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By using the site you are agreeing to this as outlined in our <a href="https://www.ebi.ac.uk/data-protection/ensembl/privacy-notice" rel=""> Privacy Policy </a> </div> </aside> </div> </div> </div> <div id="primary" class="content-area col-lg-9" itemprop="mainContentOfPage"> <h1 class="page-title">Author: <span>Aleena Mushtaq</span></h1> <div id="content" class="site-content" role="main"> <article itemscope itemtype="http://schema.org/Article" id="post-15776" class="post-15776 post type-post status-publish format-standard hentry category-07-status tag-bioinformatics tag-biomart tag-ensembl tag-release"> <header class="entry-header"> <h2 class="entry-title" itemprop="name"> <a itemprop="url" href="https://www.ensembl.info/2024/11/13/temporary-disruption-in-ensembl-biomart/" title="Permalink to Temporary disruption in Ensembl BioMart" rel="bookmark">Temporary disruption in Ensembl BioMart</a> </h2> <div class="entry-meta"><span class="entry-date"><a href="https://www.ensembl.info/2024/11/13/temporary-disruption-in-ensembl-biomart/" rel="bookmark"><time class="entry-date published" datetime="2024-11-13T11:32:09+00:00" itemprop="datepublished">13th November 2024</time></a></span> by <span class="author vcard" itemscope itemprop="author" itemtype="http://schema.org/Person"><a class="url fn n" href="https://www.ensembl.info/author/aleena/" rel="author" itemprop="url"><span itemprop="name">Aleena Mushtaq</span></a></span><span class="sep">·</span><span class="comments-link"><a href="https://www.ensembl.info/2024/11/13/temporary-disruption-in-ensembl-biomart/#respond" itemprop="discussionUrl">0 Comments</a></span></div> </header> <div class="entry-content" itemprop="articleBody"> <p>We are experiencing issues with Ensembl BioMart due to unforeseen errors. </p> <a class="btn btn-default btn-sm" href="https://www.ensembl.info/2024/11/13/temporary-disruption-in-ensembl-biomart/">Continue reading <i class="fa fa-angle-double-right"></i></a> </div> </article> <article itemscope itemtype="http://schema.org/Article" id="post-15608" class="post-15608 post type-post status-publish format-standard hentry category-02-ensembl-vep tag-bioinformatics tag-ensembl tag-variation tag-vep"> <header class="entry-header"> <h2 class="entry-title" itemprop="name"> <a itemprop="url" href="https://www.ensembl.info/2024/08/09/cool-stuff-ensembl-vep-can-do-supporting-alternative-human-assemblies/" title="Permalink to Cool stuff Ensembl VEP can do: supporting alternative human assemblies" rel="bookmark">Cool stuff Ensembl VEP can do: supporting alternative human assemblies</a> </h2> <div class="entry-meta"><span class="entry-date"><a href="https://www.ensembl.info/2024/08/09/cool-stuff-ensembl-vep-can-do-supporting-alternative-human-assemblies/" rel="bookmark"><time class="entry-date published" datetime="2024-08-09T08:22:00+01:00" itemprop="datepublished">9th August 2024</time></a></span> by <span class="author vcard" itemscope itemprop="author" itemtype="http://schema.org/Person"><a class="url fn n" href="https://www.ensembl.info/author/aleena/" rel="author" itemprop="url"><span itemprop="name">Aleena Mushtaq</span></a></span><span class="sep">·</span><span class="comments-link"><span>Comments Off<span class="screen-reader-text"> on Cool stuff Ensembl VEP can do: supporting alternative human assemblies</span></span></span></div> </header> <div class="entry-content" itemprop="articleBody"> <p>The Ensembl VEP command-line tool can annotate and filter variants called against the latest human assemblies, including the telomere-to-telomere assembly of the CHM13 cell line (T2T-CHM13). In this blog post, we provide examples of how to run Ensembl VEP with these new assemblies and list the additional annotations supported via plugins.</p> <a class="btn btn-default btn-sm" href="https://www.ensembl.info/2024/08/09/cool-stuff-ensembl-vep-can-do-supporting-alternative-human-assemblies/">Continue reading <i class="fa fa-angle-double-right"></i></a> </div> </article> <article itemscope itemtype="http://schema.org/Article" id="post-15429" class="post-15429 post type-post status-publish format-standard hentry category-01-release tag-bioinformatics tag-ensembl tag-ensembl-genomes tag-genomics tag-plants tag-release tag-rest-api tag-vep"> <header class="entry-header"> <h2 class="entry-title" itemprop="name"> <a itemprop="url" href="https://www.ensembl.info/2024/05/13/ensembl-112-has-been-released/" title="Permalink to Ensembl 112 has been released." rel="bookmark">Ensembl 112 has been released.