Select Publications

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, 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, 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, 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, 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://www.biomedcentral.com/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


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