{"id":66145,"date":"2024-02-05T16:23:14","date_gmt":"2024-02-05T15:23:14","guid":{"rendered":"https:\/\/www.embl.org\/news\/?p=66145"},"modified":"2024-06-12T12:57:43","modified_gmt":"2024-06-12T10:57:43","slug":"we-are-embl-jacqueline-toussaint-embl-phd","status":"publish","type":"post","link":"https:\/\/www.embl.org\/news\/lab-matters\/we-are-embl-jacqueline-toussaint-embl-phd\/","title":{"rendered":"We are EMBL: Jacqueline Toussaint on strange bacteria and bioinformatics"},"content":{"rendered":"\n<h3 class=\"wp-block-heading\">Tell us a little bit about your background.<\/h3>\n\n\n\n<p>I studied biochemistry with a minor in microbiology at Montana State University, USA. After my graduation in 2022, I was keen to get some hands-on experience and work on my own independent project, which is what attracted me to <a href=\"https:\/\/www.embl.org\/about\/info\/embl-international-phd-programme\/\">EMBL\u2019s international PhD programme<\/a>.&nbsp;<\/p>\n\n\n\n<h3 class=\"wp-block-heading\">How has your experience in the EMBL PhD programme been so far?<\/h3>\n\n\n\n<p>I started in 2022, and so far it\u2019s been great. It was a bit challenging in the beginning, because I didn\u2019t come from a computational background, so I had to work hard to get my skills up to speed. However, my supervisor and colleagues at EMBL-EBI are super helpful and always willing to discuss my work and point me in the right direction if I\u2019m feeling a bit lost. I value the supportive and open working environment at EMBL.&nbsp;<\/p>\n\n\n\n<p>Two of the things I found appealing about the programme were, first, that there is no compulsory teaching element \u2013 which allows you to focus on your science \u2013 and second, that there are no rotations \u2013 so you can really concentrate on your project, without the work becoming too fragmented.<\/p>\n\n\n\n<h3 class=\"wp-block-heading\">What are you currently working on?<\/h3>\n\n\n\n<p>I work on bacterial genomics with a focus on how we can better human health. Specifically, the main project I\u2019m working on now focuses on developing methods for bacterial genome-wide association studies (GWAS). It aims to look at the genotype of a bacterium and correlate it with resulting phenotypes, or traits \u2013 for example, antimicrobial resistance or virulence (a microorganism\u2019s ability to cause damage to a host).&nbsp;<\/p>\n\n\n\n<p>The goal is to get a better scientific understanding of the causal genetic mechanisms of specific phenotypes. So these studies might then help you predict, for example, antimicrobial resistance for a bacterial sample you\u2019ve isolated from a patient. This could have practical applications for guiding patient treatment in the future.<\/p>\n\n\n\n<p>I\u2019m currently working on a Bayesian model based on the theory of how bacterial genotypes and phenotypes are correlated. I\u2019m using a pre-existing software called Stan in which anyone can implement their Bayesian model. If you input genotype and phenotype data into the model, it gives you an association score for each of the genetic variants and the phenotype. You can also input new query genotypes to receive a predicted phenotype that the genotype is likely to result in and an estimate of the heritability of the phenotype.&nbsp;<\/p>\n\n\n\n<h3 class=\"wp-block-heading\">What data are you using to test the model?<\/h3>\n\n\n\n<p>I\u2019m using public, open-source datasets, some of which are archived in EMBL-EBI\u2019s <a href=\"https:\/\/www.ebi.ac.uk\/ena\/browser\/\">European Nucleotide Archive<\/a>. So far I\u2019ve used datasets focusing on antimicrobial resistance because it\u2019s heavily genetically based, which makes it a good phenotype to test with. I\u2019ve tested the model using data from a few different bacteria, including <em>Mycobacterium tuberculosis<\/em> and <em>Streptococcus pneumoniae<\/em>.