Jakob Schnabl-Baumgartner

Congratulations! Exciting times ahead 🧠🪱

I'm thrilled to announce that I'll be starting my lab as a SNSF starting grant professor at the Center for Integrative Genomics in Lausanne! I'm looking for PhD students who are fascinated about the neuronal basis of behaviour across species @fbm-unil.bsky.social

We’re excited to share our latest preprint on Fractal: our approach towards FAIR bioimage analysis at scale with OME-Zarr-native workflows.

Fractal defines interoperable tasks on OME-Zarr and provides a platform for TB-scale image analysis.

(1 / 10🧵)

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

A consortium of group leaders from IMP, IMBA (Vienna BioCenter) and ISTA has been awarded an FWF Emerging Fields grant to study how germ cells safeguard and pass on genetic information across generations.

MycoMobilome: a community-focused non-redundant database of transposable element consensus sequences for the fungal kingdom Abstract. Transposable elements (TEs) are found in nearly all eukaryotic genomes. Despite significant advances in the sequencing of genomes, TE resources r

Need to annotate transposons in fungal genomes? 🧬
Good news #MycoMobilome is now live! Check it out here: doi.org/10.1093/narg...
Access the sequences through our Zenodo community (you can also contribute seqs with credit), and synchronisation with @dfam.bsky.social!

w/ @danielcroll.bsky.social

With Eugene Koonin, we propose a concept of “the selfish ribosome”, under which evolution of life is viewed as a ribosomal takeover, where the ribosome evolved to consume most of the cell’s resources, while other cellular componentry ensures the propagation of the ribosome. arxiv.org/abs/2602.23268

Our Lab is searching a postdoc for an exciting ERC-funded project that will start this summer. Apply if you’re passionate about multi-omics, cutting-edge computational approaches, and exploring biological questions across the animal 🪼 🪱 🐞 🦎 🦋 🕷️ tree of life www.biozentrum.unibas.ch/open-positio...

LINE-L1, HIV, Ty3 retrotransposons in insects.
several of these genomes are > 40% adenosine!

What is the molecular origin & evolutionary pressure resulting in A-rich genomes of retrotransposons & some retroviruses?

it must be so hardwired that hosts exploit this bias for genome defense

any ideas?

The political effects of X’s feed algorithm - Nature Among users initially on a chronological feed, 7 weeks of exposure to X’s algorithmic feed in 2023 shifted political attitudes and account-following behaviour in a more conservative direction compared...

Brainwashing, 2026 edition. This paper shows how X's algorithmic feed shifts people's views rightwards. It's a sophisticated, highly effective form of reorientation. And it is utterly chilling.
If you're still on that platform, unhook yourself now.
www.nature.com/articles/s41...

The human BAF chromatin remodeler processes nucleosomes bound by pioneer transcription factors OCT4–SOX2 Weiss et al. structurally and functionally characterize the interplay between the human BAF chromatin remodeler and nucleosome-bound pioneer transcription factors, uncovering a highly dynamic remodeling process in which nucleosome-bound transcription factors bias the direction of BAF remodeling to regulate genome access.

The human BAF chromatin remodeler processes nucleosomes bound by pioneer transcription factors OCT4–SOX2

The spring call for the ELBE Postdoctoral Fellows Program is open now: www.csbdresden.de/join-us/as-a.... Join the @csbdresden.bsky.social for a fully funded fellowship. @mpi-cbg.de @mpipks.bsky.social

Started this project years ago, but now everything is deposited on @addgene.bsky.social and a short @protocolsio.bsky.social is online. Try it out to make your own (cheap) homemade nuclease/Benzonase!

dx.doi.org/10.17504/protocols.io.261ged7xov47/v2

Thank you @jcoker10.bsky.social and Michael Lim!

How does the piRNA pathway solve the self vs. non-self problem? 🧬

Since piRNAs come from single-stranded RNA, how does the cell choose the right ones? For years, "piRNA clusters" were seen as THE privileged source. But are they really special and earmarked for biogenesis? (1/19)

A small polymerase ribozyme that can synthesize itself and its complementary strand The emergence of a chemical system capable of self-replication and evolution is a critical event in the origin of life. RNA polymerase ribozymes can replicate RNA, but their large size and structural ...

Ooooh. Cool new paper on origins of life. A simple 45-nucleotide RNA molecule that can perfectly copy itself.

www.science.org/doi/10.1126/...

🚀 We’re hiring! The Structural Biology Platform is seeking a Project Leader to advance cryo-electron tomography and expand capabilities at the FMI. Join a vibrant research community at the interface of structural biology, cell biology & disease mechanisms. Apply at: www.fmi.ch/education-ca...

