Judith Kribelbauer

@jk-swietek.bsky.social

Gabilan Assistant Professor of Molecular and Cellular Biosciences & Quantitative and Computational Biology @ USC Prior @EPFL & @Columbia University #GeneRegulation #NonCodingMechanisms #TranscriptionFactors

Obviously a strong supporter of this type of tool, but troubled by the literature review. No reference to @chribue.bsky.social work on combinatorial enhancers, and our EXTRA-seq -> kilobase-scale E-P landscapes in a native locus (no minP). Same principle, just ONT.

Jay Shendure@jshendure.bsky.social · 6d ago

New preprint from Shendure Lab on Locus-Scale aka Long-@$$ MPRAs led by the amazing Abby McGee & @carinabiar.bsky.social Most MPRAs test ~300 bp fragments next to a promoter. But real enhancers are bigger, act combinatorially and from a distance. 1/n www.biorxiv.org/content/10.6...

Recommend read! Struggling to implement code/bring your thoughts on paper is what builds topic-level expertise. Great tool for everyone already on the other side of the learning journey, but what about trainees? Would I have wanted it for myself when I started out? Not entirely sure.

Sasha Gusev@sashagusevposts.bsky.social · 2mo ago

I wrote about AI in academia. "PhD-level thinking", LLM bias, grunt work, alignment, AGI, data center water use, AI politics -- something for everyone.

It's some AI scientists/investor hype imo. The model is as good as the data we feed it. We create experimental benchmarking data and let's just say the accuracy for predicting non-coding variant effects are not that great, even when cellular context remains unchanged, but no one wants a buzzkill...

Jason Moore@moorejh.bsky.social · 4mo ago

Is it AI that needs the dose of skepticism or the pervasive reductionism in genetics & genomics? stevensalzberg.substack.com/p/ai-is-star... #genetic #genomics #ai

🧵 CTCF is essential for embryonic development, but why has remained unclear. By combining gastruloids with a temporal degron system, we uncovered a surprising dual function — and it changes how we think about CTCF's role in development. 1/8 www.biorxiv.org/content/10.6...

A dual role for CTCF in development

CTCF is an essential DNA binding protein whose absence leads to embryonic lethality. CTCF is primarily known for its role in 3D genome organization where its N-terminal domain interacts with cohesin to anchor chromatin loops. How CTCF facilitates proper embryonic development remains unclear, necessitating temporal control to resolve its stage-specific functions. By combining gastruloids, an in vitro model of embryonic development, with a degron system to rapidly deplete CTCF at defined timepoints, we show that early CTCF depletion impairs early gastruloid morphogenesis. Surprisingly, ATAC-seq and time-resolved RNA-seq revealed that differentiation was unaffected. CTCF binding is strongly enriched at promoters of downregulated genes. Re-expression of a CTCF variant with an N-terminal truncation, incapable of looping, was sufficient to rescue the expression of CTCF-promoter bound genes and the defects in morphogenesis. However, extended culture (up to 168 hours) of gastruloids reconstituted with N-terminal truncated CTCF led to their collapse. Our work shows that CTCF has a dual function in early mammalian development: at early stages CTCF regulates developmentally important genes through promoter binding, while at later stages its looping function is required for correct development. ### Competing Interest Statement The authors have declared no competing interest. European Research Council, https://ror.org/0472cxd90, 637587, 865459 Dutch Research Council, https://ror.org/04jsz6e67, 016.161.316, VI.C.222.049 Dutch Cancer Society, https://ror.org/0368jnd28, N/A

biorxiv.org

Every grant I applied for had an unprecedented number of applications this year, while simultaneously there is less overall funding. Very discouraging when putting in the effort no longer matters and blasting the system with AI written grants becomes the winning strategy.

Martin Bulla@martinbulla.bsky.social · 6mo ago

Is #AI turning grant evaluation into a lottery? 🎲 The 2025 generative AI improvement coincides with ~20% of proposals scoring >95% in EU #MSCA call. We’ve reached "excellence saturation." Time to rethink funding? 👉 doi.org/10.31222/osf... w/ @birder158.bsky.social #MetaScience #AcademicSky

Computer science needs more biologists. They are used to: - study systems that are mindbogglingly complex and complicated, - use reductionism to study and describe such systems, using famously clumsy and fiddly tools to collect noisy and incomplete data, (1/2)

Agreed! Great we have this model & kudos to the developers (especially for user-friendly implementation😀), but let's not abuse it as an excuse to stop trying to understand the actual mechanisms! Yes, gene regulation is complicated, but still rooted in the biophysics of molecular interactions...

Philip Ball@philipcball.bsky.social · 6mo ago

I had intended to post something about this new Google DeepMind paper that appeared yesterday in Nature, but the press coverage has added to what there is to say. So this is a long 🧵 www.nature.com/articles/s41...

Surprised (but also not that surprised) that the AlphaGenome paper didn't officially cite any of the primary data used for training their model (see Fig. 1, thousands of datasets made with tremendous time and effort over >15yrs). What's up with that @nature.com ? www.nature.com/articles/s41...

Advancing regulatory variant effect prediction with AlphaGenome - Nature

AlphaGenome, a deep learning model that inputs 1-Mb DNA sequence to predict functional genomic tracks at single-base resolution across diverse modalities, outperforms existing models in variant effect...

nature.com

Great collaboration! 📠+🧬 Experiments and ML go hand-in-hand. Hopefully more to come in the future!

Luca Pinello@lucapinello.bsky.social · 7mo ago

1/ Thrilled to share our DNA-Diffusion paper, co-led by Lucas Ferreira and @ssenan.bsky.social is now out in @NatureGenet! New experimental results: STARR-Seq validation across 3 cell types (episomal) and EXTRA-Seq for endogenous activation of AXIN2, a leukemia protective gene! x.com/lucapinello/...

"Our findings argue against a strict reg. role for TAD boundaries in controlling gene expression [...] TADs appear to serve primarily to organize chrom. topology at a global scale"- taking it as support from the '3Ders' for my love of TFs as prime regulatory suspects😉 www.biorxiv.org/content/10.6...

TAD boundary architecture and gene activity are uncoupled

Topologically associating domains (TADs) are prominent features of genome organization. A proposed function of TADs is to contribute to gene regulation by promoting chromatin interactions within a TAD...

biorxiv.org