&nbsp;<\/p>\n\n\n\n<h3 class=\"wp-block-heading\">Where does your interest in bacteria spark from?<\/h3>\n\n\n\n<p>I\u2019ve always thought that bacteria make up some of the more interesting subjects of biochemistry because they can have so many improbable biological functions. Take extremophiles for example, which can live in hot geothermal springs or polar ice. When I learned about horizontal gene transfer \u2013 the movement of genetic information between organisms \u2013 it just blew my mind. For example, this process can enable the spread of antibiotic resistance genes among bacteria. I\u2019m fascinated by the strange world of bacteria and the diversity that exists within it.<\/p>\n\n\n\n<h3 class=\"wp-block-heading\">In EMBL\u2019s 50th anniversary year, how do you think molecular biology is going to change in the future?<\/h3>\n\n\n\n<p>I think that the scale at which data is going to be produced, stored, and processed will be beyond our comprehension. It may also get easier to do bioinformatics. In the past, bioinformatics software often had a high barrier to entry and it could be extremely difficult to get even simple things done. I think, in the future, development might be as simple as plug \u2018n\u2019 play, which would open up the field to a lot more people.&nbsp;&nbsp;&nbsp;<\/p>\n","protected":false},"excerpt":{"rendered":"<p>Jacqueline shares her experience of EMBL&#8217;s international PhD programme.<\/p>\n","protected":false},"author":47,"featured_media":66159,"comment_status":"closed","ping_status":"closed","sticky":false,"template":"","format":"standard","meta":{"_acf_changed":false,"footnotes":""},"categories":[3,17593],"tags":[580,28,189,5780,36,17289,42,5776,14003],"embl_taxonomy":[2906,11964],"class_list":["post-66145","post","type-post","status-publish","format-standard","has-post-thumbnail","hentry","category-lab-matters","category-people-perspectives","tag-bacteria","tag-bioinformatics","tag-computational-biology","tag-data-science","tag-embl-ebi","tag-embl50","tag-genomics","tag-microbial-ecosystems","tag-we-are-embl","embl_taxonomy-embl-ebi","embl_taxonomy-lees-group"],"acf":{"featured":true,"show_featured_image":false,"field_target_display":"both","field_article_language":{"value":"english","label":"English"},"article_intro":"<p>Jacqueline Toussaint is a predoctoral fellow in the <a href=\"https:\/\/www.ebi.ac.uk\/research\/lees\/\" target=\"_blank\" rel=\"noopener\">Lees group at EMBL-EBI<\/a>, studying pathogenic bacteria. Here, she shares her experience of EMBL\u2019s international PhD programme and her deep dive into the world of bioinformatics.<\/p>\n","related_links":[{"link_description":"EMBL PhD programme","link_url":"https:\/\/www.embl.org\/about\/info\/embl-international-phd-programme\/"},{"link_description":"Lees research group ","link_url":"https:\/\/www.ebi.ac.uk\/research\/lees\/"}],"source_article":false,"in_this_article":false,"press_contact":"None","article_translations":false,"languages":"","vf_locked":false},"embl_taxonomy_terms":[{"uuid":"a:3:{i:0;s:36:\"b14d3f13-5670-44fb-8970-e54dfd9c921a\";i:1;s:36:\"89e00fee-87f4-482e-a801-4c3548bb6a58\";i:2;s:36:\"a99d1a7c-ca83-4c00-ab61-d082d3e41ce3\";}","parents":[],"name":["EMBL-EBI"],"slug":"embl-ebi","description":"Where &gt; All EMBL sites &gt; EMBL-EBI"},{"uuid":"a:3:{i:0;s:36:\"302cfdf7-365b-462a-be65-82c7b783ebf7\";i:1;s:36:\"442a4893-2c31-4523-b9eb-fb1ee4bd2037\";i:2;s:36:\"232c135e-2db9-4a81-b72d-656b5ae845e5\";}","parents":[],"name":["Lees Group"],"slug":"lees-group","description":"What &gt; EMBL-EBI Research &gt; Lees Group"}],"yoast_head":"<!