Ulrich’s research will help advance our understanding of RNA biology & gene regulation, as well as how these mechanisms might be altered during viral infections & other diseases.
@hohmannulrich.bsky.social comes from the @impvienna.bsky.social / @imbavienna.bsky.social

www.imb.de/about-imb/ne...

Fun fuels collaboration Coordination and collaboration between biological systems is shaped over time by environmental pressures. Collaborations between scientists also evolve and grow in directions that would have been hard to predict from their outset. Sara Miller spoke with Felicia Basilicata and Claudia Keller Valsecchi about their long-term collaboration. The two started working together as postdocs and started their independent groups in Mainz, Germany and are now navigating continued collaboration after relocating to institutions in different cities.

Fun fuels collaboration

Really excited to join IMB for this new scientific endeavour!

Episode 0 of new Florian Krammer podcast viroLOGICAL is online: “This first episode is a little longer and gives a general overview of viruses and viral diseases.“
virological.podigee.io

Would anyone out there be able to share some Mus Spretus DNA with us? 🐀🧬 Any tissue of origin, for PCR amplification of selected genomic regions. Many thanks in advance!

🍄Transposon traffic in the mycocosmos🍄
Fascinating work reveals extensive horizontal TE transfer across fungi (@jromeijn.bsky.social, Iñigo Bañales & @mfseidl.bsky.social; doi.org/10.1016/j.cu...). I wrote a Dispatch to prime non-specialists,check it out here: doi.org/10.1016/j.cu....
#TEworldwide

GitHub - TobyBaril/EarlGrey: Earl Grey: A fully automated TE curation and annotation pipeline Earl Grey: A fully automated TE curation and annotation pipeline - TobyBaril/EarlGrey

☕Earl Grey v7.0.0 brewed fresh☕

Nested TEs finally get the treatment they deserve: iterative detection of deep nesting, cleaner GFF annotations, and coverage stats that don’t double-count genomic space + a RepeatCraft edge-case fix.

Happy new year to the TE folks! 🧬

github.com/TobyBaril/Ea...

Characterization of RNA interference in the cnidarian Nematostella vectensis reveals partial target silencing but lack of small RNA amplification RNA interference is an ancestral antiviral mechanism that degrades viral RNA through siRNAs, but its role in cnidarians has been unclear. This study shows that Nematostella vectensis likely possesses ...

1/3 🚨New paper from our lab!🔥
Most textbooks will tell you that invertebrates employ #RNAi as antiviral mechanism. Yet, do 🪸🪼 actually do it? Well, the answer is complicated. We show that in #Nematostella dsRNA induces RNAi 🧵
journals.plos.org/plosbiology/...

The transcription of a single olfactory receptor per neuron is enforced by epigenetic silencing of their enhancers The ability to discriminate thousands of odors in our environment requires each olfactory neuron to express a single olfactory receptor from hundreds of available genes. The biochemical mechanism enfo...

This went under the radar but answers a fundamental question in Epigenetics...

From many hundreds of olfactory receptor genes, each neuron selects expression of only single one (near-randomly). How?

Outstanding work from Mathieu Boulard and colleagues

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

Modern biology research is biased towards investigating genes that are widely conserved and present in humans. What about genes that ARE widely conserved but NOT present in humans? Can genes missing from humans tell us something about what makes our biology different from that of other animals? 1/8

Do transcriptional activators work on any promoter? Our data says no. 🙅‍♂️
Despite driving ~2/3 of mammalian genes, CpG island (CGI) promoters have remained a puzzle. We identified >50 activators that are exclusively compatible with this promoter class. 🧬

Activator-promoter compatibility in mammals: a CpG-Island-specific co-activator directly bridges transcription factors to TFIID Transcription from CpG island (CGI) promoters controls the expression of two-thirds of mammalian genes, yet despite their prevalence, it remains unknown whether CGI-specific co-activators with intrins...

Activator-promoter compatibility in mammals - Hcfc1 is a key and intrinsically CGI-promoter-specific co-activator that cannot activate non-CGI promoters. Lead by @nemcko.bsky.social & Kevin Sabath in collab. with @plaschkalab.bsky.social @impvienna.bsky.social www.biorxiv.org/content/10.6... (1/2)

Intrigued by a long-standing conundrum in small RNA biology—how nuclear Argonaute proteins silence transposons when they *need* target transcription for their own recruitment—we studied the piRNA pathway.

And found a hidden RNA-decay axis from Piwi to the RNA exosome.

📢 Please help spread the word: We’re hiring a Head of Student & Postdoc Affairs to coordinate our international PhD program, provide guidance & career counseling, lead training programs, collaborate on EDI initiatives, and manage alumni relations. Apply at www.fmi.ch/education-ca...