Professor James Cotton

Professor (Evolution & Diversity)

Biography

I completed my PhD on gene family evolution at the University of Glasgow with Rod Page, followed by post-docs in various topics in phylogenetics and molecular evolution at the Natural History Museum in London (with Mark Wilkinson) and National University of Ireland, Maynooth (With James McInerney). I was a tenure-track academic fellow at Queen Mary, University of London for a few years before moving to the Wellcome Sanger Institute, where I was a member of the parasite genomics group for ten years. I returned to Glasgow in 2022.

Research interests

I work on the genetics and genomics of eukaryotic parasites, particularly on parasites that cause neglected tropical diseases. I particularly enjoy working collaboratively, on projects that have both some implications for reducing the burder of NTDs but also raise interesting questions about the genetics or biology of the parasites themselves, or at least require some fun analyses.

My research has focused on building genomic data resources for eukaryotic parasites, and then using those tools to understand various aspects of parasite biology. I am particularly interested in generating large-scale data on parasite genetic variation, and in understanding parasite population genetics, evolution and epidemiology. I have worked on quite a wide range of organisms. A long-term interest is in Leishmania, particularly in Ethiopia where I have active projects on both cutaneous and visceral leishmaniasis. I am particularly interested in anthelminthic drug resistance, and have been working on the gastro-intestinal nematode of small ruminants Haemonchus contortus as a model for the genetics and evolution of resistance, and more recently on the genetics of Schistosoma with a view to developing genetic/genomic surveillance as an early warning system for the emergence of resistance.

You can read more about my research at my personal site

Research groups

Publications

List by: Type | Date

Jump to: 2024 | 2023 | 2022 | 2021 | 2020 | 2019 | 2018 | 2017 | 2016 | 2015 | 2014 | 2013 | 2012 | 2011 | 2010 | 2009 | 2008 | 2007 | 2006 | 2005 | 2004 | 2003 | 2002 | 2001

Number of items: 123.

2024

Attenborough, T., Rawlinson, K. A., Diaz Soria, C. L., Ambridge, K., Sankaranarayanan, G., Graham, J., Cotton, J. A. , Doyle, S. R., Rinaldi, G. and Berriman, M. (2024) A single-cell atlas of the miracidium larva of the human blood fluke Schistosoma mansoni: cell types, developmental pathways and tissue architecture. eLife, 13, RP95628. (doi: 10.7554/eLife.95628) (PMID:39190022) (PMCID:PMC11349301)

Yimer, M. et al. (2024) Demographic characteristics and prevalence of asymptomatic Leishmania donovani infection in migrant workers working in an endemic area in Northwest Ethiopia. Frontiers in Epidemiology, 4, 1367387. (doi: 10.3389/fepid.2024.1367387) (PMID:38655403) (PMCID:PMC11035784)

2023

Heeren, S. et al. (2023) Diversity and dissemination of viruses in pathogenic protozoa. Nature Communications, 14, 8343. (doi: 10.1038/s41467-023-44085-2) (PMID:38102141) (PMCID:PMC10724245)

Carey, M., Tuhinur, A., Cotton, J. A. , Alam, M., Kabir, M., Faruque, A. S.G., Haque, R., Petri, W. A. and Gilchrist, C. A. (2023) Genomic heterogeneity of Cryptosporidium parvum isolates from children in Bangladesh: implications for parasite biology and human infection. Journal of Infectious Diseases, 228(9), pp. 1292-1298. (doi: 10.1093/infdis/jiad257) (PMID:37832036) (PMCID:PMC10629705)

Yizengaw, E. et al. (2023) Cutaneous leishmaniasis in a newly established treatment centre in the Lay Gayint district, Northwest Ethiopia. Skin Health and Disease, 3(4), e229. (doi: 10.1002/ski2.229) (PMID:37538321) (PMCID:PMC10395643)

Van den Broeck, F. et al. (2023) Genome analysis of triploid hybrid Leishmania parasite from the Neotropics. Emerging Infectious Diseases, 29(5), pp. 1076-1078. (doi: 10.3201/eid2905.221456) (PMID:37081624) (PMCID:PMC10124652)

Takele, Y. et al. (2023) Recurrent visceral leishmaniasis relapses in HIV co-infected patients are characterized by less efficient immune responses and higher parasite load. iScience, 26(2), 105867. (doi: 10.1016/j.isci.2022.105867) (PMID:36685039) (PMCID:PMC9845767)

2022

Doyle, S. R. et al. (2022) Genomic landscape of drug response reveals mediators of anthelmintic resistance. Cell Reports, 41(3), 111522. (doi: 10.1016/j.celrep.2022.111522) (PMID:36261007) (PMCID:PMC9597552)

Wit, J. et al. (2022) Genomic signatures of selection associated with benzimidazole drug treatments in Haemonchus contortus field populations. International Journal for Parasitology, 52(10), pp. 677-689. (doi: 10.1016/j.ijpara.2022.07.004) (PMID:36113620)

Takele, Y., Adem, E., Mulaw, T., Müller, I., Cotton, J. A. and Kropf, P. (2022) Following successful anti-leishmanial treatment, neutrophil counts, CD10 expression and phagocytic capacity remain reduced in visceral leishmaniasis patients co-infected with HIV. PLoS Neglected Tropical Diseases, 16(8), e0010681. (doi: 10.1371/journal.pntd.0010681) (PMID:35969625) (PMCID:PMC9410551)

