I created a little letter maze generator for my son Jakob christophsturm.com/jakobs-labyr... github.com/christophstu... enjoy if you find it useful.

Still cooler then outside. It's Gazpacho time.

Since the 1960s, the genetic code has been used to predict protein sequences from DNA and mRNA sequences. Our @nature.com article demonstrates that these predictions miss thousands of protein sequences present in human tissues. www.nature.com/articles/s41... 1/

Nikolai Slavov@slavov-n.bsky.social · 2y ago

We report many proteins not predicted by the genetic code. They are stable & abundant O( 10³ ) copies / cell. Generative mechanisms include codon-anticodon mismatches & RNA modifications. Their abundance depends on codon frequency & protein stability. www.biorxiv.org/content/10.1...

I made a multi-lingual language learner app that let's you create (via LLM qwen 2.5:7b) vocabulary, sentence, grammar, conjugation lessons for many languages (in principle ...). A couple of nice lessons are available online at raim.github.io/dreizunge e.g. for ...

The way to accelerate science is to SLOW it down. Fewer papers please! We’re drowning in meaningless text. One GREAT paper per lab per decade is more than enough. q.e.d 👇

Opposing Copy Number Variation Dynamics Shape Adaptation to Glucose and Galactose in Diploid Yeast https://www.biorxiv.org/content/10.1101/2025.10.01.679718v1

When the cell needs to respond to the environment: A chromatin-splicing love affair

When the cell needs to respond to the environment: A chromatin-splicing love affair

Alternative splicing allows rapid phenotypic adaptation, but the underlying mechanisms remain unclear. Moreau et al. highlight new findings on the critical role of chromatin modifications and 3D nuclear organization in regulating splicing dynamics. Understanding these chromatin-mediated processes provides insights into how organisms sustainably adapt to environmental challenges for rapid responses.

dlvr.it

Please re-post: Interested in chromatin and its evolution? Good news! There's still time to join us in beautiful Catalonia (9-12 Dec) to discuss eukaryotic, bacterial, archaeal, and viral chromatin and how it all hangs together meetings.embo.org/event/24-evo... Abstract deadline: 30 September

EvoChromo: Evolutionary approaches to research in chromatin

Chromatin is the complex of DNA, RNA and protein that is found making up the chromosomes in eukaryotic cells. Chromatin is essential for proper genome function and is involved in chromosome segregati…

meetings.embo.org

Please re-post: If you know (or are!) somebody who might fancy doing a PhD (Oct 2026 start) in my group @oxfordbiochemistry.bsky.social, working on chromatin evolution in prokaryotes (or other things we're interested in), please have a look at www.bioch.ox.ac.uk/supervisors-...

Supervisors and Projects

bioch.ox.ac.uk

To know what WoodstockBio2 & Night Science was really like - you had to be there! As you read about it in @nature.com, be aware that none if this would have happened without the vision, hard work, leadership & passion of @svobodalab.bsky.social Who was there - knows! www.nature.com/articles/d41...

Scientific bedlam at the world’s weirdest and wildest research conference

Woodstock Bio2 + Night Science aimed to encourage collaborations through creativity. The walk-on music for presentations was fun, too.

nature.com

Finding causal structures behind correlations is a key task of science. In biology, we have to do that for evolved, highly connected homeostatic feedback systems. How? Moving from "pseudo steady state" assumptions to time series may be the only option.

Unpopular opinion: I love posters and find them underrated as a form of less linear science communication. There should be platforms to publish in poster format, with supporting online material. My latest one, I loved to present in the Bohemian woods #theconferencetoendallconferences #tcteac

So cool, a novel archaeon with a super small genome and no metabolic genes! "An unprecedented level of metabolic dependence on a host, a condition that challenges the functional distinctions between minimal cellular life and viruses." www.biorxiv.org/content/10.1...

A cellular entity retaining only its replicative core: Hidden archaeal lineage with an ultra-reduced genome

Defining the minimal genetic requirements for cellular life remains a fundamental question in biology. Genomic exploration continually reveals novel microbial lineages, often exhibiting extreme genome...

biorxiv.org

We have several open postdoc positions! We do computational biology 🧬🖥️ and deep learning to understand the genomics of genome instability and (somatic) genome evolution in ageing and cancer. Interested? 👉🏻 more details: tu-dresden.de/cmcb/biotec/...

