Dr Bruno Gaeta

Dr Bruno Gaeta

Senior Lecturer

BSc (Hons) (Biochemistry) and University Medal, UNSW (1986)

PhD (Molecular Genetics), UNSW (1992)

Computer Science and Engineering

I am a Senior Lecturer in Bioinformatics and Director of Studies (Bioinformatics Engineering) with the School of Computer Science and Engineering.

Research Interest

My main research interest is in the engineering of computer methods and software to better understand the immune system and especially the basis for the "memory" of the immune system and vaccines.

This includes software for analysing immunoglobulins, both at the genetic level and at the protein level.

I am especially interested in the design of algorithms for analysing large datasets of rearranged immunoglobulin genes for the purpose of understanding genetic variation in these genes, diversity generation events, and binding specificity.

I am also more widely interested in applications of computational methods to molecular biology, especially to gene expression, and, in collaboration with Professor Sri Parameswaran, the development of specialised hardware for bioinformatics analysis.

Professional Organisations and Consulting Positions

I am very active in the promotion and advocacy for the disciplines of computational biology and bioinformatics, through involvement in the leading professional societies and conferences in the field:

  • International Society for Computational Biology (ISCB): Director and Co-chair of the Affiliates Committee 
  • Intelligent Systems in Molecular Biology (ISMB) conference (2017-present): Steering Committee Member

Past Appointments and Contributions

  • 2017-2021: Treasurer and Executive Committee Member, International Society for Computational Biology (ISCB)
  • 2008-2019: Executive Committee Member, Asia-Pacific Bioinformatics Network (APBioNet)
  • 2016-2019: Operational Board Member, Global Organisation for Bioinformatics Learning, Education and Training (GOBLET)
  • 2006: Conference chair, Bioinformatics Australia conference (Sydney)
  • 2005-2010: Management committee, Bioinformatics Australia
  • 2002: Advisory Board, Thailand National Bioinformatics Helpdesk
  • 2001-2002: Adjunct Lecturer, School of Molecular and Microbial Biosciences, University of Sydney 
  • 1999-2001: Adjunct Lecturer, School of Microbiology, University of Sydney 
  • 1999-2001: Director of Education and Senior Scientist, eBioinformatics Pty Ltd (re-named Entigen Inc)
  • 2000: Adviser/consultant for the Biotechnology program of the Thailand-Australia Science and Engineering Assistance Project 
  • 1993-1998: Liaison Officer and Education Officer, Australian Genomic Information Centre, University of Sydney.
  • 1991-1993: Post-Doctoral Research Officer, Heart Research Institute, Camperdown, NSW

Program Committee member for conferences and workshops including Pattern Recognition in Bioinformatics, International Conference on Bioinformatics (InCoB), GIW, Computational Models for Life Sciences, and International Conference on Intelligent Sensing and Information Processing, International Conference on Artificial Immune Systems

Manuscript reviewer for PLoS Computational Biology, Bioinformatics, Briefings in Bioinformatics, BMC Bioinformatics, Journal of Theoretical Biology and Comparative and Functional Genomics

