Nina Dombrowski

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

European Bioconductor Conference 2025 – EuroBioC2025 The European Bioconductor Conference (EuroBioC2025) will take place on September 17th to 19th, 2025, in Barcelona, Spain. EuroBioC2025 will bring together the Bioconductor community to showcase the…

⏳ 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/

Job opportunity Postdoctoral Researcher (m/f/div) in Gut Microbiome Metabolomics at Leibniz HKI Jobportal Wissenschaft/Forschung in Jena

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...

Protein structure alignment significance is often exaggerated Machine learning has generated millions of high-quality predicted protein structures, creating a need for computationally efficient structure search algorithms and robust estimates of statistical sign...

"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...

YouTube video by Study Hall How to Become: a Marine Biologist

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...

Genomes of nitrogen-fixing eukaryotes reveal an alternate path for organellogenesis | PNAS Endosymbiotic gene transfer (EGT) and import of host-encoded proteins have been considered hallmarks of organelles necessary for stable integration...

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

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/...

DPANN Archaea and CPR Bacteria: insights into early cellular evolution? | Philosophical Transactions of the Royal Society B: Biological Sciences Cultivation-independent techniques have facilitated the discovery of a diversity of thus far uncultivated organisms and led to the identification of new branches within the tree of life. This has resh...

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

AI Carpentry? Helping learners make better choices with genAI. In two recent community discussion sessions, we explored what mental model of machine learning/deep learning we could teach to learners already familiar with the basics of programming, to help them sa...

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

Caliditerrarchaeota, a new sister to Nanohaloarchaeota, provides insights into the evolution of DPANN halophily The Nanohaloarchaeota are a clade of halophilic symbionts with small cells and genomes. Originally placed within the Euryarchaeota, they are now widely thought to belong to the DPANN archaea. However,...

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...

Publish a Quarto project using GitHub Pages+GitHub Actions in 6 minutes (no need to render locally!) Enjoy the videos and music you love, upload original content, and share it all with friends, family, and the world on YouTube.

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

Reply to: Reply to: False positives in the study of memory-related gene expression In the Nature paper “Spatial transcriptomics reveal neuron–astrocyte synergy in long-term memory” published on March 14th, 2024, authors Sun et al. claimed to identify cell-type specifi…

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:>

A graphic announcing the 'FULL PROGRAM LAUNCH' for 'posit conf (2025)'. Below the text is a stylized white outline of a city skyline. At the bottom left is the 'posit' logo followed by 'conf (2025)'. On the bottom right, in white text, are the dates 'SEPTEMBER 16-18' above 'Atlanta', accompanied by a small yellow cube.

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

Growth of public metagenomes over time

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