Dr James Cotton | Senior Staff Scientist

Cotton, James

I'm involved in a range of projects across a diverse array of parasitic species, including nematodes, schistosomes and kinetoplastids. I play a leading role in a number of de novo genome sequencing projects, but particularly focus on projects with a strong comparative or population genomics component.

My research at the Sanger Institute is on evolutionary genomics of parasites, and particularly on parasites that cause neglected tropical diseases. This work covers a wide range of organisms from parasitic protozoa such as Leishmania to complex multicellular helminths, but they are united by a strong emphasis on either comparative or population genomic questions.

I studied biology at Oxford, and then did a PhD on gene family evolution with Rod Page at the University of Glasgow, followed by post-docs at the Natural History Museum in London and at the National University of Ireland, Maynooth, working on various topics in phylogenetics and molecular evolution. I was subsequently an RCUK Fellow at Queen Mary, University of London for three years before joining the parasite genomics group in 2010.

Publications

  • Whole genome resequencing of the human parasite Schistosoma mansoni reveals population history and effects of selection.

    Crellen T, Allan F, David S, Durrant C, Huckvale T et al.

    Scientific reports 2016;6;20954

  • Evolutionary genomics of epidemic visceral leishmaniasis in the Indian subcontinent.

    Imamura H, Downing T, Van den Broeck F, Sanders MJ, Rijal S et al.

    eLife 2016;5

  • Whipworm genome and dual-species transcriptome analyses provide molecular insights into an intimate host-parasite interaction.

    Foth BJ, Tsai IJ, Reid AJ, Bancroft AJ, Nichol S et al.

    Nature genetics 2014;46;7;693-700

  • The genome and life-stage specific transcriptomes of Globodera pallida elucidate key aspects of plant parasitism by a cyst nematode.

    Cotton JA, Lilley CJ, Jones LM, Kikuchi T, Reid AJ et al.

    Genome biology 2014;15;3;R43

  • Genomic confirmation of hybridisation and recent inbreeding in a vector-isolated Leishmania population.

    Rogers MB, Downing T, Smith BA, Imamura H, Sanders M et al.

    PLoS genetics 2014;10;1;e1004092

  • Genome sequence of the tsetse fly (Glossina morsitans): vector of African trypanosomiasis.

    International Glossina Genome Initiative

    Science (New York, N.Y.) 2014;344;6182;380-6

  • The peculiar epidemiology of dracunculiasis in Chad.

    Eberhard ML, Ruiz-Tiben E, Hopkins DR, Farrell C, Toe F et al.

    The American journal of tropical medicine and hygiene 2014;90;1;61-70

  • Genome-wide signatures of convergent evolution in echolocating mammals.

    Parker J, Tsagkogeorga G, Cotton JA, Liu Y, Provero P et al.

    Nature 2013;502;7470;228-31

  • The genome and transcriptome of Haemonchus contortus, a key model parasite for drug and vaccine discovery.

    Laing R, Kikuchi T, Martinelli A, Tsai IJ, Beech RN et al.

    Genome biology 2013;14;8;R88

  • Whole genome sequencing of multiple Leishmania donovani clinical isolates provides insights into population structure and mechanisms of drug resistance.

    Downing T, Imamura H, Decuypere S, Clark TG, Coombs GH et al.

    Genome research 2011;21;12;2143-56

  • Evolutionary genomics of epidemic visceral leishmaniasis in the Indian subcontinent.

    Imamura H, Downing T, Van den Broeck F, Sanders MJ, Rijal S et al.

    eLife 2016;5

  • In vitro selection of miltefosine resistance in promastigotes of Leishmania donovani from Nepal: genomic and metabolomic characterization.

    Shaw CD, Lonchamp J, Downing T, Imamura H, Freeman TM et al.

    Molecular microbiology 2016;99;6;1134-48

  • Whole genome resequencing of the human parasite Schistosoma mansoni reveals population history and effects of selection.

    Crellen T, Allan F, David S, Durrant C, Huckvale T et al.

    Scientific reports 2016;6;20954

  • Modelling the effects of mass drug administration on the molecular epidemiology of schistosomes.

    Lamberton PH, Crellen T, Cotton JA and Webster JP

    Advances in parasitology 2015;87;293-327

  • Mosaic aneuploidy in Leishmania: the perspective of whole genome sequencing.

    Dujardin JC, Mannaert A, Durrant C and Cotton JA

    Trends in parasitology 2014;30;12;554-5

  • Whipworm genome and dual-species transcriptome analyses provide molecular insights into an intimate host-parasite interaction.

