Postdoctoral Research Fellow
Overview
Dr Gabriel Foley is a Postdoctoral Research Fellow at the School of Chemistry and Molecular Biosciences at The University of Queensland. His research focuses on ancestral sequence reconstruction - predicting the properties of ancient forms of proteins in order to understand their evolution and engineer proteins with novel and improved functions. His current research focuses on optimising proteins that are capable of producing sustainable biofuels.
Gabriel was awarded his PhD from The University Of Queensland in 2022, in which he developed and employed a novel method for ancestral prediction - Graphical Representation of Ancestral Sequence Predictions (GRASP). Gabriel previously completed a Bachelor of Biotechnology (First Class Honours) from The University of Queensland.
Research Interests
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Ancestral sequence reconstruction
Computational methods to predict the ancestral forms of biological sequences (proteins / DNA). -
Protein engineering
Computational manipulation of proteins in order to improve or alter their functional properties. -
Phylogenetics
Evolutionary relationships between modern day species, genes, and proteins.
Research Impacts
Graphical Representation of Ancestral Sequence Predictions (GRASP) is an open-source computational tool for the prediction fo ancestral forms of protein sequences. It is capable of processing previously unattainable scales of data as well as incorporating diversity from evolutionary insertion and deletion events that are critical to understanding how proteins evolve. It is implemented with an easy to use graphical interface to allow this research to be carried out by researchers, companies, and individuals across the world.
Qualifications
- Doctor of Philosophy of Bioinformatics, The University of Queensland
Publications
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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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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 (2024). Engineering Biocatalysts for the C‐H Activation of Fatty Acids by Ancestral Sequence Reconstruction. Angewandte Chemie International Edition, e202314869. doi: 10.1002/anie.202314869
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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
Grants
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Broad-spectrum vaccine design for flaviviruses and henipaviruses
(2023–2025) NHMRC MRFF EMCR - Early to Mid-Career Researchers
Supervision
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Dual-function ribonucleases: unexpected agents of antibiotic resistance
Doctor Philosophy
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Finding meaningful variation in biological data by deep learning
Doctor Philosophy
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Using Statistical Models to Integrate Epigenetic Information by Distinguishing Sources of Variability
Doctor Philosophy
Publications
Featured Publications
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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
Book Chapter
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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
Journal Article
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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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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 (2024). Engineering Biocatalysts for the C‐H Activation of Fatty Acids by Ancestral Sequence Reconstruction. Angewandte Chemie International Edition, e202314869. doi: 10.1002/anie.202314869
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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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Harris, 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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NAD+ cleavage activity by animal and plant TIR domains in cell death pathways
Horsefield, 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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Foley, 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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Sützl, 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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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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Structure and function of the TIR domain from the grape NLR protein RPV1
Williams, 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
Other Outputs
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Methods for ancestral sequence reconstruction of large and complex protein families
Foley, 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
Grants (Administered at UQ)
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Broad-spectrum vaccine design for flaviviruses and henipaviruses
(2023–2025) NHMRC MRFF EMCR - Early to Mid-Career Researchers
PhD and MPhil Supervision
Current Supervision
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Dual-function ribonucleases: unexpected agents of antibiotic resistance
Doctor Philosophy — Associate Advisor
Other advisors:
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Finding meaningful variation in biological data by deep learning
Doctor Philosophy — Associate Advisor
Other advisors:
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Using Statistical Models to Integrate Epigenetic Information by Distinguishing Sources of Variability
Doctor Philosophy — Associate Advisor
Other advisors:
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Evolution of cytochrome P450 enzymes in response to dietary and environmental chemicals
Doctor Philosophy — Associate Advisor
Other advisors:
