Thomas Keane - Publications

Affiliations: 
Biology National University of Ireland Maynooth, Maynooth, County Kildare, Ireland 

58 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 Lilue J, Shivalikanjli A, Adams DJ, Keane TM. Mouse protein coding diversity: What's left to discover? Plos Genetics. 15: e1008446. PMID 31725724 DOI: 10.1371/journal.pgen.1008446  0.32
2019 Allchin RL, Kelly ME, Mamand S, Doran AG, Keane T, Ahearne MJ, Wagner SD. Structural and diffusion weighted MRI demonstrates responses to ibrutinib in a mouse model of follicular helper (Tfh) T-cell lymphoma. Plos One. 14: e0215765. PMID 31013298 DOI: 10.1371/journal.pone.0215765  0.32
2018 Lilue J, Doran AG, Fiddes IT, Abrudan M, Armstrong J, Bennett R, Chow W, Collins J, Collins S, Czechanski A, Danecek P, Diekhans M, Dolle DD, Dunn M, Durbin R, ... ... Keane TM, et al. Sixteen diverse laboratory mouse reference genomes define strain-specific haplotypes and novel functional loci. Nature Genetics. PMID 30275530 DOI: 10.1038/s41588-018-0223-8  0.32
2018 Dykes IM, Szumska D, Kuncheria L, Puliyadi R, Chen CM, Papanayotou C, Lockstone H, Dubourg C, David V, Schneider JE, Keane TM, Adams DJ, Brown SDM, Mercier S, Odent S, et al. A Requirement for Zic2 in the Regulation of Nodal Expression Underlies the Establishment of Left-Sided Identity. Scientific Reports. 8: 10439. PMID 29992973 DOI: 10.1038/s41598-018-28714-1  0.32
2018 Gstrein T, Edwards A, Přistoupilová A, Leca I, Breuss M, Pilat-Carotta S, Hansen AH, Tripathy R, Traunbauer AK, Hochstoeger T, Rosoklija G, Repic M, Landler L, Stránecký V, Dürnberger G, ... Keane TM, et al. Publisher Correction: Mutations in Vps15 perturb neuronal migration in mice and are associated with neurodevelopmental disease in humans. Nature Neuroscience. PMID 29875394 DOI: 10.1038/s41593-018-0170-9  0.32
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  0.32
2018 Gstrein T, Edwards A, Přistoupilová A, Leca I, Breuss M, Pilat-Carotta S, Hansen AH, Tripathy R, Traunbauer AK, Hochstoeger T, Rosoklija G, Repic M, Landler L, Stránecký V, Dürnberger G, ... Keane TM, et al. Mutations in Vps15 perturb neuronal migration in mice and are associated with neurodevelopmental disease in humans. Nature Neuroscience. PMID 29311744 DOI: 10.1038/s41593-017-0053-5  0.32
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  0.4
2017 Ibarra-Soria X, Nakahara TS, Lilue J, Jiang Y, Trimmer C, Souza MA, Netto PH, Ikegami K, Murphy NR, Kusma M, Kirton A, Saraiva LR, Keane TM, Matsunami H, Mainland J, et al. Variation in olfactory neuron repertoires is genetically controlled and environmentally modulated. Elife. 6. PMID 28438259 DOI: 10.7554/eLife.21476  0.32
2016 Forment JV, Herzog M, Coates J, Konopka T, Gapp BV, Nijman SM, Adams DJ, Keane TM, Jackson SP. Genome-wide genetic screening with chemically mutagenized haploid embryonic stem cells. Nature Chemical Biology. PMID 27820796 DOI: 10.1038/nchembio.2226  0.32
2016 Morgan AP, Didion JP, Doran AG, Holt JM, McMillan L, Keane TM, Pardo-Manuel de Villena F. Genome Report: Whole Genome Sequence of Two Wild-Derived Mus musculus domesticus Inbred Strains, LEWES/EiJ and ZALENDE/EiJ, with Different Diploid Numbers. G3 (Bethesda, Md.). PMID 27765810 DOI: 10.1534/g3.116.034751  0.32
