toad.social

Boas PuckerT-DNA insertions: more surprises than you think 🌱🧬. PCR can miss extra T-DNAs & complex rearrangements. Long-read sequencing captures the full picture. Still super relevant for plant genomics! 🔗 <a href="https://doi.org/10.1186/s12864-021-07877-8" rel="nofollow noopener" translate="no" target="_blank">https://doi.org/10.1186/s12864-021-07877-8</a> <a href="https://mastodon.social/tags/PlantScience" class="mention hashtag" rel="nofollow noopener" target="_blank">#PlantScience</a> <a href="https://mastodon.social/tags/Genotyping" class="mention hashtag" rel="nofollow noopener" target="_blank">#Genotyping</a> <a href="https://mastodon.social/tags/LongReadSequencing" class="mention hashtag" rel="nofollow noopener" target="_blank">#LongReadSequencing</a> <a href="https://mastodon.social/tags/Arabidopsis" class="mention hashtag" rel="nofollow noopener" target="_blank">#Arabidopsis</a> <a href="https://genomic.social/@PuckerLab" class="u-url mention" rel="nofollow noopener" target="_blank">@PuckerLab</a>

Dining & CookingScientists map the genes behind diet and dementia risk <a href="https://www.diningandcooking.com/2220248/scientists-map-the-genes-behind-diet-and-dementia-risk/" rel="nofollow noopener" translate="no" target="_blank">https://www.diningandcooking.com/2220248/scientists-map-the-genes-behind-diet-and-dementia-risk/</a> <a href="https://vive.im/tags/aging" class="mention hashtag" rel="nofollow noopener" target="_blank">#aging</a> <a href="https://vive.im/tags/Autosomal" class="mention hashtag" rel="nofollow noopener" target="_blank">#Autosomal</a> <a href="https://vive.im/tags/blood" class="mention hashtag" rel="nofollow noopener" target="_blank">#blood</a> <a href="https://vive.im/tags/ClinicalTrial" class="mention hashtag" rel="nofollow noopener" target="_blank">#ClinicalTrial</a> <a href="https://vive.im/tags/CognitiveFunction" class="mention hashtag" rel="nofollow noopener" target="_blank">#CognitiveFunction</a> <a href="https://vive.im/tags/dementia" class="mention hashtag" rel="nofollow noopener" target="_blank">#dementia</a> <a href="https://vive.im/tags/diet" class="mention hashtag" rel="nofollow noopener" target="_blank">#diet</a> <a href="https://vive.im/tags/dna" class="mention hashtag" rel="nofollow noopener" target="_blank">#dna</a> <a href="https://vive.im/tags/DNAExtraction" class="mention hashtag" rel="nofollow noopener" target="_blank">#DNAExtraction</a> <a href="https://vive.im/tags/Efficacy" class="mention hashtag" rel="nofollow noopener" target="_blank">#Efficacy</a> <a href="https://vive.im/tags/Frequency" class="mention hashtag" rel="nofollow noopener" target="_blank">#Frequency</a> <a href="https://vive.im/tags/genes" class="mention hashtag" rel="nofollow noopener" target="_blank">#genes</a> <a href="https://vive.im/tags/Genetic" class="mention hashtag" rel="nofollow noopener" target="_blank">#Genetic</a> <a href="https://vive.im/tags/Genotyping" class="mention hashtag" rel="nofollow noopener" target="_blank">#Genotyping</a> <a href="https://vive.im/tags/Mediterranean" class="mention hashtag" rel="nofollow noopener" target="_blank">#Mediterranean</a> <a href="https://vive.im/tags/MediterraneanDiet" class="mention hashtag" rel="nofollow noopener" target="_blank">#MediterraneanDiet</a> <a href="https://vive.im/tags/metabolism" class="mention hashtag" rel="nofollow noopener" target="_blank">#metabolism</a> <a href="https://vive.im/tags/MindDiet" class="mention hashtag" rel="nofollow noopener" target="_blank">#MindDiet</a> <a href="https://vive.im/tags/nutrients" class="mention hashtag" rel="nofollow noopener" target="_blank">#nutrients</a> <a href="https://vive.im/tags/nutrition" class="mention hashtag" rel="nofollow noopener" target="_blank">#nutrition</a> <a href="https://vive.im/tags/OliveOil" class="mention hashtag" rel="nofollow noopener" target="_blank">#OliveOil</a> <a href="https://vive.im/tags/QC" class="mention hashtag" rel="nofollow noopener" target="_blank">#QC</a> <a href="https://vive.im/tags/QualityControl" class="mention hashtag" rel="nofollow noopener" target="_blank">#QualityControl</a> <a href="https://vive.im/tags/Vegetables" class="mention hashtag" rel="nofollow noopener" target="_blank">#Vegetables</a> <a href="https://vive.im/tags/Wine" class="mention hashtag" rel="nofollow noopener" target="_blank">#Wine</a>

