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Reposted by Alex Stark

Evgeny Kvon @evgenykvon.bsky.social · 25/08/2026

First synthetic mouse enhancers active in defined embryonic tissues! Great collaboration led by @alex-stark.bsky.social lab now at @natgenet.nature.com

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Reposted by Alex Stark

Shenzhi Chen @shenzhichen1999.bsky.social · 25/08/2026

Excited to share our paper in @natgenet.nature.com on the de novo design of tissue-specific mammalian enhancers that function in vivo in mouse embryos. 🧬🐭 www.nature.com/articles/s41...

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Reposted by Alex Stark

IMP @impvienna.bsky.social · 25/08/2026

The IMP lab of Alexander Stark used AI to design enhancers—DNA switches controlling gene activity—for specific mouse tissues: the first from-scratch design in a mammal. News: imp.ac.at/news/article/ai-learns-to-write-code-that-activates-genes-in-mammals Paper: nature.com/articles/s41588-026-02729-1

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Reposted by Alex Stark

Franzi Lorbeer @florbeer.bsky.social · 21/08/2026

0/ New preprint from the Stark and Grün labs! @reyna-rosales.bsky.social @dominicgrun.bsky.social @alex-stark.bsky.social We developed BARe-seq to ask what in the DNA controls transcriptional bursting - key findings for anyone working on transcription, gene regulation, or cis-regulatory elements 🧵

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Reposted by Alex Stark

bioRxivpreprint @biorxivpreprint.bsky.social · 20/08/2026

BARe-seq enables high-throughput dissection of cis-regulatory control of transcriptional bursting www.biorxiv.org/content/10.64898/20…

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Reposted by Alex Stark

Mikko Taipale @miketilapia.bsky.social · 30/06/2026

Our evil ORFeome paper is out! In collaboration with @alex-stark.bsky.social, we screened ~4,000 viral proteins and secreted effectors from bacteria and parasites, covering hundreds of diverse pathogens, for phenotypes in human cells.

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Reposted by Alex Stark

Biozentrum, University of Basel @biozentrum.unibas.ch · 24/06/2026

Last Discovery Seminar before the summer break: On Friday, July 3, Prof. Alexander Stark from the Research Institute of Molecular Pathology @impvienna.bsky.social will talk about “Decoding Transcription Regulation.” Everyone is welcome!

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Reposted by Alex Stark

Alex Stark @alex-stark.bsky.social · 24/12/2025

Our preprint "Predictive design of tissue-specific mammalian enhancers that function in vivo in the mouse embryo" is on bioRxiv: www.biorxiv.org/content/10.6... . Amazing collaboration by @shenzhichen1999.bsky.social, Vincent Loubiere (@impvienna.bsky.social,@viennabiocenter.bsky.social),... (1/2)

biorxiv.org

Predictive design of tissue-specific mammalian enhancers that function in vivo in the mouse embryo

Enhancers control tissue-specific gene expression across metazoans. Although deep learning has enabled enhancer prediction and design in mammalian cell lines and invertebrate systems, it remains uncle...

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Reposted by Alex Stark

Alex Stark @alex-stark.bsky.social · 29/12/2025

Join @stirlingchurchman.bsky.social, @moffittlab.bsky.social, @saramostafavi.bsky.social, me and all speakers for the 2026 CSHL meeting Systems Biology: Global Regulation of Gene Expression, March 11-14. Abstract deadline January 9! More infos and registration at meetings.cshl.edu/meetings.asp...

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Reposted by Alex Stark

Filip Nemcko @nemcko.bsky.social · 29/12/2025

Using Hcfc1 as a model, we show it functions as a molecular bridge: it connects CGI-bound TFs directly to TFIID. This recruitment overcomes a rate-limiting step unique to CGI promoters, enabling transcription initiation. 🧬🌉

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Reposted by Alex Stark

Filip Nemcko @nemcko.bsky.social · 29/12/2025

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. 🧬

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Alex Stark @alex-stark.bsky.social · 29/12/2025

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Reposted by Alex Stark

László Tora @tlaszlo.bsky.social · 24/12/2025

Read our new preprint where we uncover a hierarchy in human PIC assembly and establish a quantitative framework that connects factor exchange kinetics to the regulation of Pol II activity in living human cells. doi: doi.org/10.64898/202... By A. Oravecz and our collaborators @molinalab.bsky.social

doi.org

RNA polymerase II initiation factors show different dynamic behaviour upon induced transcription in live cells

Transcription by RNA polymerase II (Pol II) requires the ordered action of general transcription factors (GTFs) forming the pre-initiation complex (PIC). How these events unfold kinetically remains un...