2016 Doran AG, Wong K, Flint J, Adams DJ, Hunter KW, Keane TM. Deep genome sequencing and variation analysis of 13 inbred mouse strains defines candidate phenotypic alleles, private variation and homozygous truncating mutations. Genome Biology. 17: 167. PMID 27480531 DOI: 10.1186/s13059-016-1024-y  0.4
2016 Bai L, Yang HH, Hu Y, Shukla A, Ha NH, Doran A, Faraji F, Goldberger N, Lee MP, Keane T, Hunter KW. An Integrated Genome-Wide Systems Genetics Screen for Breast Cancer Metastasis Susceptibility Genes. Plos Genetics. 12: e1005989. PMID 27074153 DOI: 10.1371/journal.pgen.1005989  0.4
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  0.4
2015 Adams DJ, Doran AG, Lilue J, Keane TM. The Mouse Genomes Project: a repository of inbred laboratory mouse strain genomes. Mammalian Genome : Official Journal of the International Mammalian Genome Society. PMID 26123534 DOI: 10.1007/s00335-015-9579-6  0.4
2015 Iyer V, Shen B, Zhang W, Hodgkins A, Keane T, Huang X, Skarnes WC. Off-target mutations are rare in Cas9-modified mice. Nature Methods. 12: 479. PMID 26020497 DOI: 10.1038/nmeth.3408  0.4
2015 Puddu F, Oelschlaegel T, Guerini I, Geisler NJ, Niu H, Herzog M, Salguero I, Ochoa-Montaño B, Viré E, Sung P, Adams DJ, Keane TM, Jackson SP. Synthetic viability genomic screening defines Sae2 function in DNA repair. The Embo Journal. 34: 1509-22. PMID 25899817 DOI: 10.15252/embj.201590973  0.32
2015 Karreth FA, Reschke M, Ruocco A, Ng C, Chapuy B, Léopold V, Sjoberg M, Keane TM, Verma A, Ala U, Tay Y, Wu D, Seitzer N, Velasco-Herrera Mdel C, Bothmer A, et al. The BRAF pseudogene functions as a competitive endogenous RNA and induces lymphoma in vivo. Cell. 161: 319-32. PMID 25843629 DOI: 10.1016/j.cell.2015.02.043  0.32
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  0.4
2015 Aoude LG, Pritchard AL, Robles-Espinoza CD, Wadt K, Harland M, Choi J, Gartside M, Quesada V, Johansson P, Palmer JM, Ramsay AJ, Zhang X, Jones K, Symmons J, Holland EA, ... ... Keane TM, et al. Nonsense mutations in the shelterin complex genes ACD and TERF2IP in familial melanoma. Journal of the National Cancer Institute. 107. PMID 25505254 DOI: 10.1093/jnci/dju408  0.32
2015 Westcott PM, Halliwill KD, To MD, Rashid M, Rust AG, Keane TM, Delrosario R, Jen KY, Gurley KE, Kemp CJ, Fredlund E, Quigley DA, Adams DJ, Balmain A. The mutational landscapes of genetic and chemical models of Kras-driven lung cancer. Nature. 517: 489-92. PMID 25363767 DOI: 10.1038/nature13898  0.32
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  0.4
2014 Keane TM, Wong K, Adams DJ, Flint J, Reymond A, Yalcin B. Identification of structural variation in mouse genomes. Frontiers in Genetics. 5: 192. PMID 25071822 DOI: 10.3389/fgene.2014.00192  0.4
2014 Dove WF, Shedlovsky A, Clipson L, Amos-Landgraf JM, Halberg RB, Krentz KJ, Boehm FJ, Newton MA, Adams DJ, Keane TM. A strategy to identify dominant point mutant modifiers of a quantitative trait. G3 (Bethesda, Md.). 4: 1113-21. PMID 24747760 DOI: 10.1534/g3.114.010595  0.4
2014 Robles-Espinoza CD, Harland M, Ramsay AJ, Aoude LG, Quesada V, Ding Z, Pooley KA, Pritchard AL, Tiffen JC, Petljak M, Palmer JM, Symmons J, Johansson P, Stark MS, Gartside MG, ... ... Keane TM, et al. POT1 loss-of-function variants predispose to familial melanoma. Nature Genetics. 46: 478-81. PMID 24686849 DOI: 10.1038/ng.2947  0.4
