Francesca Finotello 🖥️🧬

🖥️🧬 New preprint with expanded study is now online ✨
www.biorxiv.org/content/10.1...

🧬🖥️🧪 Interested in single-cell-informed cell-type #deconvolution? Have a look at our enhanced benchmarking study and #omnideconv ecosystem!

www.biorxiv.org/content/10.1...

Hello Jeremy! Thanks for your feedback. It's an interesting angle indeed, but not yet supported by NovumRNA. It works on the single-sample level to assemble the isoforms and also account for single-point variants.

👏 Congratulations to Markus Ausserhofer for leading this effort! I am extremely grateful for the amazing support we had through this journey from all our collaborators, supporting institutions, and funding agencies! @uniinnsbruck.bsky.social @fwf-at.bsky.social @erc.europa.eu @oenb.at @ec.europa.eu

These results highlight not only the value of NovumRNA for the identification of novel #immunotherapy targets, but also for the selection of drugs that can synergize with immunotherapy

👉 You can read the full paper on iScience: doi.org/10.1016/j.is...

We extensively benchmarked NovumRNA on public and newly generated datasets, confirming its accuracy

Analysis of hard-to-treat #cancers demonstrated that NovumRNA can be used to identify candidate tumor-antigen targets also in tumors with low mutational burden and to detect therapy-induced ncTSAs

Non-canonical tumor-specific antigens (ncTSAs) represent an untapped pool of targets for cancer immunotherapy, but their reliable prediction is challenging. With NovumRNA, we introduce a fully automated #Nextflow pipeline that predicts different classes of ncTSAs directly from patients’ RNA-seq data

🖥️🧬🧪 Publication Alert!

I’m very excited to share our latest paper: “NovumRNA: Accurate prediction of non-canonical #tumor #antigens from RNA #sequencing data”

🎉 scverse conference 2025 Registration & Call for Abstracts NOW OPEN! 🎉
We're excited to announce that registration and the call for abstracts are officially open for the scverse Conference 2025!
Details in thread!
🧵 1/3

Amazing conference! Don't miss this opportunity! ✨

🖥️🧬 The University of Innsbruck is offering PostDoc fellowships for women: www.uibk.ac.at/en/research/...

Do you have a strong plan for a bioinformatics project (e.g. spatial/single-cell/multiomic data analysis, AI for oncology, immunogenomics)? I would be happy to support you with your application!

🖥️🧬 The University of Innsbruck is offering PostDoc fellowships for women: www.uibk.ac.at/en/research/...

Do you have a strong plan for a bioinformatics project (e.g. spatial/single-cell/multiomic data analysis, AI for oncology, immunogenomics)? I would be happy to support you with your application!

Interested in unraveling specificity in epitope recognition by TCRs and KIRs in the context of graft-versus-host diseases. We have an open post-doc position in the group. Do not hesitate to share the word.

🧬🖥️🧪 Interested in single-cell-informed cell-type #deconvolution? Have a look at our enhanced benchmarking study and #omnideconv ecosystem!

www.biorxiv.org/content/10.1...

Editorial - A stronger Europe starts with science As leaders from industry, policy and science gathered in Brussels for a lively exchange this spring, o

“Europe’s success depends on treating #science and #research as tools for competitiveness and on recognising them as foundational to Europe’s long-term strategy” erc.europa.eu/news-events/... @erc.europa.eu

📢 Announcing the MOPITAS Autumn School on Spatial Transcriptomics Data Analysis – taking place November 12–14, in Munich. Don't miss this excellent opportunity to deepen your expertise in data science and multi-OMICS analysis - especially as a PhD student in the data science community.

Join us for a series of presentations from leading data science experts, including @francescafinotello.bsky.social, @dominicgrun.bsky.social, Johanna Klughammer, Malte Lücken, @fabiantheis.bsky.social and @jwrth.genomic.social.ap.brid.gy.

Thanks @itisalist.bsky.social for your great talk and for the insightful discussions. I am excited we are making our collaboration even stronger. And you should definitely come back to enjoy a sunnier scenery :)

We are delighted to welcome Prof. @itisalist.bsky.social to the University of Innsbruck.
Looking forward to inspiring discussions and promising ideas for future collaborations!

Today, Prof. Markus List @itisalist.bsky.social will be giving a talk at Universität Innsbruck: "Data leakage is a widespread issue in machine learning in the biomedical domain: How to spot it, avoid it, and fix it"
🎤 Hosted by Prof. Francesca Finotello @francescafinotello.bsky.social See you there!

Colorful liquid flowing from one bottle into another, as an illustration for (data) leakage.

Traveling to Innsbruck by invitation of @francescafinotello.bsky.social to talk about data leakage, a widespread issue in biomedical machine learning applications. I'll talk about challenges in protein-protein interaction (doi.org/10.1093/bib/...) and drug response prediction (upcoming preprint!).

🧬 🖥️ Thrilled to share our recent work on TME heterogeneity, published on iScience:

t.co/whajXd0SjU

A joint effort with Federica Eduati's lab
Follow the thread for more🧵👇

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Benchmarking second-generation methods for cell-type deconvolution of transcriptomic data https://www.biorxiv.org/content/10.1101/2024.06.10.598226v1 🧬🖥️🧪
omnideconv #Rstats pkg https://github.com/omnideconv/deconvBench
Nextflow pipeline https://github.com/omnideconv/deconvBench

🧬 🖥️ If you are looking for more tools, resources, and insights about next-generation #deconvolution, have a look at our #omnideconv website: omnideconv.org

Great idea! I am an assistant professor in #bioinformatics and group leader at the University of Innsbruck, Austria. I develop and apply computational tools to advance precision medicine and immuno-oncology 🧬🖥️🧪👩‍🔬

Zero-shot evaluation reveals limitations of single-cell foundation models - Genome Biology Foundation models such as scGPT and Geneformer have not been rigorously evaluated in a setting where they are used without any further training (i.e., zero-shot). Understanding the performance of mode...

genomebiology.biomedcentral.com/articles/10....

Quite an indictment of some of the current single cell "virtual cell" foundation models. Even for the relatively mundane applications, cell labeling, batch correction etc, they are poor compared to much simpler & cheaper methods.

12. Like art, music, philosophy, and literature, science is literally part of humanity's heritage.

My colleagues and I have had the amazing opportunity to be part of something vastly larger than ourselves, with meaning that transcends any state, regime, or generation.

They can't take that away.

1. For the past thirty years I've had the best job in the world.


I've had the opportunity to follow my curiosity; explore the workings of nature and society; mentor students and junior colleagues in the same process; and teach generations of students about it all.

Wish that you spent your Friday doing something besides checking if TikTok was banned or not?

Try out @skylight.social — a video app built upon the same open network as Bluesky. You can login with your Bluesky account, and all of your followers seamlessly come with you.

Biggest commitment to a 3 second joke I've ever seen