Alexander Stark retweeted
It was a special privilege to witness the Career Lecture of Prof Laszlo Tora at the 6thDanube Epigenetics Meeting and FEBS Advanced Lecture Course in Budapest this week.
For over 40 years, Laszlo has been one of the most accomplished and prolific Hungarian scientist abroad. His lab at the CNRS has led the world in the golden age the discovery and biochemical characterization of transcription coactivator complexes and general transcription factors. His lab discovered the TATA-box binding protein, and TFIID component TBP, the SAGA complex and other GCN5-containing complexes, multiple activation domains in the estrogen receptor, among others. In recent work they pioneered the model of co-translational folding and assembly of TFIID and other complexes, which solved the long-standing problem in the field of how insoluble, aggregation-prone proteins can assemble into soluble functional complexes.
A remarkable feature of his Career Lecture was that Laszlo paid much gratitude both forwards and backwards. Forward to the many accomplished trainees and young scientists who worked in his lab, and backward to the giants who trained him, including the late Pierre Chambon and István Financsek.
Congratulation on an inspiring career, Laszlo, and thank you for the many insights, both professional and human!
Shoutout the Ferenc Muller for the introduction!
@FEBSnews @LaszloTora @ferencmueller @bulutkarslioglu @MariekeOudelaar
Alexander Stark retweeted
Are weak TF motifs important? @ZeitlingerLab use deep learning to systematically map low-affinity pioneer binding sites in mESCs and show that they cooperate with strong motifs to open chromatin. Preview w/ @gracecbower: cell.com/cell-genomics/fullt… Paper: cell.com/cell-genomics/fullt…
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…
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…
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.🧵
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
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
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.
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…
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…
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
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 🧵.
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…
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/…
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/
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…
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…
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…
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!
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/





