+61 2 9385 7213
401C, K17
  • Book Chapters | 2021
    Gaeta B, 2021, 'Undergraduate Education in Bioinformatics - Progress and Lessons Learnt from an Engineering Degree', in Suravajhala PN (ed.), Your Passport to a Career in Bioinformatics, Springer Nature, pp. 73 - 78
  • Journal articles | 2023
    Işık EB; Brazas MD; Schwartz R; Gaeta B; Palagi PM; van Gelder CWG; Suravajhala P; Singh H; Morgan SL; Zahroh H; Ling M; Satagopam VP; McGrath A; Nakai K; Tan TW; Gao G; Mulder N; Schönbach C; Zheng Y; De Las Rivas J; Khan AM, 2023, 'Grand challenges in bioinformatics education and training', Nature Biotechnology, 41, pp. 1171 - 1174, http://dx.doi.org/10.1038/s41587-023-01891-9
    Journal articles | 2022
    Ye C; Hu W; Gaeta B, 2022, 'Prediction of Antibody-Antigen Binding via Machine Learning: Development of Data Sets and Evaluation of Methods', JMIR Bioinformatics and Biotechnology, 3, http://dx.doi.org/10.2196/29404
    Journal articles | 2020
    Gamaarachchi H; Bayat A; Gaeta B; Parameswaran S, 2020, 'Cache Friendly Optimisation of de Bruijn Graph Based Local Re-Assembly in Variant Calling', IEEE/ACM Transactions on Computational Biology and Bioinformatics, 17, pp. 1125 - 1133, http://dx.doi.org/10.1109/TCBB.2018.2881975
    Journal articles | 2019
    Bayat A; Gaëta B; Ignjatovic A; Parameswaran S, 2019, 'Pairwise alignment of nucleotide sequences using maximal exact matches', BMC Bioinformatics, 20, pp. 261, http://dx.doi.org/10.1186/s12859-019-2827-0
    Journal articles | 2019
    Wang H; Chu W; Ye C; Gaeta B; Tao H; Wang M; Qiu Z, 2019, 'Chlorogenic acid attenuates virulence factors and pathogenicity of Pseudomonas aeruginosa by regulating quorum sensing', Applied Microbiology and Biotechnology, 103, pp. 903 - 915, http://dx.doi.org/10.1007/s00253-018-9482-7
    Journal articles | 2018
    Frenkel-Morgenstern M; Welch L; Gaeta B; Kovats DE, 2018, 'Art in Science Competition invites artworks to the annual exhibition on ISMB 2018 in Chicago', PLoS Computational Biology, 14, http://dx.doi.org/10.1371/journal.pcbi.1006139
    Journal articles | 2018
    Mulder N; Schwartz R; Brazas MD; Brooksbank C; Gaeta B; Morgan SL; Pauley MA; Rosenwald A; Rustici G; Sierk M; Warnow T; Welch L, 2018, 'The development and application of bioinformatics core competencies to improve bioinformatics training and education', PLoS Computational Biology, 14, http://dx.doi.org/10.1371/journal.pcbi.1005772
    Journal articles | 2017
    Bayat A; Gaëta B; Ignjatovic A; Parameswaran S, 2017, 'Improved VCF normalization for accurate VCF comparison.', Bioinformatics, 33, pp. 964 - 970, http://dx.doi.org/10.1093/bioinformatics/btw748
    Journal articles | 2017
    Berger B; Gaasterland T; Lengauer T; Orengo CA; Gaeta B; Markel S; Valencia A, 2017, 'ISCB's initial reaction to New England Journal of Medicine editorial on data sharing', BIOINFORMATICS, 33, pp. 2968 - 2968, http://dx.doi.org/10.1093/bioinformatics/btw090
    Journal articles | 2017
    Gaëta BA; De Las Rivas J; Horton P; Meysman P; Mulder N; Romano P; Welch L, 2017, 'Ten simple rules for forming a scientific professional society', PLoS Computational Biology, 13, pp. e1005226, http://dx.doi.org/10.1371/journal.pcbi.1005226
    Journal articles | 2016
    Berger B; Gaasterland T; Lengauer T; Orengo C; Gaeta B; Markel S; Valencia A, 2016, 'ISCB’s Initial Reaction to The New England Journal of Medicine Editorial on Data Sharing', PLoS Computational Biology, 12, http://dx.doi.org/10.1371/journal.pcbi.1004816
    Journal articles | 2016
    Welch L; Brooksbank C; Schwartz R; Morgan SL; Gaeta B; Kilpatrick AM; Mietchen D; Moore BL; Mulder N; Pauley M; Pearson W; Radivojac P; Rosenberg N; Rosenwald A; Rustici G; Warnow T, 2016, 'Applying, Evaluating and Refining Bioinformatics Core Competencies (An Update from the Curriculum Task Force of ISCB’s Education Committee)', PLoS Computational Biology, 12, http://dx.doi.org/10.1371/journal.pcbi.1004943
