Publications

E. Yizengaw, B. Gashaw, M. Yimer, Y. Takele, E. Nibret, G. Yismaw, E. Cruz Cervera, K. Ejigu, D. Tamiru, A. Munshea, I. Müller, R. Weller, James Cotton, L. A. C. Chapman, P. Kropf (2024). Demographic characteristics and clinical features of patients presenting with different forms of cutaneous leishmaniasis, in Lay Gayint, Northern Ethiopia. medRxiv.

PDF Project DOI medRxiv

M. Yimer, Y. Takele, E. Yizengaw, E. Nibret, P. Sumova, P. Volf, G. Yismaw, M. Alehegn, A. Rowan, I. Müller, James Cotton, L. A. C. Chapman, P. Kropf (2024). Demographic characteristics and prevalence of asymptomatic Leishmania donovani infection in migrant workers working in an endemic area in Northwest Ethiopia. medRxiv.

PDF Project DOI medRxiv

T. Attenborough, K. A. Rawlinson, C. L. Diaz Soria,, K. Ambridge, G. Sankaranarayanan, J. Graham, James Cotton, S. R. Doyle, G. Rinaldi, M. Berriman (2024). A single-cell atlas of the miracidium larva of the human blood fluke Schistosoma mansoni: cell types, developmental pathways and tissue architecture. bioRxiv.

PDF DOI bioRxiv

S. Heeren, I. Maes, M. Sanders, L.-F. Lye, V. Adaui, J. Arevalo, A. Llanos-Cuentas, L. Garcia, P. Lemey, S. M. Beverley, James Cotton, J.-C. Dujardin,, F. Van den Broeck (2023). Diversity and dissemination of viruses in pathogenic protozoa. In Nature Communications 14:8343.

PDF DOI publisher bioRxiv Senne Heeren

M. Carey, T. Arju, J. A Cotton, M. Alam, M. Kabir, A. S. G. Faruque, R. Haque, W. A. Petri Jr, C. A. Gilchrist (2023). Genomic Heterogeneity of Cryptosporidium parvum Isolates From Children in Bangladesh: Implications for Parasite Biology and Human Infection. In Journal of Infectious Diseases 228(9):1292–1298.

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F. Van den Broeck, S. Heeren, I. Maes, M. Sanders, J. A. Cotton, E. Cupolillo, E. Alvarez, L. Garcia, M. Tasia, A. Marneffe, J.-C. Dujardin,, G. Van der Auwera (2023). Genome Analysis of Triploid Hybrid Leishmania Parasite from the Neotropics. In Emerging Infectious Diseases 29(5):1076-1078.

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E. Yizengaw, E. Nibret, G. Yismaw, B. Gashaw, D. Tamiru, A. Munshea, Y. Takele, I. Müller, L. Chapman, R. Weller, James Cotton, P. Kropf (2023). Cutaneous leishmaniasis in a newly established treatment centre in the Lay Gayint district, Northwest Ethiopia. In Skin Health and Disease 3(4):e229.

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Y. Takele, T. Mulaw, E. Adem, R. Womersley, M. Kaforou, S. U. Franssen, M. Levin, G. P. Taylor, I. Müller, James Cotton, P. Kropf (2022). Recurrent visceral leishmaniasis relapses in HIV co-infected patients are characterized by less efficient immune responses and higher parasite load. In iScience 26(2):105867.

PDF Project DOI publisher Yegnasew Takele

S. R. Doyle, R. Laing, D. Bartley, A. Morrison, N. Holroyd, K. Maitland, A. Antonopoulos, U. Chaudhry, I. Flis, S. Howell, J. McIntyre, J. S. Gilleard, A. Tait, B. Mable, R. Kaplan, N. Sargison, C. Britton, M. Berriman, E. Devaney, James Cotton (2022). Genomic landscape of drug response reveals mediators of anthelmintic resistance. In Cell Reports 41(3):111522.

PDF Project DOI publisher Roz Laing Steve Doyle

S. M. Coker, E. K. Box, N. Stilwell, E. A. Thiele, James Cotton, E. Haynes, M. J. Yabsley, C. A. Cleveland (2022). Development and validation of a quantitative PCR for the detection of Guinea worm (Dracunculus medinensis). In PLoS Neglected Tropical Diseases 16(10):e0010830.

PDF Project DOI publisher Chris Cleveland Sarah Coker

J. Wit, M. L. Workentine, E. Redman, R. Laing, L. Stevens, James Cotton, U. Chaudhry, Q. Ali, E. C. Andersen, S. Yeaman, J. D. Wasmuth, J. S. Gilleard (2022). Genomic signatures of selection associated with benzimidazole drug treatments in Haemonchus contortus field populations. In International Journal for Parasitology 52(10):677-689.

PDF Project DOI publisher John Gilleard Janneke Wit

T. J. Vianney, D. J. Berger, S. R. Doyle, G. Sankaranarayanan, J. Serubanja, P. K. Nakawungu, F. Besigye, R. E. Sanya, N. Holroyd, F. Allan, E. L. Webb, A. M. Elliott, M. Berriman, James Cotton (2022). Genome-wide analysis of Schistosoma mansoni reveals population structure and praziquantel drug selection pressure within Ugandan hot-spot communities. In PLoS Neglected Tropical Diseases 16(8):e0010188..

PDF DOI publisher bioRxiv Tushabe John Vianney

D. J. Berger, E. Léger, G. Sankaranarayanan, M. Sène, N. D. Diouf, M. Rabone, A. Emery, F. Allan, James Cotton, M. Berriman, J. P. Webster (2022). Genomic evidence of contemporary hybridization between Schistosoma species. In PLoS Pathogens 18(8):e1010706.

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Y. Takele, E. Adem, S. U. Franssen, R. Womersley, M. Kaforou, M. Levin, I. Müller, James Cotton, P. Kropf (2022). Impaired in vitro Interferon-gamma production in patients with visceral leishmaniasis is improved by inhibition of PD1/PDL-1 ligation. In PLoS Neglected Tropical Diseases 16(6):e0010544.