Berger, D. J. et al. (2022) Genomic evidence of contemporary hybridization between Schistosoma species. PLoS Pathogens, 18(8), e1010706. (doi: 10.1371/journal.ppat.1010706) (PMID:35939508) (PMCID:PMC9387932)

Vianney, T. J. et al. (2022) Genome-wide analysis of Schistosoma mansoni reveals limited population structure and possible praziquantel drug selection pressure within Ugandan hot-spot communities. PLoS Neglected Tropical Diseases, 16(8), e0010188. (doi: 10.1371/journal.pntd.0010188) (PMID:35981002) (PMCID:PMC9426917)

Valdivia, H. O., Roatt, B. M., Baptista, R. d. P., Ottino, J., Coqueiro-dos-Santos, A., Sanders, M. J., Reis, A. B., Cotton, J. A. and Bartholomeu, D. C. (2022) Replacement of Leishmania (Leishmania) infantum populations in an endemic focus of visceral Leishmaniasis in Brazil. Frontiers in Cellular and Infection Microbiology, 12, 900084. (doi: 10.3389/fcimb.2022.900084) (PMID:35811682) (PMCID:PMC9263273)

Takele, Y., Adem, E., Ursula Franssen, S., Womersley, R., Kaforou, M., Levin, M., Müller, I., Cotton, J. A. and Kropf, P. (2022) Impaired in vitro Interferon-γ production in patients with visceral leishmaniasis is improved by inhibition of PD1/PDL-1 ligation. PLoS Neglected Tropical Diseases, 16(6), e0010544. (doi: 10.1371/journal.pntd.0010544) (PMID:35749568) (PMCID:PMC9262188)

Cotton, J. A. and Doyle, S. R. (2022) A genetic TRP down the channel to praziquantel resistance. Trends in Parasitology, 38(5), pp. 351-352. (doi: 10.1016/j.pt.2022.02.006) (PMID:35246385)

Roberts, A. J., Ong, H. B., Clare, S., Brandt, C., Harcourt, K., Franssen, S. U., Cotton, J. A. , Müller-Sienerth, N. and Wright, G. J. (2022) Systematic identification of genes encoding cell surface and secreted proteins that are essential for in vitro growth and infection in Leishmania donovani. PLoS Pathogens, 18(2), e1010364. (doi: 10.1371/journal.ppat.1010364) (PMID:35202447) (PMCID:PMC8903277)

Coker, S. M., Box, E. K., Stilwell, N., Thiele, E. A., Cotton, J. A. , Haynes, E., Yabsley, M. J. and Cleveland, C. A. (2022) Development and validation of a quantitative PCR for the detection of Guinea worm (Dracunculus medinensis). PLoS Neglected Tropical Diseases, 16(10), e0010830. (doi: 10.1371/journal.pntd.0010830) (PMID:36206300) (PMCID:PMC9581357)

2021

Ribado, J. V. et al. (2021) Linked surveillance and genetic data uncovers programmatically relevant geographic scale of Guinea worm transmission in Chad. PLoS Neglected Tropical Diseases, 15(7), e0009609. (doi: 10.1371/journal.pntd.0009609) (PMID:34310598) (PMCID:PMC8341693)

Franssen, S. U., Takele, Y., Adem, E., Sanders, M. J., Müller, I., Kropf, P., Cotton, J. A. and Weiss, L. M. (2021) Diversity and within-host evolution of Leishmania donovani from visceral leishmaniasis patients with and without HIV coinfection in northern Ethiopia. mBio, 12(3), e00971-21. (doi: 10.1128/mBio.00971-21) (PMID:34182785) (PMCID:PMC8262925)

Sloan, M. A. , Sadlova, J., Lestinova, T., Sanders, M. J., Cotton, J. A. , Volf, P. and Ligoxygakis, P. (2021) The Phlebotomus papatasi systemic transcriptional response to trypanosomatid-contaminated blood does not differ from the non-infected blood meal. Parasites and Vectors, 14, 15. (doi: 10.1186/s13071-020-04498-0) (PMID:33407867) (PMCID:PMC7789365)

Skalicky, T. et al. (2021) Endosymbiont Capture, a Repeated Process of Endosymbiont Transfer with Replacement in Trypanosomatids Angomonas spp. Pathogens, 10(6), 702. (doi: 10.3390/pathogens10060702) (PMID:34200026) (PMCID:PMC8229890)

2020

Doyle, S. R. et al. (2020) Genomic and transcriptomic variation defines the chromosome-scale assembly of Haemonchus contortus, a model gastrointestinal worm. Communications Biology, 3, 656. (doi: 10.1038/s42003-020-01377-3) (PMID:33168940) (PMCID:PMC7652881)

Basáñez, M.-G. et al. (2020) Population genomic evidence that human and animal infections in Africa come from the same populations of Dracunculus medinensis. PLoS Neglected Tropical Diseases, 14(11), e0008623. (doi: 10.1371/journal.pntd.0008623) (PMID:33253172) (PMCID:PMC7728184)

Van den Broeck, F. et al. (2020) Ecological divergence and hybridization of Neotropical Leishmania parasites. Proceedings of the National Academy of Sciences of the United States of America, 117(40), pp. 25159-25168. (doi: 10.1073/pnas.1920136117) (PMID:32958676) (PMCID:PMC7547230)