    Journal articles | 2015
    Atwood TK; Bongcam-Rudloff E; Brazas ME; Corpas M; Gaudet P; Lewitter F; Mulder N; Palagi PM; Schneider MV; van Gelder CWG; Attwood TK; Banag C; Blackford S; Blatter MC; Brazas MD; Brooksbank C; Budd A; Charleston M; Christoffels A; Conesa A; Crowe M; Davies A; de Crecy-Lagard V; De Las Rivas J; Doyle M; Edwards R; Facchiano A; Fernandes P; Gaeta B; Heger A; Herringa J; Hughes D; Jimenez RC; Kille P; Korpelainen E; Kumuthini J; MacLean D; Martinez SAR; McGrath A; Michalopoulos I; Mulder N; Ouellette BF; Palagi PM; Pearson WR; Qi W; Romano P; Rother K; Sansone SA; Schneider MV; Schönbach C; Tastan-Bishop O; Trelles O; Twells R; Via A; Vriend G; Warnow T; Watson M; Westervelt N; Zanzoni A, 2015, 'GOBLET: The Global Organisation for Bioinformatics Learning, Education and Training', PLoS Computational Biology, 11, http://dx.doi.org/10.1371/journal.pcbi.1004143
    Journal articles | 2015
    Corpas M; Jimenez RC; Bongcam-Rudloff E; Budd A; Brazas MD; Fernandes PL; Gaeta B; Van Gelder C; Korpelainen E; Lewitter F; McGrath A; MacLean D; Palagi PM; Rother K; Taylor J; Via A; Watson M; Schneider MV; Attwood TK, 2015, 'The GOBLET training portal: A global repository of bioinformatics training materials, courses and trainers', Bioinformatics, 31, pp. 140 - 142, http://dx.doi.org/10.1093/bioinformatics/btu601
    Journal articles | 2014
    Ballouz S; Liu JY; Oti M; Gaeta B; Fatkin D; Bahlo M; Wouters MA, 2014, 'Candidate disease gene prediction using : application to a genome-wide association study on coronary artery disease', Molecular Genetics & Genomic Medicine, 2, pp. 44 - 57, http://dx.doi.org/10.1002/mgg3.40
    Journal articles | 2014
    Wang Y; Jackson KJL; Davies J; Chen Z; Gaeta BA; Rimmer J; Sewell WA; Collins AM, 2014, 'IgE-associated IGHV genes from venom and peanut allergic individuals lack mutational evidence of antigen selection', PLoS ONE, 9, http://dx.doi.org/10.1371/journal.pone.0089730
    Journal articles | 2014
    Welch L; Lewitter F; Schwartz R; Brooksbank C; Radivojac P; Gaeta B; Schneider MV, 2014, 'Bioinformatics Curriculum Guidelines: Toward a Definition of Core Competencies', PLoS Computational Biology, 10, http://dx.doi.org/10.1371/journal.pcbi.1003496
    Journal articles | 2014
    Zhou L; Griffith R; Gaeta B, 2014, 'Combining spatial and chemical information for clustering pharmacophores', BMC Bioinformatics, 15, pp. s5, http://dx.doi.org/10.1186/1471-2105-15-S16-S5
    Journal articles | 2013
    Ballouz S; Liu JY; George RA; Bains N; Liu A; Oti M; Gaeta B; Fatkin D; Wouters MA, 2013, 'Gentrepid V2.0: A web server for candidate disease gene prediction', BMC Bioinformatics, 14, pp. 249, http://dx.doi.org/10.1186/1471-2105-14-249
    Journal articles | 2012
    Jackson KJ; Wang Y; Gaeta BA; Pomat W; Siba PM; Sewell WA; Collins AM, 2012, 'Divergent human populations show extensive shared IGK rearrangements in peripheral blood B cells', Immunogenetics, 64, pp. 3 - 14, http://dx.doi.org/10.1007/s00251-011-0559-z
    Journal articles | 2010
    Boyd S; Gaeta BA; Jackson KJ; Fire AZ; Marshall EL; Merker JD; Maniar JM; Zhang LN; Sahaf B; Jones CD; Simen BB; Hanczaruk B; Nguyen KD; Nadeau KC; Egholm M; Miklos DB; Zehnder JL; Collins AM, 2010, 'Individual variation in the germline immunoglobulin gene repertoire inferred from Variable Region gene rearrangements', Journal of Immunology, 184, pp. 6986 - 6992, http://dx.doi.org/10.4049/jimmunol.1000445
    Journal articles | 2010
    Jackson KJ; Boyd S; Gaeta BA; Collins AM, 2010, 'Benchmarking the performance of human antibody gene alignment utilities using a 454 sequence dataset', Bioinformatics, 26, pp. 3129 - 3130, http://dx.doi.org/10.1093
