🆕 and #OpenAccess in "Ecological Monographs"⤵️

Tiberius makes it a bit "prematurely dead" - but it's coming. It won't be more accurate than BRAKER3. But it will be shiny. Scalable. Maintainable. Bring the UTRs and downstream statistics, and the full isoseq integration. Happy Easter! BRAKER4 coming soon. #genomeannotation #BRAKER

Our takeaway: if we want to understand forest soils, we need to look beyond fungi. Metatranscriptomics reveal important players that PCR-based approaches miss. Really happy to share our new article: Protistan Predators Outshine Fungi in Forest Soil Activity. #ProtistsOnSky #MicrobialEcology #Soil

Protists accounted for ~20.1% of reads, while fungi accounted for merely ~9.1%. Among eukaryotes, Arcellinida stood out as the most abundant order, not fungi! Protists are not just bystanders, they are important predators that may strongly shape forest soil food webs! (pic:Arcellinida feeding hypha)

We all know #fungi are the dominant microbial #eukaryotes in #forest #soils… or are they really? In our new paper, we revisited 51 forest metatranscriptomes from 4 European and North American forest regions - and found that protistan predators outshine fungi in activity!

What I love about academia: within a few constraints, you can just go and pursue what you love to do, what you find captivating and fascinating, or what needs fixing. What I hate about academia: the endless to do list resulting from this freedom.

Thrilled to see this work published: Rapid ecological and evolutionary divergence during a poleward range expansion doi.org/10.1002/ecm.... with @uhl-lab.bsky.social , Monica Sheffer & other wonderful colleagues

No one could have foreseen this. www.science.org/doi/10.1126/...

ANNEVO uses a deep learning approach to advance accurate and scalable ab initio gene annotation of evolutionarily diverse genomes. www.nature.com/articles/s41...

I wrote a short Nature Methods News & Views piece on deep learning based gene finders such as ANNEVO. www.nature.com/articles/s41...

Good Morning, Greifswald…

4/ It ended up in someone else's published tool. That's the thing about sharing your work publicly. You never know who finds it useful. A throwaway tutorial you wrote on a random Tuesday can end up in someone's analysis pipeline years later.

As genome annotation scientist, I want on woman’s day draw your attention to women who impact(-ed) eukaryotic genome annotation:

Excited to share this preprint that describes my latest work on using GPUs to accelerate processing of RNA-seq data. The title says it all: "RNA-seq analysis in seconds using GPUs" now on biorxiv www.biorxiv.org/content/10.6... and github github.com/pachterlab/k... Figure 1 shows they key result

Involuntarily learnt a lot about xylitol induced insulin secretion jn dogs during the weekend. Luckily the little patient is recovering well. (We will never know what she ate… but a chewing gum seems realistic.)

So how many of my colleagues are PAYING OpenAI to use their LLM again???? You see where your money is going?

Hey #Physco sphere! What's your favorite protocol for purifying total RNA (or mRNA) from moss gametophores?

Our chairgroup Bioinformatics at Wageningen University changed leadership: prof. Dick de Ridder (@dickderidder.bsky.social) moved on to become Dean of Education and is now followed up by prof. Marnix Medema. Congrats @marnixmedema.bsky.social! www.wur.nl/en/news/marn...

Daylight during our morning walk 😁

New paper alert! The latest from my lab describing atypicalities in the processing of cues in the PFC and V1 of preterm mice trained on a visual discrimination task: www.nature.com/articles/s41...

Gestern hab ich bekannt gegeben, dass ich spätestens 2028 aus der Wissenschaft aussteigen werd — darüber schreibt @evamurasov.bsky.social nun im @tagesspiegel.de. Zig Kommentare & Nachrichten zeigen mir: Sehr viele Wissenschaftler_innen hadern. Bedingungen müssen dringend besser werden! #IchBinHanna

do nextflow pipeline developers consider temporary storage needs when developing pipelines? I love nextflow, but I feel like the modular structure encourages design choices that cause temporary storage to explode.

Scientists have seen Asgard archaea crawling for the first time. When it comes to the origin of eukaryotes, this is like seeing a feathered dinosaur in the wild. (Video courtesy of Philipp Ralder)

Congratulations to @stepbystepsolution.bsky.social to the manuscript on genome annotation of 200 insect genomes, a result his work within of @gevol.bsky.social ! doi.org/10.1038/s415...

