Publications

(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

(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

(2021). Immunological factors, but not clinical features, predict visceral leishmaniasis relapse in patients co-infected with HIV. bioRxiv.

PDF Project DOI bioRxiv Yegnasew Takele

(2021). Long-read assembly and comparative evidence-based reanalysis of Cryptosporidium genome sequences reveal new biological insights. bioRxiv 428682.

PDF DOI bioRxiv Kissinger lab

(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

(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

(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.

PDF Cite DOI publisher

(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

(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

(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.

PDF Cite DOI biorxiv publisher

(2020). A Way Straight-Forward for Leishmania Genetics. In Trends in Parasitology 36:719–721.

PDF Cite DOI publisher

(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

(2020). Novel 2D and 3D Assays to Determine the Activity of Anti-Leishmanial Drugs. In Microorganisms 8.

PDF Cite publisher

(2020). Nearly Complete Genome Sequence of Brugia malayi Strain FR3. In Microbiology Resource Announcements 9.

PDF Cite DOI publisher Elodie Ghedin

(2020). Sex chromosome evolution in parasitic nematodes of humans. In Nat Commun 11:1964.

PDF Cite DOI publisher Alex Grote

(2020). Genomic analysis of natural intra-specific hybrids among Ethiopian isolates of Leishmania donovani. In PLoS Neglected Tropical Diseases 14:e0007143.

PDF Cite Project DOI publisher

(2020). Global genome diversity of the Leishmania donovani complex. In Elife 9.

PDF Cite Project DOI publisher github

(2019). Genomic and Metabolomic Polymorphism among Experimentally Selected Paromomycin-Resistant Leishmania donovani Strains. In Antimicrobial Agents and Chemotherapy 64:e00904-19.

PDF Cite DOI publisher

(2019). Genomes of Leishmania parasites directly sequenced from patients with visceral leishmaniasis in the Indian subcontinent. In PLoS Neglected Tropical Diseases 13:e0007900.

PDF Cite DOI publisher

(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

(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

(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

(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

(2019). Genome-wide Approaches to Investigate Anthelmintic Resistance. In Trends Parasitol 35:289–301.

PDF Cite DOI publisher Steve Doyle

(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 DOI publisher Steve Doyle Chris Illingworth Gilleard lab

(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

(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.

PDF Cite Project DOI publisher

(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

(2018). Eradication genomics-lessons for parasite control. In Science 361:130–131.

PDF Cite DOI publisher

(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

(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.),.

PDF DOI publisher

(2018). Transcriptomic profiling of nematode parasites surviving vaccine exposure. In International Journal of Parasitology 48:395–402.

PDF Cite DOI publisher Guillaume Sallé

(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 DOI publisher Simone Coughlan Downing lab

(2018). Complete avian malaria parasite genomes reveal features associated with lineage-specific evolution in birds and mammals. In Genome Research 28:547–560.

PDF Cite DOI publisher

(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

(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 DOI publisher bioRxiv Neil Sargison Steve Doyle

(2018). Genome wide comparison of Ethiopian Leishmania donovani strains reveals differences potentially related to parasite survival. In PLoS Genetics 14:e1007133.

PDF Cite DOI publisher

(2017). Gene Expression in Leishmania Is Regulated Predominantly by Gene Dosage. In mBio 8.

PDF Cite DOI publisher Michael Grigg

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

PDF Cite DOI publisher

(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

(2017). The genome of Leishmania adleri from a mammalian host highlights chromosome fission in Sauroleishmania. In Sci Rep 7:43747.

PDF Cite DOI publisher Simone Coughlan Downing lab

(2017). Plasmodium malariae and P. ovale genomes provide insights into malaria parasite evolution. In Nature 542:101–104.

PDF Cite DOI publisher Thomas Otto

(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

(2016). The genome of Onchocerca volvulus, agent of river blindness. In Nature Microbiology 2:16216.