Imamura, H., Monsieurs, P., Jara, M., Sanders, M., Maes, I., Vanaerschot, M., Berriman, M., Cotton, J. A. , Dujardin, J.-C. and Domagalska, M. A. (2020) Evaluation of whole genome amplification and bioinformatic methods for the characterization of Leishmania genomes at a single cell level. Scientific Reports, 10, 15043. (doi: 10.1038/s41598-020-71882-2) (PMID:32929126) (PMCID:PMC7490275)

Cotton, J. A. and Franssen, S. U. (2020) A way straight-forward for Leishmania genetics. Trends in Parasitology, 36(9), pp. 719-721. (doi: 10.1016/j.pt.2020.07.005) (PMID:32741600)

Tracey, A. et al. (2020) Nearly complete genome sequence of Brugia malayi strain FR3. Microbiology Resource Announcements, 9(24), e00154-20. (doi: 10.1128/MRA.00154-20) (PMID:32527783) (PMCID:PMC7291094)

O’Keeffe, A., Hale, C., Cotton, J. A. , Yardley, V., Gupta, K., Ananthanarayanan, A., Murdan, S. and Croft, S. L. (2020) Novel 2D and 3D assays to determine the activity of anti-leishmanial drugs. Microorganisms, 8(6), 831. (doi: 10.3390/microorganisms8060831) (PMID:32492796) (PMCID:PMC7356592)

Foster, J. M. et al. (2020) Sex chromosome evolution in parasitic nematodes of humans. Nature Communications, 11, 1964. (doi: 10.1038/s41467-020-15654-6) (PMID:32327641) (PMCID:PMC7181701)

Cotton, J. A. et al. (2020) Genomic analysis of natural intra-specific hybrids among Ethiopian isolates of Leishmania donovani. PLoS Neglected Tropical Diseases, 14(4), e0007143. (doi: 10.1371/journal.pntd.0007143) (PMID:32310945) (PMCID:PMC7237039)

Franssen, S. U. et al. (2020) Global genome diversity of the Leishmania donovani complex. eLife, 9, e51243. (doi: 10.7554/elife.51243) (PMID:32209228) (PMCID:PMC7105377)

2019

Shaw, C. D. et al. (2019) Genomic and metabolomic polymorphism among experimentally selected paromomycin-resistant Leishmania donovani strains. Antimicrobial Agents and Chemotherapy, 64(1), e00904-19. (doi: 10.1128/AAC.00904-19) (PMID:31658971) (PMCID:PMC7187574)

Domagalska, M. A. et al. (2019) Genomes of Leishmania parasites directly sequenced from patients with visceral leishmaniasis in the Indian subcontinent. PLoS Neglected Tropical Diseases, 13(12), e0007900. (doi: 10.1371/journal.pntd.0007900) (PMID:31830038) (PMCID:PMC6932831)

Sloan, M. A. , Brooks, K., Otto, T. D. , Sanders, M. J., Cotton, J. A. and Ligoxygakis, P. (2019) Transcriptional and genomic parallels between the monoxenous parasite Herpetomonas muscarum and Leishmania. PLoS Genetics, 15(11), e1008452. (doi: 10.1371/journal.pgen.1008452) (PMID:31710597) (PMCID:PMC6872171)

Sallé, G., Doyle, S.R., Cortet, J., Cabaret, J., Berriman, M., Holroyd, N. and Cotton, J.A. (2019) The global diversity of Haemonchus contortus is shaped by human intervention and climate. Nature Communications, 10, 4811. (doi: 10.1038/s41467-019-12695-4) (PMID:31641125) (PMCID:PMC6805936)

Rezansoff, A. M. et al. (2019) The confounding effects of high genetic diversity on the determination and interpretation of differential gene expression analysis in the parasitic nematode Haemonchus contortus. International Journal for Parasitology, 49(11), pp. 847-858. (doi: 10.1016/j.ijpara.2019.05.012) (PMID:31525371)

Doyle, S. R. et al. (2019) Evaluation of DNA extraction methods on individual helminth egg and larval stages for whole-genome sequencing. Frontiers in Genetics, 10, 826. (doi: 10.3389/fgene.2019.00826) (PMID:31616465) (PMCID:PMC6764475)

Inbar, E. et al. (2019) Whole genome sequencing of experimental hybrids supports meiosis-like sexual recombination in Leishmania. PLoS Genetics, 15(5), e1008042. (doi: 10.1371/journal.pgen.1008042) (PMID:31091230) (PMCID:PMC6519804)

Doyle, S. R. and Cotton, J. A. (2019) Genome-wide approaches to investigate anthelmintic resistance. Trends in Parasitology, 35(4), pp. 289-301. (doi: 10.1016/j.pt.2019.01.004) (PMID:30733094)

Doyle, S. R. et al. (2019) Population genomic and evolutionary modelling analyses reveal a single major QTL for ivermectin drug resistance in the pathogenic nematode, Haemonchus contortus. BMC Genomics, 20, p. 218. (doi: 10.1186/s12864-019-5592-6) (PMID:30876405) (PMCID:PMC6420744)

International Helminth Genomes Consortium, et al. (2019) Comparative genomics of the major parasitic worms. Nature Genetics, 51(1), pp. 163-174. (doi: 10.1038/s41588-018-0262-1) (PMID:30397333) (PMCID:PMC6349046)

