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#FunctionalGenomics

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Victoria Stuart 🇨🇦 🏳️‍⚧️<p>AlphaGenome: AI for better understanding the genome - Google DeepMind<br><a href="https://deepmind.google/discover/blog/alphagenome-ai-for-better-understanding-the-genome" rel="nofollow noopener noreferrer" translate="no" target="_blank"><span class="invisible">https://</span><span class="ellipsis">deepmind.google/discover/blog/</span><span class="invisible">alphagenome-ai-for-better-understanding-the-genome</span></a><br><a href="https://news.ycombinator.com/item?id=44387659" rel="nofollow noopener noreferrer" translate="no" target="_blank"><span class="invisible">https://</span><span class="ellipsis">news.ycombinator.com/item?id=4</span><span class="invisible">4387659</span></a></p><p>Comment: even in well-studied organisms (E. coli; yeast: Saccharomyces; minimal synthetic cells ...) the function of a staggering number of essential genes is unknown.</p><p><a href="https://mastodon.social/tags/AlphaGenome" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>AlphaGenome</span></a> <a href="https://mastodon.social/tags/DeepMind" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>DeepMind</span></a> <a href="https://mastodon.social/tags/MolecularGenetics" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>MolecularGenetics</span></a> <a href="https://mastodon.social/tags/Genomics" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>Genomics</span></a> <a href="https://mastodon.social/tags/FunctionalGenomics" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>FunctionalGenomics</span></a></p>
Thomas Sandmann<p>Today, I reread Fulco et al's 2019 paper on "Activity-by-contact model of enhancer–promoter regulation from thousands of CRISPR perturbation" <a href="https://www.nature.com/articles/s41588-019-0538-0" rel="nofollow noopener noreferrer" translate="no" target="_blank"><span class="invisible">https://www.</span><span class="ellipsis">nature.com/articles/s41588-019</span><span class="invisible">-0538-0</span></a> Still one of my favorites, because the authors combined innovative functional genomics with down-to-earth computational approaches - and obtained a highly usable method to predict enhancer -&gt; gene interactions (the ABC model). <a href="https://genomic.social/tags/functionalgenomics" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>functionalgenomics</span></a> <a href="https://genomic.social/tags/epigenetics" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>epigenetics</span></a> <a href="https://genomic.social/tags/literature" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>literature</span></a> <a href="https://genomic.social/tags/science" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>science</span></a></p>
Paul L. Maurizio<p><a href="https://genomic.social/tags/newHere" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>newHere</span></a> <a href="https://genomic.social/tags/hashtags" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>hashtags</span></a></p><p>Some interests:</p><p><a href="https://genomic.social/tags/singleCell" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>singleCell</span></a> <a href="https://genomic.social/tags/bayesian" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>bayesian</span></a> <a href="https://genomic.social/tags/stats" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>stats</span></a> <a href="https://genomic.social/tags/ancestry" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>ancestry</span></a> <a href="https://genomic.social/tags/genetics" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>genetics</span></a> <a href="https://genomic.social/tags/popgen" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>popgen</span></a> <a href="https://genomic.social/tags/geneRegulation" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>geneRegulation</span></a> <a href="https://genomic.social/tags/systemsGenetics" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>systemsGenetics</span></a> <a href="https://genomic.social/tags/functionalGenomics" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>functionalGenomics</span></a> <a href="https://genomic.social/tags/biology" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>biology</span></a> <a href="https://genomic.social/tags/immunology" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>immunology</span></a> <a href="https://genomic.social/tags/vaccines" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>vaccines</span></a> <a href="https://genomic.social/tags/infection" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>infection</span></a> <a href="https://genomic.social/tags/viruses" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>viruses</span></a> <a href="https://genomic.social/tags/influenza" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>influenza</span></a> <a href="https://genomic.social/tags/tuberculosis" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>tuberculosis</span></a> <a href="https://genomic.social/tags/TB" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>TB</span></a> <a href="https://genomic.social/tags/malaria" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>malaria</span></a> <a href="https://genomic.social/tags/NTDs" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>NTDs</span></a> <a href="https://genomic.social/tags/fitness" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>fitness</span></a> <a