Robert Davies | Senior Scientific Manager

Davies, Robert

Sequence Analysis and Management (SAM)

My group contributes to various software packages for processing DNA sequence data, including samtools, htslib, biobambam and the Staden package. We also submit raw sequencing data to the EBI on behalf of the research groups.

Publications

  • Genome-wide end-sequenced BAC resources for the NOD/MrkTac() and NOD/ShiLtJ() mouse genomes.

    Steward CA, Humphray S, Plumb B, Jones MC, Quail MA et al.

    Genomics 2010;95;2;105-10

    PUBMED: 19909804; PMC: 2824108; DOI: 10.1016/j.ygeno.2009.10.004

  • A genome-wide, end-sequenced 129Sv BAC library resource for targeting vector construction.

    Adams DJ, Quail MA, Cox T, van der Weyden L, Gorick BD et al.

    Genomics 2005;86;6;753-8

    PUBMED: 16257172; DOI: 10.1016/j.ygeno.2005.08.003

  • The genome of the kinetoplastid parasite, Leishmania major.

    Ivens AC, Peacock CS, Worthey EA, Murphy L, Aggarwal G et al.

    Science (New York, N.Y.) 2005;309;5733;436-42

    PUBMED: 16020728; PMC: 1470643; DOI: 10.1126/science.1112680

  • The genome of the African trypanosome Trypanosoma brucei.

    Berriman M, Ghedin E, Hertz-Fowler C, Blandin G, Renauld H et al.

    Science (New York, N.Y.) 2005;309;5733;416-22

    PUBMED: 16020726; DOI: 10.1126/science.1112642

  • Complex haplotypes, copy number polymorphisms and coding variation in two recently divergent mouse strains.

    Adams DJ, Dermitzakis ET, Cox T, Smith J, Davies R et al.

    Nature genetics 2005;37;5;532-6

    PUBMED: 15852006; DOI: 10.1038/ng1551

  • Mutagenic insertion and chromosome engineering resource (MICER).

    Adams DJ, Biggs PJ, Cox T, Davies R, van der Weyden L et al.

    Nature genetics 2004;36;8;867-71

    PUBMED: 15235602; DOI: 10.1038/ng1388

  • The DNA sequence of chromosome I of an African trypanosome: gene content, chromosome organisation, recombination and polymorphism.

    Hall N, Berriman M, Lennard NJ, Harris BR, Hertz-Fowler C et al.

    Nucleic acids research 2003;31;16;4864-73

    PUBMED: 12907729; PMC: 169939

  • Sequence of Plasmodium falciparum chromosomes 1, 3-9 and 13.

    Hall N, Pain A, Berriman M, Churcher C, Harris B et al.

    Nature 2002;419;6906;527-31

    PUBMED: 12368867; DOI: 10.1038/nature01095

  • Complete genome sequence of a multiple drug resistant Salmonella enterica serovar Typhi CT18.

    Parkhill J, Dougan G, James KD, Thomson NR, Pickard D et al.

    Nature 2001;413;6858;848-52

    PUBMED: 11677608; DOI: 10.1038/35101607

  • Genome sequence of Yersinia pestis, the causative agent of plague.

    Parkhill J, Wren BW, Thomson NR, Titball RW, Holden MT et al.

    Nature 2001;413;6855;523-7

    PUBMED: 11586360; DOI: 10.1038/35097083

  • An SNP map of human chromosome 22.

    Mullikin JC, Hunt SE, Cole CG, Mortimore BJ, Rice CM et al.

    Nature 2000;407;6803;516-20

    PUBMED: 11029003; DOI: 10.1038/35035089

  • Complete DNA sequence of a serogroup A strain of Neisseria meningitidis Z2491.

    Parkhill J, Achtman M, James KD, Bentley SD, Churcher C et al.

    Nature 2000;404;6777;502-6

    PUBMED: 10761919; DOI: 10.1038/35006655

  • The genome sequence of the food-borne pathogen Campylobacter jejuni reveals hypervariable sequences.

    Parkhill J, Wren BW, Mungall K, Ketley JM, Churcher C et al.

    Nature 2000;403;6770;665-8

    PUBMED: 10688204; DOI: 10.1038/35001088

  • The complete nucleotide sequence of chromosome 3 of Plasmodium falciparum.

    Bowman S, Lawson D, Basham D, Brown D, Chillingworth T et al.

    Nature 1999;400;6744;532-8

    PUBMED: 10448855; DOI: 10.1038/22964

  • Deciphering the biology of Mycobacterium tuberculosis from the complete genome sequence.

    Cole ST, Brosch R, Parkhill J, Garnier T, Churcher C et al.

