James A. Cotton - Publications

Affiliations: 
Wellcome Trust Sanger Institute, England, United Kingdom 
Area:
Phlyogenetics, Genome Evolution

57 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
2016 Eves-van den Akker S, Laetsch DR, Thorpe P, Lilley CJ, Danchin EG, Da Rocha M, Rancurel C, Holroyd NE, Cotton JA, Szitenberg A, Grenier E, Montarry J, Mimee B, Duceppe MO, Boyes I, et al. The genome of the yellow potato cyst nematode, Globodera rostochiensis, reveals insights into the basis of parasitism and virulence. Genome Biology. 17: 124. PMID 27286965 DOI: 10.1186/S13059-016-0985-1  1
2016 Imamura H, Downing T, Van den Broeck F, Sanders MJ, Rijal S, Sundar S, Mannaert A, Vanaerschot M, Berg M, De Muylder G, Dumetz F, Cuypers B, Maes I, Domagalska M, Decuypere S, ... ... Cotton JA, et al. Evolutionary genomics of epidemic visceral leishmaniasis in the Indian subcontinent. Elife. 5. PMID 27003289 DOI: 10.7554/Elife.12613  1
2016 Crellen T, Allan F, David S, Durrant C, Huckvale T, Holroyd N, Emery AM, Rollinson D, Aanensen DM, Berriman M, Webster JP, Cotton JA. Whole genome resequencing of the human parasite Schistosoma mansoni reveals population history and effects of selection. Scientific Reports. 6: 20954. PMID 26879532 DOI: 10.1038/Srep20954  1
2016 Hunt VL, Tsai IJ, Coghlan A, Reid AJ, Holroyd N, Foth BJ, Tracey A, Cotton JA, Stanley EJ, Beasley H, Bennett HM, Brooks K, Harsha B, Kajitani R, Kulkarni A, et al. The genomic basis of parasitism in the Strongyloides clade of nematodes. Nature Genetics. PMID 26829753 DOI: 10.1038/Ng.3495  1
2016 Shaw CD, Lonchamp J, Downing T, Imamura H, Freeman TM, Cotton JA, Sanders M, Blackburn G, Dujardin JC, Rijal S, Khanal B, Illingworth CJ, Coombs GH, Carter KC. In vitro selection of miltefosine resistance in promastigotes of Leishmania donovani from Nepal: genomic and metabolomic characterization. Molecular Microbiology. 99: 1134-48. PMID 26713880 DOI: 10.1111/Mmi.13291  1
2016 Laing R, Martinelli A, Tracey A, Holroyd N, Gilleard JS, Cotton JA. Haemonchus contortus: Genome Structure, Organization and Comparative Genomics Advances in Parasitology. DOI: 10.1016/bs.apar.2016.02.016  1
2015 Kuo HC, Chen SF, Fang YP, Cotton JA, Parker JD, Csorba G, Lim BK, Eger JL, Chen CH, Chou CH, Rossiter SJ. Speciation processes in putative island endemic sister bat species: false impressions from mitochondrial DNA and microsatellite data. Molecular Ecology. PMID 26475683 DOI: 10.1111/Mec.13425  1
2015 Lamberton PH, Crellen T, Cotton JA, Webster JP. Modelling the effects of mass drug administration on the molecular epidemiology of schistosomes. Advances in Parasitology. 87: 293-327. PMID 25765198 DOI: 10.1016/Bs.Apar.2014.12.006  1
2014 Dujardin JC, Mannaert A, Durrant C, Cotton JA. Mosaic aneuploidy in Leishmania: the perspective of whole genome sequencing. Trends in Parasitology. 30: 554-5. PMID 25458156 DOI: 10.1016/J.Pt.2014.09.004  1
2014 Foth BJ, Tsai IJ, Reid AJ, Bancroft AJ, Nichol S, Tracey A, Holroyd N, Cotton JA, Stanley EJ, Zarowiecki M, Liu JZ, Huckvale T, Cooper PJ, Grencis RK, Berriman M. Whipworm genome and dual-species transcriptome analyses provide molecular insights into an intimate host-parasite interaction. Nature Genetics. 46: 693-700. PMID 24929830 DOI: 10.1038/Ng.3010  1
2014 Watanabe J, Hattori M, Berriman M, Lehane MJ, Hall N, Solano P, Aksoy S, Hide W, Touré Y, Attardo GM, Darby AC, Toyoda A, Hertz-Fowler C, Larkin DM, Cotton JA, et al. Genome sequence of the tsetse fly (Glossina morsitans ): Vector of African trypanosomiasis Science. 344: 380-386. PMID 24763584 DOI: 10.1126/Science.1249656  1