href="https://genomic.social/tags/evolution" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>evolution</span></a> <a href="https://genomic.social/tags/dominance" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>dominance</span></a> <a href="https://genomic.social/tags/stress" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>stress</span></a> <a href="https://genomic.social/tags/aging" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>aging</span></a> <a href="https://genomic.social/tags/mosquitoes" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>mosquitoes</span></a> <a href="https://genomic.social/tags/mice" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>mice</span></a> <a href="https://genomic.social/tags/macaques" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>macaques</span></a></p><p><a href="https://genomic.social/tags/academic" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>academic</span></a> <a href="https://genomic.social/tags/dei" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>dei</span></a> <a href="https://genomic.social/tags/diversity" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>diversity</span></a> <a href="https://genomic.social/tags/equity" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>equity</span></a> <a href="https://genomic.social/tags/inclusion" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>inclusion</span></a> <a href="https://genomic.social/tags/blackLivesMatter" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>blackLivesMatter</span></a> <a href="https://genomic.social/tags/firstGen" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>firstGen</span></a> <a href="https://genomic.social/tags/asian" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>asian</span></a> <a href="https://genomic.social/tags/aapi" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>aapi</span></a> <a href="https://genomic.social/tags/multi" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>multi</span></a> <a href="https://genomic.social/tags/access2meds" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>access2meds</span></a> <a href="https://genomic.social/tags/globalHealth" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>globalHealth</span></a> <a href="https://genomic.social/tags/swarthmore" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>swarthmore</span></a> <a href="https://genomic.social/tags/johnsHopkins" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>johnsHopkins</span></a> <a href="https://genomic.social/tags/unc" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>unc</span></a> <a href="https://genomic.social/tags/chicago" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>chicago</span></a> <a href="https://genomic.social/tags/washingtonDC" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>washingtonDC</span></a> <a href="https://genomic.social/tags/moco" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>moco</span></a></p>
Tamas Nagy<p>It's been years in the making (literally, my PR was ~ two years old 😅 ), but I finally updated Crispulator.jl to work with <a href="https://mas.to/tags/julialang" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>julialang</span></a> 1.0+.</p><p>It's ready to help you simulate your pooled <a href="https://mas.to/tags/CRISPR" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>CRISPR</span></a> screens for <a href="https://mas.to/tags/functionalgenomics" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>functionalgenomics</span></a> so that you can make sure they'll work before you pour many months into them!</p><p>Check out the refreshed docs: <a href="https://tamasnagy.com/Crispulator.jl/dev/" rel="nofollow noopener noreferrer" target="_blank"><span class="invisible">https://</span><span class="ellipsis">tamasnagy.com/Crispulator.jl/d</span><span class="invisible">ev/</span></a></p>
Lars Barquist<p>I guess I should do an <a href="https://mstdn.science/tags/introduction" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>introduction</span></a> -- I'm a computational biologist working at the intersection of bacterial <a href="https://mstdn.science/tags/PathogenGenomics" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>PathogenGenomics</span></a> and <a href="https://mstdn.science/tags/FunctionalGenomics" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>FunctionalGenomics</span></a>, mostly on sequencing-based technologies, and run a research group at the Helmholtz Institute for RNA-based Infection Research in Würzburg. </p><p>We dabble in <a href="https://mstdn.science/tags/MachineLearning" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>MachineLearning</span></a>, <a href="https://mstdn.science/tags/BayesianStatistics" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>BayesianStatistics</span></a>, and <a href="https://mstdn.science/tags/DataVisualization" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>DataVisualization</span></a>, figuring out ways to apply these techniques to investigate <a href="https://mstdn.science/tags/Pathogen" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>Pathogen</span></a> <a href="https://mstdn.science/tags/GeneRegulation" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>GeneRegulation</span></a> and <a href="https://mstdn.science/tags/Evolution" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>Evolution</span></a>.</p>
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