Reposted by Jean MonlongXian Chang @xian-chang.bsky.social · 02/10/2025🦒Long read giraffe is out!🦒 Mapping long reads to pangenome graphs is ~10x faster than with GraphAligner, with veeery slightly better mapping accuracy, short variant calling, and SV genotyping than GraphAligner or Minimap2 14222
Reposted by Jean MonlongZeqian Li @zeqianli.bsky.social · 20/07/2025New tgv release: local cache! tgv download hg38 Download UCSC reference genomes to a local sqlite db for much faster browsing. Awesome Rust tools (twobit, bigtools) made this simple. github.com/zeqianli/tgvgithub.comGitHub - zeqianli/tgv: Explore 5,000+ genomes in the terminal. Light, blazing fast 🚀, vim-motion.Explore 5,000+ genomes in the terminal. Light, blazing fast 🚀, vim-motion. - zeqianli/tgv 0298
Reposted by Jean MonlongXian Chang @xian-chang.bsky.social · 14/02/2025New figure for my thesis showing why Giraffe is the best long read pangenome mapper. No further evidence will be provided. 141
Reposted by Jean MonlongRita Rebollo @ritarebollo.bsky.social · 31/01/2025A couple of months ago I tried the @peercommunityin.bsky.social publishing system & I can only recommend it (pun intended). Please see below to change how we publish science 1/n 11210
Reposted by Jean MonlongUC Santa Cruz Genomics Institute @ucscgenomics.bsky.social · 24/01/2025Researchers at @ucsantacruz.bsky.social have demonstrated how long-read sequencing could improve detection of diseases that have eluded diagnosis, at a fraction of the cost. New clinical tests could be on the way. 🗞 news.ucsc.edu/2025/01/pate... 👏🏼👏🏿👏🏾 @khmiga.bsky.social @benedictpaten.bsky.social 0157
Reposted by Jean MonlongAnthony Herzig @anthony-herzig.bsky.social · 29/11/2024Organising the EMGM in Brest next year: emgm2025.sciencesconf.orgemgm2025.sciencesconf.org53rd European Mathematical Genetics Meeting - Sciencesconf.org 012
Reposted by Jean MonlongYves Clément @yvesclement.bsky.social · 29/11/2024Hurray for cats (and regulatory mutations) 043
Reposted by Jean MonlongZamin Iqbal @zaminiqbal.bsky.social · 28/11/2024"We engineered approximately 45,000 insertions, 6,000 deletions and 41,000 amino acid substitutions across the nearly 2,200 coding positions of the Enterovirus A71 proteome, quantifying their effects on viral fitness" www.nature.com/articles/s41...nature.comDeep mutation, insertion and deletion scanning across the Enterovirus A proteome reveals constraints shaping viral evolution - Nature MicrobiologyDeep mutational scanning of Enterovirus A71 maps and quantifies the impact of genomic insertions, deletions and substitutions on virus fitness and highlights the role of insertions and deletions in th... 0298
Reposted by Jean MonlongJeffrey Ross-Ibarra @jrossibarra.bsky.social · 26/11/202440 years later, and we still don't have a good answer. (original article is quite fun: www.jstor.org/stable/24084...) 5219
Reposted by Jean MonlongeLife @elife.bsky.social · 26/11/20241/ 🧵 Free resources for scientists 💡 Covering research skills, careers, #SciComm, leadership, activism and more, everything in this thread appears on our Learning Resources page, with tips for researchers and academics at any career stage. #AcademicChatter #ECRChat buff.ly/4f8vIpkbuff.lyLearning resources for scientists · eLifeA collections of articles that provide practical resources and guidance for researchers and academics 1115075
Reposted by Jean MonlongJon Lim, FRCP PhD @drjonlim.bsky.social · 23/11/2024🎨 In case anyone need… The NIH BioArt Source is an awesome library of *free* professionally drawn illustrations for scientific presentations or figures. Downloadable in HD. Thank you NIH for this invaluable tool 🙏! Check it out 👇 bioart.niaid.nih.gov 441197491
Reposted by Jean MonlongMiriam @mirischreiber.bsky.social · 14/11/2024The barley pangenome paper is finally out. 🎉 #genomics rdcu.be/d0eczrdcu.beStructural variation in the pangenome of wild and domesticated barleyNature - A pangenome analysis of 76 wild and domesticated barley accessions in combination with short-read sequence data of 1,315 barley genotypes indicates that allelic diversity at structurally... 12212
Reposted by Jean MonlongPierre Peterlongo @pierrepeterlongo.bsky.social · 11/11/2024🧬🔍There are 50 petabases of freely-available DNA sequencing data. We introducing Logan Search which allows you to search for any DNA sequence in minutes, bringing Earth’s largest genomic resource to your fingertips. 🏔️ logan-search.org 🏔️ #Genomics #Bioinformatics #OpenScience 211156
Reposted by Jean MonlongRyan Layer @ryanlayer.bsky.social · 21/11/2024We have a method for fast GWAS data access. STABIX adds a p-value index that with a position index (what TABIX has) allows you to quickly retrieve, eg. all significant SNPs in a target gene. Also column compression to reduce the size. www.biorxiv.org/content/10.1... github.com/kristen-schn...biorxiv.orgSTABIX: Summary statistic-based GWAS indexing and compressionGenome-Wide Association Studies (GWAS) are widely used to investigate the role of genetics in disease traits, but the resulting file sizes from these studies are large, posing barriers to efficient st... 0165
Reposted by Jean MonlongMarieke Oudelaar @mariekeoudelaar.bsky.social · 22/11/2024📣 Preprint alert! We have studied the formation of pair-wise and multi-way enhancer-promoter interactions in the #3Dgenome in a lymphoid-to-myeloid transdifferentiation system and learned interesting new things about their function in #GeneRegulation. 1/10 www.biorxiv.org/content/10.1...biorxiv.org 26222