List of works by James A. Cotton

An expressed, endogenous Nodavirus-like element captured by a retrotransposon in the genome of the plant parasitic nematode Bursaphelenchus xylophilus

scientific article

Analytical methods for detecting paralogy in molecular datasets

scientific article

Cetaceans on a molecular fast track to ultrasonic hearing

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

Comparative genomics of canine-isolated Leishmania (Leishmania) amazonensis from an endemic focus of visceral leishmaniasis in Governador Valadares, southeastern Brazil.

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

Convergent sequence evolution between echolocating bats and dolphins.

scientific article

Discriminating supported and unsupported relationships in supertrees using triplets

scientific article

Ecological divergence and hybridization of Neotropical Leishmania parasites

scientific article published on 21 September 2020

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

scientific article (publication date: 5 October 2010)

Evaluation of DNA Extraction Methods on Individual Helminth Egg and Larval Stages for Whole-Genome Sequencing

scientific article published on 20 September 2019

Evolutionary genomics of epidemic visceral leishmaniasis in the Indian subcontinent

scientific article

Experimental design in caecilian systematics: phylogenetic information of mitochondrial genomes and nuclear rag1

scientific article

Experimental design in phylogenetics: testing predictions from expected information

scientific article

Gene tree parsimony vs uninode coding for phylogenetic reconstruction

scientific article

Genetic analysis of the cytoplasmic dynein subunit families

scientific article

Genome-wide signatures of convergent evolution in echolocating mammals

scientific article

Genomes of Leishmania parasites directly sequenced from patients with visceral leishmaniasis in the Indian subcontinent

scientific article published on 12 December 2019

Genomic analysis of natural intra-specific hybrids among Ethiopian isolates of Leishmania donovani

scientific article published on 20 April 2020

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

Genomic confirmation of hybridisation and recent inbreeding in a vector-isolated Leishmania population

scientific article

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

scientific article

Global genome diversity of the Leishmania donovani complex

scientific article published on 25 March 2020

Going nuclear: gene family evolution and vertebrate phylogeny reconciled

scientific article (publication date: 7 August 2002)

Haemonchus contortus: Genome Structure, Organization and Comparative Genomics.

scientific article

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

scientific article

Linked surveillance and genetic data uncovers programmatically relevant geographic scale of Guinea worm transmission in Chad

scientific article published on 26 July 2021

Majority-rule supertrees

scientific article

Measuring support and finding unsupported relationships in supertrees

scientific article

Modelling the effects of mass drug administration on the molecular epidemiology of schistosomes

scientific article published on 7 February 2015

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

scientific article

Mosaic aneuploidy in Leishmania: the perspective of whole genome sequencing

scientific article published on 22 October 2014

New approaches for unravelling reassortment pathways

scientific article

Phylogenomic analyses elucidate the evolutionary relationships of bats

scientific article

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

scientific article

Population genomic evidence that human and animal infections in Africa come from the same populations of Dracunculus medinensis

scientific article published on 30 November 2020

Properties of supertree methods in the consensus setting

scientific article

Rates and patterns of gene duplication and loss in the human genome

scientific article (publication date: 7 February 2005)

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

scientific article

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

scientific article (publication date: 22 October 2007)

Speciation processes in putative island endemic sister bat species: false impressions from mitochondrial DNA and microsatellite data

scientific article

Stage-Specific Transcriptome and Proteome Analyses of the Filarial Parasite Onchocerca volvulus and Its Wolbachia Endosymbiont

scientific article

Stops making sense: translational trade-offs and stop codon reassignment

scientific article (publication date: 29 July 2011)

Supertrees disentangle the chimerical origin of eukaryotic genomes

scientific article

Supertrees join the mainstream of phylogenetics

scientific article published on 18 November 2008

Tempo and mode of diversification of lake Tanganyika cichlid fishes

scientific article (publication date: 5 March 2008)

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

scientific article

The Expanding World of Human Leishmaniasis

scientific article

The evolution of bat vestibular systems in the face of potential antagonistic selection pressures for flight and echolocation

scientific article (publication date: 2013)

The evolution of color vision in nocturnal mammals

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

scientific article

The genome of Leishmania adleri from a mammalian host highlights chromosome fission in Sauroleishmania

scientific article published on 03 March 2017

The genome of Onchocerca volvulus, agent of river blindness

scientific article published on 21 November 2016

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

The genomic basis of parasitism in the Strongyloides clade of nematodes

scientific article published in February 2016

The hearing gene Prestin reunites echolocating bats

scientific article

The information content of trees and their matrix representations

scientific article

The peculiar epidemiology of dracunculiasis in Chad

scientific article

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

scientific article published on 25 March 2008

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 shape of human gene family phylogenies

scientific article (publication date: 29 August 2006)

The shape of supertrees to come: tree shape related properties of fourteen supertree methods

scientific article

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

scientific article published on 12 November 2008

Transcriptional and genomic parallels between the monoxenous parasite Herpetomonas muscarum and Leishmania

scientific article published on 11 November 2019

Whipworm genome and dual-species transcriptome analyses provide molecular insights into an intimate host-parasite interaction

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

Whole genome sequencing of experimental hybrids supports meiosis-like sexual recombination in Leishmania

scientific article published on 15 May 2019

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

scientific article

Whole-genome sequencing of Schistosoma mansoni reveals extensive diversity with limited selection despite mass drug administration

scientific article published on 06 August 2021

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