Vienna, Austria
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- Followers 2,877
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Alexander Stark retweeted
This paper from the Stark lab introduces BARe-seq, extending MPRAs by preserving the distribution of transcriptional output across individual plasmids rather than aggregating, allowing them to decompose mean expression into burst size and burst frequency.
biorxiv.org/content/10.64898…
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Alexander Stark retweeted
Pierre Chambon was one of the driving architects of modern molecular biology, whose scientific vision transformed the understanding of gene regulation in eukaryotic cells. His passing in May 2026 represents the loss of an extraordinary scientist. doi.org/10.1038/s41588-026-0…
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Alexander Stark retweeted
It is clear that people are using AI to review papers and grants. Often as a tool, not as an off the bottle answer for review (though some do). One of the signs of this is the detail of the negative comments and the errors, often minor and irrelevant to the conclusions.🧵
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Alexander Stark retweeted
Excited to release AlphaGenome Atlas 🧬 We used AlphaGenome to predict the regulatory impact of all 9B possible SNVs in the human genome. We collaborated with amazing scientists to analyze and apply it, and developed a portal to browse the genome using this new lens 🔬
🌐 Portal: alphagenome.google/atlas
📖 Blog: goo.gle/4heuCvn
📄 Preprint: deepmind.google/blog/alphage…
🧵 1/6
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Alexander Stark retweeted
Excited to see PISA officially out! This was a very fruitful collaboration between my lab and @anshulkundaje, bringing together deep learning models and the biology of gene regulation in a visual way. Grateful to everyone who contributed! 🙏
NEW #Research published @NatureComms: Scientists in the @ZeitlingerLab developed PISA, a new #AI interpretation method that lets researchers see, at high resolution, what AI models learn from DNA sequences. Using that insight, the team discovered they could better control what the models learn next.
By separating the biology they wanted to study from bias introduced by the experiment, the researchers were able to train a more focused model and uncover patterns in DNA they didn’t see before.
That clearer view led to a surprising biological insight with implications for understanding gene regulation and, potentially, genetic disease: the way #DNA is wrapped around nucleosomes may help predict how it is organized in 3D inside the nucleus.
Hear Investigator @JuliaZeitlinger, Ph.D., explain how PISA could become a broadly useful tool for scientists to help bridge the gap between powerful AI models and the biological mechanisms researchers want to understand.
🔗bit.ly/4gwN0Oy
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Alexander Stark retweeted
Excited to attend the EMBL Transcription and Chromatin meeting #EMBLtranscript @EMBLEvents
Come to see my poster #287 if you are interested in genetic screening and high-throughput functional protein tagging.
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Alexander Stark retweeted
First synthetic mouse enhancers active in defined embryonic tissues! Great collaboration led by @stark_lab @AlexanderStark8 now at @NatureGenet
🚀 Thrilled to share that our work is now published in @NatureGenet on the de novo design of tissue-specific mammalian enhancers that function in vivo in mouse embryos.
nature.com/articles/s41588-0…
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Alexander Stark retweeted
🚀 Thrilled to share that our work is now published in @NatureGenet on the de novo design of tissue-specific mammalian enhancers that function in vivo in mouse embryos.
nature.com/articles/s41588-0…
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Alexander Stark retweeted
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-le…
Paper: nature.com/articles/s41588-0…
Made with AI
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Alexander Stark retweeted
New preprint from a wonderful collaboration with
@AlexanderStark8 led by Franzisake Lorbeer and
@ReynaERosales. We developed BARe-seq to ask what in the DNA controls transcriptional bursting - key findings for anyone working on transcription or cis-regulatory elements. See 🧵.
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Alexander Stark retweeted
In our newest study from @HippenmeyerLab @ISTAustria we quantitatively assessed emergence and development of cortical projection neuron lineages in self-organizing organoid system side-by-side in vivo cerebral cortex development.
nature.com/articles/s41586-0…
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Alexander Stark retweeted
An updated version of this blog post is now out with higher-resolution figures!
Turns out that trying to simplify things only works for S2F models, not for images in markdown.
New Genomics x AI blog post!
@jmschreiber91 presents cherimoya an efficient seq2fun model for local regulatory function prediction!
Great contribution. Love the thoroughness of hyperparam exploration and efficiency gains. Worth a read and studying repo!
genomicsxai.github.io/blogs/…
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Alexander Stark retweeted
If u have deep expertise in genomic data processing with agentic platforms, DNALMs, S2F models & interested in joining us please reach out. I'll be hiring 1-2 postdocs/staff scientists for this project. Please RT 7/
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Alexander Stark retweeted
Excited to share that our work on identifying key driver genes in breast cancer is out @Nature! Incredibly grateful to my postdoc mentors @DanielSchramek and Jeff Wrana and to all of the collaborators and funding sources that made this possible nature.com/articles/s41586-0…
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Alexander Stark retweeted
I am thrilled to share our paper out in @CellCellPress: "Systematic Discovery of Pathogen Effector Functions across Human Pathogens and Pathways." (1/4)
cell.com/cell/fulltext/S0092…
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Alexander Stark retweeted
Pathogens have spent millions of years learning how to hijack human cells. Now, researchers from the Stark lab at the IMP and the Taipale lab at the Donnelly Centre, University of Toronto, have built a platform to systematically discover how they do it: cell.com/cell/fulltext/S0092…
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Alexander Stark retweeted
tangermeme v1.4.0 is out!
This release focuses on supporting agentic usage of genomic sequence-to-function models, with installable skills w/ progressive disclosure to guide them to the right functions.
All you need to do is include `using tangermeme` in your prompts!
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Alexander Stark retweeted
Just want to give a shout-out to David Kelley @drklly who I think often does not get the credit he deserves (outside our core community).
I want to highlight why I think he is such a fantastic scientist and leader in regulatory genomics. 1/
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Alexander Stark retweeted
Not to mention the ridiculous move to open an "ERC Plus" scheme rather than invest more money into the already well functioning programs to fund more research.
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Alexander Stark retweeted
This gives incredible power to the panelists. They will literally determine if a lab survives or not with the 3 year ban. I don't think a couple of people should have this power. @ERC_Research
I don’t know if you saw the MASSIVE news announced by @ERC_Research today: from now on,if you get a B at step 1 you are eligible to apply at N+3(!!!) years. Say you got a B in STG2026 step 1, you thought you could apply in STG2028, but no: only in STG2029! erc.europa.eu/news-events/ne…
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