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H. O. Valdivia, B. M. Roatt, R. de Paula Baptista, J. Ottino, A. Coqueiro-dos-Santos, M. J. Sanders, A. B. Reis, James Cotton, D. C. Bartholomeu (2022). Replacement of Leishmania (Leishmania) infantum Populations in an Endemic Focus of Visceral Leishmaniasis in Brazil. In Frontiers in Cellular and Infection Microbiology 12:9000084.

PDF Project DOI publisher Daniella Bartholomeu Hugo Valdivia

R. Laing, S. R. Doyle, J. McIntyre, K. Maitland, A. Morrison, D. J. Bartley, R. Kaplan, U. Chaudry, N. Sargison, A. Tait, James Cotton, C. Britton, E. Devaney (2022). Transcriptomic analyses implicate neuronal plasticity and chloride homeostasis in ivermectin resistance and response to treatment in a parasitic nematode. In PLoS Pathogens 18(6):e1010545..

PDF Project publisher Roz Laing Steve Doyle

S. U. Franssen, M. J. Sanders, M. Berriman, C. A. Petersen, James Cotton (2022). Geographic Origin and Vertical Transmission of Leishmania infantum Parasites in Hunting Hounds, United States. In Emerging Infectious Diseases 2022 28(6):1211–1223..

PDF Project DOI publisher Christy Petersen

James Cotton, S. R. Doyle (2022). A genetic TRP down the channel to praziquantel resistance. In Trends in Parasitology 38(5):351-352.

PDF Project publisher Steve Doyle

Y. Takele, T. Mulaw, E. Adem, R. Womersley, M. Kaforou, S. U. Franssen, M. Levin, G. P. Taylor, I. Müller, James Cotton, P. Kropf (2021). HIV-1 co-infection increases relapse rate and shortens survival in patients with visceral leishmaniasis. medRxiv.

PDF Project DOI medRxiv Yegnasew Takele

D. J. Berger, T. Crellen, P. H. L. Lamberton, F. Allan, A. Tracey, J. D. Noonan, N. B. Kabatereine, E. M. Tukahebwa, M. Adriko, N. Holroyd, J. P. Webster, M. Berriman, James Cotton (2021). Whole-genome sequencing of Schistosoma mansoni reveals extensive diversity with limited selection despite mass drug administration. In Nature Communications 12:4776.

PDF Cite Code DOI publisher Duncan Berger ERR code Tom Crellen Webster lab

T. Skalický, J. M. P. Alves, A. C. Morais, J. Režnarová, A. Butenko, J. Lukeš, M. G. Serrano, G. A. Buck, M. M. G. Teixeira, E. P. Camargo, M. Sanders, James Cotton, V. Yurchenko, A. Y. Kostygov (2021). Endosymbiont Capture, a Repeated Process of Endosymbiont Transfer with Replacement in Trypanosomatids Angomonas spp.. In Pathogens 10(6): 702.

PDF Cite DOI publisher Tomáš Skalický Yurchenko lab

S. U. Franssen, Y. Takele, E. Adem, M. J. Sanders, I. Müller, P. Kropf, James Cotton (2021). Diversity and Within-Host Evolution of Leishmania donovani from Visceral Leishmaniasis Patients with and without HIV Coinfection in Northern Ethiopia. In mBio 12:3.

PDF Cite Project DOI publisher medRxiv Yegnasew Takele Suse Franssen

Y. Takele, T. Mulaw, E. Adem, C. J. Shaw, S. U. Franssen, R. Womersley, M. Kaforou, G. P. Taylor, M. Levin, I. Müller, James Cotton, P. Kropf (2021). Immunological factors, but not clinical features, predict visceral leishmaniasis relapse in patients co-infected with HIV. In Cell Reports Medicine 3(1):100487.

PDF Project DOI bioRxiv publisher Yegnasew Takele

R. P. Baptista, Y. Li, A. Sateriale, M. J. Sanders, K. L. Brooks, A. Tracey, B. R. E. Ansell, A. R. Jex, G. W. Cooper, E. D. Smith, R. Xiao, J. E. Dumaine, M. Berriman, B. Striepen, James Cotton, J. C. Kissinger (2021). Long-read assembly and comparative evidence-based reanalysis of Cryptosporidium genome sequences reveal new biological insights. bioRxiv 428682.

PDF DOI bioRxiv Kissinger lab

A. Hefnawy, G. Negreira, M. Jara, James Cotton, I.Maes, E. D’ Haenens, H. Imamura, B. Cuypers, P. Monsieurs, C. Mouchtoglou, H. De Winter, M. Berriman, M. Sanders, J. Martin, G. de Muylder, J.-C. Dujardin,, Y. G.-J. Sterckx, M. A. Domagalska (2021). Genomic and phenotypic characterization of experimentally selected resistant Leishmania donovani reveals a role for dynamin-1 like protein in the mechanism of resistance to a novel anti-leishmanial compound. bioRxiv 425522.

PDF DOI bioRxiv Jean-Claude Dujardin

M. A. Sloan, J. Sadlova, T. Lestinova, M. J. Sanders, James Cotton, P. Volf, P. Ligoxygakis (2021). The Phlebotomus papatasi systemic transcriptional response to trypanosomatid-contaminated blood does not differ from the non-infected blood meal. In Parasites and Vectors 14:15.

PDF Cite DOI publisher Megan Sloan

C. Durrant, E. A. Thiele, N. Holroyd, S. R. Doyle, G. Sallé, A. Tracey, G. Sankaranarayanan, M. E. Lotkowska, H. M. Bennett, T. Huckvale, Z. Abdellah, O. Tchindebet, M. Wossen, M. S. Y. Logora, C. O. Coulibaly, A. Weiss, A. I. Schulte-Hostedde, J. M. Foster, C. A. Cleveland, M. J. Yabsley, E. Ruiz-Tiben, M. Berriman, M. L. Eberhard, James Cotton (2020). Population genomic evidence that human and animal infections in Africa come from the same populations of Dracunculus medinensis. In PLoS Neglected Tropical Diseases 14:e0008623.

