Horizontal gene transfer is often depicted as a process distributing pre-existing functions to novel genetic backgrounds. Yet HGT can also increase the rate of functional innovation after transfer. Here's a brief review on the topic: ecoevorxiv.org/repository/v... #evosky #microsky

You can now view a tree of 2,399,238 bacterial genomes we made from AllTheBacteria (on the great Taxonium): taxonium.org/atb That's a big tree! (unless you're used to SC2 trees)

New preprint where @lbobay.bsky.social and I were motivated by the fact that non-synonymous substitutions are commonly analyzed in molecular evolution studies, but the similarity of the amino acids being substituted is an understudied area. doi.org/10.64898/202...

Now out & nicely formatted in @isme-microbes.bsky.social A big analysis of ocean genomes & metagenomes co-led by former postdocs, now PIs, @gmdouglas.bsky.social & @cyanophage.bsky.social along with co-PIs @lbobay.bsky.social & Samuel Chaffron. A few highlights... 🧵 (1/n) doi.org/10.1093/isme...

Join us for the first PCI Genomics Recommenders' Meeting happening on Feb 9th and 11th!

Seeking expressions of interest from researchers abroad for a Canada Impact+ Research Chair ($1M/year × 8 + up to $6M CFI) in AI-enabled antibiotic discovery and/or AMR, phage & phage-based derivatives. Email me a short vision, CV, and 3–5 key papers. Deadline: March 10, 2026 (Intake 2: June 15).

Hot off the press! Our latest paper led by @fernpizza.bsky.social, understanding how plasmids evolve inside cells. These small, self-replicating DNA circles live inside bacteria and carry antibiotic resistance genes, but also compete with one another to replicate. 1/ www.science.org/doi/10.1126/...

Our latest paper is out with @adiop.bsky.social and @gmdouglas.bsky.social. We analyzed the extent of homologous recombination between bacterial species (introgression) and how it affects species borders (it can vary a lot depending on the approach used to classify species!). rdcu.be/eQAMf

My department at UT Austin is looking to hire an Assistant Professor in Evolutionary Biology, broadly defined. Feel free to reach out to me with any questions you may have. apply.interfolio.com/177547

New diamond open access journal Replication Research welcomes reports of replication of previous works. #academicchatter https://www.uni-muenster.de/Ejournals/index.php/replicationresearch/index

Proud of the latest edition of my free intro biostats book. gitrepo: github.com/ybrandvain/b... book: ybrandvain.github.io/biostats/ Not complete but at a good point to take a break, and I think its quite usable dm me with comments , ideas etc

Too many authors use a scientific paper's Discussion to thoroughly shred their own work. That, and two more common mistakes in writing Discussions:

I'm super bummed to be missing #ESEB2025 @eseb2025.bsky.social due to a cancelled flight! Here's a quick overview of my talk "Gene- and genome-focused perspectives on microbial pangenomes" slated to be part of The Evolution of Microbial Pangenomes -- which I recommend you attend tomorrow (Fri) ! 1/n

In case you missed it, check out my latest #substack on life, entropy, and the arrow of time. Trying to get a bit more poetic with this one. If this isn't your thing, stay tuned next week, for another prose post. gibbological.substack.com/p/on-life-en...

Obligatory new job swag and selfie. Excited to start as an Assistant Professor at the University of New Brunswick in Fredericton, Canada! Come work with me! douglaslab.ca

Lopezguerra & Douglas recommend the high-quality Xylocopa violacea reference genome by Nash et al., 2024, Heredity, the first annotated pseudo-chromosomal assembly for any Xylocopa bee! 🐝 A crucial step for pollinator research, conservation, and even cancer therapy studies #ERGA tinyurl.com/vwknzu2b

At PCI Genomics, we are pleased to have recommended all ERGA manuscripts and publications to date, helping to bring together this vital body of work at the heart of European biodiversity genomics. 🔗 genomics.peercommunityin.org #ERGA #Genomics #Biodiversity #PCIGenomics #OpenScience

An update on open postdoc positions, in my group and the adjacent group of Howard Ochman, here at UT-Austin. #SymbioSky Mine: insect-bacterial symbiosis with emphasis on intracellular endosymbionts and molecular mechanisms. web.biosci.utexas.edu/moran/contac...

Howard's: evolution of microbial genes, genomes and communities. Can be experimental or computational. If interested, contact Howard Ochman, [email protected] Homepage: web.biosci.utexas.edu/ochman/index...

We just published our first paper in the Peer Community Journal - diamond open access, no APCs! Awesome experience, with less than a week from submission after receommendation by #pcigenomics. Highly recommended! #molpalmuc @lmumuenchen.bsky.social @peercommunityin.bsky.social

Come join us at @mcgill.ca as an assistant professor in virus-host interactions! Please share widely. mcgill.wd3.myworkdayjobs.com/en-US/McGill...

New preprint (and brief🧵)! “Co-occurrence drives horizontal gene transfer (HGT) among marine prokaryotes”. doi.org/10.1101/2025...