2018

Thiele, E. A., Eberhard, M. L., Cotton, J. A. , Durrant, C., Berg, J., Hamm, K. and Ruiz-Tiben, E. (2018) Population genetic analysis of Chadian Guinea worms reveals that human and non-human hosts share common parasite populations. PLoS Neglected Tropical Diseases, 12(10), e0006747. (doi: 10.1371/journal.pntd.0006747) (PMID:30286084) (PMCID:PMC6191157)

Cuypers, B. et al. (2018) Integrated genomic and metabolomic profiling of ISC1, an emerging Leishmania donovani population in the Indian subcontinent. Infection, Genetics and Evolution, 62, pp. 170-178. (doi: 10.1016/j.meegid.2018.04.021) (PMID:29679745) (PMCID:PMC6261844)

Gilchrist, C. A. et al. (2018) Genetic diversity of Cryptosporidium hominis in a Bangladeshi community as revealed by whole-genome sequencing. Journal of Infectious Diseases, 218(2), pp. 259-264. (doi: 10.1093/infdis/jiy121) (PMID:29514308) (PMCID:PMC6009673)

Cotton, J. A. , Berriman, M., Dalén, L. and Barnes, I. (2018) Eradication genomics-lessons for parasite control. Science, 361(6398), pp. 130-131. (doi: 10.1126/science.aar6609) (PMID:30002241)

Böhme, U. et al. (2018) Complete avian malaria parasite genomes reveal features associated with lineage specific evolution in birds and mammals. Genome Research, 28(4), pp. 547-560. (doi: 10.1101/gr.218123.116) (PMID:29500236) (PMCID:PMC5880244)

Coughlan, S., Taylor, A. S., Fearne, E., Sanders, M., Schonian, G., Cotton, J. A. and Downing, T. (2018) Leishmania naiffi and Leishmania guyanensis reference genomes highlight genome structure and gene evolution in the Viannia subgenus. Royal Society Open Science, 5(4), 172212. (doi: 10.1098/rsos.172212) (PMID:29765675) (PMCID:PMC5936940)

Sallé, G. et al. (2018) Transcriptomic profiling of nematode parasites surviving vaccine exposure. International Journal for Parasitology, 48(5), pp. 395-402. (doi: 10.1016/j.ijpara.2018.01.004) (PMID:29534987) (PMCID:PMC5909036)

Doyle, S. R. et al. (2018) A genome resequencing-based genetic map reveals the recombination landscape of an outbred parasitic nematode in the presence of polyploidy and polyandry. Genome Biology and Evolution, 10(2), pp. 396-409. (doi: 10.1093/gbe/evx269) (PMID:29267942) (PMCID:PMC5793844)

Sargison, N. D., Redman, E., Morrison, A. A., Bartley, D. J., Jackson, F., Naghra-van Gijzel, H., Holroyd, N., Berriman, M., Cotton, J. A. and Gilleard, J. S. (2018) A method for single pair mating in an obligate parasitic nematode. International Journal for Parasitology, 48(2), pp. 159-165. (doi: 10.1016/j.ijpara.2017.08.010) (PMID:29111440)

Zackay, A., Cotton, J. A. , Sanders, M., Hailu, A., Nasereddin, A., Warburg, A. and Jaffe, C. L. (2018) Genome wide comparison of Ethiopian Leishmania donovani strains reveals differences potentially related to parasite survival. PLoS Genetics, 14(1), e1007133. (doi: 10.1371/journal.pgen.1007133) (PMID:29315303) (PMCID:PMC5777657)

2017

Iantorno, S. A. et al. (2017) Gene expression in Leishmania is regulated predominantly by gene dosage. mBio, 8(5), e01393-17. (doi: 10.1128/mBio.01393-17) (PMID:28900023) (PMCID:PMC5596349)

Dumetz, F. et al. (2017) Modulation of aneuploidy in leishmania donovani during adaptation to different in vitro and in vivo environments and its impact on gene expression. mBio, 8(3), e00599-17. (doi: 10.1128/mBio.00599-17) (PMID:28536289) (PMCID:PMC5442457)

Cotton, J. A. (2017) The expanding world of human Leishmaniasis. Trends in Parasitology, 33(5), pp. 341-344. (doi: 10.1016/j.pt.2017.02.002) (PMID:28319012)

Coughlan, S., Mulhair, P., Sanders, M., Schonian, G., Cotton, J. A. and Downing, T. (2017) The genome of Leishmania adleri from a mammalian host highlights chromosome fission in Sauroleishmania. Scientific Reports, 7, 43747. (doi: 10.1038/srep43747) (PMID:28256610) (PMCID:PMC5335649)

Rutledge, G. G. et al. (2017) Plasmodium malariae and P. ovale genomes provide insights into malaria parasite evolution. Nature, 542(7639), pp. 101-104. (doi: 10.1038/nature21038) (PMID:28117441) (PMCID:PMC5326575)

Valdivia, H. O. et al. (2017) Comparative genomics of canine-isolated Leishmania (Leishmania) amazonensis from an endemic focus of visceral leishmaniasis in Governador Valadares, southeastern Brazil. Scientific Reports, 7, 40804. (doi: 10.1038/srep40804) (PMID:28091623) (PMCID:PMC5238499)