    Foth BJ, Tsai IJ, Reid AJ, Bancroft AJ, Nichol S et al.

    Nature genetics 2014;46;7;693-700

  • The genome and life-stage specific transcriptomes of Globodera pallida elucidate key aspects of plant parasitism by a cyst nematode.

    Cotton JA, Lilley CJ, Jones LM, Kikuchi T, Reid AJ et al.

    Genome biology 2014;15;3;R43

  • The peculiar epidemiology of dracunculiasis in Chad.

    Eberhard ML, Ruiz-Tiben E, Hopkins DR, Farrell C, Toe F et al.

    The American journal of tropical medicine and hygiene 2014;90;1;61-70

  • Genomic confirmation of hybridisation and recent inbreeding in a vector-isolated Leishmania population.

    Rogers MB, Downing T, Smith BA, Imamura H, Sanders M et al.

    PLoS genetics 2014;10;1;e1004092

  • Phylogenomic analyses elucidate the evolutionary relationships of bats.

    Tsagkogeorga G, Parker J, Stupka E, Cotton JA and Rossiter SJ

    Current biology : CB 2013;23;22;2262-7

  • Genome-wide signatures of convergent evolution in echolocating mammals.

    Parker J, Tsagkogeorga G, Cotton JA, Liu Y, Provero P et al.

    Nature 2013;502;7470;228-31

  • The genome and transcriptome of Haemonchus contortus, a key model parasite for drug and vaccine discovery.

    Laing R, Kikuchi T, Martinelli A, Tsai IJ, Beech RN et al.

    Genome biology 2013;14;8;R88

  • Characterization and comparative analysis of the complete Haemonchus contortus β-tubulin gene family and implications for benzimidazole resistance in strongylid nematodes.

    Saunders GI, Wasmuth JD, Beech R, Laing R, Hunt M et al.

    International journal for parasitology 2013;43;6;465-75

  • The evolution of bat vestibular systems in the face of potential antagonistic selection pressures for flight and echolocation.

    Davies KT, Bates PJ, Maryanto I, Cotton JA and Rossiter SJ

    PloS one 2013;8;4;e61998

  • New approaches for unravelling reassortment pathways.

    Svinti V, Cotton JA and McInerney JO

    BMC evolutionary biology 2013;13;1

  • Experimental design in phylogenetics: testing predictions from expected information.

    San Mauro D, Gower DJ, Cotton JA, Zardoya R, Wilkinson M and Massingham T

    Systematic biology 2012;61;4;661-74

  • Parallel signatures of sequence evolution among hearing genes in echolocating mammals: an emerging model of genetic convergence.

    Davies KT, Cotton JA, Kirwan JD, Teeling EC and Rossiter SJ

    Heredity 2012;108;5;480-9

  • Comparative genomics of the apicomplexan parasites Toxoplasma gondii and Neospora caninum: Coccidia differing in host range and transmission strategy.

    Reid AJ, Vermont SJ, Cotton JA, Harris D, Hill-Cawthorne GA et al.

    PLoS pathogens 2012;8;3;e1002567

  • Whole genome sequencing of multiple Leishmania donovani clinical isolates provides insights into population structure and mechanisms of drug resistance.

    Downing T, Imamura H, Decuypere S, Clark TG, Coombs GH et al.

    Genome research 2011;21;12;2143-56

  • Genomic insights into the origin of parasitism in the emerging plant pathogen Bursaphelenchus xylophilus.

    Kikuchi T, Cotton JA, Dalzell JJ, Hasegawa K, Kanzaki N et al.

    PLoS pathogens 2011;7;9;e1002219

  • Stops making sense: translational trade-offs and stop codon reassignment.

    Johnson LJ, Cotton JA, Lichtenstein CP, Elgar GS, Nichols RA et al.

    BMC evolutionary biology 2011;11;227

  • Cetaceans on a molecular fast track to ultrasonic hearing.

    Liu Y, Rossiter SJ, Han X, Cotton JA and Zhang S

    Current biology : CB 2010;20;20;1834-9

  • Eukaryotic genes of archaebacterial origin are more important than the more numerous eubacterial genes, irrespective of function.

    Cotton JA and McInerney JO

    Proceedings of the National Academy of Sciences of the United States of America 2010;107;40;17252-5

  • Convergent sequence evolution between echolocating bats and dolphins.