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S. R. Doyle, A. Tracey, R. Laing, N. Holroyd, D. Bartley, W. Bazant, H. Beasley, R. Beech, C. Britton, K. Brooks, U. Chaudhry, K. Maitland, A. Martinelli, J. D. Noonan, M. Paulini, M. A. Quail, E. Redman, F. H. Rodgers, G. Sallé, M. Z. Shabbir, G. Sankaranarayanan, J. Wit, K. L. Howe, N. Sargison, E. Devaney, M. Berriman, J. S. Gilleard, James Cotton (2020). Genomic and transcriptomic variation defines the chromosome-scale assembly of Haemonchus contortus, a model gastrointestinal worm. In Communications Biology 3:656.

PDF Cite Project DOI publisher github Steve Doyle

F. Van den Broeck, N. J. Savill, H. Imamura, M. Sanders, I. Maes, S. Cooper, D. Mateus, M. Jara, V. Adaui, J. Arevalo, A. Llanos-Cuentas, L. Garcia, E. Cupolillo, M. Miles, M. Berriman, A. Schnaufer, James Cotton, J.-C. Dujardin, (2020). Ecological divergence and hybridization of Neotropical Leishmania parasites. In Proc Natl Acad Sci U S A 117:25159–25168.

PDF Cite DOI biorxiv publisher Frederik Van den Broeck

H. Imamura, P. Monsieurs, M. Jara, M. Sanders, I. Maes, M. Vanaerschot, M. Berriman, James Cotton, J.-C. Dujardin,, M. A. Domagalska (2020). Evaluation of whole genome amplification and bioinformatic methods for the characterization of Leishmania genomes at a single cell level. In Scientific Reports 10:15043.

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James Cotton, S. U. Franssen (2020). A Way Straight-Forward for Leishmania Genetics. In Trends in Parasitology 36:719–721.

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J. V. Ribado, N. Li, E. Thiele, H. Lyons, James Cotton, A. Weiss, P. Tchindebet Ouakou, T. Moundai, H. Zirimwabagabo, S. A. J. Guagliardo, G. Chabot-Couture, J. L. Proctor (2020). Linked surveillance and genetic data uncovers programmatically relevant geographic scale of Guinea worm transmission in Chad. In PLoS Neglected Tropical Diseases 15:e0009609.

PDF Cite Project DOI publisher medRxiv Jessica Ribado

A. O'Keeffe, C. Hale, James Cotton, V. Yardley, K. Gupta, A. Ananthanarayanan, S. Murdan, S. L. Croft (2020). Novel 2D and 3D Assays to Determine the Activity of Anti-Leishmanial Drugs. In Microorganisms 8.

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A. Tracey, J. M. Foster, M. Paulini, A. Grote, J. Mattick, Y. C. Tsai, M. Chung, James Cotton, T. A. Clark, A. Geber, N. Holroyd, J. Korlach, S. Libro, S. Lustigman, M. L. Michalski, M. B. Rogers, A. Twaddle, J. C. Dunning Hotopp, M. Berriman, E. Ghedin (2020). Nearly Complete Genome Sequence of Brugia malayi Strain FR3. In Microbiology Resource Announcements 9.

PDF Cite Project DOI publisher Elodie Ghedin

J. M. Foster, A. Grote, J. Mattick, A. Tracey, Y. C. Tsai, M. Chung, James Cotton, T. A. Clark, A. Geber, N. Holroyd, J. Korlach, Y. Li, S. Libro, S. Lustigman, M. L. Michalski, M. Paulini, M. B. Rogers, L. Teigen, A. Twaddle, L. Welch, M. Berriman, J. C. Dunning Hotopp, E. Ghedin (2020). Sex chromosome evolution in parasitic nematodes of humans. In Nat Commun 11:1964.

PDF Cite DOI publisher Alex Grote

James Cotton, C. Durrant, S. U. Franssen, T. Gelanew, A. Hailu, D. Mateus, M. J. Sanders, M. Berriman, P. Volf, M. A. Miles, M. Yeo (2020). Genomic analysis of natural intra-specific hybrids among Ethiopian isolates of Leishmania donovani. In PLoS Neglected Tropical Diseases 14:e0007143.

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S. U. Franssen, C. Durrant, O. Stark, B. Moser, T. Downing, H. Imamura, J.-C. Dujardin,, M. J. Sanders, I. Mauricio, M. A. Miles, L. F. Schnur, C. L. Jaffe, A. Nasereddin, H. Schallig, M. Yeo, T. Bhattacharyya, M. Z. Alam, M. Berriman, T. Wirth, G. Schönian, James Cotton (2020). Global genome diversity of the Leishmania donovani complex. In Elife 9.

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C. D. Shaw, H. Imamura, T. Downing, G. Blackburn, G. D. Westrop, James Cotton, M. Berriman, M. Sanders, S. Rijal, G. H. Coombs, J.-C. Dujardin,, K. C. Carter (2019). Genomic and Metabolomic Polymorphism among Experimentally Selected Paromomycin-Resistant Leishmania donovani Strains. In Antimicrobial Agents and Chemotherapy 64:e00904-19.

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M. A. Domagalska, H. Imamura, M. Sanders, F. Van den Broeck, N. R. Bhattarai, M. Vanaerschot, I. Maes, E. D'Haenens, K. Rai, S. Rijal, M. Berriman, James Cotton, J.-C. Dujardin, (2019). Genomes of Leishmania parasites directly sequenced from patients with visceral leishmaniasis in the Indian subcontinent. In PLoS Neglected Tropical Diseases 13:e0007900.