2016

Cotton, J. A. , Steinbiss, S., Yokoi, T., Tsai, I. J. and Kikuchi, T. (2016) An expressed, endogenous nodavirus-like element captured by a retrotransposon in the genome of the plant parasitic nematode Bursaphelenchus xylophilus. Scientific Reports, 6, 39749. (doi: 10.1038/srep39749) (PMID:28004836) (PMCID:PMC5177903)

Bennuru, S. et al. (2016) Stage-specific transcriptome and proteome analyses of the filarial parasite Onchocerca volvulus and its Wolbachia endosymbiont. mBio, 7(6), e02028-16. (doi: 10.1128/mBio.02028-16) (PMID:27881553) (PMCID:PMC5137501)

Cotton, J. A. et al. (2016) The genome of Onchocerca volvulus, agent of river blindness. Nature Microbiology, 2, 16216. (doi: 10.1038/nmicrobiol.2016.216) (PMID:27869790) (PMCID:PMC5310847)

Crellen, T., Walker, M., Lamberton, P. H.L. , Kabatereine, N. B., Tukahebwa, E. M., Cotton, J. A. and Webster, J. P. (2016) Reduced efficacy of praziquantel against Schistosoma mansoniis associated with multiple rounds of mass drug administration. Clinical Infectious Diseases, 63(9), pp. 1151-1159. (doi: 10.1093/cid/ciw506) (PMID:27470241) (PMCID:PMC5064161)

Eves-van den Akker, S. et al. (2016) The genome of the yellow potato cyst nematode, Globodera rostochiensis, reveals insights into the basis of parasitism and virulence. Genome Biology, 17, 124. (doi: 10.1186/s13059-016-0985-1) (PMID:27286965) (PMCID:PMC4901422)

Mondelaers, A. et al. (2016) Genomic and molecular characterization of miltefosine resistance in Leishmania infantum strains with either natural or acquired resistance through experimental selection of intracellular amastigotes. PLoS ONE, 11(4), e0154101. (doi: 10.1371/journal.pone.0154101) (PMID:27123924) (PMCID:PMC4849676)

Imamura, H. et al. (2016) Evolutionary genomics of epidemic visceral leishmaniasis in the Indian subcontinent. eLife, 5, e12613. (doi: 10.7554/eLife.12613) (PMID:27003289) (PMCID:PMC4811772)

Hunt, V. L. et al. (2016) The genomic basis of parasitism in the Strongyloides clade of nematodes. Nature Genetics, 48(3), pp. 299-307. (doi: 10.1038/ng.3495) (PMID:26829753) (PMCID:PMC4948059)

Shaw, C.D. et al. (2016) In vitro selection of miltefosine resistance in promastigotes of Leishmania donovani from Nepal: genomic and metabolomic characterization. Molecular Microbiology, 99(6), pp. 1134-1148. (doi: 10.1111/mmi.13291) (PMID:26713880) (PMCID:PMC4832254)

Crellen, T. et al. (2016) Whole genome resequencing of the human parasite Schistosoma mansoni reveals population history and effects of selection. Scientific Reports, 6, 20954. (doi: 10.1038/srep20954) (PMID:26879532) (PMCID:PMC4754680)

Laing, R. , Martinelli, A., Tracey, A., Holroyd, N., Gilleard, J.S. and Cotton, J.A. (2016) Haemonchus contortus: genome structure, organization and comparative genomics. In: Gasser, R. B. and von Samson-Himmelstjerna, G. (eds.) Haemonchus contortus and Haemonchosis – Past, Present and Future Trends. Series: Advances in parasitology (93). Elsevier: Amsterdam, pp. 569-598. ISBN 9780128103951 (doi: 10.1016/bs.apar.2016.02.016)

2015

Kuo, H.-C. et al. (2015) Speciation processes in putative island endemic sister bat species: false impressions from mitochondrial DNA and microsatellite data. Molecular Ecology, 24(23), pp. 5910-5926. (doi: 10.1111/mec.13425) (PMID:26475683)

Lamberton, P. H.L. , Crellen, T., Cotton, J. A. and Webster, J. P. (2015) Modelling the effects of mass drug administration on the molecular epidemiology of schistosomes. In: Anderson, R. M. and Basáñez, M. G. (eds.) Mathematical Models for Neglected Tropical Diseases: Essential Tools for Control and Elimination, Part A. Series: Advances in parasitology (87). Elsevier, pp. 293-327. ISBN 9780128032565 (doi: 10.1016/bs.apar.2014.12.006)

2014

Dujardin, J.-C., Mannaert, A., Durrant, C. and Cotton, J. A. (2014) Mosaic aneuploidy in Leishmania: the perspective of whole genome sequencing. Trends in Parasitology, 30(12), pp. 554-555. (doi: 10.1016/j.pt.2014.09.004) (PMID:25458156)

Foth, B. J. et al. (2014) Whipworm genome and dual-species transcriptome analyses provide molecular insights into an intimate host-parasite interaction. Nature Genetics, 46(7), pp. 693-700. (doi: 10.1038/ng.3010) (PMID:24929830) (PMCID:PMC5012510)

Attardo, G. M. et al. (2014) Genome sequence of the Tsetse fly (Glossina morsitans): vector of African trypanosomiasis. Science, 344(6182), pp. 380-386. (doi: 10.1126/science.1249656) (PMID:24763584) (PMCID:PMC4077534)