Open positions

We are looking for Postdocs! If you are interested in the lab in general as a postdoc, please feel free to apply with an open application, including a letter of motivation and a CV …

tu-dresden.de

🧬🌽 Happy Transposon Day! 🌽🧬 Today we celebrate the birthday of Barbara McClintock - scientist extraordinaire and discoverer of jumping genes. Still the only woman to have an unshared Nobel Prize in the biomedical sciences #TransposonDay2025

Indeed Oded. Some Will think of #TCTeAC as escapism, but I think it was showing us how beautiful we can make this world if the guiding values are respect & trust, and if world leaders would adopt a vision that is based on hope instead of hatred. On collaboration instead of competition. 💚

This seems like a very solid DIY benchtop reactor design, including a jacketed vessel that allows for calorimetry: www.biorxiv.org/content/10.1...

A very short summary of "Data Visualization against fascism": Fascism conceals truths, disregards evidence-based decision-making, and jeopardizes the education of the next generation. Standing up against means: MONITOR, EXPOSE, and EDUCATE. As scientists we are ready for this! #TCTeAC

How was your conference? Mine was #TCTeAC

Everybody is just talking about the fun #TCTeAC but the high quality of science, across a diverse range of fields, was equally impressive. Thanks to the organizers, such a unique event.

More support for the relevance of the twin-domain model of transcription by Sam Meyer's lab: gyrase binding is increased many kb downstream of highly expressed genes, topoI upstream. Context matters. academic.oup.com/nar/article/...

LTR transposons are really versatile mobile elements: www.biorxiv.org/content/10.1...

Ancient co-option of LTR retrotransposons as yeast centromeres

The evolutionary origins of the genetic point centromere in the brewer’s yeast Saccharomyces cerevisiae, a member of the order Saccharomycetales, are still unknown. Competing hypotheses suggest that t...

biorxiv.org

Psoralen's use in genomewide footprinting of torsional strain (TMP-seq) has been limited. It seems that beautiful data can be obtained with a good reference measurement. Now, we can start to study the twin domain model on a genome-wide scale. elifesciences.org/reviewed-pre...

A woman studies embryos for decades, struggles for funding and respect. She publishes under her husband’s name, until they divorce. A single mother, she moves across an ocean to continue her studies. It all sounds quite modern, until you learn that she also worried she’d be burned as a witch. 🧵 1/15

@tbadet.bsky.social and I have a preprint out on transposon silencing in fungi! Genome size evolution is fascinating and showcases the dynamic nature of transposon activation. What we understand less are the dynamics of transposon defense systems encoded by the genomes. doi.org/10.1101/2025...

First #bluetorial. 🎉🎉 We’re very happy to share our latest biorxiv #preprint, just in time before the holiday season. We explored how transposable elements (TEs) diversify eukaryotic proteomes and found a cool case in nematode F-box genes. #TEsky #evosky #Celegans Short 🧵 with highlights.

bioRxivpreprint@biorxivpreprint.bsky.social · 2y ago

Transposable elements drive regulatory and functional innovation of F-box genes https://www.biorxiv.org/content/10.1101/2024.12.17.628972v1

Cool, elegant paper. Inverted repeat transposon near EFR affects chromatin organization and gene expression to fine-tune immune responses. #MPMI #plantimmunity www.nature.com/articles/s41...

Transposon-triggered epigenetic chromatin dynamics modulate EFR-related pathogen response - Nature Structural & Molecular Biology

Here, the authors show that an inverted-repeat transposon located next to the pattern recognition receptor ELONGATION FACTOR-TU RECEPTOR (EFR)-encoding gene in Arabidopsis controls chromatin organizat...

nature.com

super proud - our new work about the invasions triggered by two troublesome TEs in Nat. Comm. www.nature.com/articles/s41...

Double trouble: two retrotransposons triggered a cascade of invasions in Drosophila species within the last 50 years - Nature Communications

Horizontal transfer of genetic material in eukaryotes has rarely been documented over short evolutionary timescales. Here, the authors show that two transposable elements, Shellder and Spoink, invaded...

nature.com

New Bergman Lab paper now online at GBE: "Horizontal transfer and recombination fuel Ty4 retrotransposon evolution in Saccharomyces"

Horizontal transfer and recombination fuel Ty4 retrotransposon evolution in Saccharomyces

Abstract. Horizontal transposon transfer (HTT) plays an important role in the evolution of eukaryotic genomes, however the detailed evolutionary history an

academic.oup.com

Chromosomal inversions mediated by tandem insertions of transposable elements https://www.biorxiv.org/content/10.1101/2025.01.09.631634v1