Select Publications

by Dr Bruno Andre Gaeta

Journal articles

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; Bongcam-Rudloff E; Brazas MD; Brooksbank C; Budd A; Charleston M; Christoffels A; Conesa A; Corpas M; Crowe M; Davies A; de Crecy-Lagard V; De Las Rivas J; Doyle M; Edwards R; Facchiano A; Fernandes P; Gaeta B; Gaudet P; Heger A; Herringa J; Hughes D; Jimenez RC; Kille P; Korpelainen E; Kumuthini J; Lewitter F; 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; van Gelder CWG; 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, no. 4,

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, no. 1, pp. 140 - 142,

Zhou L; Griffith R; Gaeta B, 2014, 'Combining spatial and chemical information for clustering pharmacophores', BMC Bioinformatics, vol. 15, no. 16,

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, no. 2,

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, no. 3,

Ballouz S; Liu JY; Oti M; Gaeta B; Fatkin D; Bahlo M; Wouters MA, 2014, 'Candidate disease gene prediction using Gentrepid: application to a genome-wide association study on coronary artery disease.', Molecular Genetics and Genomic Medicine, vol. 2, no. 1, pp. 44 - 57,

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, no. 1,

Jackson KJL; Wang Y; Gaeta BA; Pomat W; Siba P; Rimmer J; Sewell WA; Collins AM, 2012, 'Divergent human populations show extensive shared IGK rearrangements in peripheral blood B cells', Immunogenetics, vol. 64, no. 1, pp. 3 - 14,

Boyd SD; Gaëta 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 Ig gene repertoire inferred from variable region gene rearrangements', Journal of Immunology, vol. 184, no. 12, pp. 6986 - 6992,

Jackson KJL; Boyd S; Gaëta BA; Collins AM, 2010, 'Benchmarking the performance of human antibody gene alignment utilities using a 454 sequence dataset', Bioinformatics, vol. 26, no. 24, pp. 3129 - 3130,

Kadupitige SR; Leung KC; Sellmeier J; Sivieng J; Catchpoole DR; Bain ME; Gaëta BA, 2009, 'MINER: Exploratory analysis of gene interaction networks by machine learning from expression data', BMC Genomics, vol. 10, no. SUPPL. 3

Fei W; Shui G; Gaeta B; Du X; Kuerschner L; Li P; Brown AJ; Wenk MR; Parton RG; Yang H, 2008, 'Fld1p, a functional homologue of human seipin, regulates the size of lipid droplets in yeast', The Journal of Cell Biology, vol. 180, no. 3, pp. 473 - 482,

Gaëta BA; Malming HR; Jackson KJL; Bain ME; Wilson P; Collins AM, 2007, 'iHMMune-align: Hidden Markov model-based alignment and identification of germline genes in rearranged immunoglobulin gene sequences', Bioinformatics, vol. 23, no. 13, pp. 1580 - 1587,

Jackson KJL; Gaëta 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, no. 1-2, pp. 26 - 37,

Lee CEH; Gaëta B; Malming HR; 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, no. 12, pp. 917 - 925,

Collins AM; Ikutani M; Puiu D; Buck GA; Nadkarni A; Gaeta B, 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, no. 1, pp. 340 - 348

Jackson KJL; Gaeta B; Sewell W; Collins AM, 2004, 'Exonuclease activity and P nucleotide addition in the generation of the expressed immunoglobulin repertoire', BMC Immunology, vol. 5,

Littlejohn T; Gaëta B, 2001, 'A bioinformatics perspective on the complexity of being human', Today's Life Science, vol. 13, no. 2, pp. 26 - 33

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, no. 30, pp. 4135 - 4142,

Gaëta BA, 2000, 'BLAST on the Web.', BioTechniques: the journal of laboratory technology for bioresearch, vol. 28, no. 3, pp. 436 - 440

Gaëta B, 2000, 'BLAST ... what next?', BioTechniques: the journal of laboratory technology for bioresearch, vol. 28, no. 5, pp. 874 - 876

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, vol. 6, no. 4, pp. 211 - 217

GAETA BA, 1995, 'DATABASE SIMILARITY SEARCHING USING BLAST AND FASTA', Australasian Biotechnology, vol. 5, no. 5, pp. 282 - 290,

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', Biochimica et Biophysica Acta: Gene Regulatory Mechanisms, vol. 1219, no. 2, pp. 307 - 313,

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, no. 6, pp. 1541 - 1548

Valencia A; Markel S; Gaeta B; Gaasterland T; Lengauer T; Berger B; Orengo C, 'ISCB’s initial reaction to New England Journal of Medicine editorial on data sharing', F1000 Research,

Conference Papers

Chen Z; Collins AM; Wang Y; Gata BA, 2010, 'Clustering-based identification of clonally-related immunoglobulin gene sequence sets', in Immunome Research,

Helal M; El-Gindy H; Mullin L; Gaeta B, 2008, 'Parallelizing optimal multiple sequence alignment by dynamic programming', in Proceedings of the 2008 International Symposium on Parallel and Distributed Processing with Applications, ISPA 2008, pp. 669 - 674,

Helal M; Mullin LR; El-Gindy H; Gaëta B, 2007, 'Optimal distributed multiple sequence alignment using conformal computing methods', in International Conference on High Performance Computing, Networking and Communication Systems 2007, HPCNCS 2007, pp. 120 - 127

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; 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, presented at Workshop on Intelligent systems for bioinformatics, 2006, Hobart, 4 December 2006

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, pp. C193 - C193, presented at 90th Annual Meeting of the American-Association-for-Immunologists, DENVER, COLORADO, 6 - 10 May 2003,

Bain ME; Gaeta BA, 2003, 'Learning Quantitative Gene Interactions from Microarray Data', in 2003 Congress on Evolutionary Computation CEC 2003, presented at IEEE Congress on Evolutionary Computation (CEC 2003), Canberra, 8 - 12 December 2003

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