🖥️🧬 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...

🖥️🧬🧪 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...

“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.

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!

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/

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 🧬🖥️🧪👩‍🔬

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

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

🧬🖥️ #iHet code is available at: github.com/Computationa...

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/

🖌️ ... 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

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

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/

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/

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/

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...

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 🧪

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

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/

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 ⏬

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

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/

🚨 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:

… and systematically assess how deconvolution performance is affected by different sources of variation and bias 4/

Second-generation #deconvolution methods can be trained with scRNA-seq data to estimate the cellular composition of bulk RNA-seq samples This flexibility can unlock the deconvolution of any cell type, tissue, and organism… but poses major challenges to methods benchmarking 2/

We put together a unique set of real and simulated datasets to comprehensively benchmark second-generation deconvolution tools in different scenarios... 3/

📢 Preprint alert: #Benchmarking second-generation methods for cell-type #deconvolution of #transcriptomic data t.co/MhLf5Eo3yY A thread 🧵👇 1/

What if we could look at a human tissue image🔬and quantify its biological age?🧬 And how could we get the same insights without collecting the tissue sample? In our new @biorxivpreprint, we create "tissue clocks" ⏳to do just that! www.biorxiv.org/content/10.1... 📝 #aging #tissue thread below⬇️

By the way, we also have a lab account on bluesky now. Follow @daisybio.de to get more news about our activities. We are also on LinkedIn: www.linkedin.com/company/dais...

"Adaptations of #neutrophils in #cancer" Ng et al, 2025 A great new review on these fascinating immune cells! In the first #Immunity issue of this year - with lots of other amazing immunology 🧪 check it out 🤩 @cp-immunity.bsky.social www.cell.com/immunity/iss... www.cell.com/immunity/abs...

Bizarre tumor immunology accident. Surgeon injures hand while resecting malignant histiocytoma and finds an inflamed mass at the site of prior injury. Tumor cells transplanted, patient & surgeon HLA mismatched causing intense yet insufficient host-vs-graft response: www.nejm.org/doi/full/10....

I have 7.5K subscribers for my chatomics channel, which I started last April. I am well on the track to gain 10K subscribers in April 2025. I made a video a week, and I have over 100 videos now. No shortcut, just show up: #bioinformatics subscribe here www.youtube.com/@chatomics/...

When groups meet to brainstorm, good ideas are lost. People bite their tongues due to conformity pressure, noise, and ego threat. A better approach is brainwriting: generate ideas separately, then meet to assess and refine. Group wisdom begins with individual creativity.