</a> </h2> <div class="entry-meta"><span class="entry-date"><a href="https://www.ensembl.info/2024/05/13/ensembl-112-has-been-released/" rel="bookmark"><time class="entry-date published" datetime="2024-05-13T15:33:16+01:00" itemprop="datepublished">13th May 2024</time></a></span> by <span class="author vcard" itemscope itemprop="author" itemtype="http://schema.org/Person"><a class="url fn n" href="https://www.ensembl.info/author/aleena/" rel="author" itemprop="url"><span itemprop="name">Aleena Mushtaq</span></a></span><span class="sep">·</span><span class="comments-link"><span>Comments Off<span class="screen-reader-text"> on Ensembl 112 has been released.</span></span></span></div> </header> <div class="entry-content" itemprop="articleBody"> <p>We are pleased to announce the release of Ensembl 112, and the corresponding release of Ensembl Genomes 59. We have some exciting new fish species, many more drosophila species and some incredible VEP updates.</p> <a class="btn btn-default btn-sm" href="https://www.ensembl.info/2024/05/13/ensembl-112-has-been-released/">Continue reading <i class="fa fa-angle-double-right"></i></a> </div> </article> <article itemscope itemtype="http://schema.org/Article" id="post-15366" class="post-15366 post type-post status-publish format-standard hentry category-04-training tag-bioinformatics tag-ensembl tag-ensembl-genomes tag-genomics tag-rest-api tag-vep"> <header class="entry-header"> <h2 class="entry-title" itemprop="name"> <a itemprop="url" href="https://www.ensembl.info/2024/04/05/free-ensembl-browser-and-rest-api-virtual-workshops-in-may-2/" title="Permalink to Free Ensembl Browser and REST API virtual workshops in May" rel="bookmark">Free Ensembl Browser and REST API virtual workshops in May</a> </h2> <div class="entry-meta"><span class="entry-date"><a href="https://www.ensembl.info/2024/04/05/free-ensembl-browser-and-rest-api-virtual-workshops-in-may-2/" rel="bookmark"><time class="entry-date published" datetime="2024-04-05T15:25:44+01:00" itemprop="datepublished">5th April 2024</time></a></span> by <span class="author vcard" itemscope itemprop="author" itemtype="http://schema.org/Person"><a class="url fn n" href="https://www.ensembl.info/author/aleena/" rel="author" itemprop="url"><span itemprop="name">Aleena Mushtaq</span></a></span><span class="sep">·</span><span class="comments-link"><span>Comments Off<span class="screen-reader-text"> on Free Ensembl Browser and REST API virtual workshops in May</span></span></span></div> </header> <div class="entry-content" itemprop="articleBody"> <p>Sign up for our virtual series covering the Ensembl genome browser and accessing Ensembl data via its REST API. Both workshops will be held from Tuesday to Thursday, with the browser course running from <strong>7th to 9th May</strong> and REST API from <strong>14th to 16th May 2024</strong> (14:00-17:00 BST). Read on for more information and how to register.</p> <a class="btn btn-default btn-sm" href="https://www.ensembl.info/2024/04/05/free-ensembl-browser-and-rest-api-virtual-workshops-in-may-2/">Continue reading <i class="fa fa-angle-double-right"></i></a> </div> </article> <article itemscope itemtype="http://schema.org/Article" id="post-15342" class="post-15342 post type-post status-publish format-standard hentry category-01-release tag-bioinformatics tag-ensembl tag-ensembl-genomes tag-gencode tag-plants tag-release tag-rest-api tag-variation tag-vep"> <header class="entry-header"> <h2 class="entry-title" itemprop="name"> <a itemprop="url" href="https://www.ensembl.info/2024/03/25/whats-coming-in-ensembl-release-112-ensembl-genomes-59/" title="Permalink to What鈥檚 coming in Ensembl release 112 / Ensembl Genomes 59?" rel="bookmark">What鈥檚 coming in Ensembl release 112 / Ensembl Genomes 59?</a> </h2> <div class="entry-meta"><span class="entry-date"><a href="https://www.ensembl.info/2024/03/25/whats-coming-in-ensembl-release-112-ensembl-genomes-59/" rel="bookmark"><time class="entry-date published" datetime="2024-03-25T16:00:13+00:00" itemprop="datepublished">25th March 2024</time></a></span> by <span class="author vcard" itemscope itemprop="author" itemtype="http://schema.org/Person"><a class="url fn n" href="https://www.ensembl.info/author/aleena/" rel="author" itemprop="url"><span itemprop="name">Aleena Mushtaq</span></a></span><span class="sep">·</span><span class="comments-link"><span>Comments Off<span class="screen-reader-text"> on What鈥檚 coming in Ensembl release 112 / Ensembl Genomes 59?