The Genome Analysis Centre | TGAC

Burlinson P., Studholme D., Cambray-Young J., Heavens D., Rathjen J., Hodgkin J., Preston G. M.,
Pseudomonas fluorescens NZI7 repels grazing by C. elegans, a natural predator., (2013)
The International Society for Microbial Ecology Journal 7 6

An S. Q., Febrer M., McCarthy Y., Tang D. J., Clissold L., Kaithakottil G., Swarbreck D., Tang J. L., Rogers J., Dow J. M., Ryan R. P.,
High-resolution transcriptional analysis of the regulatory influence of cell-to-cell signalling reveals novel genes that contribute to Xanthomonas phytopathogenesis., (2013)
Molecular Microbiology

Baker K. S., Leggett R. M., Bexfield N. H., Alston M., Daly G., Todd S., Tachedjian M., Holmes C. E., Crameri S., Wang L. F., Heeney J. L., Suu-Ire R., Kellam P., Cunningham A. A., Wood J. L., Caccamo M., Murcia P. R.,
Metagenomic study of the viruses of African straw-coloured fruit bats: Detection of a chiropteran poxvirus and isolation of a novel adenovirus., (2013)
Virology

Belova T., Zhan B., Wright J., Caccamo M., Asp T., Imková H., Kent M., Bendixen C., Panitz F., Lien S., Dole El J., Olsen O. A., Sandve S. R.,
Integration of mate pair sequences to improve shotgun assemblies of flow-sorted chromosome arms of hexaploid wheat., (2013)
BMC Genomics 14 1

Seipke R. F., Barke J., Heavens D., Yu D. W., Hutchings M. I.,
Analysis of the bacterial communities associated with two ant-plant symbioses., (2013)
Microbiologyopen 2 2

Ramirez-Gonzalez R., Yu D. W., Bruce C., Heavens D., Caccamo M., Emerson B. C.,
PyroClean: Denoising Pyrosequences from Protein-Coding Amplicons for the Recovery of Interspecific and Intraspecific Genetic Variation., (2013)
PLoS ONE 8 3

Marron A. O., Alston M. J., Heavens D., Akam M., Caccamo M., Holland P. W., Walker G.,
A family of diatom-like silicon transporters in the siliceous loricate choanoflagellates., (2013)
Proceedings of the Royal Society B: Biological Sciences 280 1756

MacLean D., Yoshida K., Edwards A., Crossman L. C., Clavijo B., Clark M., Swarbreck D., Bashton M., Chapman P., Gijzen M., Caccamo M., Downie A., Kamoun S., Saunders D. G. O.,
Crowdsourcing genomic analyses of ash and ash dieback – power to the people, (2013)
Gigascience 2 2013, 2:2

International Barley Sequencing Consortium I. B. S., Sampath D., Ayling S., Swarbreck D., Febrer M., Caccamo M., Rogers J.,
A physical, genetic and functional sequence assembly of the barley genome., (2012)
Nature 11543

Crossman L. C., Chen H., Cerdeno-Tarraga A., Brooks K., Quail M., Pineiro S., Hobley L., Sockett R. E., Bentley S. D., Parkhill J., Williams H. N., Stine O. C.,
A small predatory core genome in the divergent marine Bacteriovorax marinus SJ and the terrestrial Bdellovibrio bacteriovorus, (2012)
The ISME Journal (Nature group) http://www.nature.com/doifinder/10.1038/ismej.2012 6th September advance online

Sasidharan R., Nepusz T., Swarbreck D., Huala E., Paccanaro A.,
GFam: a platform for automatic annotation of gene families., (2012)
Nucleic Acids Research

Murcia P. R., Hughes J., Battista P., Lloyd L., Baillie G. J., Ramirez-Gonzalez R. H., Ormond D., Oliver K., Elton D., Mumford J. A., Caccamo M., Kellam P., Grenfell B. T., Holmes E. C., Wood J. L.,
Evolution of an Eurasian avian-like influenza virus in naïve and vaccinated pigs, (2012)
PLoS Pathogens 8 5

Sato S., Rogers J., Dalmay T., Mohorianu I.,
The tomato genome sequence provides insights into fleshy fruit evolution., (2012)
Nature 485 7400