PDF Cite DOI publisher Sara Lustigman

(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

(2016). Reduced Efficacy of Praziquantel Against Schistosoma mansoni Is Associated With Multiple Rounds of Mass Drug Administration. In Clinical Infectious Diseases 63:1151–1159.

PDF Cite DOI publisher Tom Crellen Martin Walker Webster lab

(2016). Next Generation Systematics.

PDF DOI publisher

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

PDF DOI publisher

(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.

PDF Cite DOI publisher Sebastian Eves-van den Akker John Jones

(2016). The genomic basis of parasitism in the Strongyloides clade of nematodes. In Nat Genet 48:299–307.

PDF Cite DOI publisher Hunt lab Viney lab

(2016). In vitro selection of miltefosine resistance in promastigotes of Leishmania donovani from Nepal: genomic and metabolomic characterization. In Molecular Microbiology 99:1134–1148.

PDF Cite DOI publisher

(2016). Evolutionary genomics of epidemic visceral leishmaniasis in the Indian subcontinent. In Elife 5.

PDF Cite Project DOI publisher Hideo Imamura Jean-Claude Dujardin

(2016). Whole genome resequencing of the human parasite Schistosoma mansoni reveals population history and effects of selection. In Sci Rep 6:20954.

PDF Cite DOI publisher Tom Crellen

(2016). Haemonchus contortus: Genome Structure, Organization and Comparative Genomics. In Advances in Parasitology 93:569–598.

PDF Cite DOI publisher Roz Laing

(2015). Speciation processes in putative island endemic sister bat species: false impressions from mitochondrial DNA and microsatellite data. In Molecular Ecology 24:5910–5926.

PDF Cite DOI publisher Steve Rossiter

(2015). Modelling the effects of mass drug administration on the molecular epidemiology of schistosomes. In Advances in Parasitology 87:293–327.

PDF Cite DOI publisher Lamberton lab Webster lab

(2014). Mosaic aneuploidy in Leishmania: the perspective of whole genome sequencing. In Trends in Parasitology 30:554–555.

PDF Cite DOI publisher Jean-Claude Dujardin

(2014). Whipworm genome and dual-species transcriptome analyses provide molecular insights into an intimate host-parasite interaction. In Nature Genetics 46:693–700.

PDF Cite DOI publisher Bernardo Foth

(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.

PDF Cite DOI publisher John Jones Urwin lab

(2014). The peculiar epidemiology of dracunculiasis in Chad. In American Journal of Tropical Medicine and Hygiene 90:61–70.

PDF Cite DOI publisher

(2014). Genomic confirmation of hybridisation and recent inbreeding in a vector-isolated Leishmania population. In PLoS Genetics 10:e1004092.

PDF Cite DOI publisher Matt Rogers

(2013). Phylogenomic analyses elucidate the evolutionary relationships of bats. In Current Biology 23:2262–2267.

PDF Cite DOI publisher Georgia Tsagkogeorga Steve Rossiter

(2013). Genome-wide signatures of convergent evolution in echolocating mammals. In Nature 502:228–231.

PDF Cite publisher Joe Parker Steve Rossiter

(2013). The genome and transcriptome of Haemonchus contortus, a key model parasite for drug and vaccine discovery. In Genome Biology 14:R88.

PDF Cite DOI publisher Roz Laing Gilleard lab

(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.

PDF Cite DOI publisher Gary Saunders Gilleard lab

(2013). New approaches for unravelling reassortment pathways. In BMC Evolutionary Biology 13:1.

PDF Cite DOI publisher James McInerney McInerney lab

(2012). Experimental design in phylogenetics: testing predictions from expected information. In Systematic Biology 61:661–674.

PDF Cite DOI publisher Diego San Mauro

(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.

PDF Cite DOI publisher Adam Reid

(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.

PDF Cite Project publisher Downing lab

(2011). Genomic insights into the origin of parasitism in the emerging plant pathogen Bursaphelenchus xylophilus. In PLoS Pathogens 7:e1002219.

