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Thomas Keane - Publications

Affiliations: 
Biology National University of Ireland Maynooth, Maynooth, County Kildare, Ireland 
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25 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2019 Amid C, Alako BTF, Balavenkataraman Kadhirvelu V, Burdett T, Burgin J, Fan J, Harrison PW, Holt S, Hussein A, Ivanov E, Jayathilaka S, Kay S, Keane T, Leinonen R, Liu X, et al. The European Nucleotide Archive in 2019. Nucleic Acids Research. PMID 31722421 DOI: 10.1093/Nar/Gkz1063  0.324
2018 Harrison PW, Alako B, Amid C, Cerdeño-Tárraga A, Cleland I, Holt S, Hussein A, Jayathilaka S, Kay S, Keane T, Leinonen R, Liu X, Martínez-Villacorta J, Milano A, Pakseresht N, et al. The European Nucleotide Archive in 2018. Nucleic Acids Research. PMID 30395270 DOI: 10.1093/Nar/Gky1078  0.302
2018 Fiddes IT, Armstrong J, Diekhans M, Nachtweide S, Kronenberg ZN, Underwood JG, Gordon D, Earl D, Keane T, Eichler EE, Haussler D, Stanke M, Paten B. Comparative Annotation Toolkit (CAT)-simultaneous clade and personal genome annotation. Genome Research. PMID 29884752 DOI: 10.1101/Gr.233460.117  0.402
2018 Thybert D, Roller M, Navarro FCP, Fiddes I, Streeter I, Feig C, Martin-Galvez D, Kolmogorov M, Janoušek V, Akanni W, Aken B, Aldridge S, Chakrapani V, Chow W, Clarke L, ... ... Keane TM, et al. Repeat associated mechanisms of genome evolution and function revealed by theandgenomes. Genome Research. PMID 29563166 DOI: 10.1101/Gr.234096.117  0.648
2017 Collins C, Hurley R, Almutlaqah N, O'Keeffe G, Keane TM, Fitzpatrick DA, Owens RA. Proteomic Characterization of Armillaria mellea Reveals Oxidative Stress Response Mechanisms and Altered Secondary Metabolism Profiles. Microorganisms. 5. PMID 28926970 DOI: 10.3390/microorganisms5030060  0.394
2016 Hunter KW, Bai L, Yang HH, Hu Y, Shukla A, Ha N, Doran A, Faraji F, Goldberger N, Lee MP, Keane T. Abstract IA21: An integrated genome-wide systems genetics screen for breast cancer metastasis susceptibility genes Cancer Research. 76. DOI: 10.1158/1538-7445.Tummet15-Ia21  0.315
2015 Owens RA, O'Keeffe G, Smith EB, Dolan SK, Hammel S, Sheridan KJ, Fitzpatrick DA, Keane TM, Jones GW, Doyle S. Interplay between Gliotoxin Resistance, Secretion, and the Methyl/Methionine Cycle in Aspergillus fumigatus. Eukaryotic Cell. 14: 941-57. PMID 26150413 DOI: 10.1128/EC.00055-15  0.395
2015 Jeffares DC, Rallis C, Rieux A, Speed D, P?evorovský M, Mourier T, Marsellach FX, Iqbal Z, Lau W, Cheng TM, Pracana R, Mülleder M, Lawson JL, Chessel A, Bala S, ... ... Keane T, et al. The genomic and phenotypic diversity of Schizosaccharomyces pombe. Nature Genetics. 47: 235-41. PMID 25665008 DOI: 10.1038/Ng.3215  0.396
2014 O'Keeffe G, Hammel S, Owens RA, Keane TM, Fitzpatrick DA, Jones GW, Doyle S. RNA-seq reveals the pan-transcriptomic impact of attenuating the gliotoxin self-protection mechanism in Aspergillus fumigatus. Bmc Genomics. 15: 894. PMID 25311525 DOI: 10.1186/1471-2164-15-894  0.392
2013 Baud A, Hermsen R, Guryev V, Stridh P, Graham D, McBride MW, Foroud T, Calderari S, Diez M, Ockinger J, Beyeen AD, Gillett A, Abdelmagid N, Guerreiro-Cacais AO, ... ... Keane T, et al. Combined sequence-based and genetic mapping analysis of complex traits in outbred rats. Nature Genetics. 45: 767-75. PMID 23708188 DOI: 10.1038/Ng.2644  0.313
2013 Collins C, Keane TM, Turner DJ, O'Keeffe G, Fitzpatrick DA, Doyle S. Genomic and proteomic dissection of the ubiquitous plant pathogen, Armillaria mellea: toward a new infection model system. Journal of Proteome Research. 12: 2552-70. PMID 23656496 DOI: 10.1021/pr301131t  0.487
