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List of works by James A. Cotton

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Whole genome sequencing of multiple Leishmania donovani clinical isolates provides insights into population structure and mechanisms of drug resistance

scientific article
Genomic insights into the origin of parasitism in the emerging plant pathogen Bursaphelenchus xylophilus

scientific article
Genetic analysis of the cytoplasmic dynein subunit families

scientific article
Genome-wide signatures of convergent evolution in echolocating mammals

scientific article
The genome and transcriptome of Haemonchus contortus, a key model parasite for drug and vaccine discovery

scientific article
Convergent sequence evolution between echolocating bats and dolphins.

scientific article
The Ediacaran emergence of bilaterians: congruence between the genetic and the geological fossil records

scientific article
Supertrees disentangle the chimerical origin of eukaryotic genomes

scientific article
The genome and life-stage specific transcriptomes of Globodera pallida elucidate key aspects of plant parasitism by a cyst nematode

scientific article
The evolution of color vision in nocturnal mammals

scientific article
Comparative genomics of the apicomplexan parasites Toxoplasma gondii and Neospora caninum: Coccidia differing in host range and transmission strategy

scientific article published in 2012
The genomic basis of parasitism in the Strongyloides clade of nematodes

scientific article published in February 2016
Whipworm genome and dual-species transcriptome analyses provide molecular insights into an intimate host-parasite interaction

scientific article
The hearing gene Prestin reunites echolocating bats

scientific article
Phylogenomic analyses elucidate the evolutionary relationships of bats

scientific article
The prokaryotic tree of life: past, present... and future?

scientific article published on 25 March 2008
Tempo and mode of diversification of lake Tanganyika cichlid fishes

scientific article (publication date: 5 March 2008)
Genomic confirmation of hybridisation and recent inbreeding in a vector-isolated Leishmania population

scientific article
Plasmodium malariae and P. ovale genomes provide insights into malaria parasite evolution

scientific article
Going nuclear: gene family evolution and vertebrate phylogeny reconciled

scientific article (publication date: 7 August 2002)
The genome of the yellow potato cyst nematode, Globodera rostochiensis, reveals insights into the basis of parasitism and virulence.

scientific article published on 10 June 2016
New approaches for unravelling reassortment pathways

scientific article
Eukaryotic genes of archaebacterial origin are more important than the more numerous eubacterial genes, irrespective of function

scientific article (publication date: 5 October 2010)
Evolutionary genomics of epidemic visceral leishmaniasis in the Indian subcontinent

scientific article
The genome of Onchocerca volvulus, agent of river blindness

scientific article published on 21 November 2016
The shape of supertrees to come: tree shape related properties of fourteen supertree methods

scientific article published in June 2005
The peculiar epidemiology of dracunculiasis in Chad

scientific article
Modulation of Aneuploidy in Leishmania donovani during Adaptation to Different In Vitro and In Vivo Environments and Its Impact on Gene Expression

scientific article
Reduced Efficacy of Praziquantel Against Schistosoma mansoni Is Associated With Multiple Rounds of Mass Drug Administration

scientific article
Measuring support and finding unsupported relationships in supertrees

scientific article published in October 2005
Cetaceans on a molecular fast track to ultrasonic hearing

scientific article
Genomic and Molecular Characterization of Miltefosine Resistance in Leishmania infantum Strains with Either Natural or Acquired Resistance through Experimental Selection of Intracellular Amastigotes

scientific article
Relative time scales reveal multiple origins of parallel disjunct distributions of African caecilian amphibians

scientific article (publication date: 22 October 2007)
Rates and patterns of gene duplication and loss in the human genome

scientific article (publication date: 7 February 2005)
Experimental design in caecilian systematics: phylogenetic information of mitochondrial genomes and nuclear rag1

scientific article
In vitro selection of miltefosine resistance in promastigotes of Leishmania donovani from Nepal: genomic and metabolomic characterization.

scientific article
Majority-rule supertrees

scientific article published in June 2007
Stage-Specific Transcriptome and Proteome Analyses of the Filarial Parasite Onchocerca volvulus and Its Wolbachia Endosymbiont

scientific article
Characterization and comparative analysis of the complete Haemonchus contortus β-tubulin gene family and implications for benzimidazole resistance in strongylid nematodes.

scientific article published on 14 February 2013
Properties of supertree methods in the consensus setting

scientific article
Whole genome resequencing of the human parasite Schistosoma mansoni reveals population history and effects of selection

scientific article published on 16 February 2016
The evolution of bat vestibular systems in the face of potential antagonistic selection pressures for flight and echolocation

scientific article (publication date: 2013)
Comparative genomics of canine-isolated Leishmania (Leishmania) amazonensis from an endemic focus of visceral leishmaniasis in Governador Valadares, southeastern Brazil

scientific article
The tree of genomes: an empirical comparison of genome-phylogeny reconstruction methods

scientific article published on 12 November 2008
The genome of Leishmania adleri from a mammalian host highlights chromosome fission in Sauroleishmania

scientific article published on 03 March 2017
The role of Notch signalling and numb function in mechanosensory organ formation in the spider Cupiennius salei

scientific article published on 16 December 2008
The Expanding World of Human Leishmaniasis

scientific article
Discriminating supported and unsupported relationships in supertrees using triplets

scientific article published in April 2006
Gene tree parsimony vs uninode coding for phylogenetic reconstruction

scientific article
Analytical methods for detecting paralogy in molecular datasets

scientific article

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