    Liu Y, Cotton JA, Shen B, Han X, Rossiter SJ and Zhang S

    Current biology : CB 2010;20;2;R53-4

  • Experimental design in caecilian systematics: phylogenetic information of mitochondrial genomes and nuclear rag1.

    San Mauro D, Gower DJ, Massingham T, Wilkinson M, Zardoya R and Cotton JA

    Systematic biology 2009;58;4;425-38

  • The evolution of color vision in nocturnal mammals.

    Zhao H, Rossiter SJ, Teeling EC, Li C, Cotton JA and Zhang S

    Proceedings of the National Academy of Sciences of the United States of America 2009;106;22;8980-5

  • The role of Notch signalling and numb function in mechanosensory organ formation in the spider Cupiennius salei.

    Gold K, Cotton JA and Stollewerk A

    Developmental biology 2009;327;1;121-31

  • Supertrees join the mainstream of phylogenetics.

    Cotton JA and Wilkinson M

    Trends in ecology & evolution 2009;24;1;1-3

  • The hearing gene Prestin reunites echolocating bats.

    Li G, Wang J, Rossiter SJ, Jones G, Cotton JA and Zhang S

    Proceedings of the National Academy of Sciences of the United States of America 2008;105;37;13959-64

  • The prokaryotic tree of life: past, present... and future?

    McInerney JO, Cotton JA and Pisani D

    Trends in ecology & evolution 2008;23;5;276-81

  • The Ediacaran emergence of bilaterians: congruence between the genetic and the geological fossil records.

    Peterson KJ, Cotton JA, Gehling JG and Pisani D

    Philosophical transactions of the Royal Society of London. Series B, Biological sciences 2008;363;1496;1435-43

  • The tree of genomes: an empirical comparison of genome-phylogeny reconstruction methods.

    McCann A, Cotton JA and McInerney JO

    BMC evolutionary biology 2008;8;312

  • Tempo and mode of diversification of lake Tanganyika cichlid fishes.

    Day JJ, Cotton JA and Barraclough TG

    PloS one 2008;3;3;e1730

  • Relative time scales reveal multiple origins of parallel disjunct distributions of African caecilian amphibians.

    Loader SP, Pisani D, Cotton JA, Gower DJ, Day JJ and Wilkinson M

    Biology letters 2007;3;5;505-8

  • Supertrees disentangle the chimerical origin of eukaryotic genomes.

    Pisani D, Cotton JA and McInerney JO

    Molecular biology and evolution 2007;24;8;1752-60

  • Majority-rule supertrees.

    Cotton JA and Wilkinson M

    Systematic biology 2007;56;3;445-52

  • Properties of supertree methods in the consensus setting.

    Wilkinson M, Cotton JA, Lapointe FJ and Pisani D

    Systematic biology 2007;56;2;330-7

  • Discriminating supported and unsupported relationships in supertrees using triplets.

    Cotton JA, Slater CS and Wilkinson M

    Systematic biology 2006;55;2;345-50

  • The shape of human gene family phylogenies.

    Cotton JA and Page RD

    BMC evolutionary biology 2006;6;66

  • Measuring support and finding unsupported relationships in supertrees.

    Wilkinson M, Pisani D, Cotton JA and Corfe I

    Systematic biology 2005;54;5;823-31

  • The shape of supertrees to come: tree shape related properties of fourteen supertree methods.

    Wilkinson M, Cotton JA, Creevey C, Eulenstein O, Harris SR et al.

    Systematic biology 2005;54;3;419-31

  • Rates and patterns of gene duplication and loss in the human genome.

    Cotton JA and Page RD

    Proceedings. Biological sciences / The Royal Society 2005;272;1560;277-83

  • Analytical methods for detecting paralogy in molecular datasets.

    Cotton JA

    Methods in enzymology 2005;395;700-24

  • Gene tree parsimony vs uninode coding for phylogenetic reconstruction.

    Cotton JA and Page RD

    Molecular phylogenetics and evolution 2003;29;2;298-308

  • Going nuclear: gene family evolution and vertebrate phylogeny reconciled.

    Cotton JA and Page RD

    Proceedings. Biological sciences / The Royal Society 2002;269;1500;1555-61

  • Vertebrate phylogenomics: reconciled trees and gene duplications.

    Page RD and Cotton JA

    Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing 2002;536-47

Cotton, James
James's Timeline
2010

Joined Parasite Genomics group

2007

moved to RCUK academic fellowship at Queen Mary, University of London

2003

awarded PhD, University of Glasgow

1997

graduated with a BA in Biological Sciences from the University of Oxford