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#bioinformatics

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Victoria Stuart 🇨🇦 🏳️‍⚧️<p>GREmLN: A Cellular Regulatory Network-Aware Transcriptomics Foundation Model<br><a href="https://www.biorxiv.org/content/10.1101/2025.07.03.663009v1?rss=1" rel="nofollow noopener" translate="no" target="_blank"><span class="invisible">https://www.</span><span class="ellipsis">biorxiv.org/content/10.1101/20</span><span class="invisible">25.07.03.663009v1?rss=1</span></a></p><p>Comments<br>* really brilliant work: LLM + neural transformer architecture<br>* a molecular biologist, I long-thought (no time to learn / program) flux-based analysis / ODE models<br>* this type of modeling is foundational to in silico modeling<br>* huge proponent of graphs - add LLM, attention heads - brilliant! 😀 👍️ kudos</p><p><a href="https://mastodon.social/tags/BiologicalModeling" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>BiologicalModeling</span></a> <a href="https://mastodon.social/tags/FoundationModels" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>FoundationModels</span></a> <a href="https://mastodon.social/tags/LLM" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>LLM</span></a> <a href="https://mastodon.social/tags/attention" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>attention</span></a> <a href="https://mastodon.social/tags/GraphTheory" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>GraphTheory</span></a> <a href="https://mastodon.social/tags/bioinformatics" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>bioinformatics</span></a></p>
UK<p><a href="https://www.europesays.com/uk/240940/" rel="nofollow noopener" translate="no" target="_blank"><span class="invisible">https://www.</span><span class="">europesays.com/uk/240940/</span><span class="invisible"></span></a> The role of untranslated region variants in Mendelian disease: a review <a href="https://pubeurope.com/tags/Bioinformatics" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>Bioinformatics</span></a> <a href="https://pubeurope.com/tags/Biomedicine" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>Biomedicine</span></a> <a href="https://pubeurope.com/tags/Cytogenetics" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>Cytogenetics</span></a> <a href="https://pubeurope.com/tags/DiseaseGenetics" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>DiseaseGenetics</span></a> <a href="https://pubeurope.com/tags/GeneExpression" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>GeneExpression</span></a> <a href="https://pubeurope.com/tags/GeneRegulation" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>GeneRegulation</span></a> <a href="https://pubeurope.com/tags/general" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>general</span></a> <a href="https://pubeurope.com/tags/Genetics" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>Genetics</span></a> <a href="https://pubeurope.com/tags/HumanGenetics" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>HumanGenetics</span></a> <a href="https://pubeurope.com/tags/Science" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>Science</span></a> <a href="https://pubeurope.com/tags/UK" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>UK</span></a> <a href="https://pubeurope.com/tags/UnitedKingdom" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>UnitedKingdom</span></a></p>
Dr. Robert M Flight<p>So, redesigning a few classes in my <a href="https://mastodon.social/tags/RStats" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>RStats</span></a> categoryCompare2 📦 actually fixed all the issues I was seeing trying to manage different types of annotation enrichments, with very little effort (hypergeometric, GSEA, and binomial).</p><p>Tests are passing, just need to fix up the vignettes, and then we can merge!</p><p><a href="https://mastodon.social/tags/bioinformatics" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>bioinformatics</span></a></p>
Alexis SimonBioinformatics research engineer position, 18 Months, France
Eli Roberson (he/him)<p><a href="https://genomic.social/tags/Bioinformatics" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>Bioinformatics</span></a><br><a href="https://genomic.social/tags/Genomics" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>Genomics</span></a><br><a href="https://genomic.social/tags/Academia" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>Academia</span></a></p><p>A few years ago the PI of my grad lab moved to the NIH. The institute he was at shut down their servers and presumably wiped them. Unfortunately, they had hosted multiple web tools that were lost. The one I built I had the code for. I am going through my digital hoarding to clean out space in my emails. I just randomly came across an email that had zip attachments of the source for TWO LOST TOOLS.</p><p>Time to dockerize them.</p>
