Publications by authors named "Thomas M Keane"

58Publications

Transcriptional activity and strain-specific history of mouse pseudogenes.

Nat Commun 2020 07 29;11(1):3695. Epub 2020 Jul 29.

Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, 06520, USA.

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http://dx.doi.org/10.1038/s41467-020-17157-wDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7392758PMC
July 2020

Mouse protein coding diversity: What's left to discover?

PLoS Genet 2019 11 14;15(11):e1008446. Epub 2019 Nov 14.

European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, Cambridge, United Kingdom.

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http://dx.doi.org/10.1371/journal.pgen.1008446DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6855407PMC
November 2019

Genome-wide genetic screening with chemically mutagenized haploid embryonic stem cells.

Nat Chem Biol 2017 Jan 31;13(1):12-14. Epub 2016 Oct 31.

The Wellcome Trust and Cancer Research UK Gurdon Institute, and Department of Biochemistry, University of Cambridge, Cambridge, UK.

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http://dx.doi.org/10.1038/nchembio.2226DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5164930PMC
January 2017

Whole Genome Sequence of Two Wild-Derived Mus musculus domesticus Inbred Strains, LEWES/EiJ and ZALENDE/EiJ, with Different Diploid Numbers.

G3 (Bethesda) 2016 12 7;6(12):4211-4216. Epub 2016 Dec 7.

Department of Genetics, Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina 27599-7264

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http://g3journal.org/lookup/doi/10.1534/g3.116.034751
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http://dx.doi.org/10.1534/g3.116.034751DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5144988PMC
December 2016

The Mouse Genomes Project: a repository of inbred laboratory mouse strain genomes.

Mamm Genome 2015 Oct 30;26(9-10):403-12. Epub 2015 Jun 30.

Wellcome Trust Sanger Institute, Hinxton, Cambridge, CB10 1HH, UK.

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http://link.springer.com/10.1007/s00335-015-9579-6
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http://dx.doi.org/10.1007/s00335-015-9579-6DOI Listing
October 2015

Synthetic viability genomic screening defines Sae2 function in DNA repair.

EMBO J 2015 Jun 21;34(11):1509-22. Epub 2015 Apr 21.

The Gurdon Institute and Department of Biochemistry, University of Cambridge, Cambridge, UK The Wellcome Trust Sanger Institute, Hinxton Cambridge, UK

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http://dx.doi.org/10.15252/embj.201590973DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4474527PMC
June 2015

Nonsense mutations in the shelterin complex genes ACD and TERF2IP in familial melanoma.

J Natl Cancer Inst 2015 Feb 13;107(2). Epub 2014 Dec 13.

Affiliations of authors: QIMR Berghofer Medical Research Institute, Brisbane, Australia (LGA, ALP, MG, PJ, JMP, JS, VB, SW, KDR, MSS, GWM, NGM, NKH); Wellcome Trust Sanger Institute, Hinxton, Cambridge, UK (CDRE, TMK, DJA); Department of Clinical Genetics, Rigshospitalet, Copenhagen, Denmark (KW, AMG); Leeds Institute of Cancer and Pathology, University of Leeds, Leeds, UK (MH, HSn, DTB, JANB); Laboratory of Translational Genomics, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD (JC, KMB); Departamento de Bioquímica y Biología Molecular, Instituto Universitario de Oncología del Principado de Asturias (IUOPA) Universidad de Oviedo, Oviedo, Spain (VQ, AJR, CLO); Cancer Genomics Research Laboratory, NCI Frederick, SAIC-Frederick Inc., Frederick MD (XZ, KJ); Department of Dermatology, Leiden University Medical Centre, Leiden, the Netherlands (RvD, NAG); Department of Clinical Sciences Lund, Division of Oncology and Pathology, Lund University, Lund, Sweden (HO, CI, ÅB, GJ); Translational Genomics Institute, Phoenix, AZ (JMT); University of Sydney at Westmead Millennium Institute, Westmead, Sydney, NSW, Australia (EAH, HSc, GJM); Melanoma Institute Australia, North Sydney, NSW, Australia (EAH, HSc, GJM).

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http://dx.doi.org/10.1093/jnci/dju408DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4334787PMC
February 2015

The mutational landscapes of genetic and chemical models of Kras-driven lung cancer.

Nature 2015 Jan 2;517(7535):489-92. Epub 2014 Nov 2.

1] Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, California 94158, USA [2] Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, California 94158, USA.