Cotton, J. A. et al. (2014) The genome and life-stage specific transcriptomes of Globodera pallida elucidate key aspects of plant parasitism by a cyst nematode. Genome Biology, 15(3), R43. (doi: 10.1186/gb-2014-15-3-r43) (PMID:24580726) (PMCID:PMC4054857)

Eberhard, M. L. et al. (2014) The peculiar epidemiology of dracunculiasis in Chad. American Journal of Tropical Medicine and Hygiene, 90(1), pp. 61-70. (doi: 10.4269/ajtmh.13-0554) (PMID:24277785) (PMCID:PMC3886430)

Rogers, M. B., Downing, T., Smith, B. A., Imamura, H., Sanders, M., Svobodova, M., Volf, P., Berriman, M., Cotton, J. A. and Smith, D. F. (2014) Genomic confirmation of hybridisation and recent inbreeding in a vector-isolated Leishmania population. PLoS Genetics, 10(1), e1004092. (doi: 10.1371/journal.pgen.1004092) (PMID:24453988) (PMCID:PMC3894156)

2013

Tsagkogeorga, G., Parker, J., Stupka, E., Cotton, J. A. and Rossiter, S. J. (2013) Phylogenomic analyses elucidate the evolutionary relationships of bats. Current Biology, 23(22), pp. 2262-2267. (doi: 10.1016/j.cub.2013.09.014) (PMID:24184098)

Parker, J., Tsagkogeorga, G., Cotton, J. A. , Liu, Y., Provero, P., Stupka, E. and Rossiter, S. J. (2013) Genome-wide signatures of convergent evolution in echolocating mammals. Nature, 502(7470), pp. 228-231. (doi: 10.1038/nature12511) (PMID:24005325) (PMCID:PMC3836225)

Laing, R. et al. (2013) The genome and transcriptome of haemonchus contortus, a key model parasite for drug and vaccine discovery. Genome Biology, 14(8), R88. (doi: 10.1186/gb-2013-14-8-r88) (PMID:23985316) (PMCID:PMC4054779)

Saunders, G. I., Wasmuth, J. D., Beech, R., Laing, R. , Hunt, M., Naghra, H., Cotton, J. A. , Berriman, M., Britton, C. and Gilleard, J. S. (2013) 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(6), pp. 465-475. (doi: 10.1016/j.ijpara.2012.12.011) (PMID:23416426)

Davies, K. T.J., Bates, P. J.J., Maryanto, I., Cotton, J. A. and Rossiter, S. J. (2013) The evolution of bat vestibular systems in the face of potential antagonistic selection pressures for flight and echolocation. PLoS ONE, 8(4), e61998. (doi: 10.1371/journal.pone.0061998) (PMID:23637943) (PMCID:PMC3634842)

Svinti, V., Cotton, J. A. and McInerney, J. O. (2013) New approaches for unravelling reassortment pathways. BMC Evolutionary Biology, 13, 1. (doi: 10.1186/1471-2148-13-1) (PMID:23279962) (PMCID:PMC3541980)

2012

Mauro, D. S., Gower, D. J., Cotton, J. A. , Zardoya, R., Wilkinson, M. and Massingham, T. (2012) Experimental design in phylogenetics: testing predictions from expected information. Systematic Biology, 61(4), pp. 661-674. (doi: 10.1093/sysbio/sys028) (PMID:22328568)

Davies, K.T.J., Cotton, J.A. , Kirwan, J.D., Teeling, E.C. and Rossiter, S.J. (2012) Parallel signatures of sequence evolution among hearing genes in echolocating mammals: an emerging model of genetic convergence. Heredity, 108(5), pp. 480-489. (doi: 10.1038/hdy.2011.119) (PMID:22167055) (PMCID:PMC3330687)

Reid, A. J. et al. (2012) Comparative genomics of the apicomplexan parasites Toxoplasma gondii and neospora caninum: Coccidia differing in host range and transmission strategy. PLoS Pathogens, 8(3), e1002567. (doi: 10.1371/journal.ppat.1002567) (PMID:22457617) (PMCID:PMC3310773)

2011

Downing, T. et al. (2011) Whole genome sequencing of multiple Leishmania donovani clinical isolates provides insights into population structure and mechanisms of drug resistance. Genome Research, 21(12), pp. 2143-2156. (doi: 10.1101/gr.123430.111) (PMID:22038251) (PMCID:PMC3227103)

Kikuchi, T. et al. (2011) Genomic insights into the origin of parasitism in the emerging plant pathogen Bursaphelenchus xylophilus. PLoS Pathogens, 7(9), e1002219. (doi: 10.1371/journal.ppat.1002219) (PMID:21909270) (PMCID:PMC3164644)

Johnson, L. J., Cotton, J. A. , Lichtenstein, C. P., Elgar, G. S., Nichols, R. A., Polly, P. D. and Le Comber, S. C. (2011) Stops making sense: translational trade-offs and stop codon reassignment. BMC Evolutionary Biology, 11, 227. (doi: 10.1186/1471-2148-11-227) (PMID:21801361) (PMCID:PMC3161013)

Loader, S. P., Wilkinson, M., Cotton, J. A. , Measey, G. J., Menegon, M., Howell, K. M., Müller, H. and Gower, D. J. (2011) Molecular phylogenetics of Boulengerula (Amphibia: Gymnophiona: Caeciliidae) and implications for taxonomy, biogeography and conservation. Herpetological Journal, 21(1), pp. 5-16.

