Sebastian Falk

@sebastianfalk.bsky.social

🏳️‍🌈 Assoc. Prof @Max Perutz Labs Vienna, Biochemist & Structural Biologist, #RNA & #protein, Tennis addict, 🐈❤️,all time skeptic 🤨

I’m very happy to be part of our FWF “Emerging Fields” consortium! Together with @gekaragoz.bsky.social, @sebastianfalk.bsky.social and CCRI/CeMM/VetMedUni colleagues Eleni Tomazou, @dseruggia.bsky.social and @floriangrebien.bsky.social, we will study the ribosome code in pediatric cancers.

Max Perutz Labs Vienna@maxperutzlabs.ac.at · 6mo ago

A strong Perutz presence in a new @fwf-at.bsky.social consortium: @elifkaragoz.bsky.social will coordinate the Emerging Fields project 'Translating the Ribosome Code of Pediatric Cancers' 🤝 The team includes @sebastianfalk.bsky.social and @marco.heinlab.org ➡️ tinyurl.com/3d6z3ry5

GERMAN PRESIDENT STEINMEIER: “.. the United States has broken with the values that it helped to establish .. “.. we have now moved beyond the stage where we can lament the lack of respect for international law or the erosion of the international order; we are far beyond that, I believe.”

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.

bioRxivpreprint@biorxivpreprint.bsky.social · 9mo ago

RNA decay via the nuclear exosome is essential for piwi-mediated transposon silencing https://www.biorxiv.org/content/10.64898/2025.12.16.694471v1

📢 New preprint: Experiment-guided AlphaFold3 resolves accurate protein ensembles. doi.org/10.1101/2025... AlphaFold3 is incredible, but has crucial limitations: it typically collapses to a single conformation, ignoring the inherent dynamics of proteins. And it can be wrong. Here's a solution. 🧵👇

Structures from AlphaFold3 - while often impressively good - tend to fail representing the dynamic ensembles accurately. And often parts of the structure are not correct.
Adding experimental data, directly in AlphaFold's diffusion step, provides physically realistic protein ensembles. This image shows two cases where AlphaFold3-only structures were largely improved by guiding with experimental data.

When transposons jump, genomes diverge - even in cultured cells. I am happy to share our new preprint: a chromosome-scale genome assembly for Drosophila OSC cells, one of the key model systems in the piRNA field, especially for nuclear piRNA biology. 🧬🧵 (1/12)

Graphical abstract: The Drosophila OSC Genome as a resource for transposon and piRNA biology. The figure illustrates the workflow and key findings. Left: De novo genome assembly using Oxford Nanopore Technologies (ONT) long reads and Hi-C data generates a phased assembly distinguishing unique (blue) and repetitive (orange) sequences. Dot plot comparison between OSC-r1.01 and dm6 reference genomes shows overall synteny with extensive structural variation. Middle: A freely accessible UCSC genome browser session displays multi-omics data tracks including gene models, transposon insertions, chromatin accessibility, transcription, small RNAs, and histone modifications. Right: New insights into flamenco piRNA cluster biology reveal >730 kb transcribed from a single promoter without major splicing. Tethering assays demonstrate long-range silencing effects across the locus, and genome browser tracks show coordinated regulation of piRNA production, transcription, and chromatin state. This resource enables comprehensive studies of transposon regulation and piRNA pathway function in a widely-used Drosophila cell line.