Rectangle: robust and scalable multiscale deconvolution informed by single-cell RNA sequencing data https://www.biorxiv.org/content/10.64898/2026.07.07.736950v1
Francesca Finotello 🖥️🧬
@francescafinotello.bsky.social
Assistant Professor leading the Computational Biomedicine Group at the University of Innsbruck • Data scientist at the Digital Science Center (DiSC) • Precision medicine and cancer immunotherapy • Mother 🧬🖥️ https://computationalbiomedicinegroup.github.io/
Rectangle: robust and scalable multiscale deconvolution informed by single-cell RNA sequencing data https://www.biorxiv.org/content/10.64898/2026.07.07.736950v1
Rectangle: robust and scalable multiscale deconvolution informed by single-cell RNA sequencing data #SingleCell 🧪🧬🖥️ https://www.biorxiv.org/content/10.64898/2026.07.07.736950v1
📝 omnideconv – a unifying framework for using and benchmarking single-cell-informed deconvolution of bulk RNA-seq data ✍️ RNA-Seq Blog
omnideconv – a unifying framework for using and benchmarking single-cell-informed deconvolution of bulk RNA-seq data
Article de RNA-Seq Blog
rna-seqblog.com
This started as a collaboration with biocypher (@slobentanzer.bsky.social) at a @scverse.bsky.social hackathon, was then advanced by @valeriiadragan.bsky.social as a master thesis project and finally pushed over the finish line by Raphael De Gottardi
Happy to announce the release of IggyTop, a metadatabase for immune receptor–epitope interactions. It's integrated with scirpy v0.24 so you can readily use it to annotate your single-cell TCR datasets. iggytop.readthedocs.io/en/latest/
🖥️🧬🚀 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...
doi.org
Francesca Finotello 🖥️🧬@francescafinotello.bsky.social · 2y ago📢 Preprint alert: #Benchmarking second-generation methods for cell-type #deconvolution of #transcriptomic data t.co/MhLf5Eo3yY A thread 🧵👇 1/
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...
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...
doi.org
Francesca Finotello 🖥️🧬@francescafinotello.bsky.social · 2y ago📢 Preprint alert: #Benchmarking second-generation methods for cell-type #deconvolution of #transcriptomic data t.co/MhLf5Eo3yY A thread 🧵👇 1/
🖥️🧬 New preprint with expanded study is now online ✨ www.biorxiv.org/content/10.1...
omnideconv: a unifying framework for using and benchmarking single-cell-informed deconvolution of bulk RNA-seq data
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 u...
biorxiv.org
Francesca Finotello 🖥️🧬@francescafinotello.bsky.social · 2y ago🧬 🖥️ If you are looking for more tools, resources, and insights about next-generation #deconvolution, have a look at our #omnideconv website: omnideconv.org
🧬🖥️🧪 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...
omnideconv: a unifying framework for using and benchmarking single-cell-informed deconvolution of bulk RNA-seq data
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...
biorxiv.org
Francesca Finotello 🖥️🧬@francescafinotello.bsky.social · 2y ago📢 Preprint alert: #Benchmarking second-generation methods for cell-type #deconvolution of #transcriptomic data t.co/MhLf5Eo3yY A thread 🧵👇 1/
🖥️🧬🧪 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!
UIBK - FemCareer - Fellowship
Three-year career development programme at the UIBK for external, female early career postdocs
uibk.ac.at
🖥️🧬 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
uibk.ac.at
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...
omnideconv: a unifying framework for using and benchmarking single-cell-informed deconvolution of bulk RNA-seq data
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...
biorxiv.org
Francesca Finotello 🖥️🧬@francescafinotello.bsky.social · 2y ago📢 Preprint alert: #Benchmarking second-generation methods for cell-type #deconvolution of #transcriptomic data t.co/MhLf5Eo3yY A thread 🧵👇 1/
“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
📢 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.
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 · last yr.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!
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!
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🧵👇 1/
🧬 🖥️ If you are looking for more tools, resources, and insights about next-generation #deconvolution, have a look at our #omnideconv website: omnideconv.org
Francesca Finotello 🖥️🧬@francescafinotello.bsky.social · 2y ago📢 Preprint alert: #Benchmarking second-generation methods for cell-type #deconvolution of #transcriptomic data t.co/MhLf5Eo3yY A thread 🧵👇 1/
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 🧬🖥️🧪👩🔬
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