2010

Liu, Y., Rossiter, S. J., Han, X., Cotton, J. A. and Zhang, S. (2010) Cetaceans on a molecular fast track to ultrasonic hearing. Current Biology, 20(20), pp. 1834-1839. (doi: 10.1016/j.cub.2010.09.008) (PMID:20933423)

Cotton, J. A. and McInerney, J. O. (2010) 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(40), pp. 17252-17255. (doi: 10.1073/pnas.1000265107) (PMID:20852068) (PMCID:PMC2951413)

Liu, Y., Cotton, J. A. , Shen, B., Han, X., Rossiter, S. J. and Zhang, S. (2010) Convergent sequence evolution between echolocating bats and dolphins. Current Biology, 20(2), R53-R54. (doi: 10.1016/j.cub.2009.11.058) (PMID:20129036)

2009

Peterson, K. J., Cotton, J. A. , Gehling, J. G. and Pisani, D. (2009) The Ediacaran emergence of bilaterians: congruence between the genetic and the geological fossil records. In: Telford, M. J. and Littlewood, D.T.J. (eds.) Animal Evolution: Genomes, Fossils, and Trees. Series: Oxford biology. Oxford University Press: Oxford, pp. 15-23. ISBN 9780199549429 (doi: 10.1093/acprof:oso/9780199549429.003.0002)

San Mauro, D., Gower, D. J., Massingham, T., Wilkinson, M., Zardoya, R. and Cotton, J. A. (2009) Experimental design in caecilian systematics: phylogenetic information of mitochondrial genomes and nuclear rag1. Systematic Biology, 58(4), pp. 425-438. (doi: 10.1093/sysbio/syp043) (PMID:20525595)

Zhao, H., Rossiter, S. J., Teeling, E. C., Li, C., Cotton, J. A. and Zhang, S. (2009) The evolution of color vision in nocturnal mammals. Proceedings of the National Academy of Sciences of the United States of America, 106(22), pp. 8980-8985. (doi: 10.1073/pnas.0813201106) (PMID:19470491) (PMCID:PMC2690009)

Gold, K., Cotton, J. A. and Stollewerk, A. (2009) The role of Notch signalling and numb function in mechanosensory organ formation in the spider Cupiennius salei. Developmental Biology, 327(1), pp. 121-131. (doi: 10.1016/j.ydbio.2008.12.004) (PMID:19121304)

Cotton, J. A. and Wilkinson, M. (2009) Supertrees join the mainstream of phylogenetics. Trends in Ecology and Evolution, 24(1), pp. 1-3. (doi: 10.1016/j.tree.2008.08.006) (PMID:19022523)

2008

McCann, A., Cotton, J. A. and McInerney, J. O. (2008) The tree of genomes: an empirical comparison of genome-phylogeny reconstruction methods. BMC Evolutionary Biology, 8, 312. (doi: 10.1186/1471-2148-8-312) (PMID:19014489) (PMCID:PMC2592249)

Li, G., Wang, J., Rossiter, S. J., Jones, G., Cotton, J. A. and Zhang, S. (2008) The hearing gene Prestin reunites echolocating bats. Proceedings of the National Academy of Sciences of the United States of America, 105(37), pp. 13959-13964. (doi: 10.1073/pnas.0802097105) (PMID:18776049) (PMCID:PMC2544561)

McInerney, J. O., Cotton, J. A. and Pisani, D. (2008) The prokaryotic tree of life: past, present…and future? Trends in Ecology and Evolution, 23(5), pp. 276-281. (doi: 10.1016/j.tree.2008.01.008) (PMID:18367290)

Peterson, K. J., Cotton, J. A. , Gehling, J. G. and Pisani, D. (2008) The Ediacaran emergence of bilaterians: congruence between the genetic and the geological fossil records. Philosophical Transactions of the Royal Society B: Biological Sciences, 363(1496), pp. 1435-1443. (doi: 10.1098/rstb.2007.2233) (PMID:18192191) (PMCID:PMC2614224)

Day, J. J., Cotton, J. A. and Barraclough, T. G. (2008) Tempo and mode of diversification of Lake Tanganyika cichlid fishes. PLoS ONE, 3(3), e1730. (doi: 10.1371/journal.pone.0001730) (PMID:18320049) (PMCID:PMC2248707)

Cotton, J. A. and Wilkinson, M. (2008) Quantifying the potential utility of phylogenetic characters. Taxon, 57(1), pp. 131-136.