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http://dx.doi.org/10.1038/nature13898DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4304785PMC
January 2015

RNA-seq reveals the pan-transcriptomic impact of attenuating the gliotoxin self-protection mechanism in Aspergillus fumigatus.

BMC Genomics 2014 Oct 14;15:894. Epub 2014 Oct 14.

Department of Biology, National University of Ireland Maynooth, Maynooth, Co, Kildare, Ireland.

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http://dx.doi.org/10.1186/1471-2164-15-894DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4209032PMC
October 2014

Identification of structural variation in mouse genomes.

Front Genet 2014 2;5:192. Epub 2014 Jul 2.

Center for Integrative Genomics, University of Lausanne Lausanne, Switzerland ; Institute of Genetics and Molecular and Cellular Biology Illkirch, France.

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http://journal.frontiersin.org/article/10.3389/fgene.2014.00
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http://dx.doi.org/10.3389/fgene.2014.00192DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4079067PMC
July 2014

Genomic and proteomic dissection of the ubiquitous plant pathogen, Armillaria mellea: toward a new infection model system.

J Proteome Res 2013 Jun 28;12(6):2552-70. Epub 2013 May 28.

Department of Biology, National University of Ireland Maynooth, Maynooth, Co Kildare, Ireland.

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http://dx.doi.org/10.1021/pr301131tDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3679558PMC
June 2013

Go retro and get a GRIP.

Genome Biol 2013 Mar 19;14(3):108. Epub 2013 Mar 19.

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http://dx.doi.org/10.1186/gb-2013-14-3-108DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3663096PMC
March 2013

RetroSeq: transposable element discovery from next-generation sequencing data.

Bioinformatics 2013 Feb 10;29(3):389-90. Epub 2012 Dec 10.

Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, UK.

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http://dx.doi.org/10.1093/bioinformatics/bts697DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3562067PMC
February 2013

Next-generation sequencing of experimental mouse strains.

Mamm Genome 2012 Oct 7;23(9-10):490-8. Epub 2012 Jul 7.

Center for Integrative Genomics, University of Lausanne, Lausanne, Switzerland.

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http://dx.doi.org/10.1007/s00335-012-9402-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3463794PMC
October 2012

The genomic landscape shaped by selection on transposable elements across 18 mouse strains.

Genome Biol 2012 Jun 15;13(6):R45. Epub 2012 Jun 15.

MRC Functional Genomics Unit, Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, UK.

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http://dx.doi.org/10.1186/gb-2012-13-6-r45DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3446317PMC
June 2012

Multi-heuristic dynamic task allocation using genetic algorithms in a heterogeneous distributed system.

J Parallel Distrib Comput 2010 Jul;70(7):758-766

Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, CB10 1SA, UK.

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http://dx.doi.org/10.1016/j.jpdc.2010.03.011DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2927021PMC
July 2010

New insights into the blood-stage transcriptome of Plasmodium falciparum using RNA-Seq.

Mol Microbiol 2010 Apr 4;76(1):12-24. Epub 2010 Feb 4.

Parasite Genomics, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK.

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http://dx.doi.org/10.1111/j.1365-2958.2009.07026.xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2859250PMC
April 2010

Plasmodium falciparum var gene expression is modified by host immunity.

Proc Natl Acad Sci U S A 2009 Dec 11;106(51):21801-6. Epub 2009 Dec 11.

Kenya Medical Research Institute-Wellcome Trust Research Programme, 80108 Kilifi, Kenya.

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http://dx.doi.org/10.1073/pnas.0907590106DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2792160PMC
December 2009

ABACAS: algorithm-based automatic contiguation of assembled sequences.

Bioinformatics 2009 Aug 3;25(15):1968-9. Epub 2009 Jun 3.

Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge CB10 1SA, UK.

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http://dx.doi.org/10.1093/bioinformatics/btp347DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2712343PMC
August 2009

Next-generation sequencing of vertebrate experimental organisms.

Mamm Genome 2009 Jun 19;20(6):327-38. Epub 2009 May 19.

Experimental Cancer Genetics, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, UK.

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http://dx.doi.org/10.1007/s00335-009-9187-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2714443PMC
June 2009

MultiPhyl: a high-throughput phylogenomics webserver using distributed computing.

Nucleic Acids Res 2007 Jul 6;35(Web Server issue):W33-7. Epub 2007 Jun 6.

Pathogen Sequencing Unit, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, CB10 1SA Hinxton, UK.

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http://dx.doi.org/10.1093/nar/gkm359DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1933173PMC
July 2007