</span></span></span></div> </header> <div class="entry-content" itemprop="articleBody"> <p>Ensembl 112 and Ensembl Genomes 59 are expected in April 2024. Check out what we鈥檙e up to, although we can鈥檛 guarantee everything listed here will make it into the final release.</p> <a class="btn btn-default btn-sm" href="https://www.ensembl.info/2024/03/25/whats-coming-in-ensembl-release-112-ensembl-genomes-59/">Continue reading <i class="fa fa-angle-double-right"></i></a> </div> </article> <article itemscope itemtype="http://schema.org/Article" id="post-15211" class="post-15211 post type-post status-publish format-standard hentry category-07-status tag-asia-mirror tag-ensembl tag-genomics"> <header class="entry-header"> <h2 class="entry-title" itemprop="name"> <a itemprop="url" href="https://www.ensembl.info/2024/01/18/downtime-of-the-ensembl-search-and-asia-mirror/" title="Permalink to Downtime of Ensembl search" rel="bookmark">Downtime of Ensembl search</a> </h2> <div class="entry-meta"><span class="entry-date"><a href="https://www.ensembl.info/2024/01/18/downtime-of-the-ensembl-search-and-asia-mirror/" rel="bookmark"><time class="entry-date published" datetime="2024-01-18T12:14:17+00:00" itemprop="datepublished">18th January 2024</time></a></span> by <span class="author vcard" itemscope itemprop="author" itemtype="http://schema.org/Person"><a class="url fn n" href="https://www.ensembl.info/author/aleena/" rel="author" itemprop="url"><span itemprop="name">Aleena Mushtaq</span></a></span><span class="sep">·</span><span class="comments-link"><a href="https://www.ensembl.info/2024/01/18/downtime-of-the-ensembl-search-and-asia-mirror/#comments" itemprop="discussionUrl">13 Comments</a></span></div> </header> <div class="entry-content" itemprop="articleBody"> <p>We are experiencing issues with the <a href="https://www.ensembl.org/index.html" data-type="link" data-id="https://www.ensembl.org/index.html" target="_blank" rel="noreferrer noopener">Ensembl</a> search system due to unforeseen errors. The search function is currently unavailable and this may affect other functions such as the loading of variants on genomic sequences. To search for entries in Ensembl, you can do one of the following:</p> <ol> <li>Use the EMBL-EBI website: go to <a href="https://www.ebi.ac.uk/ebisearch" target="_blank" rel="noreferrer noopener">https://www.ebi.ac.uk/ebisearch</a> and enter your search terms into the text box. E.g. if you want to search for human <em>BRCA2</em> in Ensembl, enter <code>Ensembl human BRCA2</code> into the search text box.</li> <li>Use Google: to search for entries in Ensembl via Google, go to <a href="https://google.com/" target="_blank" rel="noreferrer noopener">www.google.com</a> and enter聽<code>site:https://www.ensembl.org聽[search terms]</code>. E.g. if you want to search for human <em>BRCA2</em>, enter聽<code>site:https://www.ensembl.org聽human BRCA2</code><strong><em>聽</em></strong>into Google.</li> </ol> <p>We are working to fix this issue as quickly as possible, although a timeline is still unclear for the work to be completed. Services will be resumed as soon as the issue has been resolved. If you have any questions, please contact us on the <a href="https://www.ensembl.org/Help/Contact" target="_blank" rel="noreferrer noopener">Ensembl Helpdesk</a>.</p> </div> </article> <article itemscope itemtype="http://schema.org/Article" id="post-14900" class="post-14900 post type-post status-publish format-standard hentry category-uncategorised tag-bioinformatics tag-deep-learning tag-ensembl tag-ensembl-beta tag-gencode tag-genomics tag-gsoc"> <header class="entry-header"> <h2 class="entry-title" itemprop="name"> <a itemprop="url" href="https://www.ensembl.info/2023/07/27/gsoc-2023-our-contributors-and-their-projects/" title="Permalink to GSOC 2023: Our contributors and their projects" rel="bookmark">GSOC 2023: Our contributors and their projects</a> </h2> <div class="entry-meta"><span class="entry-date"><a