Ramirez-Gonzalez R. H., Bonnal R., Caccamo M., Maclean D.,
Bio-samtools: Ruby bindings for SAMtools, a library for accessing BAM files containing high-throughput sequence alignments., (2012)
Source Code for Biology and Medicine 7 1

Bonnal R. J., Aerts J., Githinji G., Goto N., Maclean D., Miller C. A., Mishima H., Pagani M., Ramirez-Gonzalez R., Smant G., Strozzi F., Syme R., Vos R., Wennblom T. J., Woodcroft B. J., Katayama T., Prins P.,
Biogem: an effective tool-based approach for scaling up open source software development in bioinformatics., (2012)
Bioinformatics 28 7

Rogers J.,
Insights into hominid evolution from the gorilla genome sequence., (2012)
Nature 483 7388

Rolfe M. D., Rice C. J., Lucchini S., Pin C., Thompson A., Cameron A. D., Alston M., Stringer M. F., Betts R. P., Baranyi J., Peck M. W., Hinton J. C.,
Lag phase is a distinct growth phase that prepares bacteria for exponential growth and involves transient metal accumulation., (2012)
Journal of Bacteriology 194 3

Brown A. P., Kroon J. T., Swarbreck D., Febrer M., Larson T. R., Graham I. A., Caccamo M., Slabas A. R.,
Tissue-specific whole transcriptome sequencing in castor, directed at understanding triacylglycerol lipid biosynthetic pathways., (2012)
PLoS One 7 2

Trick M., Adamski N. M., Mugford S. G., Jiang C. C., Febrer M., Uauy C.,
Combining SNP discovery from next-generation sequencing data with bulked segregant analysis (BSA) to fine-map genes in polyploid wheat., (2012)
BMC Plant Biology 12 1

Iqbal Z., Caccamo M., Turner I., Flicek P., McVean G.,
De novo assembly and genotyping of variants using colored de Bruijn graphs., (2012)
Nature Genetics 44 2

Lamesch P., Berardini T. Z., Li D., Swarbreck D., Wilks C., Sasidharan R., Muller R., Dreher K., Alexander D. L., Garcia-Hernandez M., Karthikeyan A. S., Lee C. H., Nelson W. D., Ploetz L., Singh S., Wensel A., Huala E.,
The Arabidopsis Information Resource (TAIR): improved gene annotation and new tools., (2012)
Nucleic Acids Research 40 Database issue

Nasiadka A., Clark M. D.,
Zebrafish breeding in the laboratory environment., (2012)
Institute for Laboratory Animal Research Journal 53 2

Young N. D., Debellé F., Oldroyd G. E., Geurts R., Cannon S. B., Udvardi M. K., Benedito V. A., Mayer K. F., Gouzy J., Schoof H., Van de Peer Y., Proost S., Cook D. R., Meyers B. C., Spannagl M., Cheung F., De Mita S., Krishnakumar V., Gundlach H., Zhou S., Mudge J., Bharti A. K., Murray J. D., Naoumkina M. A., Rosen B., Silverstein K. A., Tang H., Rombauts S., Zhao P. X., Zhou P.,
The Medicago genome provides insight into the evolution of rhizobial symbioses., (2011)
Nature 480 7378

Assemblathon 1: a competitive assessment of de novo short read assembly methods., (2011)
Genome Research 21 12

Earl D., Bradnam K., St John J., Darling A., Lin D., Fass J., Yu H. O., Buffalo V., Zerbino D. R., Diekhans M., Nguyen N., Ariyaratne P. N., Sung W. K., Ning Z., Haimel M., Simpson J. T., Fonseca N. A., Birol I., Docking T. R., Ho I. Y., Rokhsar D. S., Chikhi R., Lavenier D., Chapuis G., Naquin D., Maillet N., Schatz M. C., Kelley D. R., Phillippy A. M., Koren S., Yang S. P., Wu W., Chou W. C., Srivastava A., Shaw T. I., Ruby J. G., Skewes-Cox P., Betegon M., Dimon M. T., Solovyev V., Seledtsov I., Kosarev P., Vorobyev D., Ramirez-Gonzalez R., Leggett R., MacLean D., Xia F., Luo R., Li Z., Xie Y.,
Assemblathon 1: a competitive assessment of de novo short read assembly methods., (2011)
Genome Research 21 12