Dr. Robert M Flight<p>Current me: Ugh, human GO terms are annotated with Uniprot, current data has Entrez, when I generate the GO annotation object I'll have to convert as part of the process.</p><p>Past me: Human GO terms are annotated with Uniprot, when we ingest this data, we should be able to provide a mapping table so that the final GO annotation object uses whatever gene IDs we want.</p><p>Current me: Thanks past me! Glad I looked at the help and the code for that function first!</p><p><a href="https://mastodon.social/tags/bioinformatics" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>bioinformatics</span></a> <a href="https://mastodon.social/tags/GeneOntology" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>GeneOntology</span></a></p>
Bioconductor<p>📝 New blog post from the Bioconductor Training Committee!</p><p>We’re collaborating with <span class="h-card" translate="no"><a href="https://ecoevo.social/@physaliacourses2" class="u-url mention" rel="nofollow noopener" target="_blank">@<span>physaliacourses2</span></a></span> to offer co-branded training in bioinformatics and computational biology.</p><p>Read more 👉 <a href="https://blog.bioconductor.org/posts/2025-06-20-physalia-collaboration/" rel="nofollow noopener" translate="no" target="_blank"><span class="invisible">https://</span><span class="ellipsis">blog.bioconductor.org/posts/20</span><span class="invisible">25-06-20-physalia-collaboration/</span></a></p><p><a href="https://genomic.social/tags/Bioinformatics" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>Bioinformatics</span></a> <a href="https://genomic.social/tags/Bioconductor" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>Bioconductor</span></a> <a href="https://genomic.social/tags/OpenScience" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>OpenScience</span></a></p>
Dr. Robert M Flight<p>It makes my blood boil when I see -omics companies report statistical results without doing correction for multiple testing.</p><p><a href="https://mastodon.social/tags/bioinformatics" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>bioinformatics</span></a></p>
Molecular Biology & Evolution<p>Is MEGA-GPT heralding a new age of accessibility in bioinformatics with dedicated chatbots to help guide users? Read more in MBE's new Highlight: "MEGA into the New Generation of Computational Genetics"</p><p>🔗 doi.org/10.1093/molbev/msaf108</p><p><a href="https://ecoevo.social/tags/evobio" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>evobio</span></a> <a href="https://ecoevo.social/tags/molbio" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>molbio</span></a> <a href="https://ecoevo.social/tags/bioinformatics" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>bioinformatics</span></a> <a href="https://ecoevo.social/tags/AI" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>AI</span></a></p>
Marc Robinson-Rechavi<p>You can still apply: Postdoc job opportunity! We're looking for early career researcher in evolutionary genomics to study the relation between intra-specific gene expression variability, polymorphism, and macro-evolutionary rates. We have all of the data in 3 fishes and amphioxus, just waiting for your expertise and enthusiasm!<br><a href="https://tinyurl.com/3aewk286" rel="nofollow noopener" translate="no" target="_blank"><span class="invisible">https://</span><span class="">tinyurl.com/3aewk286</span><span class="invisible"></span></a> <br><a href="https://ecoevo.social/tags/EvoDevo" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>EvoDevo</span></a> <a href="https://ecoevo.social/tags/MolecularEvolution" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>MolecularEvolution</span></a> <a href="https://ecoevo.social/tags/bioinformatics" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>bioinformatics</span></a> <a href="https://ecoevo.social/tags/PopulationGenomics" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>PopulationGenomics</span></a> <a href="https://ecoevo.social/tags/RNAseq" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>RNAseq</span></a> <a href="https://ecoevo.social/tags/PostDoc" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>PostDoc</span></a></p>
Mikolaj Kocikowski, PhD<p>🐶 New preprint: DoggifAI</p><p>🤖 We built a transformer model that translates antibodies from mouse/human to dog “protein language” - preserving structure while reducing immunogenicity.</p><p>📂 Open model, code + dataset of 430k canine antibody sequences (largest to date): <a href="https://www.biorxiv.org/content/10.1101/2025.05.28.656573v1" rel="nofollow noopener" translate="no" target="_blank"><span class="invisible">https://www.</span><span class="ellipsis">biorxiv.org/content/10.1101/20</span><span class="invisible">25.05.28.656573v1</span></a></p><p><a href="https://mastodon.social/tags/bioinformatics" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>bioinformatics</span></a> <a href="https://mastodon.social/tags/AI" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>AI</span></a> <a href="https://mastodon.social/tags/immunotherapy" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>immunotherapy</span></a> <a href="https://mastodon.social/tags/OpenScience" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>OpenScience</span></a> <a href="https://mastodon.social/tags/preprint" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>preprint</span></a> <a href="https://mastodon.social/tags/comparativeoncology" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>comparativeoncology</span></a> <a href="https://mastodon.social/tags/dogs" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>dogs</span></a> <a href="https://mastodon.social/tags/OpenData" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>OpenData</span></a>, <a href="https://mastodon.social/tags/cancerresearch" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>cancerresearch</span></a></p>