2014 Cotton JA, Lilley CJ, Jones LM, Kikuchi T, Reid AJ, Thorpe P, Tsai IJ, Beasley H, Blok V, Cock PJ, Eves-van den Akker S, Holroyd N, Hunt M, Mantelin S, Naghra H, et al. The genome and life-stage specific transcriptomes of Globodera pallida elucidate key aspects of plant parasitism by a cyst nematode. Genome Biology. 15: R43. PMID 24580726 DOI: 10.1186/Gb-2014-15-3-R43  1
2014 Rogers MB, Downing T, Smith BA, Imamura H, Sanders M, Svobodova M, Volf P, Berriman M, Cotton JA, Smith DF. Genomic confirmation of hybridisation and recent inbreeding in a vector-isolated Leishmania population. Plos Genetics. 10: e1004092. PMID 24453988 DOI: 10.1371/Journal.Pgen.1004092  1
2014 Eberhard ML, Ruiz-Tiben E, Hopkins DR, Farrell C, Toe F, Weiss A, Withers PC, Jenks MH, Thiele EA, Cotton JA, Hance Z, Holroyd N, Cama VA, Tahir MA, Mounda T. The peculiar epidemiology of dracunculiasis in Chad. The American Journal of Tropical Medicine and Hygiene. 90: 61-70. PMID 24277785 DOI: 10.4269/Ajtmh.13-0554  1
2013 Tsagkogeorga G, Parker J, Stupka E, Cotton JA, Rossiter SJ. Phylogenomic analyses elucidate the evolutionary relationships of bats. Current Biology : Cb. 23: 2262-7. PMID 24184098 DOI: 10.1016/J.Cub.2013.09.014  1
2013 Parker J, Tsagkogeorga G, Cotton JA, Liu Y, Provero P, Stupka E, Rossiter SJ. Genome-wide signatures of convergent evolution in echolocating mammals. Nature. 502: 228-31. PMID 24005325 DOI: 10.1038/Nature12511  1
2013 Laing R, Kikuchi T, Martinelli A, Tsai IJ, Beech RN, Redman E, Holroyd N, Bartley DJ, Beasley H, Britton C, Curran D, Devaney E, Gilabert A, Hunt M, Jackson F, ... ... Cotton JA, et al. The genome and transcriptome of Haemonchus contortus, a key model parasite for drug and vaccine discovery. Genome Biology. 14: R88. PMID 23985316 DOI: 10.1186/Gb-2013-14-8-R88  1
2013 Davies KT, Bates PJ, Maryanto I, Cotton JA, Rossiter SJ. The evolution of bat vestibular systems in the face of potential antagonistic selection pressures for flight and echolocation. Plos One. 8: e61998. PMID 23637943 DOI: 10.1371/Journal.Pone.0061998  1
2013 Saunders GI, Wasmuth JD, Beech R, Laing R, Hunt M, Naghra H, Cotton JA, Berriman M, Britton C, Gilleard JS. Characterization and comparative analysis of the complete Haemonchus contortus β-tubulin gene family and implications for benzimidazole resistance in strongylid nematodes. International Journal For Parasitology. 43: 465-75. PMID 23416426 DOI: 10.1016/J.Ijpara.2012.12.011  1
2013 Svinti V, Cotton JA, McInerney JO. New approaches for unravelling reassortment pathways. Bmc Evolutionary Biology. 13: 1. PMID 23279962 DOI: 10.1186/1471-2148-13-1  1
2012 Reid AJ, Vermont SJ, Cotton JA, Harris D, Hill-Cawthorne GA, Könen-Waisman S, Latham SM, Mourier T, Norton R, Quail MA, Sanders M, Shanmugam D, Sohal A, Wasmuth JD, Brunk B, et al. Comparative genomics of the apicomplexan parasites Toxoplasma gondii and Neospora caninum: Coccidia differing in host range and transmission strategy. Plos Pathogens. 8: e1002567. PMID 22457617 DOI: 10.1371/Journal.Ppat.1002567  1
2012 San Mauro D, Gower DJ, Cotton JA, Zardoya R, Wilkinson M, Massingham T. Experimental design in phylogenetics: testing predictions from expected information. Systematic Biology. 61: 661-74. PMID 22328568 DOI: 10.1093/Sysbio/Sys028  1
2012 Davies KT, Cotton JA, Kirwan JD, Teeling EC, Rossiter SJ. Parallel signatures of sequence evolution among hearing genes in echolocating mammals: an emerging model of genetic convergence. Heredity. 108: 480-9. PMID 22167055 DOI: 10.1038/Hdy.2011.119  1
2011 Downing T, Imamura H, Decuypere S, Clark TG, Coombs GH, Cotton JA, Hilley JD, de Doncker S, Maes I, Mottram JC, Quail MA, Rijal S, Sanders M, Schönian G, Stark O, et al. Whole genome sequencing of multiple Leishmania donovani clinical isolates provides insights into population structure and mechanisms of drug resistance. Genome Research. 21: 2143-56. PMID 22038251 DOI: 10.1101/Gr.123430.111  1
