iiinova — where your digital self keeps evolving

Reposted by Francesca Finotello 🖥️🧬

bioRxivpreprint @biorxivpreprint.bsky.social · 09/07/2026

Rectangle: robust and scalable multiscale deconvolution informed by single-cell RNA sequencing data www.biorxiv.org/content/10.64898/20…

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Reposted by Francesca Finotello 🖥️🧬

bioRxiv Bioinfo @biorxiv-bioinfo.bsky.social · 09/07/2026

Rectangle: robust and scalable multiscale deconvolution informed by single-cell RNA sequencing data www.biorxiv.org/content/10.64898/20…

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#SingleCell preprints @prepub-singlecell.bsky.social · 09/07/2026

Rectangle: robust and scalable multiscale deconvolution informed by single-cell RNA sequencing data #SingleCell 🧪🧬🖥️ www.biorxiv.org/content/10.64898/20…

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Reposted by Francesca Finotello 🖥️🧬

bioinfoblogs @bioinfoblogs.bsky.social · 29/01/2026

📝 omnideconv – a unifying framework for using and benchmarking single-cell-informed deconvolution of bulk RNA-seq data ✍️ RNA-Seq Blog

rna-seqblog.com

omnideconv – a unifying framework for using and benchmarking single-cell-informed deconvolution of bulk RNA-seq data

Article de RNA-Seq Blog

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Reposted by Francesca Finotello 🖥️🧬

Gregor Sturm @grst.bsky.social · 29/05/2026

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

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Reposted by Francesca Finotello 🖥️🧬

Gregor Sturm @grst.bsky.social · 29/05/2026

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/

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Reposted by Francesca Finotello 🖥️🧬

Stephen Turner @stephenturner.us · 12/12/2024

Benchmarking second-generation methods for cell-type deconvolution of transcriptomic data www.biorxiv.org/content/10.1101/202… 🧬🖥️🧪 omnideconv #Rstats pkg github.com/omnideconv/deconvBench Nextflow pipeline github.com/omnideconv/deconvBench

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GeneticsPapers @asimresearcher.bsky.social · 26/01/2026

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

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Reposted by Francesca Finotello 🖥️🧬

Ming Tommy Tang @tommytang.bsky.social · 10/09/2025

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

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Francesca Finotello 🖥️🧬 @francescafinotello.bsky.social · 26/09/2025

🖥️🧬🧪 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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Francesca Finotello 🖥️🧬 @francescafinotello.bsky.social · 25/08/2025

Amazing conference! Don't miss this opportunity! ✨

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Reposted by Francesca Finotello 🖥️🧬

Francesca Finotello 🖥️🧬 @francescafinotello.bsky.social · 17/07/2025

🖥️🧬 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.ac.at

UIBK - FemCareer - Fellowship

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

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Francesca Finotello 🖥️🧬 @francescafinotello.bsky.social · 17/07/2025

uibk.ac.at

UIBK - FemCareer - Fellowship

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

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Reposted by Francesca Finotello 🖥️🧬

David Gfeller @dgfeller.bsky.social · 15/07/2025

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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Reposted by Francesca Finotello 🖥️🧬

carmonasfj.bsky.social @carmonasfj.bsky.social · 13/07/2025

“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

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

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Reposted by Francesca Finotello 🖥️🧬

Stegle Lab @steglelab.bsky.social · 04/07/2025

📢 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 · 04/07/2025

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 · 27/05/2025

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!

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Reposted by Francesca Finotello 🖥️🧬

DaiSyBio @daisybio.de · 27/05/2025

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 · 27/05/2025

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 · 12/11/2024

🧬 🖥️ 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/

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Reposted by Francesca Finotello 🖥️🧬

Francesca Finotello 🖥️🧬 @francescafinotello.bsky.social · 12/11/2024

🧬 🖥️ 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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Francesca Finotello 🖥️🧬 @francescafinotello.bsky.social · 13/11/2024

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 · 20/04/2025

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.

genomebiology.biomedcentral.com

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...

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Reposted by Francesca Finotello 🖥️🧬

Carl T. Bergstrom @carlbergstrom.com · 19/03/2025

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.

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Carl T. Bergstrom @carlbergstrom.com · 19/03/2025

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.

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Reposted by Francesca Finotello 🖥️🧬

Bluesky @bsky.app · 04/04/2025

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.

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Reposted by Francesca Finotello 🖥️🧬

Oregon 🕎🎲 @oregonthedm.bsky.social · 09/04/2025

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

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Francesca Finotello 🖥️🧬 @francescafinotello.bsky.social · 18/03/2025

🧬🖥️🧪 Now I can also proudly tag @eduati.bsky.social! Welcome my friend 🤗

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Reposted by Francesca Finotello 🖥️🧬

Francesca Finotello 🖥️🧬 @francescafinotello.bsky.social · 12/11/2024

And... I had a lot of fun with my 5yo who put together a tentative cover for iHet 🖌️ This artwork represents how RNA-seq data generated from different tumors carry information on the capability of immune cells (red dots in the upper part) to infiltrate tumors... 7/

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Reposted by Francesca Finotello 🖥️🧬