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M. A. Sloan, K. Brooks, T. D. Otto, M. J. Sanders, James Cotton, P. Ligoxygakis (2019). Transcriptional and genomic parallels between the monoxenous parasite Herpetomonas muscarum and Leishmania. In PLoS Genetics 15:e1008452.

PDF Cite DOI publisher Petros Ligoxygakis Megan Sloan

G. Sallé, S. R. Doyle, J. Cortet, J. Cabaret, M. Berriman, N. Holroyd, James Cotton (2019). The global diversity of Haemonchus contortus is shaped by human intervention and climate. In Nat Commun 10:4811.

PDF Cite DOI publisher Guillaume Sallé

A. M. Rezansoff, R. Laing, A. Martinelli, S. Stasiuk, E. Redman, D. Bartley, N. Holroyd, E. Devaney, N. D. Sargison, S. Doyle, James Cotton, J. S. Gilleard (2019). The confounding effects of high genetic diversity on the determination and interpretation of differential gene expression analysis in the parasitic nematode Haemonchus contortus. In Int J Parasitol 49:847–858.

PDF Cite DOI publisher Gilleard lab

E. Inbar, J. Shaik, S. A. Iantorno, A. Romano, C. O. Nzelu, K. Owens, M. J. Sanders, D. Dobson, James Cotton, M. E. Grigg, S. M. Beverley, D. Sacks (2019). Whole genome sequencing of experimental hybrids supports meiosis-like sexual recombination in Leishmania. In PLoS Genetics 15:e1008042.

PDF Cite DOI publisher David Sacks

S. R. Doyle, James Cotton (2019). Genome-wide Approaches to Investigate Anthelmintic Resistance. In Trends Parasitol 35:289–301.

PDF Cite Project DOI publisher Steve Doyle

S. R. Doyle, C. J. R. Illingworth, R. Laing, D. J. Bartley, E. Redman, A. Martinelli, N. Holroyd, A. A. Morrison, A. Rezansoff, A. Tracey, E. Devaney, M. Berriman, N. Sargison, James Cotton, J. S. Gilleard (2019). Population genomic and evolutionary modelling analyses reveal a single major QTL for ivermectin drug resistance in the pathogenic nematode, Haemonchus contortus. In BMC Genomics 20:218.

PDF Cite Project DOI publisher Steve Doyle Chris Illingworth Gilleard lab

S. R. Doyle, G. Sankaranarayanan, F. Allan, D. Berger, P. D. Jimenez Castro, J. B. Collins, T. Crellen, M. A. Duque-Correa, P. Ellis, T. G. Jaleta, R. Laing, K. Maitland, C. McCarthy, T. Moundai, B. Softley, E. Thiele, P. T. Ouakou, J. V. Tushabe, J. P. Webster, A. J. Weiss, J. Lok, E. Devaney, R. M. Kaplan, James Cotton, M. Berriman, N. Holroyd (2019). Evaluation of DNA Extraction Methods on Individual Helminth Egg and Larval Stages for Whole-Genome Sequencing. In Frontiers in Genetics 10:826.

PDF Cite DOI publisher Steve Doyle Nancy Holroyd

International Helminth Genomes Consortium (2018). Comparative genomics of the major parasitic worms. In Nature Genetics 51:163–174.

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E. A. Thiele, M. L. Eberhard, James Cotton, C. Durrant, J. Berg, K. Hamm, E. Ruiz-Tiben (2018). Population genetic analysis of Chadian Guinea worms reveals that human and non-human hosts share common parasite populations. In PLoS Neglected Tropical Diseases 12:e0006747.

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B. Cuypers, M. Berg, H. Imamura, F. Dumetz, G. de Muylder, M. A. Domagalska, S. Rijal, N. R. Bhattarai, I. Maes, M. Sanders, James Cotton, P. Meysman, K. Laukens, J.-C. Dujardin, (2018). Integrated genomic and metabolomic profiling of ISC1, an emerging Leishmania donovani population in the Indian subcontinent. In Infect Genet Evol 62:170–178.

PDF Cite DOI publisher Bart Cuypers Jean-Claude Dujardin

James Cotton, M. Berriman, L. Dalén, I. Barnes (2018). Eradication genomics-lessons for parasite control. In Science 361:130–131.

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C. A. Gilchrist, James Cotton, C. Burkey, T. Arju, A. Gilmartin, Y. Lin, E. Ahmed, K. Steiner, M. Alam, S. Ahmed, G. Robinson, S. U. Zaman, M. Kabir, M. Sanders, R. M. Chalmers, T. Ahmed, J. Z. Ma, R. Haque, A. S. G. Faruque, M. Berriman, W. A. Petri (2018). Genetic Diversity of Cryptosporidium hominis in a Bangladeshi Community as Revealed by Whole-Genome Sequencing. In The Journal of Infectious Diseases 218:259–264.

PDF Cite DOI publisher Carol Gilchrist Petri lab

G. Schönian, J. Lukeš, O. Stark, James Cotton (2018). Molecular Evolution and Phylogeny of Leishmania. in Drug Resistance in Leishmania Parasites: Consequences, Molecular Mechanisms and Possible Treatments, A. Ponte-Sucre, M. Padrón-Nieves (eds.),.

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G. Sallé, R. Laing, James Cotton, K. Maitland, A. Martinelli, N. Holroyd, A. Tracey, M. Berriman, W. D. Smith, G. F. J. Newlands, E. Hanks, E. Devaney, C. Britton (2018). Transcriptomic profiling of nematode parasites surviving vaccine exposure. In International Journal of Parasitology 48:395–402.

PDF Cite DOI publisher Guillaume Sallé

S. Coughlan, A. S. Taylor, E. Feane, M. Sanders, G. Schönian, James Cotton, T. Downing (2018). Leishmania naiffi and Leishmania guyanensis reference genomes highlight genome structure and gene evolution in the Viannia subgenus. In Royal Society Open Science 5:172212.