2011 Kikuchi T, Cotton JA, Dalzell JJ, Hasegawa K, Kanzaki N, McVeigh P, Takanashi T, Tsai IJ, Assefa SA, Cock PJ, Otto TD, Hunt M, Reid AJ, Sanchez-Flores A, Tsuchihara K, et al. Genomic insights into the origin of parasitism in the emerging plant pathogen Bursaphelenchus xylophilus. Plos Pathogens. 7: e1002219. PMID 21909270 DOI: 10.1371/Journal.Ppat.1002219  1
2011 Johnson LJ, Cotton JA, Lichtenstein CP, Elgar GS, Nichols RA, Polly PD, Le Comber SC. Stops making sense: translational trade-offs and stop codon reassignment. Bmc Evolutionary Biology. 11: 227. PMID 21801361 DOI: 10.1186/1471-2148-11-227  1
2011 Loader SP, Wilkinson M, Cotton JA, John Measey G, Menegon M, Howell KM, Müller H, Gower DJ. Molecular phylogenetics of Boulengerula (Amphibia: Gymnophiona: Caeciliidae) and implications for taxonomy, biogeography and conservation Herpetological Journal. 21: 5-16.  1
2010 Liu Y, Rossiter SJ, Han X, Cotton JA, Zhang S. Cetaceans on a molecular fast track to ultrasonic hearing. Current Biology : Cb. 20: 1834-9. PMID 20933423 DOI: 10.1016/J.Cub.2010.09.008  1
2010 Cotton JA, McInerney JO. Eukaryotic genes of archaebacterial origin are more important than the more numerous eubacterial genes, irrespective of function. Proceedings of the National Academy of Sciences of the United States of America. 107: 17252-5. PMID 20852068 DOI: 10.1073/Pnas.1000265107  1
2010 Liu Y, Cotton JA, Shen B, Han X, Rossiter SJ, Zhang S. Convergent sequence evolution between echolocating bats and dolphins. Current Biology : Cb. 20: R53-4. PMID 20129036 DOI: 10.1016/J.Cub.2009.11.058  1
2009 San Mauro D, Gower DJ, Massingham T, Wilkinson M, Zardoya R, Cotton JA. Experimental design in caecilian systematics: phylogenetic information of mitochondrial genomes and nuclear rag1. Systematic Biology. 58: 425-38. PMID 20525595 DOI: 10.1093/Sysbio/Syp043  1
2009 Zhao H, Rossiter SJ, Teeling EC, Li C, Cotton JA, Zhang S. The evolution of color vision in nocturnal mammals. Proceedings of the National Academy of Sciences of the United States of America. 106: 8980-5. PMID 19470491 DOI: 10.1073/Pnas.0813201106  1
2009 Gold K, Cotton JA, Stollewerk A. The role of Notch signalling and numb function in mechanosensory organ formation in the spider Cupiennius salei. Developmental Biology. 327: 121-31. PMID 19121304 DOI: 10.1016/J.Ydbio.2008.12.004  1
2009 Cotton JA, Wilkinson M. Supertrees join the mainstream of phylogenetics. Trends in Ecology & Evolution. 24: 1-3. PMID 19022523 DOI: 10.1016/J.Tree.2008.08.006  1
2008 McCann A, Cotton JA, McInerney JO. The tree of genomes: an empirical comparison of genome-phylogeny reconstruction methods. Bmc Evolutionary Biology. 8: 312. PMID 19014489 DOI: 10.1186/1471-2148-8-312  1
2008 Li G, Wang J, Rossiter SJ, Jones G, Cotton JA, Zhang S. The hearing gene Prestin reunites echolocating bats. Proceedings of the National Academy of Sciences of the United States of America. 105: 13959-64. PMID 18776049 DOI: 10.1073/Pnas.0802097105  1
2008 McInerney JO, Cotton JA, Pisani D. The prokaryotic tree of life: past, present... and future? Trends in Ecology & Evolution. 23: 276-81. PMID 18367290 DOI: 10.1016/J.Tree.2008.01.008  1
2008 Day JJ, Cotton JA, Barraclough TG. Tempo and mode of diversification of lake Tanganyika cichlid fishes. Plos One. 3: e1730. PMID 18320049 DOI: 10.1371/Journal.Pone.0001730  1
2008 Peterson KJ, Cotton JA, Gehling JG, Pisani D. The Ediacaran emergence of bilaterians: congruence between the genetic and the geological fossil records. Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences. 363: 1435-43. PMID 18192191 DOI: 10.1098/Rstb.2007.2233  1
