I'm both excited and a little terrified. It feels like a wave of AI-assisted tool rewrites is coming to bioinformatics whether we like it or not. We figured that the best we can do is to try to get ahead of it, so we wrote down some principles for doing it responsibly: rewrites.bio

Pretty much the same reason all the gene regulatory network inference models don't work as well as people think they do

We're thrilled to announce the Ctrl-Z Award, a US$2,500 prize for researchers “who discover substantial errors in their published work and take meaningful steps to correct the scientific record." Covered by @nature.com today; read more here: centerforscientificintegrity.org/2026/03/10/a...

Evo 2, the largest fully open biological AI model to date, is now published in @nature.com youtu.be/o_w-E--u7GQ

we talk about carcinization, but never about the many, many times plants have invented the “tree.” Tree is not a kind of plant, it is a thing plats do, and they are by and large unrelated.

So I pleased to announce the conceptual spawn of FigTree: PearTree (acronym still to be finalised). If you want to dive right in it is hosted as a web app here: artic-network.github.io/peartree (click the “Example...” button for immediate candy and then click every button you can find).

Sounds like a great opportunity for a professor position in computational biology in the Netherlands careers.universiteitleiden.nl/job/Assistan...

Students being students: I found this when logging on to the lecture room PC this morning. Translation: “R is not fun <redacted>” 😂

🎉📣 #TAIR12, the latest reannotation of the Arabidopsis thaliana genome, is now available under accession number PRJEB100887 on ENA and NCBI! Thank you all the volunteer researchers whose hard work has made this possible! #plantscience #plantbiology 🧪 bit.ly/3ZHtneT

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...

Vibecoding when you’re a proficient programmer

Nothing but respect for the authors who made the difficult call to retract published work after facing public scrutiny: www.science.org/doi/10.1126/... But also: scientific publishing is fundamentally broken if we see this case as anything other than a win for science!

Super interesting thread on vibecoding: translating an existing approach from c++ to rust. TLDR it’s not straightforward at all! Even though the information is there, many crucial parts are omitted/incorrect.

Protenix v1.0 is out with some very impressive performance numbers (exceeding AF3 performance on protein-protein complexes)

Preprint your work! TIL I learned the animal phylogenomics paper has been asked to be retracted, which might have been avoided if it was looked at by more than a handful of rushed anonymous academics.

www.wur.nl/en/vacancy/f... Become our new colleague (and next door neighbor) and lead a chair/group/department of Biophysics at Wageningen University. Reach out to me for info and please spread!!!

Sure. AI companies have ALWAYS been training their models on Wikipedia content, which under the free and open access model is available to anyone — including AI companies. Agreements like these require AI companies to limit and offset the strain they place on Wikimedia infrastructure.

I am looking for a postdoc to develop high-performance algorithms in computational genomics. Email or DM me if interested. For more information, see hlilab.github.io/vacancies. RTs appreciated!

It took me forever to realize this after reading Pearl’s The Book of Why

Now published in Algorithms for Molecular Biology: link.springer.com/article/10.1.... Key message: a tiny CNN model with 7k parameters can capture main splice signals across vertebrates+insect and halves the minimap2 & miniprot junction error rate. I always use this new feature now.

Now published in gigascience: academic.oup.com/gigascience/.... Key messages: SVs are highly enriched in low-complexity/tandem-repeat regions and are harder to call. They behave differently from transposon insertions. Always stratify if you study SVs.

I have a postdoc position in metagenomic exploration available in my group. Candidates with documented experience in phylo & metagenomics and preferably with petabase-scale data mining and GLM workflows are encouraged to apply. Come join us! 🧬🦠💻 Please repost Apply here: www.wur.nl/en/vacancy/p...

happy ‘i will reply to your email on my return’ day to all who celebrate

I’m so far removed from this field that saying “there is no causal inference” for me is at least a lukewarm take.

Apropos of nothing: I just realized serde literally derives from serializing/deserializing despite having used it a bunch. No I didn’t read the docs, yes I feel stupid 🙃

On the first day of Christmas (in about 2014), @duckswabber.bsky.social gave to me - a partridge in a pear tree. Happy Christmas everyone!

We are pleased to announce the official release of PLAZA 5.1, our plant genomics platform, which comes with a major front-end redesign. This results in improved performance, enhanced visualization tools, and refined Toolboxes. Src: www.vandepoelelab.be/plaza/news#28

Wishing everyone a safe Christmas break!

Now available online: the new 2.0 version of gutSMASH, with capabilities to detect 12 new types of catabolic gene clusters relevant to gut microbiome ecology, as well as predictions of their regulation through transcription factor binding site detection. www.sciencedirect.com/science/arti...

Paid internship opportunity for Master’s students in the Netherlands 🇳🇱 If you’re studying computer science, bioinformatics or molecular biology, this could be the perfect springboard for you. A collaboration with the Embassy of the Kingdom of the Netherlands. www.ebi.ac.uk/about/jobs/i...

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

Someone call the visualization police 🚨

My university teaches stats but not logic and honestly they could do with some jaynes

I learned about Nyguist-Shannon ~1year ago and now firmly believe everyone designing time series experiments should know this. I hardly see it being discussed in transcriptomics…

The kinds of databases: • Fancy files • 1970s stays winning • This would be so cool if it worked at scale • Oh, that's why google has a monopoly on search

We (Nordborg & Weigel labs) need input on the next generation of genome browsers & data download modes for the #Arabidopsis #1001GenomesPlus project. We have now a curated collection of over 500 long read genomes. Please help us by filling out this questionnaire: docs.google.com/forms/d/e/1F...

Live your life in a way that quotations like these don't show up in your obituary.

If ever you needed evidence of dot com 2.0

Students should absolutely have a say in evaluating their education, but standardized forms measure overall satisfaction/mood and are not a good indicator of quality

In this commentary, I argue that student-based teaching evaluations are problematic bc ✳️ systematic biases (e.g., racism, sexism) ✳️ poor construct validity ✳️ undermine standards and learning We should evaluate teaching as seriously as we do research. Or don't do teaching evaluations.

Hot off the press! Our paper, “Global comparative structural analysis of responses to protein phosphorylation”, is now out in Nature Communications! www.nature.com/articles/s41...

MMseqs2-GPU sets new standards in single query search speed, allows near instant search of big databases, scales to multiple GPUs and is fast beyond VRAM. It enables ColabFold MSA generation in seconds and sub-second Foldseek search against AFDB50. 1/n 📄 www.nature.com/articles/s41... 💿 mmseqs.com

A double edged sword: not patenting IP saves universities money, and open source is always a win

Heads up: ignore samtools dot org, similarly minimap2 dot com and likely others. It's owned by a known phishing site and while the binaries they offer look valid currently (but note they may be serving us different binaries to others), that could change. Ie: it's not us (Samtools team)! Be warned

It seems trendy lately to have visualizations of 3D proteins structures generated by AI. These show very ugly artifacts, akin to AI pictures of humans with the wrong number of fingers. It is really not hard to make a visualization of a random protein structure using free software! #AI-slop

We are looking for a 3-year postdoc to work with Daniel Probst, Justin van der Hooft and myself on an exciting project involving federated learning and integrative omics for discovery of new antibiotics from natural products. Apply here: www.wur.nl/en/vacancy/p... Please share!

We're looking for a postdoc who wants to tackle multi-modal federated learning applied to drug discovery. There will be: - A great team - Loads of data - An interesting and important application - A beautiful, modern campus ...

New RL target just dropped 🙃