href="https://www.ensembl.info/2023/07/27/gsoc-2023-our-contributors-and-their-projects/" rel="bookmark"><time class="entry-date published" datetime="2023-07-27T09:32:10+01:00" itemprop="datepublished">27th July 2023</time></a></span> by <span class="author vcard" itemscope itemprop="author" itemtype="http://schema.org/Person"><a class="url fn n" href="https://www.ensembl.info/author/aleena/" rel="author" itemprop="url"><span itemprop="name">Aleena Mushtaq</span></a></span><span class="sep">·</span><span class="comments-link"><span>Comments Off<span class="screen-reader-text"> on GSOC 2023: Our contributors and their projects</span></span></span></div> </header> <div class="entry-content" itemprop="articleBody"> <p>Today鈥檚 blog focuses on this year鈥檚 <a href="https://summerofcode.withgoogle.com/" data-type="URL" data-id="https://summerofcode.withgoogle.com/" target="_blank" rel="noreferrer noopener">Google Summer of Code (GSoC)</a>. GSoC is an international program founded by Google in 2005 with the purpose of bringing together open-source organisations, and developers interested in contributing to open-source software and getting an exposure to real-world software development techniques. Host organisations list project ideas, and applicants discuss these ideas directly with mentors from the organisations and devise a project proposal to Google, who issue a small stipend to successful applicants.</p> <a class="btn btn-default btn-sm" href="https://www.ensembl.info/2023/07/27/gsoc-2023-our-contributors-and-their-projects/">Continue reading <i class="fa fa-angle-double-right"></i></a> </div> </article> <article itemscope itemtype="http://schema.org/Article" id="post-14754" class="post-14754 post type-post status-publish format-standard hentry category-05-community category-03-other category-uncategorised tag-ensembl tag-ensembl-genomes tag-ftp tag-genomics"> <header class="entry-header"> <h2 class="entry-title" itemprop="name"> <a itemprop="url" href="https://www.ensembl.info/2023/06/01/retirement-of-neandertal-genome-website/" title="Permalink to Retirement of Neandertal Genome website" rel="bookmark">Retirement of Neandertal Genome website</a> </h2> <div class="entry-meta"><span class="entry-date"><a href="https://www.ensembl.info/2023/06/01/retirement-of-neandertal-genome-website/" rel="bookmark"><time class="entry-date published" datetime="2023-06-01T17:15:36+01:00" itemprop="datepublished">1st June 2023</time></a></span> by <span class="author vcard" itemscope itemprop="author" itemtype="http://schema.org/Person"><a class="url fn n" href="https://www.ensembl.info/author/aleena/" rel="author" itemprop="url"><span itemprop="name">Aleena Mushtaq</span></a></span><span class="sep">·</span><span class="comments-link"><span>Comments Off<span class="screen-reader-text"> on Retirement of Neandertal Genome website</span></span></span></div> </header> <div class="entry-content" itemprop="articleBody"> <p>The <a href="https://neandertal.ensemblgenomes.org/">Neandertal Genome website</a> will be retired at the end of June 2023. Details about how to access data previously hosted by this resource can be found at the <a href="https://projects.ensembl.org/neandertal/">Ensembl Neandertal Project website</a>.</p> <a class="btn btn-default btn-sm" href="https://www.ensembl.info/2023/06/01/retirement-of-neandertal-genome-website/">Continue reading <i class="fa fa-angle-double-right"></i></a> </div> </article> <article itemscope itemtype="http://schema.org/Article" id="post-14707" class="post-14707 post type-post status-publish format-standard hentry category-05-community tag-bioinformatics tag-ensembl tag-ensembl-genomes tag-genomics"> <header class="entry-header"> <h2 class="entry-title" itemprop="name"> <a itemprop="url" href="https://www.ensembl.info/2023/05/16/getting-to-know-us-jorge-alvarez-jarreta-from-ensembl-metazoa/" title="Permalink to Getting to know us: Jorge 脕lvarez Jarreta from Ensembl Metazoa" rel="bookmark">Getting to know us: Jorge 脕lvarez Jarreta from Ensembl Metazoa</a> </h2> <div class="entry-meta"><span class="entry-date"><a href="https://www.ensembl.info/2023/05/16/getting-to-know-us-jorge-alvarez-jarreta-from-ensembl-metazoa/" rel="bookmark"><time class="entry-date published" datetime="2023-05-16T10:54:30+01:00" itemprop="datepublished">16th May 2023</time></a></span> by <span class="author vcard" itemscope