UK<a href="https://www.europesays.com/uk/289381/" rel="nofollow noopener" translate="no" target="_blank">https://www.europesays.com/uk/289381/</a> Scientists open new atlas of genetic diversity with advanced sequencing <a href="https://pubeurope.com/tags/DNA" class="mention hashtag" rel="nofollow noopener" target="_blank">#DNA</a> <a href="https://pubeurope.com/tags/Genetic" class="mention hashtag" rel="nofollow noopener" target="_blank">#Genetic</a> <a href="https://pubeurope.com/tags/Genetics" class="mention hashtag" rel="nofollow noopener" target="_blank">#Genetics</a> <a href="https://pubeurope.com/tags/Genome" class="mention hashtag" rel="nofollow noopener" target="_blank">#Genome</a> <a href="https://pubeurope.com/tags/Genomic" class="mention hashtag" rel="nofollow noopener" target="_blank">#Genomic</a> <a href="https://pubeurope.com/tags/Genotyping" class="mention hashtag" rel="nofollow noopener" target="_blank">#Genotyping</a> <a href="https://pubeurope.com/tags/Medicine" class="mention hashtag" rel="nofollow noopener" target="_blank">#Medicine</a> <a href="https://pubeurope.com/tags/Science" class="mention hashtag" rel="nofollow noopener" target="_blank">#Science</a> <a href="https://pubeurope.com/tags/Technology" class="mention hashtag" rel="nofollow noopener" target="_blank">#Technology</a> <a href="https://pubeurope.com/tags/UK" class="mention hashtag" rel="nofollow noopener" target="_blank">#UK</a> <a href="https://pubeurope.com/tags/UnitedKingdom" class="mention hashtag" rel="nofollow noopener" target="_blank">#UnitedKingdom</a>

Benjamin Carr, Ph.D. 👨🏻‍💻🧬<a href="https://hachyderm.io/tags/23andMe" class="mention hashtag" rel="nofollow noopener" target="_blank">#23andMe</a> Sale Shows Your <a href="https://hachyderm.io/tags/Genetic" class="mention hashtag" rel="nofollow noopener" target="_blank">#Genetic</a> Data Is Worth $17 23andMe sold genetic data of 15M people for $256M to a <a href="https://hachyderm.io/tags/pharmaceutical" class="mention hashtag" rel="nofollow noopener" target="_blank">#pharmaceutical</a> <a href="https://hachyderm.io/tags/Regeneron" class="mention hashtag" rel="nofollow noopener" target="_blank">#Regeneron</a>. 23andMe does not perform full genome sequences. It instead does <a href="https://hachyderm.io/tags/DNA" class="mention hashtag" rel="nofollow noopener" target="_blank">#DNA</a> <a href="https://hachyderm.io/tags/genotyping" class="mention hashtag" rel="nofollow noopener" target="_blank">#genotyping</a>, which look at parts of <a href="https://hachyderm.io/tags/genome" class="mention hashtag" rel="nofollow noopener" target="_blank">#genome</a> that vary from person to person. Sale to Regeneron means <a href="https://hachyderm.io/tags/gene" class="mention hashtag" rel="nofollow noopener" target="_blank">#gene</a> data collected by 23andMe will be used for development of new <a href="https://hachyderm.io/tags/drugs" class="mention hashtag" rel="nofollow noopener" target="_blank">#drugs</a>, which felt like the most likely and perhaps best-case scenario for the company’s bankruptcy. <a href="https://www.404media.co/23andme-sale-shows-your-genetic-data-is-worth-17/" rel="nofollow noopener" translate="no" target="_blank">https://www.404media.co/23andme-sale-shows-your-genetic-data-is-worth-17/</a>