PDF Cite Project DOI publisher Simone Coughlan Downing lab

U. Böhme, T. D. Otto, James Cotton, S. Steinbiss, M. Sanders, S. O. Oyola, A. Nicot, S. Gandon, K. P. Patra, C. Herd, E. Bushell, K. K. Modrzynska, O. Billker, J. M. Vinetz, A. Rivero, C. I. Newbold, M. Berriman (2018). Complete avian malaria parasite genomes reveal features associated with lineage-specific evolution in birds and mammals. In Genome Research 28:547–560.

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N. D. Sargison, E. Redman, A. A. Morrison, D. J. Bartley, F. Jackson, H. Naghra-van Gijzel, N. Holroyd, M. Berriman, James Cotton, J. S. Gilleard (2018). A method for single pair mating in an obligate parasitic nematode. In International Journal of Parasitology 48:159–165.

PDF Cite DOI publisher Neil Sargison Gilleard lab

S. R. Doyle, R. Laing, D. J. Bartley, C. Britton, U. Chaudhry, J. S. Gilleard, N. Holroyd, B. K. Mable, K. Maitland, A. A. Morrison, A. Tait, A. Tracey, M. Berriman, E. Devaney, James Cotton, N. D. Sargison (2018). A Genome Resequencing-Based Genetic Map Reveals the Recombination Landscape of an Outbred Parasitic Nematode in the Presence of Polyploidy and Polyandry. In Genome Biology and Evolution 10:396–409.

PDF Cite Project DOI publisher bioRxiv Neil Sargison Steve Doyle

A. Zackay, James Cotton, M. Sanders, A. Hailu, A. Nasereddin, A. Warburg, C. L. Jaffe (2018). Genome wide comparison of Ethiopian Leishmania donovani strains reveals differences potentially related to parasite survival. In PLoS Genetics 14:e1007133.

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S. A. Iantorno, C. Durrant, A. Khan, M. J. Sanders, S. M. Beverley, W. C. Warren, M. Berriman, D. L. Sacks, James Cotton, M. E. Grigg (2017). Gene Expression in Leishmania Is Regulated Predominantly by Gene Dosage. In mBio 8.

PDF Cite DOI publisher Michael Grigg

James Cotton (2017). The Expanding World of Human Leishmaniasis. In Trends Parasitol 33:341–344.

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F. Dumetz, H. Imamura, M. Sanders, V. Seblova, J. Myskova, P. Pescher, M. Vanaerschot, C. J. Meehan, B. Cuypers, G. de Muylder, G. F. Späth, G. Bussotti, J. R. Vermeesch, M. Berriman, James Cotton, P. Volf, J.-C. Dujardin,, M. A. Domagalska (2017). Modulation of Aneuploidy in Leishmania donovani during Adaptation to Different In Vitro and In Vivo Environments and Its Impact on Gene Expression. In mBio 8.

PDF Cite DOI publisher Franck Dumetz

S. Coughlan, P. Mulhair, M. Sanders, G. Schönian, James Cotton, T. Downing (2017). The genome of Leishmania adleri from a mammalian host highlights chromosome fission in Sauroleishmania. In Sci Rep 7:43747.

PDF Cite Project DOI publisher Simone Coughlan Downing lab

G. G. Rutledge, U. Böhme, M. Sanders, A. J. Reid, James Cotton, O. Maiga-Ascofare, A. A. Djimdé, T. O. Apinjoh, L. Amenga-Etego, M. Manske, J. W. Barnwell, F. Renaud, B. Ollomo, F. Prugnolle, N. M. Anstey, S. Auburn, R. N. Price, J. S. McCarthy, D. P. Kwiatkowski, C. I. Newbold, M. Berriman, T. D. Otto (2017). Plasmodium malariae and P. ovale genomes provide insights into malaria parasite evolution. In Nature 542:101–104.

PDF Cite Project DOI publisher Thomas Otto

H. O. Valdivia, L. V. Almeida, B. M. Roatt, J. L. Reis-Cunha, A. A. Pereira, C. Gontijo, R. T. Fujiwara, A. B. Reis, M. J. Sanders, James Cotton, D. C. Bartholomeu (2017). Comparative genomics of canine-isolated Leishmania (Leishmania) amazonensis from an endemic focus of visceral leishmaniasis in Governador Valadares, southeastern Brazil. In Sci Rep 7:40804.

PDF Cite DOI publisher Hugo Valdivia Daniella Bartholomeu

James Cotton, S. Steinbiss, T. Yokoi, I. J. Tsai, T. Kikuchi (2016). An expressed, endogenous Nodavirus-like element captured by a retrotransposon in the genome of the plant parasitic nematode Bursaphelenchus xylophilus. In Scientific Reports 6:39749.

PDF Cite DOI publisher Taisei Kikuchi Sascha Steinbiss

James Cotton, S. Bennuru, A. Grote, B. Harsha, A. Tracey, R. Beech, S. R. Doyle, M. Dunn, J. C. Hotopp, N. Holroyd, T. Kikuchi, O. Lambert, A. Mhashilkar, P. Mutowo, N. Nursimulu, J. M. Ribeiro, M. B. Rogers, E. Stanley, L. S. Swapna, I. J. Tsai, T. R. Unnasch, D. Voronin, J. Parkinson, T. B. Nutman, E. Ghedin, M. Berriman, S. Lustigman (2016). The genome of Onchocerca volvulus, agent of river blindness. In Nature Microbiology 2:16216.

PDF Cite Project DOI publisher Sara Lustigman

S. Bennuru, James Cotton, J. M. Ribeiro, A. Grote, B. Harsha, N. Holroyd, A. Mhashilkar, D. M. Molina, A. Z. Randall, A. D. Shandling, T. R. Unnasch, E. Ghedin, M. Berriman, S. Lustigman, T. B. Nutman (2016). Stage-Specific Transcriptome and Proteome Analyses of the Filarial Parasite Onchocerca volvulus and Its Wolbachia Endosymbiont. In mBio 7.