Bioconductor<p>📝 New Bioconductor Blog Post!</p><p>We’ve just launched the first in a new series by Vince Carey, founding contributor to Bioconductor and core developer, exploring the evolving complexity and value of the Bioconductor ecosystem.</p><p>Check it out 👉 <a href="https://blog.bioconductor.org/posts/2025-05-26-ask" rel="nofollow noopener" translate="no" target="_blank"><span class="invisible">https://</span><span class="ellipsis">blog.bioconductor.org/posts/20</span><span class="invisible">25-05-26-ask</span></a></p><p><a href="https://genomic.social/tags/Bioconductor" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>Bioconductor</span></a> <a href="https://genomic.social/tags/RStats" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>RStats</span></a> <a href="https://genomic.social/tags/Bioinformatics" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>Bioinformatics</span></a> <a href="https://genomic.social/tags/DataScience" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>DataScience</span></a> <a href="https://genomic.social/tags/OpenScience" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>OpenScience</span></a></p>
Luke Pembleton<p>Anyone have any recommendations on a free online short course that they have found useful in the fields of <a href="https://genomic.social/tags/bioinformatics" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>bioinformatics</span></a> <a href="https://genomic.social/tags/genomics" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>genomics</span></a> <a href="https://genomic.social/tags/agriculture" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>agriculture</span></a> <a href="https://genomic.social/tags/rstats" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>rstats</span></a> or related?</p>
Bioconductor<p>📝 New Bioconductor blog post!</p><p>We’ve just published a recap of our first in-person course in Africa, held in Nairobi this March 🇰🇪<br>Read about the highlights, feedback, and what’s next:<br>👉 <a href="https://blog.bioconductor.org/posts/2025-05-21-kenya-course/" rel="nofollow noopener" translate="no" target="_blank"><span class="invisible">https://</span><span class="ellipsis">blog.bioconductor.org/posts/20</span><span class="invisible">25-05-21-kenya-course/</span></a></p><p><a href="https://genomic.social/tags/Bioinformatics" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>Bioinformatics</span></a> <a href="https://genomic.social/tags/BioconductorAfrica" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>BioconductorAfrica</span></a> <a href="https://genomic.social/tags/OpenScience" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>OpenScience</span></a> <a href="https://genomic.social/tags/RStats" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>RStats</span></a> <a href="https://genomic.social/tags/CapacityBuilding" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>CapacityBuilding</span></a></p>
Europe Says<p><a href="https://www.europesays.com/2095746/" rel="nofollow noopener" translate="no" target="_blank"><span class="invisible">https://www.</span><span class="">europesays.com/2095746/</span><span class="invisible"></span></a> Nitte University Centre for Science Education &amp; Research – Empowering Minds with Research-Driven Education <a href="https://pubeurope.com/tags/AdvertorialDisclaimer" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>AdvertorialDisclaimer</span></a> <a href="https://pubeurope.com/tags/america" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>america</span></a> <a href="https://pubeurope.com/tags/Bioinformatics" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>Bioinformatics</span></a> <a href="https://pubeurope.com/tags/BiomedicalScience" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>BiomedicalScience</span></a> <a href="https://pubeurope.com/tags/Biotechnology" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>Biotechnology</span></a> <a href="https://pubeurope.com/tags/CancerBiology" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>CancerBiology</span></a> <a href="https://pubeurope.com/tags/FoodScience" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>FoodScience</span></a>&amp;Technology <a href="https://pubeurope.com/tags/microbiology" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>microbiology</span></a> <a href="https://pubeurope.com/tags/science" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>science</span></a> <a href="https://pubeurope.com/tags/SMPL" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>SMPL</span></a> <a href="https://pubeurope.com/tags/technology" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>technology</span></a> <a href="https://pubeurope.com/tags/UnitedStates" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>UnitedStates</span></a> <a href="https://pubeurope.com/tags/UnitedStatesOfAmerica" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>UnitedStatesOfAmerica</span></a> <a href="https://pubeurope.com/tags/US" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>US</span></a> <a href="https://pubeurope.com/tags/USA" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>USA</span></a></p>