Daly G. M., Bexfield N., Heaney J., Stubbs S., Mayer A. P., Palser A., Kellam P., Drou N., Caccamo M., Tiley L., Alexander G. J., Bernal W., Heeney J. L.,
A viral discovery methodology for clinical biopsy samples utilising massively parallel next generation sequencing., (2011)
PLoS One 6 12

Ramirez-Gonzalez R., Caccamo M., MacLean D.,
Gee Fu: a sequence version and web-services database tool for genomic assembly, genome feature and NGS data., (2011)
Bioinformatics 27 19

Idziak D., Betekhtin A., Wolny E., Lesniewska K., Wright J., Febrer M., Bevan M. W., Jenkins G., Hasterok R.,
Painting the chromosomes of Brachypodium-current status and future prospects., (2011)
Chromosoma 120 5

Clark M. D., Guryev V., Bruijn E., Nijman I. J., Tada M., Wilson C., Deloukas P., Postlethwait J. H., Cuppen E., Stemple D. L.,
Single nucleotide polymorphism (SNP) panels for rapid positional cloning in zebrafish., (2011)
104 13

Whiteley A. R., Bhat A., Martins E. P., Mayden R. L., Arunachalam M., Uusi-Heikkilä S., Ahmed A. T., Shrestha J., Clark M., Stemple D., Bernatchez L.,
Population genomics of wild and laboratory zebrafish (Danio rerio)., (2011)
Molecular Ecology 2011 Sep 16

Crossman L. C.,
Large scale expansion of mobile elements in specific hotspot regions of the German outbreak Escherichia coli O104:H4, (2011)
Nature Precedings hdl:10101/npre.2011.6466.1 n/a

Joron M., Frezal L., Jones R. T., Chamberlain N. L., Lee S. F., Haag C. R., Whibley A., Becuwe M., Baxter S. W., Ferguson L., Wilkinson P. A., Salazar C., Davidson C., Clark R., Quail M. A., Beasley H., Glithero R., Lloyd C., Sims S., Jones M. C., Rogers J., Jiggins C. D., ffrench-Constant R. H.,
Chromosomal rearrangements maintain a polymorphic supergene controlling butterfly mimicry., (2011)
Nature 477 7363

Heavens D., Tailford L. E., Crossman L., Jeffers F., Mackenzie D. A., Caccamo M., Juge N.,
Genome sequence of the vertebrate gut symbiont Lactobacillus reuteri ATCC 53608., (2011)
Journal of Bacteriology 193 15

Danecek P., Auton A., Abecasis G., Albers C. A., Banks E., DePristo M. A., Handsaker R. E., Lunter G., Marth G. T., Sherry S. T., McVean G., Durbin R., 1000 Genomes Project Analysis Group M., Caccamo M.,
The variant call format and VCFtools., (2011)
Bioinformatics 27 15

Appia-Ayme C., Patrick E., J Sullivan M., Alston M. J., Field S. J., Abuoun M., Anjum M. F., Rowley G.,
Novel inducers of the envelope stress response BaeSR in Salmonella Typhimurium: BaeR is critically required for tungstate waste disposal, (2011)
PLoS One 6 8

Seipke R. F., Crossman L., Drou N., Heavens D., Bibb M. J., Caccamo M., Hutchings M. I.,
Draft genome sequence of Streptomyces strain S4, a symbiont of the leaf-cutting ant Acromyrmex octospinosus, (2011)
Journal of Bacteriology 193 16

Bancroft I., Morgan C., Fraser F., Higgins J., Wells R., Clissold L., Baker D., Long Y., Meng J., Wang X., Liu S., Trick M.,
Dissecting the genome of the polyploid crop oilseed rape by transcriptome sequencing., (2011)
Nature Biotechnology 29 8

Febrer M., McLay K., Caccamo M., Twomey K. B., Ryan R. P.,
Advances in bacterial transcriptome and transposon insertion-site profiling using second-generation sequencing., (2011)
Trends in Biotechnology 29 11

Hu Z. L., Ramos A. M., Humphray S. J., Rogers J., Reecy J. M., Rothschild M. F.,
Use of genome sequence information for meat quality trait QTL mining for causal genes and mutations on pig chromosome 17, (2011)
Frontiers in Genetics 2

Carter A. T., Pearson B. M., Crossman L. C., Drou N., Heavens D., Baker D., Febrer M., Caccamo M., Grant K. A., Peck M. W.,
Complete genome sequence of the proteolytic Clostridium botulinum type A5 (B3') strain H04402 065., (2011)
Journal of Bacteriology 193 9