PDF Cite DOI publisher Sasi Bennuru

T. Crellen, M. Walker, P. H. Lamberton, N. B. Kabatereine, E. M. Tukahebwa, James Cotton, J. P. Webster (2016). Reduced Efficacy of Praziquantel Against Schistosoma mansoni Is Associated With Multiple Rounds of Mass Drug Administration. In Clinical Infectious Diseases 63:1151–1159.

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Pete Olson, Joseph Hughes, James Cotton (2016). Next Generation Systematics.

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James Cotton (2016). from sequence reads to evolutionary inferences. in Next Generation Systematics, P. Olson, J. Hughes and J. Cotton, (eds).

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S. Eves-van den Akker, D. R. Laetsch, P. Thorpe, C. J. Lilley, E. G. Danchin, M. Da Rocha, C. Rancurel, N. E. Holroyd, James Cotton, A. Szitenberg, E. Grenier, J. Montarry, B. Mimee, M. O. Duceppe, I. Boyes, J. M. Marvin, L. M. Jones, H. B. Yusup, J. Lafond-Lapalme, M. Esquibet, M. Sabeh, M. Rott, H. Overmars, A. Finkers-Tomczak, G. Smant, G. Koutsovoulos, V. Blok, S. Mantelin, P. J. Cock, W. Phillips, B. Henrissat, P. E. Urwin, M. Blaxter, J. T. Jones (2016). The genome of the yellow potato cyst nematode, Globodera rostochiensis, reveals insights into the basis of parasitism and virulence. In Genome Biology 17:124.

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V. L. Hunt, I. J. Tsai, A. Coghlan, A. J. Reid, N. Holroyd, B. J. Foth, A. Tracey, James Cotton, E. J. Stanley, H. Beasley, H. M. Bennett, K. Brooks, B. Harsha, R. Kajitani, A. Kulkarni, D. Harbecke, E. Nagayasu, S. Nichol, Y. Ogura, M. A. Quail, N. Randle, D. Xia, N. W. Brattig, H. Soblik, D. M. Ribeiro, A. Sanchez-Flores, T. Hayashi, T. Itoh, D. R. Denver, W. Grant, J. D. Stoltzfus, J. B. Lok, H. Murayama, J. Wastling, A. Streit, T. Kikuchi, M. Viney, M. Berriman (2016). The genomic basis of parasitism in the Strongyloides clade of nematodes. In Nat Genet 48:299–307.

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C. D. Shaw, J. Lonchamp, T. Downing, H. Imamura, T. M. Freeman, James Cotton, M. Sanders, G. Blackburn, J.-C. Dujardin,, S. Rijal, B. Khanal, C. J. Illingworth, G. H. Coombs, K. C. Carter (2016). In vitro selection of miltefosine resistance in promastigotes of Leishmania donovani from Nepal: genomic and metabolomic characterization. In Molecular Microbiology 99:1134–1148.

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H. Imamura, T. Downing, F. Van den Broeck, M. J. Sanders, S. Rijal, S. Sundar, A. Mannaert, M. Vanaerschot, M. Berg, G. de Muylder, F. Dumetz, B. Cuypers, I. Maes, M. Domagalska, S. Decuypere, K. Rai, S. Uranw, N. R. Bhattarai, B. Khanal, V. K. Prajapati, S. Sharma, O. Stark, G. Schönian, H. P. De Koning, L. Settimo, B. Vanhollebeke, S. Roy, B. Ostyn, M. Boelaert, L. Maes, M. Berriman, J.-C. Dujardin,, James Cotton (2016). Evolutionary genomics of epidemic visceral leishmaniasis in the Indian subcontinent. In Elife 5.

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T. Crellen, F. Allan, S. David, C. Durrant, T. Huckvale, N. Holroyd, A. M. Emery, D. Rollinson, D. M. Aanensen, M. Berriman, J. P. Webster, James Cotton (2016). Whole genome resequencing of the human parasite Schistosoma mansoni reveals population history and effects of selection. In Sci Rep 6:20954.

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R. Laing, A. Martinelli, A. Tracey, N. Holroyd, J. S. Gilleard, James Cotton (2016). Haemonchus contortus: Genome Structure, Organization and Comparative Genomics. In Advances in Parasitology 93:569–598.

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H. C. Kuo, S. F. Chen, Y. P. Fang, James Cotton, J. D. Parker, G. Csorba, B. K. Lim, J. L. Eger, C. H. Chen, C. H. Chou, S. J. Rossiter (2015). Speciation processes in putative island endemic sister bat species: false impressions from mitochondrial DNA and microsatellite data. In Molecular Ecology 24:5910–5926.

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P. H. Lamberton, T. Crellen, James Cotton, J. P. Webster (2015). Modelling the effects of mass drug administration on the molecular epidemiology of schistosomes. In Advances in Parasitology 87:293–327.

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J.-C. Dujardin,, A. Mannaert, C. Durrant, James Cotton (2014). Mosaic aneuploidy in Leishmania: the perspective of whole genome sequencing. In Trends in Parasitology 30:554–555.

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B. J. Foth, I. J. Tsai, A. J. Reid, A. J. Bancroft, S. Nichol, A. Tracey, N. Holroyd, James Cotton, E. J. Stanley, M. Zarowiecki, J. Z. Liu, T. Huckvale, P. J. Cooper, R. K. Grencis, M. Berriman (2014). Whipworm genome and dual-species transcriptome analyses provide molecular insights into an intimate host-parasite interaction. In Nature Genetics 46:693–700.

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International Glossina Genome Initiative (2014). Genome Sequence of the Tsetse Fly (Glossina morsitans): Vector of African Trypanosomiasis. Science 344:380-386.