-- This site is optimized with the Yoast SEO plugin v26.2 - https:\/\/yoast.com\/wordpress\/plugins\/seo\/ -->\n<title>We are EMBL: Jacqueline Toussaint on strange bacteria and bioinformatics | EMBL<\/title>\n<meta name=\"description\" content=\"Part of the EMBL international PhD programme, Jacqueline Toussaint is using cutting-edge bioinformatics to annotate bacterial genomes.\" \/>\n<meta name=\"robots\" content=\"index, follow, max-snippet:-1, max-image-preview:large, max-video-preview:-1\" \/>\n<link rel=\"canonical\" href=\"https:\/\/www.embl.org\/news\/lab-matters\/we-are-embl-jacqueline-toussaint-embl-phd\/\" \/>\n<meta property=\"og:locale\" content=\"en_US\" \/>\n<meta property=\"og:type\" content=\"article\" \/>\n<meta property=\"og:title\" content=\"We are EMBL: Jacqueline Toussaint on strange bacteria and bioinformatics | EMBL\" \/>\n<meta property=\"og:description\" content=\"Part of the EMBL international PhD programme, Jacqueline Toussaint is using cutting-edge bioinformatics to annotate bacterial genomes.\" \/>\n<meta property=\"og:url\" content=\"https:\/\/www.embl.org\/news\/lab-matters\/we-are-embl-jacqueline-toussaint-embl-phd\/\" \/>\n<meta property=\"og:site_name\" content=\"EMBL\" \/>\n<meta property=\"article:publisher\" content=\"https:\/\/www.facebook.com\/embl.org\/\" \/>\n<meta property=\"article:published_time\" content=\"2024-02-05T15:23:14+00:00\" \/>\n<meta property=\"article:modified_time\" content=\"2024-06-12T10:57:43+00:00\" \/>\n<meta property=\"og:image\" content=\"https:\/\/www.embl.org\/news\/wp-content\/uploads\/2024\/02\/Jacqueline-Toussaint-low-res.jpg\" \/>\n\t<meta property=\"og:image:width\" content=\"1000\" \/>\n\t<meta property=\"og:image:height\" content=\"600\" \/>\n\t<meta property=\"og:image:type\" content=\"image\/jpeg\" \/>\n<meta name=\"author\" content=\"Oana Stroe\" \/>\n<meta name=\"twitter:card\" content=\"summary_large_image\" \/>\n<meta name=\"twitter:creator\" content=\"@embl\" \/>\n<meta name=\"twitter:site\" content=\"@embl\" \/>\n<meta name=\"twitter:label1\" content=\"Written by\" \/>\n\t<meta name=\"twitter:data1\" content=\"Oana Stroe\" \/>\n\t<meta name=\"twitter:label2\" content=\"Est. reading time\" \/>\n\t<meta name=\"twitter:data2\" content=\"4 minutes\" \/>\n<script type=\"application\/ld+json\" class=\"yoast-schema-graph\">{\"@context\":\"https:\/\/schema.org\",\"@graph\":[{\"@type\":\"NewsArticle\",\"@id\":\"https:\/\/www.embl.org\/news\/lab-matters\/we-are-embl-jacqueline-toussaint-embl-phd\/#article\",\"isPartOf\":{\"@id\":\"https:\/\/www.embl.org\/news\/lab-matters\/we-are-embl-jacqueline-toussaint-embl-phd\/\"},\"author\":{\"name\":\"Oana Stroe\",\"@id\":\"https:\/\/www.embl.org\/news\/#\/schema\/person\/95d28f359cc138357c5dcf79319ef414\"},\"headline\":\"We are EMBL: Jacqueline Toussaint on strange bacteria and bioinformatics\",\"datePublished\":\"2024-02-05T15:23:14+00:00\",\"dateModified\":\"2024-06-12T10:57:43+00:00\",\"mainEntityOfPage\":{\"@id\":\"https:\/\/www.embl.org\/news\/lab-matters\/we-are-embl-jacqueline-toussaint-embl-phd\/\"},\"wordCount\":687,\"publisher\":{\"@id\":\"https:\/\/www.embl.org\/news\/#organization\"},\"image\":{\"@id\":\"https:\/\/www.embl.org\/news\/lab-matters\/we-are-embl-jacqueline-toussaint-embl-phd\/#primaryimage\"},\"thumbnailUrl\":\"https:\/\/www.embl.org\/news\/wp-content\/uploads\/2024\/02\/Jacqueline-Toussaint-low-res.jpg\",\"keywords\":[\"bacteria\",\"bioinformatics\",\"computational biology\",\"data science\",\"embl-ebi\",\"embl50\",\"genomics\",\"microbial ecosystems\",\"we are embl\"],\"articleSection\":[\"Lab Matters\",\"People &amp; 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