    Nature 1998;393;6685;537-44

    PUBMED: 9634230; DOI: 10.1038/31159

  • Genome-wide end-sequenced BAC resources for the NOD/MrkTac() and NOD/ShiLtJ() mouse genomes.

    Steward CA, Humphray S, Plumb B, Jones MC, Quail MA et al.

    Genomics 2010;95;2;105-10

    PUBMED: 19909804; PMC: 2824108; DOI: 10.1016/j.ygeno.2009.10.004

  • A genome-wide, end-sequenced 129Sv BAC library resource for targeting vector construction.

    Adams DJ, Quail MA, Cox T, van der Weyden L, Gorick BD et al.

    Genomics 2005;86;6;753-8

    PUBMED: 16257172; DOI: 10.1016/j.ygeno.2005.08.003

  • The genome of the African trypanosome Trypanosoma brucei.

    Berriman M, Ghedin E, Hertz-Fowler C, Blandin G, Renauld H et al.

    Science (New York, N.Y.) 2005;309;5733;416-22

    PUBMED: 16020726; DOI: 10.1126/science.1112642

  • The genome of the kinetoplastid parasite, Leishmania major.

    Ivens AC, Peacock CS, Worthey EA, Murphy L, Aggarwal G et al.

    Science (New York, N.Y.) 2005;309;5733;436-42

    PUBMED: 16020728; PMC: 1470643; DOI: 10.1126/science.1112680

  • Complex haplotypes, copy number polymorphisms and coding variation in two recently divergent mouse strains.

    Adams DJ, Dermitzakis ET, Cox T, Smith J, Davies R et al.

    Nature genetics 2005;37;5;532-6

    PUBMED: 15852006; DOI: 10.1038/ng1551

  • Mutagenic insertion and chromosome engineering resource (MICER).

    Adams DJ, Biggs PJ, Cox T, Davies R, van der Weyden L et al.

    Nature genetics 2004;36;8;867-71

    PUBMED: 15235602; DOI: 10.1038/ng1388

  • The DNA sequence of chromosome I of an African trypanosome: gene content, chromosome organisation, recombination and polymorphism.

    Hall N, Berriman M, Lennard NJ, Harris BR, Hertz-Fowler C et al.

    Nucleic acids research 2003;31;16;4864-73

    PUBMED: 12907729; PMC: 169939

  • Sequence of Plasmodium falciparum chromosomes 1, 3-9 and 13.

    Hall N, Pain A, Berriman M, Churcher C, Harris B et al.

    Nature 2002;419;6906;527-31

    PUBMED: 12368867; DOI: 10.1038/nature01095

  • Complete genome sequence of a multiple drug resistant Salmonella enterica serovar Typhi CT18.

    Parkhill J, Dougan G, James KD, Thomson NR, Pickard D et al.

    Nature 2001;413;6858;848-52

    PUBMED: 11677608; DOI: 10.1038/35101607

  • Genome sequence of Yersinia pestis, the causative agent of plague.

    Parkhill J, Wren BW, Thomson NR, Titball RW, Holden MT et al.

    Nature 2001;413;6855;523-7

    PUBMED: 11586360; DOI: 10.1038/35097083

  • An SNP map of human chromosome 22.

    Mullikin JC, Hunt SE, Cole CG, Mortimore BJ, Rice CM et al.

    Nature 2000;407;6803;516-20

    PUBMED: 11029003; DOI: 10.1038/35035089

  • Complete DNA sequence of a serogroup A strain of Neisseria meningitidis Z2491.

    Parkhill J, Achtman M, James KD, Bentley SD, Churcher C et al.

    Nature 2000;404;6777;502-6

    PUBMED: 10761919; DOI: 10.1038/35006655

  • The genome sequence of the food-borne pathogen Campylobacter jejuni reveals hypervariable sequences.

    Parkhill J, Wren BW, Mungall K, Ketley JM, Churcher C et al.

    Nature 2000;403;6770;665-8

    PUBMED: 10688204; DOI: 10.1038/35001088

  • The complete nucleotide sequence of chromosome 3 of Plasmodium falciparum.

    Bowman S, Lawson D, Basham D, Brown D, Chillingworth T et al.

    Nature 1999;400;6744;532-8

    PUBMED: 10448855; DOI: 10.1038/22964

  • Deciphering the biology of Mycobacterium tuberculosis from the complete genome sequence.

    Cole ST, Brosch R, Parkhill J, Garnier T, Churcher C et al.

    Nature 1998;393;6685;537-44

    PUBMED: 9634230; DOI: 10.1038/31159

Davies, Robert
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