Dr 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

Publications

List by: Type | Date

Jump to: 2022 | 2021 | 2020 | 2019 | 2018 | 2017 | 2016 | 2015 | 2013 | 2011 | 2006 | 2005 | 2004 | 2003 | 2002
Number of items: 50.

2022

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)

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)

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)

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)

2017

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)

2016

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)

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)

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)

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

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)

2013

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)

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)

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)

2005

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

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)

This list was generated on Thu Aug 18 08:34:09 2022 BST.
Number of items: 50.

Articles

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)

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)

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)

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)

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)

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)

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)

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)

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)

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)

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)

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)

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)

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. 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)

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)

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)

Book Sections

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)

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)

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)

This list was generated on Thu Aug 18 08:34:09 2022 BST.