Are you (or is someone you know) teaching AI / ML / Deep Learning this year? My forthcoming book (freely available at udlbook.com) will save you a lot of time. This thread will show you why.

Many thanks to Ming "Tommy" Tang for highlighting our work! In a joint effort with @itisalist lab, we have developed 2 additional packages for: - scRNA-seq-informed deconvolution, #omnideconv: shorturl.at/fjKMU - spatial deconvolution, #spacedeconv: shorturl.at/swFIP

GitHub - omnideconv/spacedeconv: A unified interface to spatial transcriptomics deconvolution tools github.com/omnideconv/spa…

GitHub - omnideconv/spacedeconv: A unified interface to spatial transcriptomics deconvolution tools github.com/omnideconv/spa…

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/

Thank you for highlighting our work! 🙏 #spacedeconv preprint is available at: researchsquare.com/article/rs-510…

What if you could make physics diagrams come alive? At #UIST2024, we will be presenting our paper, Augmented Physics, an ML-Integrated Authoring Tool for Creating Interactive Physics Simulations from Static Diagrams Co-authors: Yi Wen Nandi Zhang Jarin Rubaiat Habib Ryo Suzuki

Interested in benchmarking computational methods in computational biology, generally? Save the date, submit an abstract, join us next March in Ascona! Conference website: sites.google.com/view/ascona2025 Please retweet and/or tell your colleagues!

RNA sequencing depth guidelines for the study of alternative splicing biorxiv.org/cgi/content/sh… #biorxiv_bioinfo

**Please Retweet (Re-X?)** 🔥Postdoc #jobs in Spatial / Single Cell Omics Looking to become a #leader in #SpatialBiology? Love NGS & #MachineLearning? #Positions Harvard Medical School Broad Institute linkedin.com/jobs/view/4038… #hiring #lab #boston #research #aiml #biotech #Science

🚀 Proud to launch ⭐Path2Space⭐ — the first AI to discover spatial biomarkers for cancer treatment! It predicts spatial gene expression from histopathology, enabling large-scale tumor microenvironment profiling. biorxiv.org/content/10.110… 🧵1/11

TCR lovers, we are delighted to share our benchmarking of TCR specificity tools using an harmonized aggregation of public databases. biorxiv.org/content/10.110…

🚀 New Tool Alert! 🚀 PENGUIN 🐧is finally published in CSBJ : PENGUIN is a rapid, efficient, and user-friendly tool for denoising and normalizing multiplexed spatial proteomics images! 🔬✨ 🔗sciencedirect.com/science/articl…

NovumRNA: accurate prediction of non-canonical tumor antigens from RNA sequencing data biorxiv.org/cgi/content/sh… #biorxiv_bioinfo

1/10 PREPRINT MONDAY at the SchubertLab Benchmarking TCR-Epitope Predictors with ePytope-TCR (doi.org/10.1101/2024.1…) Short-Summary: - 18 pre-trained public methods - evaluated on 2 benchmarking datasets - for repertoire annotation & cross-reactivity prediction

anndata 0.11 is out now: anndata.readthedocs.io/en/stable/rele…! We have some great new features to highlight as well as some breaking changes to look out for.

Benchmarking second-generation methods for cell-type deconvolution of transcriptomic data biorxiv.org/content/10.110… 🧬🖥️🧪 omnideconv #Rstats pkg github.com/omnideconv/dec… Nextflow pipeline github.com/omnideconv/dec…

Stephen Turner 🦋 @stephenturner.us Great work on the benchmarking study! ️ I'm looking forward to exploring the omnideconv package and learning more about cell-type deconvolution of transcriptomic data.

Closing 2024, scverse celebrates incredible growth and collaboration! Huge thanks to everyone on this journey and our dedicated core team & management board (Fabian Theis, Francesca Finotello, Oliver Stegle , Yosef Lab, Panos Roussos, 𝕐). Here’s to an even brighter 2025!