Gabriel Renaud

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...

I'm hiring!⭐ As part of the DFF Sapere Aude-funded project MiddleEarth, I am looking for 1 postdoctoral researcher and 1 research assistant.

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...

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....

Bioinformatician - Uppsala University Bioinformatician, Department of Organismal Biology, Uppsala University

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/...

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.

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

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...

thanks for sharing! Just Figure 1 is amazing!

🚨 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...

Come get your PhD with me, and at @stockholm-uni.bsky.social and @scilifelab.se ! :)

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.)

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 ...

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...

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/...