Claudia Kasper

moiraine: an R package to construct reproducible pipelines for the application and comparison of multi-omics integration methods academic.oup.com/bioinformati... 🧬💻🧪 #Rstats github.com/Plant-Food-R...

Recently we're working with SNPs from whole genome assemblies to estimate ARGs. It's a pain to go from alignment files to vcf, keeping track of masked and invariant sites. So we wrote a snakemake/SLURM pipeline. Hope it's useful to others, and don't hesitate to post issues if there are problems!

Control of retrotransposon-driven activation of the interferon response by the double-stranded RNA binding protein DGCR8 Abstract. The type I interferon (IFN) response is the main innate immune pathway against viruses in mammals. This pathway must be tightly regulated to prev

I'm so happy to share our latest paper! Now out in @narjournal.bsky.social 🥳

Did you know that transposable elements embedded in mRNAs can form dsRNA and activate innate immunity? 🧬🦠 Have a look! academic.oup.com/nar/article/...

#TEsky #RNAsky #RNAbiology #immunity #NAR

Join us at the EMBO Workshop “RNA-guided genome protection” 🇨🇭 June 16–20. Transposon silencing • stem cell biology • RNA-guided immunity. Keynotes: Déborah Bourc’his + Ian MacRae. Register now + submit your abstract! meetings.embo.org/event/26-gen...

DIW Berlin: Electric Mobility in Germany: Untapped Potential A rapid transition from combustion engines to electric vehicles is essential for climate protection in road transport. This report highlights current trends in electric mobility in Germany based on…

🔌🚗 Electric mobility in Germany: Untapped Potential!

Electric mobility has been slow to take off, but there are positive trends. I summarize them in the new @diw.de Weekly Report, based on data collected on the #OpenEnergyTracker. (English version of a report first published in 🇩🇪 in February)

Northern California’s first condor egg in 100 years reported in redwood tree

Who COULDN’T use some good news? ‘ Scientists with the Yurok Tribe say that two of dozens of condors released to the wild in Humboldt County since 2022, to reestablish the endangered birds, have paired up, built a nest in a redwood tree and appear to be tending to an egg.”

#californiacondor

Finally, today's offering! www.biorxiv.org/content/10.6...

This began life as a very different project which failed because we couldn't agree on defining eqtl sharing across cohorts. So two young members of the lab dug deeply into this - first @ijbeasley.bsky.social, then @patrickgibbs.bsky.social

The real problem is that we publish many more papers per scientist than before.

A two-column status table titled "Stage" and "Start Date" tracks the timeline of a manuscript submission from its preliminary data submission on October 8, 2025, to its eventual withdrawal on March 2, 2026. The log reveals a lengthy and repetitive administrative process, particularly between October 26, 2025, and February 19, 2026, where the status cycled more than ten times between "Contacting Potential Reviewers" and "Waiting for Reviewer Assignment," suggesting significant difficulty in securing peer reviewers. Following these numerous failed attempts to move into the active review phase, the final entry shows the manuscript was officially withdrawn on March 2, 2026, at 09:08:18.

My first paper had to be mailed to Stockholm, Sweden, and then mailed to reviewers around the world. Everything by mail! It was submitted, reviewed, revised, typeset, and published in 3 months. I feel bad for early-career scientists who can't find a single reviewer after 5 months. It's gotta change.

Pangenomes, really?

Most early “pangenomes” = oligogenomes (oligo, Gr., few).

More recent “pangenomes” generally = poligenomes (polis, Gr., many).

True pangenomes (pas, Gr., every/all) would be rare indeed.

🙏🏼 @zbao.bsky.social for pointing out his review.

www.nature.com/articles/s41...

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.

Hey - there's a preprint about the bioRxiv preprint server published as a preprint on the bioRxiv preprint server:

bioRxiv: the preprint server for biology www.biorxiv.org/content/10.1...

