@joshnhamm.bsky.social @ndombrowski.bsky.social @greening.bsky.social @luisvalentin.bsky.social et al. provide the first investigation into the enigmatic Terrarchaeota and insights into the evolution of high salt adaptation in Archaea. 🔗 doi.org/10.1093/molbev/msag091 #evobio #molbio #microbeSky

Our paper examining the evolution of halophily in DPANN is out now in MBE! academic.oup.com/mbe/advance-...

IQ-TREE 3: Phylogenomic Inference Software using Complex Evolutionary Models academic.oup.com/mbe/article/...

2/ Gene-level stats ≠ biological interpretation. You need pathway-level signals. That’s where gene set enrichment comes in. But most tools are: • slow • fragile with small n • stuck in R

Statistical Rethinking 2026 is done: 20 new lectures emphasizing logical and critical statistical workflow, from basics of probability theory to causal inference to reliable computation to sensitivity. It's all free, made just for you. Lecture list and links: github.com/rmcelreath/s...

🚨 Postdoctoral Opportunity for Female Scientists🚨 The University of Vienna is awarding at least 20 fully funded 4 year postdoctoral positions to outstanding female scientists Interested? Get in touch via direct message careers.univie.ac.at/en/postdoc/e... #MicroSky 🧪 #PostDoc @univie.ac.at

So it looks like i hadn't mentioned this, here, so just in case let me say this plain: Instructure, the parent company & producer of the Canvas learning management software platform, has partnered with OpenAI, as of last year. There are a number of claims being made about privacy but… well. Heads up

I'm teaching Statistical Rethinking again starting Jan 2026. This time with live lectures, divided into Beginner and Experienced sections. Will be a lot more work for me, but I hope much better for students. I will record lectures & all will be found at this link: github.com/rmcelreath/s...

Really important read for people working with long-read MAGs. www.nature.com/articles/s41...

A new year brings new opportunities: we are looking to fill a permanent professorship position with a Microbiologist preferably with expertise on archaeal biology, RNA biology or imaging techniques to unravel cell biology in prokaryotes! Please share and/or apply :)! www.nature.com/naturecareer...

💾 Prokka 1.15.6 is released! This is the last major release of Prokka. But don't be sad, because @oschwengers.bsky.social already has an excellent replacement called Bakta you can migrate to. #bioinformatics #microbiology #genomics github.com/tseemann/pro...

I'm proud to share the latest methods work from my group. Led by @revathykri.bsky.social we wrote a book chapter on how we process and analyse viromes. Thanks to co-authors @rikhaagmans.bsky.social @ryancook94.bsky.social & Alise Ponsero link.springer.com/protocol/10....

Co-occurrence is associated with horizontal gene transfer across marine bacteria independent of phylogeny academic.oup.com/ismej/advanc... #jcampubs

We are thrilled to announce the first official release (v0.1.8) of #𝗯𝗲𝗱𝗱𝗲𝗿, the successor to one of our flagship tool, #𝗯𝗲𝗱𝘁𝗼𝗼𝗹𝘀! Based on ideas we conceived of long ago (!), this was achieved thanks to the dedication of Brent Pedersen. 1/n

#Archaea, #DPANN, #phylogenetic_reconciliation New preprint online! www.biorxiv.org/content/10.1...

The detectCores() apocalypse is creeping up on us 👻🐛 As more people are getting access to 128+ CPU cores, code spinning up parallel cluster with detectCores() workers fails - not enough #RStats connections available Friends, do *not* default to detectCores(), bc www.jottr.org/2022/12/05/a...

October 2025 batch of Kraken 2 indexes, including core_nt and many others, available: benlangmead.github.io/aws-indexes/k2 Coming soon to K2: a feature for querying many K2 indexes as though they're a single index. Highly useful if the index you want to query is too big to build and/or fit in RAM.

Around 10% of your Nanopore reads (SQK-RBK114) are incorrectly trimmed. Here is why, and how our new tool Barbell solves it: www.biorxiv.org/content/10.1... Want to get started? github.com/rickbeeloo/b...

Still fascinated with #webR and its potential for teaching stats Here students can play (even from their phones) and find out themselves how the p-value depends on sample size pakillo.github.io/LM-GLM-GLMM-... #rstats

To summarise our recent pre-print: Autocycler, the automated consensus assembler, when used with Nanopore long-read only Enterobacterales assemblies, produces more complete chromosomes and plasmids, with an accuracy comparable to hybrid assemblies.

Job Alert! We're hiring a BIOINFORMATICIAN / NGS SPECIALIST to support our new Molecular Biodiversity Lab in the @terra-cluster.org at @unituebingen.bsky.social. Like the idea to use your skills for understanding biodiversity? To work on diverse questions in a wonderful place? Apply! Please repost!

New blog post! metaMDBG (@gaetanbenoit.bsky.social) and Myloasm (@jimshaw.bsky.social) have had recent releases, so I updated the benchmarks from the Autocycler paper: rrwick.github.io/2025/09/23/a... Both tools improved considerably! Time to update your conda environments 😄

contact me or @csoneson.bsky.social if you want more details

⏳ One week left to register! Join us at EuroBioC2025 in Barcelona and the Bioconductor Carpentry Workshops for hands-on learning, community building, and cutting-edge bioinformatics. 🗓️ Registration closes August 28 — don’t miss out! 🔗 eurobioc2025.bioconductor.org #EuroBioC2025 #RStats

{tinytable} 0.13.0 for #RStats can now draw interactive tables with sorting, filtering & pages! And the 📦 is still an ultra-simple, powerful, and 0-dep way to create beautiful tables in basically any format: tex, typ, docx, pdf, png, md, etc Gallery & Docs: vincentarelbundock.github.io/tinytable/

We’re hiring a Postdoc in Gut Microbiome Metabolomics! Help us decode microbial metabolism and its impact on human health @leibniz-hki.de , Jena 🇩🇪 🔗 jobs.hki-jena.de/jobs/Postdoc...

