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Reposted by Francesca Finotello 🖥️🧬

Francesca Finotello 🖥️🧬 @francescafinotello.bsky.social · Jul 15

🧬🖥️🧪 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...

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Francesca Finotello 🖥️🧬 @francescafinotello.bsky.social · 12d

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.

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Francesca Finotello 🖥️🧬 @francescafinotello.bsky.social · 12d

👏 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

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Francesca Finotello 🖥️🧬 @francescafinotello.bsky.social · 12d

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...

Redirecting

doi.org

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Francesca Finotello 🖥️🧬 @francescafinotello.bsky.social · 12d

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

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Francesca Finotello 🖥️🧬 @francescafinotello.bsky.social · 12d

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

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Francesca Finotello 🖥️🧬 @francescafinotello.bsky.social · 12d

🖥️🧬🧪 Publication Alert!

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

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Reposted by Francesca Finotello 🖥️🧬

scverse @scverse.bsky.social · Aug 2

🎉 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!
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Francesca Finotello 🖥️🧬 @francescafinotello.bsky.social · Aug 25

Amazing conference! Don't miss this opportunity! ✨

scverse @scverse.bsky.social · Aug 2

🎉 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

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Reposted by Francesca Finotello 🖥️🧬

Francesca Finotello 🖥️🧬 @francescafinotello.bsky.social · Jul 17

🖥️🧬 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!

UIBK - FemCareer - Fellowship

Three-year career development programme at the UIBK for external, female early career postdocs

www.uibk.ac.at

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Francesca Finotello 🖥️🧬 @francescafinotello.bsky.social · Jul 17

🖥️🧬 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!

UIBK - FemCareer - Fellowship

Three-year career development programme at the UIBK for external, female early career postdocs

www.uibk.ac.at

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Reposted by Francesca Finotello 🖥️🧬

David Gfeller @dgfeller.bsky.social · Jul 15

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.

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Francesca Finotello 🖥️🧬 @francescafinotello.bsky.social · Jul 15

🧬🖥️🧪 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...

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Reposted by Francesca Finotello 🖥️🧬

carmonasfj.bsky.social @carmonasfj.bsky.social · Jul 13

“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

Editorial - A stronger Europe starts with science

As leaders from industry, policy and science gathered in Brussels for a lively exchange this spring, o

erc.europa.eu

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Reposted by Francesca Finotello 🖥️🧬

Stegle Lab @steglelab.bsky.social · Jul 4

📢 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.

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Reposted by Francesca Finotello 🖥️🧬

Stegle Lab @steglelab.bsky.social · Jul 4

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.

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Francesca Finotello 🖥️🧬 @francescafinotello.bsky.social · May 29

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 :)

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Francesca Finotello 🖥️🧬 @francescafinotello.bsky.social · May 27

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!

DaiSyBio @daisybio.de · May 27

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!

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Reposted by Francesca Finotello 🖥️🧬

DaiSyBio @daisybio.de · May 27

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!

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Reposted by Francesca Finotello 🖥️🧬

Markus List @itisalist.bsky.social · May 27

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!).

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

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Reposted by Francesca Finotello 🖥️🧬

Francesca Finotello 🖥️🧬 @francescafinotello.bsky.social · Nov 12

🧬 🖥️ 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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Reposted by Francesca Finotello 🖥️🧬

Stephen Turner @stephenturner.us · Dec 12

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

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Reposted by Francesca Finotello 🖥️🧬

Francesca Finotello 🖥️🧬 @francescafinotello.bsky.social · Nov 12

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

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Reposted by Francesca Finotello 🖥️🧬

Francesca Finotello 🖥️🧬 @francescafinotello.bsky.social · Nov 13

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 🧬🖥️🧪👩‍🔬

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Reposted by Francesca Finotello 🖥️🧬

Anshul Kundaje @anshulkundaje.bsky.social · Apr 20

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.

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

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