Bruno Gaeta

Director of Studies, Bioinformatics
Senior Lecturer

I am a Senior Lecturer in Bioinformatics and Program Director (Bioinformatics) 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): Treasurer, Executive Committee Member, Director and Co-chair of the Affiliates Committee -
  • Intelligent Systems in Molecular Biology (ISMB) conference (2017-present): Steering Committee Member and Treasurer
  • Asia-Pacific Bioinformatics Network (APBioNet): Executive Committee Member
  • Global Organisation for Bioinformatics Learning, Education and Training (GOBLET): Operational Board Member (2016-2019)

Past Appointments and Contributions

  • 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

Book Chapters
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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
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
2021
Journal articles
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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, vol. 17, pp. 1125 - 1133, http://dx.doi.org/10.1109/TCBB.2018.2881975
2020
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, vol. 103, pp. 903 - 915, http://dx.doi.org/10.1007/s00253-018-9482-7
2019
Bayat A; Gaëta B; Ignjatovic A; Parameswaran S, 2019, 'Pairwise alignment of nucleotide sequences using maximal exact matches', BMC Bioinformatics, vol. 20, pp. 261, http://dx.doi.org/10.1186/s12859-019-2827-0
2019
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, vol. 14, http://dx.doi.org/10.1371/journal.pcbi.1006139
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, vol. 14, http://dx.doi.org/10.1371/journal.pcbi.1005772
2018
Bayat A; Gaëta B; Ignjatovic A; Parameswaran S, 2017, 'Improved VCF normalization for accurate VCF comparison.', Bioinformatics, vol. 33, pp. 964 - 970, http://dx.doi.org/10.1093/bioinformatics/btw748
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, vol. 13, http://dx.doi.org/10.1371/journal.pcbi.1005226
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, vol. 33, pp. 2968 - 2968, http://dx.doi.org/10.1093/bioinformatics/btw090
2017
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, vol. 12, http://dx.doi.org/10.1371/journal.pcbi.1004816
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, vol. 12, http://dx.doi.org/10.1371/journal.pcbi.1004943
2016
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, vol. 11, http://dx.doi.org/10.1371/journal.pcbi.1004143
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, vol. 31, pp. 140 - 142, http://dx.doi.org/10.1093/bioinformatics/btu601
2015
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, vol. 2, pp. 44 - 57, http://dx.doi.org/10.1002/mgg3.40
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, vol. 9, http://dx.doi.org/10.1371/journal.pone.0089730
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, vol. 10, http://dx.doi.org/10.1371/journal.pcbi.1003496
2014
Zhou L; Griffith R; Gaeta B, 2014, 'Combining spatial and chemical information for clustering pharmacophores', BMC Bioinformatics, vol. 15, http://dx.doi.org/10.1186/1471-2105-15-S16-S5
2014
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, vol. 14, http://dx.doi.org/10.1186/1471-2105-14-249
2013
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, vol. 64, pp. 3 - 14, http://dx.doi.org/10.1007/s00251-011-0559-z
2012
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, vol. 184, pp. 6986 - 6992, http://dx.doi.org/10.4049/jimmunol.1000445
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, vol. 26, pp. 3129 - 3130, http://dx.doi.org/10.1093/bioinformatics/btq604
2010
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, vol. 10 Suppl 3, pp. S17, http://dx.doi.org/10.1186/1471-2164-10-S3-S17
2009
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, vol. 180, pp. 473 - 482, http://dx.doi.org/10.1083/icb.200711136
2008
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, vol. 324, pp. 26 - 37, http://dx.doi.org/10.1016/j.jim.2007.04.011
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, vol. 23, pp. 1580 - 1587, http://dx.doi.org/10.1093/bioinformatics/btm147
2007
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, vol. 57, pp. 917 - 925, http://dx.doi.org/10.1007/s00251-005-0062-5
2006
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, vol. 172, pp. 340 - 348, http://dx.doi.org/10.4049/jimmunol.172.1.340
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], vol. 5, pp. 19 - 19, http://dx.doi.org/10.1186/1471-2172-5-19
2004
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, vol. 19, pp. 4135 - 4142, http://dx.doi.org/10.1016/S0264-410X(01)00173-6
2001
Littlejohn T; Gaëta B, 2001, 'A bioinformatics perspective on the complexity of being human', Today's Life Science, vol. 13, pp. 26 - 33
2001
Gaëta B, 2000, 'BLAST ... what next?', BioTechniques, vol. 28, pp. 874 - 876, http://dx.doi.org/10.2144/00285ir01
2000
Gaëta BA, 2000, 'BLAST on the Web.', BioTechniques, vol. 28, http://dx.doi.org/10.2144/00283ir01
2000
Littlejohn TG; Bucholtz CA; Campbell RMM; Gaëta BA; Huynh C; Kim SH, 1996, 'Computing for biotechnology - WebANGIS', Australasian Biotechnology, vol. 6, pp. 211 - 217
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
1996
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, vol. 1219, pp. 307 - 313, http://dx.doi.org/10.1016/0167-4781(94)90053-1
1994
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, vol. 18, pp. 1541 - 1548, http://dx.doi.org/10.1093/nar/18.6.1541
1990
Conference Papers
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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
2010
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, pp. 669 - 674, http://dx.doi.org/10.1109/ISPA.2008.93
2008
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, pp. 120 - 127, presented at International conference on high performance computing, networking and communication systems 2007, Orlando, Florida, USA, 09 July 2007 - 12 July 2007
2007
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
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
2006
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
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, DENVER, COLORADO, pp. C193 - C193, presented at 90th Annual Meeting of the American-Association-for-Immunologists, DENVER, COLORADO, 06 May 2003 - 10 May 2003, http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=LinksAMR&KeyUT=WOS:000182367000893&DestLinkType=FullRecord&DestApp=ALL_WOS&UsrCustomerID=891bb5ab6ba270e68a29b250adbe88d1
2003

Bioinformatics & education, especially curriculum design for bioinformatics.

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 Bioinformatics Methods and Applications
  • BINF3020/9020 Computational Bioinformatics
  • BINF6111 Genome Informatics Engineering Design Project
  • BINF6112 Computational Biology Engineering Design Project
  • COMP4920 Management and Ethics