{"id":75,"date":"2021-12-02T14:40:17","date_gmt":"2021-12-02T14:40:17","guid":{"rendered":"https:\/\/www.ebi.ac.uk\/research-beta\/lees\/?page_id=75"},"modified":"2026-01-13T13:54:50","modified_gmt":"2026-01-13T13:54:50","slug":"selected-publications","status":"publish","type":"page","link":"https:\/\/www.ebi.ac.uk\/research\/lees\/selected-publications\/","title":{"rendered":"Selected Publications"},"content":{"rendered":"\n<div class=\"vf-grid | vf-grid__col-3\"><div class=\"vf-grid__col--span-2\"><!--[vf\/content]-->\n<div class=\"vf-content\">\n\n<div class=\"wp-block-group\"><div class=\"wp-block-group__inner-container is-layout-flow wp-block-group-is-layout-flow\">\n<div class=\"wp-block-group\"><div class=\"wp-block-group__inner-container is-layout-flow wp-block-group-is-layout-flow\">\n<h3 class=\"wp-block-heading\">See <a href=\"https:\/\/www.bacpop.org\/publications\/\">https:\/\/www.bacpop.org\/publications\/<\/a> for an annotated list, or <a href=\"https:\/\/scholar.google.co.uk\/citations?user=UVV3P4UAAAAJ&amp;hl=en\" data-type=\"URL\" data-id=\"https:\/\/scholar.google.co.uk\/citations?user=UVV3P4UAAAAJ&amp;hl=en\">here<\/a> for google scholar.<\/h3>\n\n\n\n<p>For a background to our work, the following may be of interest:<\/p>\n\n\n\n<p>Hunt, M., Lima, L., Anderson, D., Bouras, G., Hall, M. B., Hawkey, J., Schwengers, O., Shen, W., Lees, J., &amp; Iqbal, Z. (2024). A<strong>llTheBacteria &#8211; all bacterial genomes assembled, available and searchable. <\/strong>In <em>bioRxiv<\/em> (p. 2024.03.08.584059). <\/p>\n\n\n\n<p><a href=\"https:\/\/doi.org\/10.1101\/2024.03.08.584059\">https:\/\/doi.org\/10.1101\/2024.03.08.584059<\/a><br><a href=\"https:\/\/www.allthebacteria.org\">https:\/\/www.allthebacteria.org<\/a><br><\/p>\n\n\n\n<p>John A Lees, Timothy W Russell, Liam P Shaw, Joel Hellewell (2024). <strong>Recent approaches in computational modelling for controlling pathogen threats<\/strong> <em>Life Science Alliance<\/em> 7(9) e202402666<\/p>\n\n\n\n<p><a href=\"https:\/\/doi.org\/10.26508\/lsa.202402666\">https:\/\/doi.org\/10.26508\/lsa.202402666<\/a><\/p>\n\n\n\n<p>Romain Derelle, Johanna von Wachsmann, Tommi M\u00e4klin, Joel Hellewell, Timothy Russell, Ajit Lalvani, Leonid Chindelevitch, Nicholas J. Croucher, Simon R. Harris, John A. Lees (2024). <strong>Seamless, rapid and accurate analyses of outbreak genomic data using Split K-mer Analysis (SKA)<\/strong> <em>bioRxiv<\/em><\/p>\n\n\n\n<p><a href=\"https:\/\/www.biorxiv.org\/content\/10.1101\/2024.03.25.586631.abstract\">https:\/\/www.biorxiv.org\/content\/10.1101\/2024.03.25.586631.abstract<\/a><\/p>\n<\/div><\/div>\n\n\n\n<p>Samuel T. Horsfield, Nicholas J. Croucher and John A. Lees (2023). <strong>Accurate and fast graph-based pangenome annotation and clustering with ggCaller<\/strong> <em>Genome Research<\/em> 33: 1622-1637<\/p>\n\n\n\n<p><a href=\"https:\/\/genome.cshlp.org\/content\/33\/9\/1622\">https:\/\/genome.cshlp.org\/content\/33\/9\/1622<\/a><\/p>\n<\/div><\/div>\n\n<\/div>\n<\/div>\n\n\n<div><!--[vf\/content]-->\n<div class=\"vf-content\">\n\n<\/div>\n<\/div>\n<\/div>\n\n\n\n<p><\/p>\n","protected":false},"excerpt":{"rendered":"","protected":false},"author":6,"featured_media":0,"parent":0,"menu_order":0,"comment_status":"closed","ping_status":"closed","template":"template-title-left-aligned.php","meta":{"_acf_changed":false,"footnotes":""},"embl_taxonomy":[],"class_list":["post-75","page","type-page","status-publish","hentry"],"acf":[],"embl_taxonomy_terms":[],"_links":{"self":[{"href":"https:\/\/www.ebi.ac.uk\/research\/lees\/wp-json\/wp\/v2\/pages\/75","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/www.ebi.ac.uk\/research\/lees\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/www.ebi.ac.uk\/research\/lees\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/www.ebi.ac.uk\/research\/lees\/wp-json\/wp\/v2\/users\/6"}],"replies":[{"embeddable":true,"href":"https:\/\/www.ebi.ac.uk\/research\/lees\/wp-json\/wp\/v2\/comments?post=75"}],"version-history":[{"count":11,"href":"https:\/\/www.ebi.ac.uk\/research\/lees\/wp-json\/wp\/v2\/pages\/75\/revisions"}],"predecessor-version":[{"id":21981,"href":"https:\/\/www.ebi.ac.uk\/research\/lees\/wp-json\/wp\/v2\/pages\/75\/revisions\/21981"}],"wp:attachment":[{"href":"https:\/\/www.ebi.ac.uk\/research\/lees\/wp-json\/wp\/v2\/media?parent=75"}],"wp:term":[{"taxonomy":"embl_taxonomy","embeddable":true,"href":"https:\/\/www.ebi.ac.uk\/research\/lees\/wp-json\/wp\/v2\/embl_taxonomy?post=75"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}