Francesca Finotello 🖥️🧬

🖥️🧬🚀 I am excited to share that our #omnideconv study is finally published on Genome Biology: doi.org/10.1186/s130...

omnideconv: a unifying framework for using and benchmarking single-cell-informed deconvolution of bulk RNA-seq data - Genome Biology Background In silico cell-type deconvolution from bulk transcriptomics data is a powerful technique to gain insights into the cellular composition of complex tissues. While first-generation methods us...

Our omnideconv study is finally published on Genome Biology: doi.org/10.1186/s130... 🚀

omnideconv: a unifying framework for using and benchmarking single-cell-informed deconvolution of bulk RNA-seq data - Genome Biology Background In silico cell-type deconvolution from bulk transcriptomics data is a powerful technique to gain insights into the cellular composition of complex tissues. While first-generation methods us...

Now finally published in Genome Biology: doi.org/10.1186/s130... 🚀

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

omnideconv: a unifying framework for using and benchmarking single-cell-informed deconvolution of bulk RNA-seq data https://pubmed.ncbi.nlm.nih.gov/41582216/

omnideconv is an ecosystem of user-friendly tools and resources for cell-type deconvolution. (bulk RNAseq, spatial data)
omnideconv.org/

🖥️🧬🚀 I am excited to share that our #omnideconv study is finally published on Genome Biology: doi.org/10.1186/s130...

🖥️🧬 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”

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