💻🧬 Keen to learn about eukaryotic genome annotation? Registration is now open for our 2026 online #genomeannotation course, led by our core #bioinformatics team. ➡️ buff.ly/sonWCgT

The new diatom Tiberius parameters for unmasked genomes illustrate the gain in accuracy that we often observe compared to parameters for unmasked genomes. #geneprediction #genomeannotation #diatoms #bacillariophyta github.com/Gaius-August...

We have a new insect parameter set for unmasked genomes and a new fungal parameter set for unmasked genomes. Both deliver accuracy superior to previous models for insects and fungi. #genomeannotation #geneprediction github.com/Gaius-August...

What we more recently learnt about Tiberius: the models trained on softmasked genomes are very sensitive to how the genome was masked for inference. It seems safer to use models trained on unmasked genomes. #genomeannotation #geneprediction github.com/Gaius-August...

I am very, very happy! I got a pull up bar for x-mas, and today, my dear husband installed it. It’s so much easier to grip than those cheap gymnastics rings that I have used until now. Can I do a pull up? No. But the pathetic-looking attempts have changed my life. Pain is gone since I started trying

This article is now published! academic.oup.com/nargab/artic... We’ve added a few new analyses. First off, we show that, while gene presence absence variation (PAV) scales with evolutionary distance in both plants and animals, the base level and rate of accrual are both twice as high in plants.

#ProtistsOnSky no 'swimming' by 𝘝𝘢𝘮𝘱𝘺𝘳𝘦𝘭𝘭𝘢, definitively no 'staying still'. just a relaxed walk towards the lunch...

Tiberius parameters for fungi incertae sedis will soon be available on Github.

"Once you get to the top, you get to ski all the way back down the mountain!" Read @lsubiosci.bsky.social PhD student @jacobcarignan.bsky.social's interview with Quantitative Ecologist Michelle Stantial about her ski mountaineering hobby: thelattinlab.com/beyond-the-b...

These orb-weaver spiders build FAKE SPIDER DECOYS in their webs, potentially to deter predators 🤯 onlinelibrary.wiley.com/doi/10.1002/...

We ended the day on Wednesday with a computer lab session on gene expression analyses with Rachel Steward 💻📊 #evomics2026

Morning lecture by Maliheh Mehrshad (@mehrshmali.bsky.social) on metagenomics and metatranscriptomics! 🧪🧬🦠 #evomics2026

Rosa Fernández (@rosafernandez.bsky.social) introducing the field of Phylogenomics to our participants 🙌🏽🧬🌳💻 #evomics2026

Last computer lab session of the workshop we are back in the Genomics Adventure, with Guy Leonard (@guyleonard.bsky.social)!! 🙌🏽💻🙆🏻‍♀️ #evomics2026

Our closing lecture given by Nathan Clark, on Evolutionary Adaptation and Comparative Genomics 🌳🧬🙌🏽 #evomics2026

The 2026 Workshop on Genomics comes to an end! It has been two intense and inspiring weeks of Genomics in Český Krumlov. We hope everyone is going back home with a renewed excitement for science and new friends and collaborations around the world! 🙆🏻‍♀️🧬 #evomics2026

This happens if you take your kid to an art & science event one summer night. Proud of you, kid. www.instagram.com/reel/DT5IOEE...

We are hiring a postdoctoral researcher!🌲 🌳 🌍 📍Interested in boreal and temperate forest productivity and respiration? 💻 Like to work with large datasets, remote sensing and models? 🏔️ Love an alpine setting in a small town? Come and join us at KIT! Application details: t1p.de/qctj7

I worked all through x-mas break to get the Basidiomycota parameters for Tiberius for #PAG33 - but I did not get the GPU nodes in time. Here they are, Tiberius parameter for Basidiomycota, benchmarked with gffcompare on CDS exons only. Appearing on Tiberius github, soon.

On Saturday afternoon we had a session led by Dag Ahrén (@dagahren.bsky.social) on Best Practices in Bioinformatics 💻📑 #evomics2026

Surprisingly, a local town cat decided that they wanted to learn some pop gen too!! 😸

Evening practical session with Madeline Chase on Population Genomics 🐦🐦🧬💻 #evomics2026

Morning lecture on Single Cell Transcriptomics by Arnau Sebé-Pedrós (@arnausebe.bsky.social) in the Town Theatre of Český Krumlov! 🧫🧬💻 #evomics2026