I Tried to Be the Government. It Did Not Go Well. My five-month quest to monitor the weather, track inflation, and inspect milk for harmful microorganisms

in honor of a certain surgeon general nominee’s hearing today, here is the story of (among other things) the time I tried to take her advice about milk www.theatlantic.com/magazine/202...

Have you ever wondered 🤔... Does phenotypic variance respond to environmental perturbation? Does it have a genetic basis? Are mean and variance regulating loci exposed to different selection pressures? These and more questions are explored in our new preprint 🔥

www.biorxiv.org/content/10.6...

Happy Birthday!

I first read about the LTEE in high school in a science magazine my Bio teacher had in the classroom. I don't think I thought "I want to be a microbiologist," but the article planted the seed.

Amazing that it's nearly at "mid life" (by human standards)., excited for what's next!

Happy 38th birthday to the #LTEE!
#BOTD in 1988.
Keep on evolving!

#science #evolution #microbiology

DNA

obXKCD: xkcd.com/1605/

Written English has barely changed in 300 years. If you can read Harry Potter, you can read Robinson Crusoe (1719).

How far back in time can you understand English? An experiment in language change

If you liked this experiment, I published a full piece today in the same vein: a text that gets 100 years older with every section, from a modern blog post to a medieval chronicle.

It's a single story spanning 1000 years of English. See how far you get.

www.deadlanguagesociety.com/p/how-far-ba...

I'd like to go there, but not sure if I would ask for a glas of tap water.

The strongest version of this illusion I’ve seen! Absolute head-wrecker!

Health Rounds: Moderna combo flu/COVID vaccine succeeds in mid-stage trial A two-in-one mRNA vaccine developed by Moderna that targets seasonal influenza and COVID-19 produced robust and durable immune responses without safety concerns in a small mid-stage trial, the company...

More good news on vaccines

A two-in-one mRNA vaccine developed by Moderna targets seasonal influenza & COVID-19. It produced robust and durable immune responses w/o safety concerns in a small mid-stage trial.

mRNA is the future. We can’t afford to lose it.

🧪 www.reuters.com/business/hea...

One vaccine may provide broad protection against many respiratory infections and allergens Stanford Medicine researchers and their colleagues invented a new vaccine that protects mice from respiratory viruses, bacteria and allergens — the closest yet to a universal vaccine.

Exciting! Stanford researchers have developed a UNIVERSAL INTRANASAL vaccine. A study in mouse models shows that vaccinated mice were protected against Covid & other coronaviruses. Still a long way to humans. This study was #NIH funded.

A potential game changer.
🧪 med.stanford.edu/news/all-new...

BREAKING: Former South Korean President Yoon Suk Yeol has been convicted of insurrection for declaring martial law in December 2024, and has been sentenced to life in prison.

Now, I have thoughts on all this but that’s for elsewhere. What immediately strikes me most is that Dawkins was using a definition of “gene” that he admits (and Stent acknowledges) was taken from George Williams, and which was common in evolutionary biology then and still is now. But…. /9

A Shapiro-Wilk test of the response variable concludes very significant deviation of Normality. But residuals of linear model consistent with Normal distribution.

Visual check of the linear model with DHARMa

Periodic reminder that we should avoid testing the Normality of the response variable.

For a linear model, what matters is the Normality of residuals (and not that much). Visual checks better than test. #statistics

Every politician considering slowing down climate solutions, like the renewables, electric vehicle or heat pump rollout, needs to be fully informed what is at stake and what risks they are taking.
It is often compared to a ship sailing into uncharted waters with dangerous rocks below the surface.

Coral background with faint heart illustrations. A glossy male Blackbird with a bright yellow bill faces left. Large title reads: “Birds as bad exes*” Smaller text reads: “*Yes, you read that right.”

Happy Valentine’s Day, from us to you. Tag your exes. Xoxox

The strength

Happy birthday to one of my favourite haters, Charles Darwin