Associate professor in Universite Laval in Quebec City, QC, Canada. I am interested in ancient/environmental DNA, sequencing and population genomics. Bayesianist. ☕️ addict & avid traveler. husband, dad of 3https://bsky.app/profile/gabrielylr.bsky.socialhttps://bsky.app/profile/gabrielylr.bsky.social/post/3muphwovh5s2bA while back, I wrote this small program to quickly visualize the genomic distribution of BED or BAM files. Claude completely refactored it. Now it is much faster, and the plots are much more congenial: https://github.com/grenaud/bedBamAndBeyond04 Sep 2026 17:19 +0000at://did:plc:uh2wgwtffvvwbefuxconsxm4/app.bsky.feed.post/3muphwovh5s2bhttps://bsky.app/profile/gabrielylr.bsky.social/post/3mtqsmsnqgs23🧬 Ancient DNA → ancient proteins? We now have the computational toolkit to make this possible: CarpeDeam + AdDeam + AlphaFold + Foldseek. In our new preprint, we reconstruct an archaeal ATP synthase from ~2M-yo aeDNA from Greenland and predict its 3D structure. https://www.biorxiv.org/content/10.64898/2026.08.20.745946v123 Aug 2026 12:38 +0000at://did:plc:uh2wgwtffvvwbefuxconsxm4/app.bsky.feed.post/3mtqsmsnqgs23https://bsky.app/profile/gabrielylr.bsky.social/post/3m46jg5iwpc2bThrilled to see this in print! CarpeDeam is the first assembler built specifically for ancient metagenomics, as it specifically models aDNA damage. We also introduce "RYmers" (i.e., k-mers but robust to damage). Amazing work by Louis Kraft et al.! ⁠ https://genomebiology.biomedcentral.com/articles/10.1186/s13059-025-03839-527 Oct 2025 13:26 +0000at://did:plc:uh2wgwtffvvwbefuxconsxm4/app.bsky.feed.post/3m46jg5iwpc2bhttps://bsky.app/profile/gabrielylr.bsky.social/post/3luht7merwk23Thrilled to see this out in Bioinformatics! AdDeam is a powerful tool to rapidly estimate aDNA damage from BAM files and cluster them to flag outliers—great for large/small aDNA projects and ancient metagenomics to find contigs likely to be modern. Great work by Louis Kraft! https://doi.org/10.1093/bioinformatics/btaf40721 Jul 2025 10:54 +0000at://did:plc:uh2wgwtffvvwbefuxconsxm4/app.bsky.feed.post/3luht7merwk23https://bsky.app/profile/gabrielylr.bsky.social/post/3lqachfoyec27🚨 New preprint from our group! Thrilled to present CHARON, a new method to estimate the number of individuals and identify the closest population of origin in environmental & forensic human DNA—even at 2–4X coverage. #eDNA #forensics #AncientDNA https://www.biorxiv.org/content/10.1101/2025.05.26.656139v128 May 2025 13:24 +0000at://did:plc:uh2wgwtffvvwbefuxconsxm4/app.bsky.feed.post/3lqachfoyec27https://bsky.app/profile/gabrielylr.bsky.social/post/3ll72xxbm722daDNA/aeDNA folks: tired of eyeballing hundreds of damage plots? I am excited to introduce AdDeam—a tool to rapidly generate damage profiles, cluster them, and spot outliers. Great for large sample sets or flagging modern contigs in ancient metagenomics assemblies. https://www.biorxiv.org/content/10.1101/2025.03.20.644297v125 Mar 2025 10:32 +0000at://did:plc:uh2wgwtffvvwbefuxconsxm4/app.bsky.feed.post/3ll72xxbm722dhttps://bsky.app/profile/gabrielylr.bsky.social/post/3ldlfmteeu22eThrilled to share that @nicolaavogel.bsky.social just became the very first PhD graduate in our group! 🎉🎓 huge congrats to her! Onwards to an even brighter future! ✨ #eDNA #sedaDNA #aDNA #aeDNA18 Dec 2024 12:53 +0000at://did:plc:uh2wgwtffvvwbefuxconsxm4/app.bsky.feed.post/3ldlfmteeu22ehttps://bsky.app/profile/gabrielylr.bsky.social/post/3kabufbgoa72xCurious about which terrestrial animals are hidden in your modern or ancient environmental DNA? 🧬 Want to uncover signs of scavenger DNA in your aDNA datasets? Check out 'euka' – it's now available! 🔍 #eDNA #aDNA" #aeDNA https://besjournals.onlinelibrary.wiley.com/doi/10.1111/2041-210X.1421426 Sep 2023 08:09 +0000at://did:plc:uh2wgwtffvvwbefuxconsxm4/app.bsky.feed.post/3kabufbgoa72x