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4<aside class=search-modal id=search><div class=container><section class=search-header><div class="row no-gutters justify-content-between mb-3"><div class=col-6><h1>Search</h1></div><div class="col-6 col-search-close"><a class=js-search href=# aria-label=Close><i class="fas fa-times-circle text-muted" aria-hidden=true></i></a></div></div><div id=search-box><input name=q id=search-query placeholder=Search... autocapitalize=off autocomplete=off autocorrect=off spellcheck=false type=search class=form-control aria-label=Search...></div></section><section class=section-search-results><div id=search-hits></div></section></div></aside><div class=page-header><nav class="navbar navbar-expand-lg navbar-light compensate-for-scrollbar" id=navbar-main><div class=container-xl><div class="d-none d-lg-inline-flex"><a class=navbar-brand href=/>James Cotton</a></div><button type=button class=navbar-toggler data-toggle=collapse data-target=#navbar-content aria-controls=navbar aria-expanded=false aria-label="Toggle navigation">
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7<a href=# class="dropdown-item js-set-theme-auto"><span>Automatic</span></a></div></li></ul></div></nav></div><div class=page-body><div class="universal-wrapper pt-3"><h1>Projects</h1></div><div class=universal-wrapper><div><h2><a href=/project/leishethiopia/>Leishmaniasis in Ethiopia</a></h2><div class=article-style>Working with some excellent Ethiopian collaborators and in particular Pascale Kropf at Imperial college, London, we are using parasite genetics and RNA-seq of clinical samples to understand the pathogenesis and epidemiology of leishmaniasis in Ethiopia.</div></div><div><h2><a href=/project/anthelminthics/>genetics of anthelminthic drug resistance</a></h2><div class=article-style>I led the Sanger Institute involvement in the first reference genome for Haemonchus contortus. Haemonchus is widely used as a model in research on anti-nematode anthelminthics, so it was natural to try and use this resource to try and understand the genetic basis of anthelmintihcs resistance.</div></div><div><h2><a href=/project/leishevo/>evolutionary genomics of Leishmania</a></h2><div class=article-style>I was involved in the earliest work on the genomics of Leishmania populations, and with a range of collaborators have published on Leishmania populations in the Indian subcontinent, East Africa and South America, and recently the first global picture of the Leishmania donovani species complex.</div></div><div><h2><a href=/project/guineaworm/>Guinea worm eradication genomics</a></h2><div class=article-style>I was involved in attempts to provide genetic evidence to support the Guinea worm eradication program. I was initially asked whether we could show genetically that the worms then appearing in dog infections in Chad were the same - Dracunculus medinensis - as those causing human cases.</div></div><div><h2><a href=/project/refgenomes/>building reference genome and transcriptome resources</a></h2><div class=article-style>My first involvement in parasitology was through leading reference genome sequencing, assembly and annotation projects for a number of key helminth species of medical and veterinary importance. This inlucdes the nematodes Haemonchus contortus, Globodera pallida and Onchocerca volvulus.</div></div><div><h2><a href=/project/sheepscab/>ML resistance in sheep scab mites</a></h2><div class=article-style>Roz Laing, Jenni McIntyre and I have recently been awarded BBSRC funding for a project with Stew Burgess and Al Nisbet and colleagues at the Moredu

7n Research Institute and Jack Hearn at SRUC to study ivermectin resistance in sheep scab mites (Psoroptes ovis), using a combination of bulked segregant analysis and population genomics approaches.</div></div><div><h2><a href=/project/cryptosporidium/>Cryptosporidium genetics and genomics</a></h2><div class=article-style>I&rsquo;ve worked on Cryptosporidium genomics in collaboration with Carol Gilchrist and Bill Petri at the University of Virginia and their colleagues at ICDDR,B in Dhaka to generate some genomic data from a cohort of Bangaldesh children with diarrhoeal disease.</div></div></div></div><div class=page-footer><div class=container><footer class=site-footer><p class=powered-by>© 2026 James A. Cotton</p><p class=powered-by>Published with <a href="https://wowchemy.com/?utm_campaign=poweredby" target=_blank rel=noopener>Wowchemy</a> — the free, <a href=https://github.com/wowchemy/wowchemy-hugo-modules target=_blank rel=noopener>open source</a> website builder that empowers creators.</p></footer></div></div><div id=modal class="modal fade" role=dialog><div class=modal-dialog><div class=modal-content><div class=modal-header><h5 class=modal-title>Cite</h5><button type=button class=close data-dismiss=modal aria-label=Close>
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