PDF Cite DOI publisher Taisei Kikuchi

(2011). Stops making sense: translational trade-offs and stop codon reassignment. In BMC Evolutionary Biology 11:227.

PDF Cite DOI publisher Steve Le Comber Louise Johnson

(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.

PDF Cite DOI publisher James McInerney McInerney lab

(2010). Cetaceans on a molecular fast track to ultrasonic hearing. In Current Biology 20:1834–1839.

PDF Cite DOI publisher Rossiter lab

(2010). Convergent sequence evolution between echolocating bats and dolphins. In Current Biology 20:R53–54.

PDF Cite DOI publisher Rossiter lab

(2009). Experimental design in caecilian systematics: phylogenetic information of mitochondrial genomes and nuclear rag1. In Systematic Biology 58:425–438.

PDF Cite DOI publisher Diego San Mauro

(2009). The evolution of color vision in nocturnal mammals. In Proceedings of the National Academy of Science of the USA 106:8980–8985.

PDF Cite DOI publisher Rossiter lab

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

PDF Cite DOI publisher Mark Wilkinson

(2008). The tree of genomes: an empirical comparison of genome-phylogeny reconstruction methods. In BMC Evolutionary Biology 8:312.

PDF Cite DOI publisher James McInerney McInerney lab

(2008). The hearing gene Prestin reunites echolocating bats. In Proceedings of the National Academy of Science of the USA 105:13959–13964.

PDF Cite DOI publisher Rossiter lab

(2008). The prokaryotic tree of life: past, present... and future?. In Trends Ecol Evol 23:276–281.

PDF Cite DOI publisher James McInerney McInerney lab

(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.

PDF Cite DOI publisher Davide Pisani Kevin Peterson

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

PDF Cite DOI publisher

(2008). Tempo and mode of diversification of lake Tanganyika cichlid fishes. In PLoS One 3:e1730.

PDF Cite DOI publisher Day lab BarraLab

(2007). Relative time scales reveal multiple origins of parallel disjunct distributions of African caecilian amphibians. In Biology Letters 3:505–508.

PDF Cite DOI publisher Simon Loader Mark Wilkinson

(2007). Supertrees disentangle the chimerical origin of eukaryotic genomes. In Molecular Biology and Evolution 24:1752–1760.

PDF Cite DOI publisher Davide Pisani James McInerney McInerney lab

(2007). Majority-rule supertrees. In Systematic Biology 56:445–452.

PDF Cite DOI publisher Mark Wilkinson

(2007). Properties of supertree methods in the consensus setting. In Systematic Biology 56:330–337.

PDF Cite DOI publisher Mark Wilkinson

(2006). The shape of human gene family phylogenies. In BMC Evolutionay Biology 6:66.

PDF Cite DOI publisher Rod Page Rod Page

(2006). Discriminating supported and unsupported relationships in supertrees using triplets. In Systematic Biology 55:345–350.

PDF Cite DOI publisher Mark Wilkinson

(2005). Measuring support and finding unsupported relationships in supertrees. In Systematic Biology 54:823–831.

PDF Cite DOI publisher Mark Wilkinson

(2005). The shape of supertrees to come: tree shape related properties of fourteen supertree methods. In Systematic Biology 54:419–431.

PDF Cite DOI publisher Mark Wilkinson

(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.

PDF Cite DOI publisher Rod Page Rod Page

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

PDF Cite DOI publisher

(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.).

PDF DOI publisher

(2003). Gene tree parsimony vs uninode coding for phylogenetic reconstruction. In Molecular Phylogenetics and Evolution 29:298–308.

PDF Cite DOI publisher Rod Page Rod Page

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

PDF Cite DOI publisher Rod Page Rod Page

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

PDF DOI publisher

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

PDF DOI publisher

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

PDF DOI publisher

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

PDF DOI publisher

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

PDF DOI publisher

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

PDF DOI publisher

(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.).

PDF DOI publisher