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James Cotton, C. J. Lilley, L. M. Jones, T. Kikuchi, A. J. Reid, P. Thorpe, I. J. Tsai, H. Beasley, V. Blok, P. J. Cock, S. Eves-van den Akker, N. Holroyd, M. Hunt, S. Mantelin, H. Naghra, A. Pain, J. E. Palomares-Rius, M. Zarowiecki, M. Berriman, J. T. Jones, P. E. Urwin (2014). The genome and life-stage specific transcriptomes of Globodera pallida elucidate key aspects of plant parasitism by a cyst nematode. In Genome Biology 15:R43.

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M. L. Eberhard, E. Ruiz-Tiben, D. R. Hopkins, C. Farrell, F. Toe, A. Weiss, P. C. Withers, M. H. Jenks, E. A. Thiele, James Cotton, Z. Hance, N. Holroyd, V. A. Cama, M. A. Tahir, T. Mounda (2014). The peculiar epidemiology of dracunculiasis in Chad. In American Journal of Tropical Medicine and Hygiene 90:61–70.

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M. B. Rogers, T. Downing, B. A. Smith, H. Imamura, M. Sanders, M. Svobodova, P. Volf, M. Berriman, James Cotton, D. F. Smith (2014). Genomic confirmation of hybridisation and recent inbreeding in a vector-isolated Leishmania population. In PLoS Genetics 10:e1004092.

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G. Tsagkogeorga, J. Parker, E. Stupka, James Cotton, S. J. Rossiter (2013). Phylogenomic analyses elucidate the evolutionary relationships of bats. In Current Biology 23:2262–2267.

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J. Parker, G. Tsagkogeorga, James Cotton, Y. Liu, P. Provero, E. Stupka, S. J. Rossiter (2013). Genome-wide signatures of convergent evolution in echolocating mammals. In Nature 502:228–231.

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R. Laing, T. Kikuchi, A. Martinelli, I. J. Tsai, R. N. Beech, E. Redman, N. Holroyd, D. J. Bartley, H. Beasley, C. Britton, D. Curran, E. Devaney, A. Gilabert, M. Hunt, F. Jackson, S. L. Johnston, I. Kryukov, K. Li, A. A. Morrison, A. J. Reid, N. Sargison, G. I. Saunders, J. D. Wasmuth, A. Wolstenholme, M. Berriman, J. S. Gilleard, James Cotton (2013). The genome and transcriptome of Haemonchus contortus, a key model parasite for drug and vaccine discovery. In Genome Biology 14:R88.

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G. I. Saunders, J. D. Wasmuth, R. Beech, R. Laing, M. Hunt, H. Naghra, James Cotton, M. Berriman, C. Britton, J. S. Gilleard (2013). Characterization and comparative analysis of the complete Haemonchus contortus β-tubulin gene family and implications for benzimidazole resistance in strongylid nematodes. In International Journal of Parasitology 43:465–475.

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K. T. Davies, P. J. Bates, I. Maryanto, James Cotton, S. J. Rossiter (2013). The evolution of bat vestibular systems in the face of potential antagonistic selection pressures for flight and echolocation. In PLoS One 8:e61998.

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V. Svinti, James Cotton, J. O. McInerney (2013). New approaches for unravelling reassortment pathways. In BMC Evolutionary Biology 13:1.

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D. San Mauro, D. J. Gower, James Cotton, R. Zardoya, M. Wilkinson, T. Massingham (2012). Experimental design in phylogenetics: testing predictions from expected information. In Systematic Biology 61:661–674.

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K. T. Davies, James Cotton, J. D. Kirwan, E. C. Teeling, S. J. Rossiter (2012). Parallel signatures of sequence evolution among hearing genes in echolocating mammals: an emerging model of genetic convergence. In Heredity 108:480–489.

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A. J. Reid, S. J. Vermont, James Cotton, D. Harris, G. A. Hill-Cawthorne, S. Könen-Waisman, S. M. Latham, T. Mourier, R. Norton, M. A. Quail, M. Sanders, D. Shanmugam, A. Sohal, J. D. Wasmuth, B. Brunk, M. E. Grigg, J. C. Howard, J. Parkinson, D. S. Roos, A. J. Trees, M. Berriman, A. Pain, J. M. Wastling (2012). Comparative genomics of the apicomplexan parasites Toxoplasma gondii and Neospora caninum: Coccidia differing in host range and transmission strategy. In PLoS Pathogens 8:e1002567.

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T. Downing, H. Imamura, S. Decuypere, T. G. Clark, G. H. Coombs, James Cotton, J. D. Hilley, S. de Doncker, I. Maes, J. C. Mottram, M. A. Quail, S. Rijal, M. Sanders, G. Schönian, O. Stark, S. Sundar, M. Vanaerschot, C. Hertz-Fowler, J.-C. Dujardin,, M. Berriman (2011). Whole genome sequencing of multiple Leishmania donovani clinical isolates provides insights into population structure and mechanisms of drug resistance. In Genome Research 21:2143–2156.

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T. Kikuchi, James Cotton, J. J. Dalzell, K. Hasegawa, N. Kanzaki, P. McVeigh, T. Takanashi, I. J. Tsai, S. A. Assefa, P. J. Cock, T. D. Otto, M. Hunt, A. J. Reid, A. Sanchez-Flores, K. Tsuchihara, T. Yokoi, M. C. Larsson, J. Miwa, A. G. Maule, N. Sahashi, J. T. Jones, M. Berriman (2011). Genomic insights into the origin of parasitism in the emerging plant pathogen Bursaphelenchus xylophilus. In PLoS Pathogens 7:e1002219.

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L. J. Johnson, James Cotton, C. P. Lichtenstein, G. S. Elgar, R. A. Nichols, P. D. Polly, S. C. Le Comber (2011). Stops making sense: translational trade-offs and stop codon reassignment. In BMC Evolutionary Biology 11:227.

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James Cotton, J. O. McInerney (2010). Eukaryotic genes of archaebacterial origin are more important than the more numerous eubacterial genes, irrespective of function. In Proceedings of the National Academy of Sciences of the USA 107:17252–17255.

