Select Publications

Book Chapters

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

Littlejohn T; Gaëta B, 2001, 'A bioinformatics perspective on the complexity of being human', Today's Life Science, 13, pp. 26 - 33

Gaëta B, 2000, 'BLAST ... what next?', BioTechniques, 28, pp. 874 - 876, http://dx.doi.org/10.2144/00285ir01

Gaëta BA, 2000, 'BLAST on the Web.', BioTechniques, 28, http://dx.doi.org/10.2144/00283ir01

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

Littlejohn TG; Bucholtz CA; Campbell RMM; Gaëta BA; Huynh C; Kim SH, 1996, 'Computing for biotechnology - WebANGIS', Australasian Biotechnology, 6, pp. 211 - 217

GAETA BA, 1995, 'DATABASE SIMILARITY SEARCHING USING BLAST AND FASTA', AUSTRALASIAN BIOTECHNOLOGY, 5, pp. 282 - 290, https://www.webofscience.com/api/gateway?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=LinksAMR&KeyUT=WOS:A1995TF10200010&DestLinkType=FullRecord&DestApp=ALL_WOS&UsrCustomerID=891bb5ab6ba270e68a29b250adbe88d1

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

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

Conference Papers

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

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

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

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

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

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

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

Preprints

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

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


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