Giuseppe MichieliBeyond <a href="https://mstdn.science/tags/Poliomyelitis" class="mention hashtag" rel="nofollow noopener" target="_blank">#Poliomyelitis</a>: A 21-Year Study of Non-Polio <a href="https://mstdn.science/tags/Enterovirus" class="mention hashtag" rel="nofollow noopener" target="_blank">#Enterovirus</a> <a href="https://mstdn.science/tags/Genotyping" class="mention hashtag" rel="nofollow noopener" target="_blank">#Genotyping</a> and Its Relevance in <a href="https://mstdn.science/tags/AFP" class="mention hashtag" rel="nofollow noopener" target="_blank">#AFP</a> in São Paulo, <a href="https://mstdn.science/tags/Brazil" class="mention hashtag" rel="nofollow noopener" target="_blank">#Brazil</a>Source: Viruses, AbstractIn the context of the near-global eradication of wild poliovirus, the significance of non-polio enteroviruses (NPEVs) in causing acute flaccid paralysis (AFP) and their impact on public health has gained increased attention. This research, conducted from 2001 to 2021, examined stool samples from 1597 children under 15…<a href="https://etidioh.wordpress.com/2024/12/01/beyond-poliomyelitis-a-21-year-study-of-non-polio-enterovirus-genotyping-and-its-relevance-in-afp-in-sao-paulo-brazil/" rel="nofollow noopener" translate="no" target="_blank">https://etidioh.wordpress.com/2024/12/01/beyond-poliomyelitis-a-21-year-study-of-non-polio-enterovirus-genotyping-and-its-relevance-in-afp-in-sao-paulo-brazil/</a>

Luke PembletonHands up ✋ who's working on <a href="https://genomic.social/tags/polyploid" class="mention hashtag" rel="nofollow noopener" target="_blank">#polyploid</a> <a href="https://genomic.social/tags/genotyping" class="mention hashtag" rel="nofollow noopener" target="_blank">#genotyping</a> and imputation? <a href="https://genomic.social/tags/genomics" class="mention hashtag" rel="nofollow noopener" target="_blank">#genomics</a> <a href="https://genomic.social/tags/bioinformatics" class="mention hashtag" rel="nofollow noopener" target="_blank">#bioinformatics</a>

Luke PembletonWith phased/haplotype-aware genomes becoming more frequent I'm Curious 🤔 to hear from others how you have been handling SNP/variant calling against them 🧬 Are you sacrificing heterozygous calls and aligning to all haplotypes, or only using one of the haplotypes as the reference, or do you have a pipeline tool that compares and combines the haplotypes during variant calling? <a href="https://genomic.social/tags/bioinformatics" class="mention hashtag" rel="nofollow noopener" target="_blank">#bioinformatics</a> <a href="https://genomic.social/tags/genomics" class="mention hashtag" rel="nofollow noopener" target="_blank">#genomics</a> <a href="https://genomic.social/tags/genotyping" class="mention hashtag" rel="nofollow noopener" target="_blank">#genotyping</a>

in silico PlantsUsing techniques including • <a href="https://botany.social/tags/phenotyping" class="mention hashtag" rel="nofollow noopener" target="_blank">#phenotyping</a> • <a href="https://botany.social/tags/artificialIntelligence" class="mention hashtag" rel="nofollow noopener" target="_blank">#artificialIntelligence</a> (machine-learning, deep learning, neural networks) • <a href="https://botany.social/tags/digitaltwins" class="mention hashtag" rel="nofollow noopener" target="_blank">#digitaltwins</a> • <a href="https://botany.social/tags/genotyping" class="mention hashtag" rel="nofollow noopener" target="_blank">#genotyping</a> • image capture, analysis, feature extraction and annotation • image, or <a href="https://botany.social/tags/machinelearning" class="mention hashtag" rel="nofollow noopener" target="_blank">#machinelearning</a> classification • <a href="https://botany.social/tags/phenotyping" class="mention hashtag" rel="nofollow noopener" target="_blank">#phenotyping</a> • proximal or <a href="https://botany.social/tags/remoteSensing" class="mention hashtag" rel="nofollow noopener" target="_blank">#remoteSensing</a> • visualization

Luke PembletonAnd it’s finally here 🥳 {resurface} my <a href="https://genomic.social/tags/rstats" class="mention hashtag" rel="nofollow noopener" target="_blank">#rstats</a> package for imputing missing genotype allele frequencies, such as those from pooled samples or populations. Stems from some scripts I wrote nearly 10 years ago, which I can now finally say is open. I hope to progressively add more imputation options. <a href="https://genomic.social/tags/imputation" class="mention hashtag" rel="nofollow noopener" target="_blank">#imputation</a> <a href="https://genomic.social/tags/genomics" class="mention hashtag" rel="nofollow noopener" target="_blank">#genomics</a> <a href="https://genomic.social/tags/genotyping" class="mention hashtag" rel="nofollow noopener" target="_blank">#genotyping</a> <a href="https://genomic.social/tags/bioinformatics" class="mention hashtag" rel="nofollow noopener" target="_blank">#bioinformatics</a> <a href="https://github.com/lpembleton/resurface" rel="nofollow noopener" translate="no" target="_blank">https://github.com/lpembleton/resurface</a>

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