Overview
Background
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.
Availability
- Dr Gabriel Foley is:
- Available for supervision
- Media expert
Qualifications
- Doctor of Philosophy of Bioinformatics, 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).
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Protein engineering
Computational manipulation of proteins in order to improve or alter their functional properties.
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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.
Works
Search Professor Gabriel Foley’s works on UQ eSpace
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
2024
Journal Article
Optimal phylogenetic reconstruction of insertion and deletion events
Tule, Sanjana, Foley, Gabriel, Zhao, Chongting, Forbes, Michael and Bodén, Mikael (2024). Optimal phylogenetic reconstruction of insertion and deletion events. Bioinformatics, 40 (Supplement_1), i277-i286. doi: 10.1093/bioinformatics/btae254
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
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 (2024). Engineering Biocatalysts for the C‐H Activation of Fatty Acids by Ancestral Sequence Reconstruction. Angewandte Chemie International Edition, 63 (18) e202314869, e202314869. doi: 10.1002/anie.202314869
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
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 vertebrates
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
2022
Other Outputs
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
2019
Journal Article
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
2019
Journal Article
SeqScrub: a web tool for automatic cleaning and annotation of FASTA file headers for bioinformatic applications
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
2019
Journal Article
The GMC superfamily of oxidoreductases revisited: analysis and evolution of fungal GMC oxidoreductases
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
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
2016
Journal Article
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
Funding
Current funding
Supervision
Availability
- Dr Gabriel Foley is:
- Available for supervision
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Supervision history
Current supervision
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Doctor Philosophy
Evolution of cytochrome P450 enzymes in response to dietary and environmental chemicals
Associate Advisor
Other advisors: Professor Elizabeth Gillam
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Doctor Philosophy
Dual-function ribonucleases: unexpected agents of antibiotic resistance
Associate Advisor
Other advisors: Professor Phil Hugenholtz, Professor Mikael Boden
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Doctor Philosophy
Using Statistical Models to Integrate Epigenetic Information by Distinguishing Sources of Variability
Associate Advisor
Other advisors: Professor Michael Piper, Professor Mikael Boden
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Doctor Philosophy
Finding meaningful variation in biological data by deep learning
Associate Advisor
Other advisors: Professor Mikael Boden
Media
Enquiries
Contact Dr Gabriel Foley directly for media enquiries about:
- ancestral sequence reconstruction
- biofuels
- evolution
- phylogenetics
- protein engineering
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