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Reposted by Alex Stark

Evgeny Kvon @evgenykvon.bsky.social · 24/12/2025

Not that long ago, in vivo mouse enhancer design was a dream. Today, it's a reality! Using transfer deep learning to design de novo synthetic embryonic enhancers active in the heart, limb, and CNS. Great collab with @alex-stark.bsky.social lab! @ucibiosci.bsky.social @impvienna.bsky.social

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Alex Stark @alex-stark.bsky.social · 24/12/2025

biorxiv.org

Predictive design of tissue-specific mammalian enhancers that function in vivo in the mouse embryo

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Reposted by Alex Stark

Jacob Schreiber @jmschreiber91.bsky.social · 10/12/2025

After a huge amount of work w/ @alex-stark.bsky.social's group, a new version of our Ledidi preprint is now out! In an era of AI-designed proteins, the next leap will be controlling when, where, and how much of these proteins are expressed in living cells. www.biorxiv.org/content/10.1...

biorxiv.org

Programmatic design and editing of cis-regulatory elements

The development of modern genome editing and DNA synthesis has enabled researchers to edit DNA sequences with high precision but has left unsolved the problem of designing these edits. We introduce Le...

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Reposted by Alex Stark

Plaschka lab @plaschkalab.bsky.social · 21/11/2025

Messenger RNA is made in the nucleus before it is exported to the cytoplasm for translation. But how are only correctly made mRNAs chosen and remodeled in the nucleus for export? Our new paper investigates the nuclear events leading to human mRNA export. www.nature.com/articles/s41.... (1/4)

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Reposted by Alex Stark

Ulrich Hohmann @hohmannulrich.bsky.social · 19/11/2025

Lastly, I’m excited to join @imbmainz.bsky.social in 2026 to start my own lab. We'll explore new mechanisms in eukaryotic gene expression, leveraging ‘evolutionary play’ to uncover how regulation, repurposing, and hijacking shape RNA biology. tinyurl.com/y4x29ctt Thanks for reading! 20/20

Reposted by Alex Stark

Jacob Schreiber @jmschreiber91.bsky.social · 20/11/2025

My first @umasschan.bsky.social/@impvienna.bsky.social affiliated paper is up! tomtom-lite is a re-implementation of tomtom targeting the ML age of genomics. Fast annotations ("what is this motif?") and simple large-scale discovery of motifs. Check it out! academic.oup.com/bioinformati...

academic.oup.com

Tomtom-lite: accelerating Tomtom enables large-scale and real-time motif similarity scoring

AbstractSummary. Pairwise sequence similarity is a core operation in genomic analysis, yet most attention has been given to sequences made up of discrete c

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Reposted by Alex Stark

CeMM @cemm.oeaw.ac.at · 18/11/2025

🎉 Congrats to @aelewaut.bsky.social for winning the 2024 #DenisePBarlowAward! 🎖️ She carried out her PhD thesis in @obenaufa.bsky.social's lab (@impvienna.bsky.social), work published in @nature.com. 📄 Paper: rdcu.be/eQv1f ➡️ About the award: bit.ly/3iFbafP

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Reposted by Alex Stark

Mikko Taipale @miketilapia.bsky.social · 18/11/2025

Looks like the previous link is not working... here's a working link! www.biorxiv.org/content/10.1...

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Reposted by Alex Stark

Mikko Taipale @miketilapia.bsky.social · 18/11/2025

Link to preprint: www.biorxiv.org/content/2025...

biorxiv.org

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Reposted by Alex Stark

Mikko Taipale @miketilapia.bsky.social · 18/11/2025

This has been an amazing collaborative project that keeps on giving. We now have a new 3x larger eORFeome and we will dive deep into pathogen and host biology. If you are interested in scalable approaches to study effectors and their interactions with the host, get in touch! 8/8

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Reposted by Alex Stark

Mikko Taipale @miketilapia.bsky.social · 18/11/2025

Our new preprint is online! Viruses, bacteria and parasites use effector proteins to evade immunity and rewire host cell pathways. Together with @AlexanderStark8, we wondered if we could systematically map what these effectors, regardless of their origin, do in human cells. 1/8

biorxiv.org

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Alex Stark @alex-stark.bsky.social · 18/11/2025

Major new direction in the lab: hacking human cell biology with pathogen effectors (eORFs) - amazing collaboration with @miketilapia.bsky.social lab. Huge congrats to first authors Tomas & He & all co-authors! Check out the pre-print on @biorxivpreprint.bsky.social www.biorxiv.org/content/10.1...

biorxiv.org

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Reposted by Alex Stark

bioRxiv SysBio @biorxiv-sysbio.bsky.social · 18/11/2025

Systematic Discovery of Pathogen Effector Functions across Human Pathogens and Pathways www.biorxiv.org/content/10.1101/202…

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Reposted by Alex Stark

Alex Stark @alex-stark.bsky.social · 11/09/2025

Join this year's CSH Asia Systems Biology of Gene Regulation & Genome Editing meeting in beautiful Suzhou, China, Oct 20-24. Let's bring the international communities together! Abstract deadline Sept 19! Infos and registration at csh-asia.org?content/2767. Please repost!

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Alex Stark @alex-stark.bsky.social · 11/09/2025

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