Francesca Finotello 🖥️🧬 @francescafinotello.bsky.social · 12/11/2024

🖌️ ... Using a multimodal approach to analyze RNA-seq data, we derived a holistic representation of the cellular and molecular heterogeneity of tumors (bottom), which is associated with immune-cell infiltration and activity, and predicts response to immunotherapy. 8/8

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Reposted by Francesca Finotello 🖥️🧬

Francesca Finotello 🖥️🧬 @francescafinotello.bsky.social · 12/11/2024

Our work shows how #transcriptomics can be used to derive a holistic representation of TME heterogeneity and its unfolding during #cancer #immunotherapy 6/

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Francesca Finotello 🖥️🧬 @francescafinotello.bsky.social · 12/11/2024

We demonstrated that iHet has predictive value for #ICB #immunotherapy, which can be further improved by disentangling three major determinants of anticancer immune responses: - activity of immune cells - immune infiltration vs. exclusion - tumor foreignness 4/

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Francesca Finotello 🖥️🧬 @francescafinotello.bsky.social · 12/11/2024

We demonstrated that the iHet signature, despite being derived with an unsupervised approach, is conserved in different cancers and associated with antitumor immunity Through analysis of single-cell and spatial transcriptomics, we traced back the cellular origin of iHet 3/

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Francesca Finotello 🖥️🧬 @francescafinotello.bsky.social · 12/11/2024

The cellular and molecular heterogeneity of tumors is a major obstacle to cancer immunotherapy We used a systems biology approach to derive a signature (iHet) capturing the main sources of #TME #heterogeneity from lung cancer transcriptomic data 2/

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Magdalena Skipper @magdalenaskipper.bsky.social · 08/03/2025

Women in research need the credit & recognition they deserve for the amazing contributions they make. Nature Awards for Inspiring Women in Science are open for applications - take a look 👇🏻 & help spread the word #WomeninSTEM #AcademicSky 🧪 @natureportfolio.nature.com www.nature.com/immersive/in...

nature.com

Nature Awards Inspiring Women in Science

Celebrating and supporting the achievements of women in science, and all those who work to encourage girls and young women to engage with STEM subjects and stay in STEM careers around the world.

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EMBO @embo.org · 08/03/2025

On #InternationalWomensDay, nominate a female scientist for the next FEBS | EMBO Women in Science Award. Deadline is 15 May 2025: www.embo.org/the-embo-com... #WomeninScience #ForAllWomenAndGirls 🧪

embo.org

The EMBO communities – FEBS|EMBO Women in Science Awardees – EMBO

Outstanding female life scientists and role models.

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Johanna Joyce @johannajoyce.bsky.social · 07/03/2025

Ahead of International Women's Day, and with attacks on critical #DEI programs in the US, I'm resharing this article ⏬ If this regressive shift spreads, we risk undoing many hard-won advances towards gender equality around the world We cannot let this happen 💪 #Diversity #Equity #Inclusion

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Manlio De Domenico @manlius.bsky.social · 07/03/2025

In onore della mia ultima foto delle nebulose Fiamma e Testa di Cavallo, ho pensato di scrivere un thread per gli utenti 🇮🇹 che mi seguono. Lo scopo è quello di condividere la meraviglia verso il cielo stellato, che è un bene prezioso che sta scomparendo sempre più. Un piccolo viaggio. 🧵 1/

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Johanna Joyce @johannajoyce.bsky.social · 05/03/2025

Now, more than ever, the #global #science community needs to stand together - #united against those who attack science 🧪, who seek to diminish #scientists, who destroy critical programs that advance #equality, #diversity and #inclusion Please consider to join us in signing the #MilanDeclaration ⏬

febs.org

Milan Declaration - FEBS

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Francesca Finotello 🖥️🧬 @francescafinotello.bsky.social · 12/11/2024

Great collaboration with @itisalist.bsky.social ✨ We hope our study and set of tools and resources can be helpful to the scientific community 💫 📝 preprint: doi.org/10.1101/2024... 🛠️ omnideconv ecosystem: omnideconv.org Please repost and help us spread the word! 6/6

doi.org

Benchmarking second-generation methods for cell-type deconvolution of transcriptomic data

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 used precompu...

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Reposted by Francesca Finotello 🖥️🧬

Francesca Finotello 🖥️🧬 @francescafinotello.bsky.social · 12/11/2024

We provide the scientific community with an ecosystem of tools and resources, #omnideconv, that strongly simplifies the application, benchmarking, and optimization of deconvolution methods: omnideconv.org 5/

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Achim Zeileis @zeileis.org · 24/02/2025

🚨 The "penguins" data is coming to the base #rstats{datasets} in 4.5.0! @ellakaye.co.uk & @HeathrTurnr.fosstodon.org.ap.brid.gy r prepared an adapted and a raw version of the data set based on the {palmerpenguins} 📦 by @allisonhorst.bsky.social @apreshill.com and Kristen Gorman. 📈 Scatter plot:

Scatter plot of bill depth vs. length by species (color) and sex (symbol). It shows positive correlations for all species with males tending to have bigger bills than females.

sym <- c(1, 16)
pal <- c("darkorange","purple","cyan4")
plot(bill_dep ~ bill_len, data = penguins, pch = sym[sex], col = pal[species])

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