Anna Poetsch

I am looking to get my hands on some #Illumina 5-base methylation data - does anyone have a bam file that I could use for some testing? Please RT for reach!

Thank you for having me, it was really a very informative, stimulating and motivating few days!

It was a pleasure to talk Genome Stability for a few days with the DFG - FOR5504 for. It is really exciting to see the community in and around Cologne looking for genome stability in whole organisms and the context of the sequence. I am excited about what else is going to come.

Me: I got a new type of compliment from an audience member: "Your talk was so Gen Z"
My lab: This was not a compliment...
Me: 🥲 (but..., but..., I still think it was meant to be one...)

(S+) Künstliche Intelligenz: KI-designtes Virus tötet Kolibakterien US-Forscher haben mithilfe von künstlicher Intelligenz Viren hergestellt und ihnen bestimmte Eigenschaften gegeben, weltweit sind sie damit wohl die Ersten. Die Möglichkeit KI-generierten Lebens schei...

I am happy to share some thoughts on using AI to generate viruses (in German). www.spiegel.de/wissenschaft...

Die ersten KI-generierten Viren als Hoffnung im Kampf gegen resistente Bakterien Forschende aus Stanford haben erstmals Viren entwickelt, die von einer KI entworfen wurden. Einige dieser KI-Viren konnten antibiotikaresistente Bakterien infizieren und abtöten - ein möglicher Durchb...

The ARD Wissenschaftsredaktion talked to me about AI generated viruses. Interested? Here you can listen to it (in German). www.swr.de/leben/gesund...

There is a new Master of Physics of Life in the house. Congratulations, Adnan! Well done! It was really a superb Defense!
@poldresden.bsky.social

Die ersten KI-generierten Viren als Hoffnung im Kampf gegen resistente Bakterien Forschende aus Stanford haben erstmals Viren entwickelt, die von einer KI entworfen wurden. Einige dieser KI-Viren konnten antibiotikaresistente Bakterien infizieren und abtöten - ein möglicher Durchb...

The ARD Wissenschaftsredaktion talked to me about AI generated viruses. Interested? Here you can listen to it (in German). www.swr.de/leben/gesund...

(S+) Künstliche Intelligenz: KI-designtes Virus tötet Kolibakterien US-Forscher haben mithilfe von künstlicher Intelligenz Viren hergestellt und ihnen bestimmte Eigenschaften gegeben, weltweit sind sie damit wohl die Ersten. Die Möglichkeit KI-generierten Lebens schei...

I am happy to share some thoughts on using AI to generate viruses (in German). www.spiegel.de/wissenschaft...

Dear CRC TRR 341, thanks for having me. It was fascinating to learn more about the genomes of plants in their ecological context!

I have already been part of your movement without knowing :-)

PhD Student in Mutational Processes Driving Somatic Evolution

Would you like to do some unique experiments in cancer genomics and mutagenesis, in beautiful Munich? Well then apply for this PhD position: jobs.dkfz.de/en/jobs/1679...

You'll learn a lot and it'll be fun and interesting!
#DKTK @dkfz.bsky.social @lmumuenchen.bsky.social

Exciting to see the @grunewaldlab.bsky.social finding new target candidates against metastases of Ewing sarcoma.
It makes one wonder how general this pathway disruption might be and whether it may work with other sarcomas or metastatic cancers in general… 🤔

"i think every participant will treasure the experience forever ❤️"
Yes ☺️

We have a postdoc position for a project that is very analogous. The deadline has passed, but feel free to still apply, if you are interested. 🧵 6/6

Such an interdisciplinary interaction also makes ways back to the clinic short, so we hope that these findings can lead to predictive biomarkers for treatment response. Or does modulating NFkB signaling maybe even have potential as a co-treatment strategy 🤔? 🧵 5/6

A big shoutout to the Stange Lab at UK Dresden (www.uniklinikum-dresden.de/de/das-klini...), who are building up a very valuable resource with models for gastrointestinal tumours, on which studies like this are based. 🧵 4/6

We find changes in the clonal dynamics, but the most striking treatment-related change is the downregulation of inflammatory NFkB signaling in a subpopulation of cells, independent of the genetics of the tumor. This transcriptional memory persists in the organoids without an immune system. 🧵 3/6

In this paper we used data from patient derived organoids from adenomas of the gastroesophageal junction treated with neoadjuvant FLOT chemotherapy in the patient, or of the organoids from the untreated tumour. We reconstructed the clonal dynamics and integrated the single cell transcriptomes.🧵 2/6

Tumor clone dynamics in gastro-esophageal cancer organoids reveal a non-genetic memory of neoadjuvant chemotherapy via downregulation of NFκB signaling Adenocarcinomas of the gastroesophageal junction exhibit genetic and non-genetic heterogeneity that impact clinical outcomes, though the underlying mechanisms behind drug resistance remain poorly unde...

We are happy to present a new paper on gastric tumour evolution in response to peri-operative chemotherapy. www.biorxiv.org/content/10.1... 🧵 1/6

We find that both the 🧬 sequence and the epigenome contribute essential information and the models perform best, when trained on both. But who contributes what? To answer this, interpretable machine learning helps and it is in the paper 😉 🧵 4/4

DNA language model GROVER learns sequence context in the human genome - Nature Machine Intelligence Genomes can be modelled with language approaches by treating nucleotide bases A, C, G and T like text, but there is no natural concept of what the words would be and whether there is even a ‘language’...

For this we use our 🧬-language model, GROVER www.nature.com/articles/s42..., and classical machine learning. 🧵 3/4

In this paper we disentangle what determines the genomic location of 🧬-double strand breaks looking at the 🧬 sequence and the epigenome 🧵 2/4

Using the DNA language model, GROVER, to parse sequence and epigenetic effects on genome stability Genome stability is shaped by DNA sequence and epigenomic context, but their relative contributions to double-strand break (DSB) sensitivity remain unclear. We show that the DNA language model, GROVER...

We are happy to present a new paper on the sequence dependence of 🧬-double strand breaks. www.biorxiv.org/content/10.1...
🧵 1/4

Usually aggressive food preparation (vegetarian)

I do. Only the tips, but recurrently so.
Also 🐙, if you can call the tips of the arms fingers….

Last year I was writing a grant in an outdoor swimming pool to escape my overheated office.
It was super productive!
🏊‍♂️ ✍️ 🏊‍♂️ ✍️ 🏊‍♂️

Hi Craig, these are great news, congratulations! By the way, I am DKTK too, in case you want to write a grant together ;-)

The Company of Biologists 100 logo to the left and QR code to the right. Portrait of Helena Jambor to the left, text to the right 100 extraordinary biologists Helena Jambor Helena Jambor has written many 'How to' posts on the Node, presented a FocalPlane features... webinar and authored Perspective articles for Journal of Cell Science. Helena is an Associate Professor at the University of Applied Sciences of the Grisons, Switzerland, and is an advocate for accessibility and interpretability of image data. #100biologists #biologists100

This week, we are highlighting Helena Jambor, a prolific contributor to our community sites @the-node.bsky.social and
@focalplane.bsky.social, as an extraordinary biologist. #100biologists

@helenajambor.bsky.social

🚨 #JobAlert. please share: The DRESDEN-concept Genome Center (DcGC) 🧬 @dcgenomecenter.bsky.social is looking for the new Head of Facility!

🗓️ Deadline for applications: August 11

More information here ➡️ tud.link/fz5hr8

@tudresden.bsky.social @mpi-cbg.de