Jim Rose<p>As a scientist working on a mix of bespoke data analysis and reproducible pipeline creation this article ressonates. Very different skillsets! <a href="https://genomic.social/tags/bioinformatics" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>bioinformatics</span></a> <a href="https://genomic.social/tags/genomics" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>genomics</span></a> <a href="https://genomic.social/tags/datasci" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>datasci</span></a> <a href="https://www.counting-stuff.com/as-a-mostly-ad-hocer-ive-got-workflow-issues/" rel="nofollow noopener" translate="no" target="_blank"><span class="invisible">https://www.</span><span class="ellipsis">counting-stuff.com/as-a-mostly</span><span class="invisible">-ad-hocer-ive-got-workflow-issues/</span></a></p>
Duncan MacCannell<p>This special issue highlights more than a decade of progress in applying <a href="https://mstdn.science/tags/genomics" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>genomics</span></a> and advanced <a href="https://mstdn.science/tags/bioinformatics" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>bioinformatics</span></a> to <a href="https://mstdn.science/tags/publichealth" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>publichealth</span></a>. It includes real-world examples of how technologies are transforming <a href="https://mstdn.science/tags/surveillance" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>surveillance</span></a>, <a href="https://mstdn.science/tags/outbreak" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>outbreak</span></a> response, <a href="https://mstdn.science/tags/antimicrobialresistance" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>antimicrobialresistance</span></a> monitoring, and <a href="https://mstdn.science/tags/pandemic" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>pandemic</span></a> preparedness.</p>
Dr. Robert M Flight<p>Alternatively, setup the recount3 mono-rail pipeline locally and just run it on your samples, trusting what they did (at least for basic quantitation), for human and mouse.</p><p><a href="https://genomic.social/@tangming2005/114523472124005574" rel="nofollow noopener" translate="no" target="_blank"><span class="invisible">https://</span><span class="ellipsis">genomic.social/@tangming2005/1</span><span class="invisible">14523472124005574</span></a></p><p><a href="https://mastodon.social/tags/bioinformatics" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>bioinformatics</span></a></p>
Dr. Robert M Flight<p>Some late night <a href="https://mastodon.social/tags/bioinformatics" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>bioinformatics</span></a></p><p>Collaborators had some samples sequenced to check if it was even possible. Two samples from a single patient (different locations of tissue), and one other sample from another patient.</p><p>The other patient (C on this plot) has only 9000 genes with read counts &gt; 10, where the other two have 21,000 (no real idea why the discrepancy). </p><p>Very visible on this intensity histogram of counts.</p>
Marc Robinson-Rechavi<p>Postdoc job opportunity! We're looking for early career researcher in evolutionary genomics to study the relation between intra-specific gene expression variability, polymorphism, and macro-evolutionary rates. We have all of the data in 3 fishes and amphioxus, just waiting for your expertise and enthusiasm!<br><a href="https://tinyurl.com/3aewk286" rel="nofollow noopener" translate="no" target="_blank"><span class="invisible">https://</span><span class="">tinyurl.com/3aewk286</span><span class="invisible"></span></a> <br><a href="https://ecoevo.social/tags/EvoDevo" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>EvoDevo</span></a> <a href="https://ecoevo.social/tags/MolecularEvolution" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>MolecularEvolution</span></a> <a href="https://ecoevo.social/tags/bioinformatics" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>bioinformatics</span></a> <a href="https://ecoevo.social/tags/PopulationGenomics" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>PopulationGenomics</span></a> <a href="https://ecoevo.social/tags/RNAseq" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>RNAseq</span></a> <a href="https://ecoevo.social/tags/PostDoc" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>PostDoc</span></a></p>