Gabriel Renaud
@gabrielylr.bsky.social
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 3
A 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: github.com/grenaud/bedB...
GitHub - grenaud/bedBamAndBeyond
Contribute to grenaud/bedBamAndBeyond development by creating an account on GitHub.
github.com
🧬 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. www.biorxiv.org/content/10.6...
Ancient Reconstructed Proteins: A Framework for Resurrecting Protein Structures from Million-Year-Old Metagenomes
DNA sequences derived from ancient samples provide insights into human history, paleoenvironments, and evolutionary biology. Advances in laboratory techniques and computational tools have established ...
biorxiv.org
PhD position available in Pleistocene animal genomics, combining cutting-edge deep sequencing and pangenome analysis approaches. Join us! careers.univie.ac.at/en/praedoc/s...
Vienna Doctoral School of Ecology and Evolution
The Vienna Doctoral School of Ecology and Evolution is dedicated to educating students to advance our understanding of the ecology and evolution of extant and ancestral organisms, populations, and communities. In Ecology, the focus is on uncovering the mechanistic and evolutionary drivers of patterns and processes across biological scales, from gene regulation to ecosystem structure and function, including the role of communities in biogeochemical cycles and their adaptive responses to environmental change. In Evolution, we investigate the processes shaping changes in organization and dynamics of organisms, populations, and species at molecular, developmental, morphological, and physiological levels.
careers.univie.ac.at
I'm hiring!⭐ As part of the DFF Sapere Aude-funded project MiddleEarth, I am looking for 1 postdoctoral researcher and 1 research assistant.
Thrilled 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.! genomebiology.biomedcentral.com/articles/10....
CarpeDeam: a de novo metagenome assembler for heavily damaged ancient datasets - Genome Biology
De novo assembly of ancient metagenomic datasets is a challenging task. Ultra-short fragment size and characteristic postmortem damage patterns of sequenced ancient DNA molecules leave current tools i...
genomebiology.biomedcentral.com
The @scilifelab.se ancient DNA unit is looking for an bioinformatician placed at Uppsala University. This is a great way to be part of diverse #aDNA research projects as a staff scientist with permanent (!!) employment: www.uu.se/en/about-uu/...
Bioinformatician - Uppsala University
Bioinformatician, Department of Organismal Biology, Uppsala University
uu.se
I am starting a computational lab at LIOS, Riga, Latvia, and going to recruit a few people. Please DM if you are interested in a postdoc or PhD position in my Metabolic Research Group within the TARGETWISE project. I can highly recommend Riga, it is a beautiful city with very good living conditions.
Thrilled 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! doi.org/10.1093/bioi...
AdDeam: A Fast and Scalable Tool for Estimating and Clustering Reference-Level Damage Profiles
AbstractMotivation. DNA damage patterns, such as increased frequencies of C→T and G→A substitutions at fragment ends, are widely used in ancient DNA studie
doi.org
🚨 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 www.biorxiv.org/content/10.1...
biorxiv.org
Come get your PhD with me, and at @stockholm-uni.bsky.social and @scilifelab.se ! :)
Mafalda S Ferreira@mafaldaferreira.bsky.social · last yr.We are recruiting PhD student to work on genomics of seasonal camouflage in ptarmigan! There is still a week to apply! #Genomics #PopGen #Evolution #Camouflage #Birds #PhDPosition #PhDStudent
A reminder to SAMtools / HTSlib users, from the next release (probably April 2025) CRAM 3.1 will be the default version used. Use "samtools view -O cram,version=3.0" to switch back to the current 3.0. (But note 3.1 should be smaller and faster, especially on Illumina.)
aDNA/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. www.biorxiv.org/content/10.1...
AdDeam: A Fast and Scalable Tool for Estimating and Clustering Reference-Level Damage Profiles
Motivation DNA damage patterns, such as increased frequencies of C>T and G>A substitutions at fragment ends, are widely used in ancient DNA studies to assess authenticity and detect contamination. In ...
biorxiv.org
Thrilled 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 #aeDNA
Curious 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 besjournals.onlinelibrary.wiley.com/doi/10.1111/...