    Journal articles | 2009
    Kadupitige ; Leung KC; Sellmeier J; Sivieng J; Catchpoole DR; Bain ME; Gaeta BA, 2009, 'MINER: exploratory analysis of gene interaction networks by machine learning from expression data', BMC Genomics, 10 Suppl 3, pp. S17, http://dx.doi.org/10.1186/1471-2164-10-S3-S17
    Journal articles | 2008
    Fei W; Shui G; Gaeta BA; Du XR; Kuerschner L; Liu P; Brown AJ; Wenk M; Parton R; Yang H, 2008, 'Fld1p, a functional homologue of human seipin, regulates the size of lipid droplets in yeast', Journal of Cell Biology, 180, pp. 473 - 482, http://dx.doi.org/10.1083/icb.200711136
    Journal articles | 2007
    Gaeta BA; Malming H; Jackson KJ; Bain ME; Wilson PD; Collins AM, 2007, 'iHMMune-align: hidden Markov model-based alignment and identification of germline genes in rearranged immunoglobulin gene sequences', Bioinformatics, 23, pp. 1580 - 1587
    Journal articles | 2007
    Jackson KJ; Gaeta BA; Collins AM, 2007, 'Identifying highly mutated IGHD genes in the junctions of rearranged human immunoglobulin heavy chain genes', Journal of Immunological Methods, 324, pp. 26 - 37
    Journal articles | 2006
    Lee CE; Gaeta BA; Malming H; Bain ME; Sewell WA; Collins AM, 2006, 'Reconsidering the human immunoglobulin heavy-chain locus: 1. An evaluation of the expressed human IGHD gene repertoire', Immunogenetics, 57, pp. 917 - 925
    Journal articles | 2004
    Collins AM; Ikutani M; Puiu D; Buck G; Nadkarni A; Gaeta BA, 2004, 'Partitioning of rearranged Ig genes by mutation analysis demonstrates D-D fusion and V gene replacement in the expressed human repertoire', Journal of Immunology, 172, pp. 340 - 348
    Journal articles | 2004
    Jackson KJ; Gaeta BA; Sewell WA; Collins AM, 2004, 'Exonuclease activity and P nucleotide addition in the generation of the expressed immunoglobulin repertoire', BMC Immunology [Electronic Resource], 5, pp. 19 - 19, http://www.sciencedirect.com/science/article/B6WVB-4DCMWPN-C7/2/6ddd51d3d5a4b4c9e01603c7452ea881
    Journal articles | 2001
    Littlejohn T; Gaëta B, 2001, 'A bioinformatics perspective on the complexity of being human', Today's Life Science, 13, pp. 26 - 33
    Journal articles | 2001
    Ross BC; Czajkowski L; Hocking D; Margetts M; Webb E; Rothel L; Patterson M; Agius C; Camuglia S; Reynolds E; Littlejohn T; Gaeta B; Ng A; Kuczek ES; Mattick JS; Gearing D; Barr IG, 2001, 'Identification of vaccine candidate antigens from a genomic analysis of Porphyromonas gingivalis', Vaccine, 19, pp. 4135 - 4142, http://dx.doi.org/10.1016/S0264-410X(01)00173-6
    Journal articles | 2000
    Gaëta B, 2000, 'BLAST ... what next?', BioTechniques, 28, pp. 874 - 876, http://dx.doi.org/10.2144/00285ir01
    Journal articles | 2000
    Gaëta BA, 2000, 'BLAST on the Web.', BioTechniques, 28, http://dx.doi.org/10.2144/00283ir01
    Journal articles | 1996
    Gaëta BA; Bucholtz CA; Campbell R; Huynh C; Kim S; Reisner AH, 1996, 'Biocomputing education by the Australian National Genomic Information Service.', Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing, pp. 319 - 330
    Journal articles | 1996
    Littlejohn TG; Bucholtz CA; Campbell RMM; Gaëta BA; Huynh C; Kim SH, 1996, 'Computing for biotechnology - WebANGIS', Australasian Biotechnology, 6, pp. 211 - 217
    Journal articles | 1995
    Journal articles | 1994
    Gaëta BA; Borthwick I; Stanley KK, 1994, 'The 5′-flanking region of the α2MR/LRP gene contains an enhancer-like cluster of Sp1 binding sites', BBA - Gene Structure and Expression, 1219, pp. 307 - 313, http://dx.doi.org/10.1016/0167-4781(94)90053-1
    Journal articles | 1990
    Gaëta BA; Sharp SJ; Stewart TS, 1990, 'Saturation mutagenesis of the Drosophila tRNAArg gene B-box intragenic promoter element: Requirements for transcription activation and stable complex formation', Nucleic Acids Research, 18, pp. 1541 - 1548, http://dx.doi.org/10.1093/nar/18.6.1541