itemprop="author" itemtype="http://schema.org/Person"><a class="url fn n" href="https://www.ensembl.info/author/aleena/" rel="author" itemprop="url"><span itemprop="name">Aleena Mushtaq</span></a></span><span class="sep">·</span><span class="comments-link"><span>Comments Off<span class="screen-reader-text"> on Getting to know us: Jorge 脕lvarez Jarreta from Ensembl Metazoa</span></span></span></div> </header> <div class="entry-content" itemprop="articleBody"> <p>This month, we meet <a rel="noreferrer noopener" href="https://www.ebi.ac.uk/people/person/jorge-alvarez-jarreta/" data-type="URL" data-id="https://www.ebi.ac.uk/people/person/jorge-alvarez-jarreta/" target="_blank">Jorge 脕lvarez Jarreta</a> to talk about his professional journey, Jorge’s role in Ensembl and learn about the new and upcoming features that the Metazoa team is working on.</p> <a class="btn btn-default btn-sm" href="https://www.ensembl.info/2023/05/16/getting-to-know-us-jorge-alvarez-jarreta-from-ensembl-metazoa/">Continue reading <i class="fa fa-angle-double-right"></i></a> </div> </article> <article itemscope itemtype="http://schema.org/Article" id="post-14684" class="post-14684 post type-post status-publish format-standard hentry category-02-ensembl-vep tag-bioinformatics tag-ensembl tag-gene-annotation tag-rest-api tag-vep"> <header class="entry-header"> <h2 class="entry-title" itemprop="name"> <a itemprop="url" href="https://www.ensembl.info/2023/04/05/cool-stuff-ensembl-vep-can-do-using-gene-ontology-annotations-to-understand-gene-function/" title="Permalink to Cool stuff Ensembl VEP can do: Using Gene Ontology annotations to understand gene function" rel="bookmark">Cool stuff Ensembl VEP can do: Using Gene Ontology annotations to understand gene function</a> </h2> <div class="entry-meta"><span class="entry-date"><a href="https://www.ensembl.info/2023/04/05/cool-stuff-ensembl-vep-can-do-using-gene-ontology-annotations-to-understand-gene-function/" rel="bookmark"><time class="entry-date published" datetime="2023-04-05T15:14:14+01:00" itemprop="datepublished">5th April 2023</time></a></span> by <span class="author vcard" itemscope itemprop="author" itemtype="http://schema.org/Person"><a class="url fn n" href="https://www.ensembl.info/author/aleena/" rel="author" itemprop="url"><span itemprop="name">Aleena Mushtaq</span></a></span><span class="sep">·</span><span class="comments-link"><span>Comments Off<span class="screen-reader-text"> on Cool stuff Ensembl VEP can do: Using Gene Ontology annotations to understand gene function</span></span></span></div> </header> <div class="entry-content" itemprop="articleBody"> <p>Ensembl <a href="https://www.ensembl.org/info/docs/tools/vep/index.html">VEP</a> maps your variants to genes but what do those genes do?</p> <p>The Gene Ontology (GO) annotates genes with molecular function, the cellular location in which the gene product functions and the biological process in which the gene product is involved. In addition to <a href="https://www.ensembl.info/2019/04/26/cool-stuff-the-ensembl-vep-can-do-phenotype-and-disease-associations/" target="_blank" rel="noreferrer noopener">phenotype association information</a>, which is only available for a few genes, we now show <a href="http://geneontology.org">GO annotations</a> to help guide variant prioritisation by providing an indication of the functionality a variant may affect.</p> <a class="btn btn-default btn-sm" href="https://www.ensembl.info/2023/04/05/cool-stuff-ensembl-vep-can-do-using-gene-ontology-annotations-to-understand-gene-function/">Continue reading <i class="fa fa-angle-double-right"></i></a> </div> </article> <nav class="navigation pagination" aria-label="Posts"> <h2 class="screen-reader-text">Posts navigation</h2> <div class="nav-links"><span aria-current="page" class="page-numbers current">1</span> <a class="page-numbers" href="https://www.ensembl.info/author/aleena/page/2/">2</a> <a class="page-numbers" href="https://www.ensembl.info/author/aleena/page/3/">3</a> <a class="next page-numbers" href="https://www.ensembl.info/author/aleena/page/2/"><i class="fa fa-chevron-right"></i></a></div> </nav> </div> <footer class="site-info" itemscope itemtype="http://schema.org/WPFooter"> <a href="http://wordpress.org/" title="Semantic Personal Publishing Platform">Proudly powered by WordPress</a>. 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