2007

Loader, S. P., Pisani, D., Cotton, J. A. , Gower, D. J., Day, J. J. and Wilkinson, M. (2007) Relative time scales reveal multiple origins of parallel disjunct distributions of African caecilian amphibians. Biology Letters, 3(5), pp. 505-508. (doi: 10.1098/rsbl.2007.0266) (PMID:17609171) (PMCID:PMC2396187)

Pisani, D., Cotton, J. A. and McInerney, J. O. (2007) Supertrees disentangle the chimerical origin of eukaryotic genomes. Molecular Biology and Evolution, 24(8), pp. 1752-1760. (doi: 10.1093/molbev/msm095) (PMID:17504772)

Cotton, J. A. and Wilkinson, M. (2007) Majority-rule supertrees. Systematic Biology, 56(3), pp. 445-452. (doi: 10.1080/10635150701416682) (PMID:17558966)

Wilkinson, M., Cotton, J. A. , Lapointe, F.-J. and Pisani, D. (2007) Properties of supertree methods in the consensus setting. Systematic Biology, 56(2), pp. 330-337. (doi: 10.1080/10635150701245370) (PMID:17464887)

Wilkinson, M. and Cotton, J.A. (2007) Supertree methods for building the tree of life: divide-and-conquer approaches to large phylogenetic problems. In: Hodkinson, T. R. and Parnell, J. A.N. (eds.) Reconstructing the Tree of Life: Taxonomy and Systematics of Species Rich Taxa. Series: Systematics Association special volume (72). CRC Press: Boca Raton, Fla, pp. 61-76. ISBN 9780849395796 (doi: 10.1201/9781420009538-11)

2006

Cotton, J.A. and Page, R.D.M. (2006) The shape of human gene family phylogenies. BMC Evolutionary Biology, 6(8), p. 66. (doi: 10.1186/1471-2148-6-66) (PMID:16939643) (PMCID:PMC1618862)

Cotton, J. A. , Slater, C. S.C. and Wilkinson, M. (2006) Discriminating supported and unsupported relationships in supertrees using triplets. Systematic Biology, 55(2), pp. 345-350. (doi: 10.1080/10635150500481556) (PMID:16611604)

Pfister, K. K., Shah, P. R., Hummerich, H., Russ, A., Cotton, J. , Annuar, A. A., King, S. M. and Fisher, E. M.C. (2006) Genetic analysis of the cytoplasmic dynein subunit families. PLoS Genetics, 2(1), e1. (doi: 10.1371/journal.pgen.0020001) (PMID:16440056) (PMCID:PMC1331979)

2005

Wilkinson, M., Pisani, D., Cotton, J. A. and Corfe, I. (2005) Measuring support and finding unsupported relationships in supertrees. Systematic Biology, 54(5), pp. 823-831. (doi: 10.1080/10635150590950362) (PMID:16243766)

Wilkinson, M., Cotton, J. A. , Creevey, C., Eulenstein, O., Harris, S. R., Lapointe, F.-J., Levasseur, C., Mcinerney, J. O., Pisani, D. and Thorley, J. L. (2005) The shape of supertrees to come: tree shape related properties of fourteen supertree methods. Systematic Biology, 54(3), pp. 419-431. (doi: 10.1080/10635150590949832) (PMID:16012108)

Cotton, J. A. (2005) Analytical methods for detecting paralogy in molecular datasets. In: Zimmer, E. A. and Roalson, E. H. (eds.) Molecular Evolution: Producing the Biochemical Data. Series: Methods in enzymology (395). Elsevier Academic Press: Amsterdam, pp. 700-724. ISBN 9780121828004 (doi: 10.1016/S0076-6879(05)95036-2)

Cotton, J.A. and Page, R.D.M. (2005) Rates and patterns of gene duplication and loss in the human genome. Proceedings of the Royal Society of London Series B: Biological Sciences, 272(1560), pp. 277-283. (doi: 10.1098/rspb.2004.2969) (PMID:15705552) (PMCID:PMC1634978)

2004

Wilkinson, M., Cotton, J. A. and Thorley, J. L. (2004) The information content of trees and their matrix representations. Systematic Biology, 53(6), pp. 989-1001. (doi: 10.1080/10635150490522737) (PMID:15764566)

Cotton, J. A. and Page, R. D.M. (2004) Tangled tales from multiple markers: reconciling conflict between phylogenies to build molecular supertrees. In: Bininda-Emonds, O. R.P. (ed.) Phylogenetic Supertrees: Combining information to Reveal the Tree of Life. Series: Computational biology (4). Springer: Dordrecht, pp. 107-125. ISBN 9781402023286 (doi: 10.1007/978-1-4020-2330-9_6)

2003

Cotton, J.A. and Page, R.D.M. (2003) Gene tree parsimony vs. uninode coding for phylogenetic reconstruction. Molecular Phylogenetics and Evolution, 29(2), pp. 298-308. (doi: 10.1016/S1055-7903(03)00109-X) (PMID:13678685)

2002

Cotton, J.A. and Page, R.D.M. (2002) Going nuclear: gene family evolution and vertebrate phylogeny reconciled. Proceedings of the Royal Society of London Series B: Biological Sciences, 269(1500), pp. 1555-1561. (doi: 10.1098/rspb.2002.2074) (PMID:12184825) (PMCID:PMC1691073)

Page, R.D.M. and Cotton, J.A. (2002) Vertebrate Phylogenomics: Reconciled Trees and Gene Duplications. In: Pacific Symposium on Biocomputing 2002, Lihue, HI, USA, 03-07 Jan 2002, pp. 536-547.

2001

Cotton, J. (2001) Homologous recombination in animal mitochondria. Genome Biology, 2(10), reports0034. (doi: 10.1186/gb-2001-2-10-reports0034)

Cotton, J. (2001) A new profusion of planktonic eukaryotes. Genome Biology, 2(7), reports0016. (doi: 10.1186/gb-2001-2-7-reports0016)

Cotton, J. (2001) Retroviruses from retrotransposons. Genome Biology, 2(2), reports0006. (doi: 10.1186/gb-2001-2-2-reports0006)

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