2013 Perkins TT, Davies MR, Klemm EJ, Rowley G, Wileman T, James K, Keane T, Maskell D, Hinton JC, Dougan G, Kingsley RA. ChIP-seq and transcriptome analysis of the OmpR regulon of Salmonella enterica serovars Typhi and Typhimurium reveals accessory genes implicated in host colonization. Molecular Microbiology. 87: 526-38. PMID 23190111 DOI: 10.1111/Mmi.12111  0.345
2011 Keane TM, Goodstadt L, Danecek P, White MA, Wong K, Yalcin B, Heger A, Agam A, Slater G, Goodson M, Furlotte NA, Eskin E, NellÃ¥ker C, Whitley H, Cleak J, et al. Mouse genomic variation and its effect on phenotypes and gene regulation. Nature. 477: 289-94. PMID 21921910 DOI: 10.1038/Nature10413  0.301
2011 Petty NK, Feltwell T, Pickard D, Clare S, Toribio AL, Fookes M, Roberts K, Monson R, Nair S, Kingsley RA, Bulgin R, Wiles S, Goulding D, Keane T, Corton C, et al. Citrobacter rodentium is an unstable pathogen showing evidence of significant genomic flux. Plos Pathogens. 7: e1002018. PMID 21490962 DOI: 10.1371/Journal.Ppat.1002018  0.375
2009 Sudbery I, Stalker J, Simpson JT, Keane T, Rust AG, Hurles ME, Walter K, Lynch D, Teboul L, Brown SD, Li H, Ning Z, Nadeau JH, Croniger CM, Durbin R, et al. Deep short-read sequencing of chromosome 17 from the mouse strains A/J and CAST/Ei identifies significant germline variation and candidate genes that regulate liver triglyceride levels. Genome Biology. 10: R112. PMID 19825173 DOI: 10.1186/Gb-2009-10-10-R112  0.383
2009 Croucher NJ, Fookes MC, Perkins TT, Turner DJ, Marguerat SB, Keane T, Quail MA, He M, Assefa S, Bähler J, Kingsley RA, Parkhill J, Bentley SD, Dougan G, Thomson NR. A simple method for directional transcriptome sequencing using Illumina technology. Nucleic Acids Research. 37: e148. PMID 19815668 DOI: 10.1093/Nar/Gkp811  0.406
2009 Turner DJ, Keane TM, Sudbery I, Adams DJ. Next-generation sequencing of vertebrate experimental organisms. Mammalian Genome : Official Journal of the International Mammalian Genome Society. 20: 327-38. PMID 19452216 DOI: 10.1007/S00335-009-9187-4  0.303
2009 Parra G, Bradnam K, Ning Z, Keane T, Korf I. Assessing the gene space in draft genomes. Nucleic Acids Research. 37: 289-97. PMID 19042974 DOI: 10.1093/Nar/Gkn916  0.389
2008 Pain A, Böhme U, Berry AE, Mungall K, Finn RD, Jackson AP, Mourier T, Mistry J, Pasini EM, Aslett MA, Balasubrammaniam S, Borgwardt K, Brooks K, Carret C, Carver TJ, ... ... Keane T, et al. The genome of the simian and human malaria parasite Plasmodium knowlesi. Nature. 455: 799-803. PMID 18843368 DOI: 10.1038/Nature07306  0.347
2007 Keane TM, Naughton TJ, McInerney JO. MultiPhyl: A high-throughput phylogenomics webserver using distributed computing Nucleic Acids Research. 35: W33-W37. PMID 17553837 DOI: 10.1093/Nar/Gkm359  0.59
2006 Keane TM, Creevey CJ, Pentony MM, Naughton TJ, Mclnerney JO. Assessment of methods for amino acid matrix selection and their use on empirical data shows that ad hoc assumptions for choice of matrix are not justified. Bmc Evolutionary Biology. 6: 29. PMID 16563161 DOI: 10.1186/1471-2148-6-29  0.632
2006 Keane TM, Page AJ, Naughton TJ, Travers SAA, McInerney JO. Building large phylogenetic trees on coarse-grained parallel machines Algorithmica (New York). 45: 285-300. DOI: 10.1007/S00453-006-1215-0  0.542
2005 Keane TM, Naughton TJ, Travers SAA, McInerney JO, McCormack GP. DPRml: Distributed phylogeny reconstruction by maximum likelihood Bioinformatics. 21: 969-974. PMID 15513992 DOI: 10.1093/Bioinformatics/Bti100  0.545
2005 Keane TM, Page AJ, McInerney JO, Naughton TJ. A high-throughput bioinformatics distributed computing platform Proceedings - Ieee Symposium On Computer-Based Medical Systems. 377-382.  0.501
2003 Keane T, Allen R, Naughton TJ, McInerney J, Waldron J. Distributed Java platform with programmable MIMD capabilities Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 2604: 122-131.  0.476
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