"We show that unrelated proteins have a universal tendency towards convergent evolution of secondary and tertiary motifs, causing an excess of high-scoring FP alignment... previous methods routinely overestimate significance by up to six orders of magnitude." www.biorxiv.org/content/10.1...

IT'S HERE!!!!!!!!! I had the opportunity to work with @gostudyhall.bsky.social to film a video on How to Become a Marine Biologist a few months ago and now it's live! www.youtube.com/watch?v=ezaE...

www.pnas.org/doi/10.1073/... Genomes of nitrogen-fixing eukaryotes reveal an alternate path for organellogenesis #protistsonsky

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/...

DPANN Archaea and CPR Bacteria: insights into early cellular evolution? royalsocietypublishing.org/doi/full/10.... #jcampubs

My latest post on @carpentries.carpentries.org blog is a call to action for the community to engage in curriculum development for workshops about genAI. How can we help our target audience make more informed choices about when and how to use it? carpentries.org/blog/2025/08...

Oatk: a de novo assembly tool for complex plant organelle genomes. #DeNovoAssembly #OrganelleGenomes #Bioinformatics #GenomeBiology genomebiology.biomedcentral.com/articles/10....

I am excited to announce that the position of a senior postdoc (3 +3 years) in the field of theoretical biology is available in my group. The position provides the opportunity to closely interact with experimentalists and develop own research projects. Please RT. Details 👇: shorturl.at/iiiOv

New preprint up now! Interested in the evolution of halophily within DPANN archaea we decided to investigate the sister phylum to the Nanohaloarchaeota, GTDB phylum EX4484-52, for which we propose the name Caliditerrarchaeota www.biorxiv.org/content/10.1...

This video by Melissa Van Bussel helped me set up my very first GitHub Action to publish my site. It took exactly 10 minutes! 👉 tiny.cc/gh-actions Here’s the site I published using that workflow: 🔗 jformoso.github.io And her website, she has great resources! 🌐 www.melissavanbussel.com #RLadies

Excited to share our work on WitChi! 🛠️🖥️ We tested it on the GTDB r220 archaeal supermatrix (5,869 taxa & 10,101 cols) removing 55% of sites in <2h. The phylogeny showed several interesting groupings with overall improved branch support: #phylogenetics #ArchaeaSky #MSA #opensource #MEvoSky #MicroSky

I wrote a review of a recent paper on false discovery and multiple testing correction. liorpachter.wordpress.com/2025/06/16/r...

I’ve written threads about the GBR-MGDs pMAGs, but it also contains viruses (vMAGs), including a monophyletic clade of marine Crassvirales, chromosome-level eukaryote eMAGs, and putative plasmids. We wanted a holistic DB. One problem: some key software appear to break with long reads. A 🦠 🧵.

I'm happy to announce the latest release of the GlobDB, available at globdb.org. The GlobDB is a database of "species dereplicated" microbial genomes, and as of release 226 contains twice the number of species-representative genomes (306,260) than the latest GTDB release.

📣 We have a postdoc position in fungus-microbiota interactions! Apply here: jobportal.uni-koeln.de/bewerben/2197 ⁩ For more details, visit: bewerbungsmanagement.uni-koeln.de/ausschreibun...

New vacancy in my team! PhD student position on microbial genome evolution, focusing on the evolutionary principles underlying bacterial genome architecture. Please repost and share with talented MSc students in #evobio, bioinformatics or related :) www.uu.nl/en/organisat... #MEvoSky #MicroSky

This promises to be a cool PhD project with a very inspiring and nice PI!

Thanks to everybody who chimed in! I arrived at the conclusion that (1) there's a lot of interesting stuff about interactions and (2) the figure I was looking for does not exist. So, I made it myself! Here's a simple illustration of how to control for confounding in interactions:>

We’re excited to announce that the session catalog for posit::conf(2025) has launched! View 100+ talks, sort by day and type, and add favorites to your schedule: reg.rainfocus.com/flow/posit/p... Our Early Bird discount is still available. Get your ticket today! #RStats #Python #PositConf2025

Unique investigation of some errors in long read assemblers. In particular these remarkably chimeric contigs are 😱, if rare.... Improving long read assemblers is definitely the space to be in when it comes to the future of metagenomics, as short reads won't be part of it 😉

GTDB Release 10-RS226 (16th April 2025) has been published gtdb.ecogenomic.org

A 1.0 release for Sandpiper. 700,000 microbial community profiles (3x the last version, 4.7 Pbp metaG), searchable via the @ace-gtdb.bsky.social R226 taxonomy that just dropped. MetaGs are going exponential, but we are still nowhere near a MAG for all species. sandpiper.qut.edu.au #microsky 🧬🖥️ 1/2

#EBAME 10 Microbial Ecogenomics Workshop! Brest🇫🇷, Oct 11-25, 2025. A two-week workshop of lectures & tutorials to learn about omics data analysis for microbial ecology and evolution, all in the beautiful Brest Bay! Apply here until June 1: maignienlab.gitlab.io/ebame

🔍 "Adaptive adjustment of profile HMM significance thresholds improves functional and metabolic insights into microbial genomes"  is in Bioinformatics Advances: https://doi.org/10.1093/bioadv/vbaf039 Authors include: @merenbey.bsky.social  @bradleyph.bsky.social