2008 Cotton JA, Wilkinson M. Quantifying the potential utility of phylogenetic characters Taxon. 57: 131-136.  1
2007 Loader SP, Pisani D, Cotton JA, Gower DJ, Day JJ, Wilkinson M. Relative time scales reveal multiple origins of parallel disjunct distributions of African caecilian amphibians. Biology Letters. 3: 505-8. PMID 17609171 DOI: 10.1098/Rsbl.2007.0266  1
2007 Cotton JA, Wilkinson M. Majority-rule supertrees. Systematic Biology. 56: 445-52. PMID 17558966 DOI: 10.1080/10635150701416682  1
2007 Pisani D, Cotton JA, McInerney JO. Supertrees disentangle the chimerical origin of eukaryotic genomes. Molecular Biology and Evolution. 24: 1752-60. PMID 17504772 DOI: 10.1093/Molbev/Msm095  1
2007 Wilkinson M, Cotton JA, Lapointe FJ, Pisani D. Properties of supertree methods in the consensus setting. Systematic Biology. 56: 330-7. PMID 17464887 DOI: 10.1080/10635150701245370  1
2006 Cotton JA, Page RD. The shape of human gene family phylogenies. Bmc Evolutionary Biology. 6: 66. PMID 16939643 DOI: 10.1186/1471-2148-6-66  1
2006 Cotton JA, Slater CS, Wilkinson M. Discriminating supported and unsupported relationships in supertrees using triplets. Systematic Biology. 55: 345-50. PMID 16611604 DOI: 10.1080/10635150500481556  1
2006 Pfister KK, Shah PR, Hummerich H, Russ A, Cotton J, Annuar AA, King SM, Fisher EMC. Genetic analysis of the cytoplasmic dynein subunit families Plos Genetics. 2: e1. PMID 16440056 DOI: 10.1371/Journal.Pgen.0020001  1
2005 Wilkinson M, Pisani D, Cotton JA, Corfe I. Measuring support and finding unsupported relationships in supertrees. Systematic Biology. 54: 823-31. PMID 16243766 DOI: 10.1080/10635150590950362  1
2005 Wilkinson M, Cotton JA, Creevey C, Eulenstein O, Harris SR, Lapointe FJ, Levasseur C, McInerney JO, Pisani D, Thorley JL. The shape of supertrees to come: tree shape related properties of fourteen supertree methods. Systematic Biology. 54: 419-31. PMID 16012108 DOI: 10.1080/10635150590949832  1
2005 Cotton JA. Analytical methods for detecting paralogy in molecular datasets. Methods in Enzymology. 395: 700-24. PMID 15865991 DOI: 10.1016/S0076-6879(05)95036-2  1
2005 Cotton JA, Page RD. Rates and patterns of gene duplication and loss in the human genome. Proceedings. Biological Sciences / the Royal Society. 272: 277-83. PMID 15705552 DOI: 10.1098/Rspb.2004.2969  1
2004 Wilkinson M, Cotton JA, Thorley JL. The information content of trees and their matrix representations Systematic Biology. 53: 989-1001. PMID 15764566 DOI: 10.1080/10635150490522737  1
2003 Cotton JA, Page RD. Gene tree parsimony vs uninode coding for phylogenetic reconstruction. Molecular Phylogenetics and Evolution. 29: 298-308. PMID 13678685 DOI: 10.1016/S1055-7903(03)00109-X  1
2002 Cotton JA, Page RD. Going nuclear: gene family evolution and vertebrate phylogeny reconciled. Proceedings. Biological Sciences / the Royal Society. 269: 1555-61. PMID 12184825 DOI: 10.1098/Rspb.2002.2074  1
2002 Page RD, Cotton JA. Vertebrate phylogenomics: reconciled trees and gene duplications. Pacific Symposium On Biocomputing. Pacific Symposium On Biocomputing. 536-47. PMID 11928506  1
1999 Cotton JA, Heritage GL, Large ARG, Passmore DG. Biotic response to late Holocene floodplain evolution in the River Irthing catchment, Cumbria Geological Society Special Publication. 163: 163-178. DOI: 10.1144/GSL.SP.1999.163.01.14  0.01
1999 Cotton JA, Heritage GL, Large ARG, Passmore DG. Biotic response to late Holocene floodplain evolution in the River Irthing catchment, Cumbria Geological Society Special Publication. 163: 163-178. DOI: 10.1144/GSL.SP.1999.163.01.14  0.01
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