I'm pleased to introduce our new paper rooting the eukaryote Tree of Life (eToL) that resulted from a collaboration led by PhD student Kelsey Williamson and a large group of collaborators doi.org/10.1038/s415...htt

Big news: we are setting up a new non-profit organization to run bioRxiv and medRxiv. It's called openRxiv [no it's not a new preprint server; it's dedicated organization to oversee the servers] openrxiv.org 1/n

I am a little late, but I am very happy to see this work published. Congrats to @ellistorrance.bsky.social for all the hard work on her last chapter! doi.org/10.1093/nar/...

📑 New PCI Genomics recommendation, by Nicolas Pollet: https://buff.ly/40lxBsq On the work of Sallé et al. (2024) Spatio-temporal diversity and genetic architecture of pyrantel resistance in Cylicocyclus nassatus, the most abundant horse parasite https://buff.ly/4jCCiqK

I am looking for graduate students interested in investigating bacterial genome evolution, esp. pangenomes and intergenic regions, and the relative importance of genetic drift! https://buff.ly/3UPVcQ9

What are folks favourite *free* tools for finding potential reviewers for manuscripts? I have used JANE (https://buff.ly/2XdHUyw) previously, which is great, but I'm wondering if there are other open tools to try too.

This looks interesting: SCARAP: scalable cross-species comparative genomics of prokaryotes academic.oup.com/bioinformati...

14. There are huge benefits to converting your current journal clubs into preprint review clubs. *Share usable feedback and improve science *Help ECRs build a public track record *Actual training op-ed: buff.ly/3zjLltQ You could post the reviews to @prereview.bsky.social too! #PreprintAdvent

Reminder for newcomers that bioRxiv has Bluesky accounts in every subject category - great way to keep up (please re-skeet) connect.biorxiv.org/news/2023/09...

📑 New PCI Genomics recommendation, by Federico Hoffmann: https://buff.ly/41bWBnZ A recommendation of a thorough investigation into the factors affecting single gene tree dating, from Guillaume Louvel and Hugues Roest Crollius: https://buff.ly/4eRtARP

Really interesting episode! Disturbing to think how often this bias may occur in investigations where it's not obvious.

Peer Community In Genomics is now on Bluesky! 👋 We're a free and transparent platform for evaluating and recommending genomics preprints 📑 ✍️ Part of @peercommunityin.bsky.social , and associated with (optional) Diamond OA journal @peercomjournal.bsky.social 🎈

Microbiome FacultyJob at UC Davis in the Department of Medical Microbiology and Immunology (one of the departments where I reside ...) See recruit.ucdavis.edu/JPF06847

Anyone have thoughts on the "ordered quantile normalization"? www.tandfonline.com/doi/full/10.... It transforms data to normal distribution, and retains the order but not the scale of original data. Reasonable to use with models that assume normality, if you are interested in relative ranking?

I'm excited to be starting as an Assistant Professor (@BiologyUnb) at the University of New Brunswick (Fredericton, Canada) in July 2025! My group will be exploring the evolutionary forces driving pangenome variation in prokaryotes. Details here: https://buff.ly/3UPVcQ9

I'm hiring a postdoc! To use substitution models to understand protein evolution and/or improve phylogenetic methods. evol.mcmaster.ca/brian/evoldi...

The Canadian research funding agencies are currently re-evaluating their policy on open access publishing. I wrote this policy memo on this topic, which was just published in the Journal of Science Policy & Governance! Check it out here:

A reminder that this job posting is open for 1 more week! Come join us! #microsky #microbiome

🆕 I’m looking for a postdoc to join the group! This is for a project as part of the @multidefence.bsky.social consortium, looking at genome defences and horizontal gene transfer in Pseudomonas. Deadline 12th August. 🧵 my.corehr.com/pls/ulivrecr...

Are you going to #ISME19? Will you present a poster? Do you use #anvio for your research? If yes, yes, and yes, please consider filling out this form so we can bring stickers to your poster, say hi, and ask your advice on how to make anvi'o better. forms.gle/idoXJbN5bpUP... Thank you! 😇

Hiring a bioinformatician at @uniofexeter.bsky.social to work with the Exeter sequencing facility. Please spread the word! jobs.exeter.ac.uk/hrpr_webrecr...

Floria: fast and accurate strain haplotyping in metagenomes academic.oup.com/bioinformati... 🧬🖥️ github.com/bluenote-157...

Microflora Danica: the atlas of Danish environmental microbiomes 10,686 shotgun metagenomes from a variety of environments across Denmark www.biorxiv.org/content/10.1...

einstein sent this to curie in 1911 when she was being harassed by tabloids. it contains everything you’d want in such a letter: (1) your haters are trash (2) you’re a baller, a true queen (3) i have determined the statistical law of motion of the diatomic molecule in planck’s radiation field 🧪⚛️

Tenure track position (Assistant Prof or Associate Prof) in Science & Technology Studies at University of Lausanne, Switzerland Closing date for applications: 15.08.2024 further details: career5.successfactors.eu/career?caree... #STS #HPS

This looks fantastic from Tanya Stadler and co: decodinggenomes.org