Carter A. T., Pearson B. M., Crossman L. C., Drou N., Heavens D., Baker D., Febrer M., Caccamo M., Grant K. A., Peck M. W.,
Complete genome sequence of the proteolytic Clostridium botulinum type A5 (B3') strain H04402 065, (2011)
Journal of Bacteriology 193 9

Frank R. A., McRae A. F., Pocklington A. J., van de Lagemaat L. N., Navarro P., Croning M. D., Komiyama N. H., Bradley S. J., Challiss R. A., Armstrong J. D., Finn R. D., Malloy M. P., MacLean A. W., Harris S. E., Starr J. M., Bhaskar S. S., Howard E. K., Hunt S. E., Coffey A. J., Ranganath V., Deloukas P., Rogers J., Muir W. J., Deary I. J., Blackwood D. H., Visscher P. M., Grant S. G.,
Clustered coding variants in the glutamate receptor complexes of individuals with schizophrenia and bipolar disorder., (2011)
PLoS One 6 4

Feuillet C., Leach J. E., Rogers J., Schnable P. S., Eversole K.,
Crop genome sequencing: lessons and rationales., (2011)
Trends in Plant Science 16 2

Crossman L. C., Chaudhuri R. R., Beatson S. A., Wells T. J., Desvaux M., Cunningham A. F., Petty N. K., Mahon V., Brinkley C., Hobman J. L., Savarino S. J., Turner S. M., Pallen M. J., Penn C. W., Parkhill J., Turner A. K., Johnson T. J., Thomson N. R., Smith S. G., Henderson I. R.,
A commensal gone bad: complete genome sequence of the prototypical enterotoxigenic Escherichia coli strain H10407., (2010)
Journal of Bacteriology 192 21

Barke J., Seipke R. F., Grüschow S., Heavens D., Drou N., Bibb M. J., Goss R. J., Yu D. W., Hutchings M. I.,
A mixed community of actinomycetes produce multiple antibiotics for the fungus farming ant Acromyrmex octospinosus, (2010)
BMC Biology 8

Archibald A. L., Bolund L., Churcher C., Fredholm M., Groenen M. A., Harlizius B., Lee K. T., Milan D., Rogers J., Rothschild M. F., Uenishi H., Wang J., Schook L. B.,
Pig genome sequence--analysis and publication strategy., (2010)
BMC Genomics 11

Stephenson P., Baker D., Girin T., Perez A., Amoah S., King G. J., Østergaard L.,
A rich TILLING resource for studying gene function in Brassica rapa., (2010)
BMC Plant Biology 10

Quintana F. J., Iglesias A. H., Farez M. F., Caccamo M., Burns E. J., Kassam N., Oukka M., Weiner H. L.,
Adaptive autoimmunity and Foxp3-based immunoregulation in zebrafish., (2010)
PLoS One 5 3

Steward C. A., Humphray S., Plumb B., Jones M. C., Quail M. A., Rice S., Cox T., Davies R., Bonfield J., Keane T. M., Nefedov M., de Jong P. J., Lyons P., Wicker L., Todd J., Hayashizaki Y., Gulban O., Danska J., Harrow J., Hubbard T., Rogers J., Adams D. J.,
Genome-wide end-sequenced BAC resources for the NOD/MrkTac() and NOD/ShiLtJ() mouse genomes., (2010)
Genomics 95 2

Bouzid M., Heavens D., Elwin K., Chalmers R. M., Hadfield S. J., Hunter P. R., Tyler K. M.,
Whole genome amplification (WGA) for archiving and genotyping of clinical isolates of Cryptosporidium species., (2010)
Parasitology 137 1

Kool J., Uren A. G., Martins C. P., Sie D., de Ridder J., Turner G., van Uitert M., Matentzoglu K., Lagcher W., Krimpenfort P., Gadiot J., Pritchard C., Lenz J., Lund A. H., Jonkers J., Rogers J., Adams D. J., Wessels L., Berns A., van Lohuizen M.,
Insertional mutagenesis in mice deficient for p15Ink4b, p16Ink4a, p21Cip1, and p27Kip1 reveals cancer gene interactions and correlations with tumor phenotypes., (2010)
Cancer Research 70 2

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