  • Preprints | 2023
    Helal M; El-Gindy H; Mullin L; Gaeta B, 2023, Parallelizing Optimal Multiple Sequence Alignment by Dynamic Programming, , http://dx.doi.org/10.48550/arxiv.2311.17530
    Preprints | 2021
    Ye C; Hu W; Gaeta B, 2021, Machine learning prediction of Antibody-Antigen binding: dataset, method and testing, , http://dx.doi.org/10.1101/2021.03.19.435772
    Conference Papers | 2010
    Chen Z; Collins AM; Wang Y; Gaeta BA, 2010, 'Clustering-based identification of clonally related immunoglobulin gene sequence sets', in Immunome Research, Tokyo, Japan, pp. S4, presented at Ninth International Conference on Bioinformatics (InCoB2010), Tokyo, Japan, 26 September 2010 - 28 September 2010, http://dx.doi.org/10.1186/1745-7580-6-S1-S4
    Conference Papers | 2008
    Helal M; El-Gindy H; Mullin L; Gaeta BA, 2008, 'Parallelizing Optimal Multiple Sequence Alignment by Dynamic Programming', in PROCEEDINGS OF THE 2008 INTERNATIONAL SYMPOSIUM ON PARALLEL ANDDISTRIBUTED PROCESSING WITH APPLICATIONS, Ieee Computer Soc, Los Alamitos, http://dx.doi.org/10.1109/ISPA.2008.93
    Conference Papers | 2007
    Helal M; Mullin L; Elgindy H; Gaeta BA, 2007, 'Optimal distributed multiple sequence alignment using conformal computing methods', in 2007 International conference on high performance computing, networking and communication systems, Orlando, Florida, USA, presented at International conference on high performance computing, networking and communication systems 2007, Orlando, Florida, USA, 09 July 2007 - 12 July 2007
    Conference Papers | 2006
    Bain ME; Ahsan N; Potter JM; Gaeta BA; Temple MD; Dawes IW, 2006, 'Learning causal networks from microarray data', in Workshop on Intelligent systems for bioinformatics, 2006, Workshop on Intelligent systems for bioinformatics, 2006, Hobart, presented at Workshop on Intelligent systems for bioinformatics, 2006, Hobart, 04 December 2006
    Conference Papers | 2006
    Gaeta B; Graves J; Lee SY; Panchenko A; Nicholas F, 2006, 'Bioinfomatics Australia 2006: Inaugural National Conference - Connecting Australian Bioinformatics 21-22 November 2006, Sydney Convention & Exhibition Centre', in Australasian Biotechnology, pp. 64
    Conference Papers | 2003
    Bain ME; Gaeta BA, 2003, 'Learning Quantitative Gene Interactions from Microarray Data', in 2003 Congress on Evolutionary Computation CEC 2003, IEEE Congress on Evolutionary Computation (CEC 2003), Canberra, presented at IEEE Congress on Evolutionary Computation (CEC 2003), Canberra, 08 December 2003 - 12 December 2003
    Conference Papers | 2003
    Collins A; Ikutani M; Nadkarni A; Gaeta B; Sewell W, 2003, 'Analysis of the distribution of point mutations can be used to evaluate D segment alignments of rearranged immunoglobulin heavy chain genes', in FASEB JOURNAL, FEDERATION AMER SOC EXP BIOL, COLORADO, DENVER, pp. C193 - C193, presented at 90th Annual Meeting of the American-Association-for-Immunologists, COLORADO, DENVER, 06 May 2003 - 10 May 2003, https://www.webofscience.com/api/gateway?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=LinksAMR&KeyUT=WOS:000182367000893&DestLinkType=FullRecord&DestApp=ALL_WOS&UsrCustomerID=891bb5ab6ba270e68a29b250adbe88d1

My Research Supervision

I am currently supervising one PhD student in my group, and up to four Honours students per year.

I have previously graduated 4 PhD students and 2 MSc students.

My Teaching

I am Director of Studies for the Bioinformatics Engineering program, and for the Bioinformatics major at UNSW.

Lectures/Courses taught

  • BINF2010 Introduction to Bioinformatics
  • BINF3010/9010 Applied Bioinformatics
  • BINF3020/9020 Computational Bioinformatics
  • DESN2000 Engineering Design and Professional Practice