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Y. Liu, S. J. Rossiter, X. Han, James Cotton, S. Zhang (2010). Cetaceans on a molecular fast track to ultrasonic hearing. In Current Biology 20:1834–1839.

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Y. Liu, James Cotton, B. Shen, X. Han, S. J. Rossiter, S. Zhang (2010). Convergent sequence evolution between echolocating bats and dolphins. In Current Biology 20:R53–54.

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D. San Mauro, D. J. Gower, T. Massingham, M. Wilkinson, R. Zardoya, James Cotton (2009). Experimental design in caecilian systematics: phylogenetic information of mitochondrial genomes and nuclear rag1. In Systematic Biology 58:425–438.

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H. Zhao, S. J. Rossiter, E. C. Teeling, C. Li, James Cotton, S. Zhang (2009). The evolution of color vision in nocturnal mammals. In Proceedings of the National Academy of Science of the USA 106:8980–8985.

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K. Gold, James Cotton, A. Stollewerk (2009). The role of Notch signalling and numb function in mechanosensory organ formation in the spider Cupiennius salei. In Developmental Biology 327:121–131.

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James Cotton, M. Wilkinson (2009). Supertrees join the mainstream of phylogenetics. In Trends in Ecology and Evolution 24:1–3.

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A. McCann, James Cotton, J. O. McInerney (2008). The tree of genomes: an empirical comparison of genome-phylogeny reconstruction methods. In BMC Evolutionary Biology 8:312.

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G. Li, J. Wang, S. J. Rossiter, G. Jones, James Cotton, S. Zhang (2008). The hearing gene Prestin reunites echolocating bats. In Proceedings of the National Academy of Science of the USA 105:13959–13964.

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J. O. McInerney, James Cotton, D. Pisani (2008). The prokaryotic tree of life: past, present... and future?. In Trends Ecol Evol 23:276–281.

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K. J. Peterson, James Cotton, J. G. Gehling, D. Pisani (2008). The Ediacaran emergence of bilaterians: congruence between the genetic and the geological fossil records. In Philosophical Transactions of the Royal Society of London Series B Biological Sciences 363:1435–1443.

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James Cotton (2008). The Impact of Gene Duplication on Human Genome Evolution. im eLS (encyclopedia of Life Sciences).

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J. J. Day, James Cotton, T. G. Barraclough (2008). Tempo and mode of diversification of lake Tanganyika cichlid fishes. In PLoS One 3:e1730.

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S. P. Loader, D. Pisani, James Cotton, D. J. Gower, J. J. Day, M. Wilkinson (2007). Relative time scales reveal multiple origins of parallel disjunct distributions of African caecilian amphibians. In Biology Letters 3:505–508.

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D. Pisani, James Cotton, J. O. McInerney (2007). Supertrees disentangle the chimerical origin of eukaryotic genomes. In Molecular Biology and Evolution 24:1752–1760.

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James Cotton, M. Wilkinson (2007). Majority-rule supertrees. In Systematic Biology 56:445–452.

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M. Wilkinson, James Cotton, F. J. Lapointe, D. Pisani (2007). Properties of supertree methods in the consensus setting. In Systematic Biology 56:330–337.

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James Cotton, R. D. Page (2006). The shape of human gene family phylogenies. In BMC Evolutionay Biology 6:66.

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James Cotton, C. S. Slater, M. Wilkinson (2006). Discriminating supported and unsupported relationships in supertrees using triplets. In Systematic Biology 55:345–350.

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M. Wilkinson, D. Pisani, James Cotton, I. Corfe (2005). Measuring support and finding unsupported relationships in supertrees. In Systematic Biology 54:823–831.

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M. Wilkinson, James Cotton, C. Creevey, O. Eulenstein, S. R. Harris, F. J. Lapointe, C. Levasseur, J. O. McInerney, D. Pisani, J. L. Thorley (2005). The shape of supertrees to come: tree shape related properties of fourteen supertree methods. In Systematic Biology 54:419–431.

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James Cotton, R. D. Page (2005). Rates and patterns of gene duplication and loss in the human genome. In Proceedings of the Royal Society B:Biological Sciences 272:277–283.

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James Cotton (2005). Analytical methods for detecting paralogy in molecular datasets. In Methods in Enzymology 395:700–724.

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James Cotton, R. D. M. Page (2004). Tangled tales from multiple markers: Reconciling conflict between phylogenies to build molecular supertrees. in Phylogenetic Supertrees: combinging information to reveal the tree of life, O.R.P. Bininda-Emonds (ed.).

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James Cotton, R. D. Page (2003). Gene tree parsimony vs uninode coding for phylogenetic reconstruction. In Molecular Phylogenetics and Evolution 29:298–308.

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R. D. Page, James Cotton (2002). Vertebrate phylogenomics: reconciled trees and gene duplications. In Pac Symp Biocomput 269:536–547.

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James Cotton, R. D. Page (2002). Going nuclear: gene family evolution and vertebrate phylogeny reconciled. In Proceedings of the Royal Society B:Biological Sciences 269:1555–1561.

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James Cotton (2001). Homologous recombination in animal mitochondria. Genome Biology 2:reports0034.

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James Cotton (2001). A new profusion of planktonic eukaryotes. Genome Biology 2:reports0016.

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James Cotton (2001). Retroviruses from retrotransposons. Genome Biology 2:reports0006.

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James Cotton (2000). Oldest Archaea?. Genome Biology 1:reports0076.

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James Cotton (2000). Evolution without sex. Genome Biology 1:reports0068.

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James Cotton (2000). Towards uncultured-microbe genomics. Genome Biology 1:reports0060.

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R. D. M. Page, James Cotton (2000). Genetree: a tool for exploring gene family evolution. in Comparative Genomics: Empirical and Analytical Approaches to Gene Order Dynamics, Map Alignment and the Evolution of Gene Families, D. Sankoff and J. H. Nadeau (eds.).

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