2014 Maguire S, Estabel J, Ingham N, Pearson S, Ryder E, Carragher DM, Walker N, Bussell J, Chan WI, Keane TM, Adams DJ, Scudamore CL, Lelliott CJ, Ramírez-Solis R, et al. Targeting of Slc25a21 is associated with orofacial defects and otitis media due to disrupted expression of a neighbouring gene. Plos One. 9: e91807. PMID 24642684 DOI: 10.1371/journal.pone.0091807  0.4
2013 Halligan DL, Kousathanas A, Ness RW, Harr B, Eöry L, Keane TM, Adams DJ, Keightley PD. Contributions of protein-coding and regulatory change to adaptive molecular evolution in murid rodents. Plos Genetics. 9: e1003995. PMID 24339797 DOI: 10.1371/journal.pgen.1003995  0.4
2013 Simon MM, Greenaway S, White JK, Fuchs H, Gailus-Durner V, Wells S, Sorg T, Wong K, Bedu E, Cartwright EJ, Dacquin R, Djebali S, Estabel J, Graw J, Ingham NJ, ... ... Keane TM, et al. A comparative phenotypic and genomic analysis of C57BL/6J and C57BL/6N mouse strains. Genome Biology. 14: R82. PMID 23902802 DOI: 10.1186/gb-2013-14-7-r82  0.4
2013 Atanur SS, Diaz AG, Maratou K, Sarkis A, Rotival M, Game L, Tschannen MR, Kaisaki PJ, Otto GW, Ma MC, Keane TM, Hummel O, Saar K, Chen W, Guryev V, et al. Genome sequencing reveals loci under artificial selection that underlie disease phenotypes in the laboratory rat. Cell. 154: 691-703. PMID 23890820 DOI: 10.1016/j.cell.2013.06.040  0.4
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  0.4
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  0.4
2013 Ryder E, Wong K, Gleeson D, Keane TM, Sethi D, Vyas S, Wardle-Jones H, Bussell JN, Houghton R, Salisbury J, Harvey N, Adams DJ, Ramirez-Solis R. Genomic analysis of a novel spontaneous albino C57BL/6N mouse strain. Genesis (New York, N.Y. : 2000). 51: 523-8. PMID 23620107 DOI: 10.1002/dvg.22398  0.4
2013 Takada T, Ebata T, Noguchi H, Keane TM, Adams DJ, Narita T, Shin-I T, Fujisawa H, Toyoda A, Abe K, Obata Y, Sakaki Y, Moriwaki K, Fujiyama A, Kohara Y, et al. The ancestor of extant Japanese fancy mice contributed to the mosaic genomes of classical inbred strains. Genome Research. 23: 1329-38. PMID 23604024 DOI: 10.1101/gr.156497.113  0.4
2013 Wong K, Adams DJ, Keane TM. Go retro and get a GRIP. Genome Biology. 14: 108. PMID 23514103 DOI: 10.1186/gb-2013-14-3-108  0.4
2013 Keane TM, Wong K, Adams DJ. RetroSeq: transposable element discovery from next-generation sequencing data. Bioinformatics (Oxford, England). 29: 389-90. PMID 23233656 DOI: 10.1093/bioinformatics/bts697  0.4
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  0.4
2012 Bagley BN, Keane TM, Maklakova VI, Marshall JG, Lester RA, Cancel MM, Paulsen AR, Bendzick LE, Been RA, Kogan SC, Cormier RT, Kendziorski C, Adams DJ, Collier LS. A dominantly acting murine allele of Mcm4 causes chromosomal abnormalities and promotes tumorigenesis. Plos Genetics. 8: e1003034. PMID 23133403 DOI: 10.1371/journal.pgen.1003034  0.4
2012 Wong K, Bumpstead S, Van Der Weyden L, Reinholdt LG, Wilming LG, Adams DJ, Keane TM. Sequencing and characterization of the FVB/NJ mouse genome. Genome Biology. 13: R72. PMID 22916792 DOI: 10.1186/gb-2012-13-8-r72  0.4
2012 Yalcin B, Adams DJ, Flint J, Keane TM. Next-generation sequencing of experimental mouse strains. Mammalian Genome : Official Journal of the International Mammalian Genome Society. 23: 490-8. PMID 22772437 DOI: 10.1007/s00335-012-9402-6  0.4
2012 Nellåker C, Keane TM, Yalcin B, Wong K, Agam A, Belgard TG, Flint J, Adams DJ, Frankel WN, Ponting CP. The genomic landscape shaped by selection on transposable elements across 18 mouse strains. Genome Biology. 13: R45. PMID 22703977 DOI: 10.1186/gb-2012-13-6-r45  0.4
