.J. and Bodén, Mikael (2019). SeqScrub: a web tool for automatic cleaning and annotation of FASTA file headers for bioinformatic applications. BioTechniques, 67 (2), 50-54. doi: 10.2144/btn-2018-0188 |
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2019 Journal Article The GMC superfamily of oxidoreductases revisited: analysis and evolution of fungal GMC oxidoreductasesSützl, Leander, Foley, Gabriel, Gillam, Elizabeth M J, Bodén, Mikael and Haltrich, Dietmar (2019). The GMC superfamily of oxidoreductases revisited: analysis and evolution of fungal GMC oxidoreductases. Biotechnology for Biofuels, 12 (1) 118, 118. doi: 10.1186/s13068-019-1457-0 |
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2017 Journal Article Motivating postgrad research students to pitch their ideas: what have we learned from 'pitching research' competitions at UQ?Faff, Robert W., Babakhani, Nazila, Carrick, Robin, Chen, Angel, Dallest, Kathy, Daunt, Lisa, Escobar, Marisol, Foley, Gabe, Gill, Chelsea, Khong, Bo Xuan, Liu, Mengxi (Maggie), Mahmud, Siti, McCullough, Jon, Ndugwa, Zina, Nguyen, Bao, O'Brien, Shari, Orole, Felix, Qureshi, Asma, Rad, Hossein, Rekker, Saphira, Shahzad, Syed, Smith, Marita, Tran, Tran Le, Tunny, William and Wallin, Ann (2017). Motivating postgrad research students to pitch their ideas: what have we learned from 'pitching research' competitions at UQ?. SSRN Electronic Journal. doi: 10.2139/ssrn.2899942 |
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2016 Journal Article Structure and function of the TIR domain from the grape NLR protein RPV1Williams, Simon J., Yin, Ling, Foley, Gabriel, Casey, Lachlan W., Outram, Megan A., Ericsson, Daniel J., Lu, Jiang, Boden, Mikael, Dry, Ian B. and Kobe, Bostjan (2016). Structure and function of the TIR domain from the grape NLR protein RPV1. Frontiers in Plant Science, 7 (DECEMBER2016) 1850, 1850. doi: 10.3389/fpls.2016.01850 |