2012 Danecek P, Nellåker C, McIntyre RE, Buendia-Buendia JE, Bumpstead S, Ponting CP, Flint J, Durbin R, Keane TM, Adams DJ. High levels of RNA-editing site conservation amongst 15 laboratory mouse strains. Genome Biology. 13: 26. PMID 22524474 DOI: 10.1186/gb-2012-13-4-r26  0.4
2012 Yalcin B, Wong K, Bhomra A, Goodson M, Keane TM, Adams DJ, Flint J. The fine-scale architecture of structural variants in 17 mouse genomes. Genome Biology. 13: R18. PMID 22439878 DOI: 10.1186/gb-2012-13-3-r18  0.4
2011 Rebollo R, Karimi MM, Bilenky M, Gagnier L, Miceli-Royer K, Zhang Y, Goyal P, Keane TM, Jones S, Hirst M, Lorincz MC, Mager DL. Retrotransposon-induced heterochromatin spreading in the mouse revealed by insertional polymorphisms Plos Genetics. 7. PMID 21980304 DOI: 10.1371/journal.pgen.1002301  0.4
2011 Yalcin B, Wong K, Agam A, Goodson M, Keane TM, Gan X, Nellåker C, Goodstadt L, Nicod J, Bhomra A, Hernandez-Pliego P, Whitley H, Cleak J, Dutton R, Janowitz D, et al. Sequence-based characterization of structural variation in the mouse genome. Nature. 477: 326-9. PMID 21921916 DOI: 10.1038/nature10432  0.4
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  0.4
2010 Wong K, Keane TM, Stalker J, Adams DJ. Enhanced structural variant and breakpoint detection using SVMerge by integration of multiple detection methods and local assembly Genome Biology. 11. PMID 21194472 DOI: 10.1186/gb-2010-11-12-r128  0.4
2010 Page AJ, Keane TM, Naughton TJ. Multi-heuristic dynamic task allocation using genetic algorithms in a heterogeneous distributed system. Journal of Parallel and Distributed Computing. 70: 758-766. PMID 20862190 DOI: 10.1016/j.jpdc.2010.03.011  0.4
2010 Otto TD, Wilinski D, Assefa S, Keane TM, Sarry LR, Böhme U, Lemieux J, Barrell B, Pain A, Berriman M, Newbold C, Llinás M. New insights into the blood-stage transcriptome of Plasmodium falciparum using RNA-Seq. Molecular Microbiology. 76: 12-24. PMID 20141604 DOI: 10.1111/j.1365-2958.2009.07026.x  0.4
2010 Steward CA, Humphray S, Plumb B, Jones MC, Quail MA, Rice S, Cox T, Davies R, Bonfield J, Keane TM, Nefedov M, de Jong PJ, Lyons P, Wicker L, Todd J, et al. Genome-wide end-sequenced BAC resources for the NOD/MrkTac() and NOD/ShiLtJ() mouse genomes. Genomics. 95: 105-10. PMID 19909804 DOI: 10.1016/j.ygeno.2009.10.004  0.4
2009 Warimwe GM, Keane TM, Fegan G, Musyoki JN, Newton CR, Pain A, Berriman M, Marsh K, Bull PC. Plasmodium falciparum var gene expression is modified by host immunity. Proceedings of the National Academy of Sciences of the United States of America. 106: 21801-6. PMID 20018734 DOI: 10.1073/pnas.0907590106  0.4
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  0.4
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  0.4
2009 Assefa S, Keane TM, Otto TD, Newbold C, Berriman M. ABACAS: algorithm-based automatic contiguation of assembled sequences. Bioinformatics (Oxford, England). 25: 1968-9. PMID 19497936 DOI: 10.1093/bioinformatics/btp347  0.4
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  0.4
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  0.4
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  0.4
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  0.4
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  0.4
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