New review highlights #SARS-CoV-2 evolution and longstanding #GenomicSurveillance in Germany, emphasising the need for adaptive #PublicHealth strategies for pandemic preparedness. 📄 https://doi.org/10.1038/s43856-025-01093-1  👤 EVBC members: Max von Kleist, Thorsten Wolff

HLA micropolymorphisms confine neoantigen conformational adaptability and guide T cell receptor selectivity https://www.biorxiv.org/content/10.64898/2025.12.22.696040v1

#WeekendRead! #SmartTumor #EveryCellIsAnImmuneCell! Levy & (many) friends show @cp-cell.bsky.social that melanoma tumors release large extracellular vesicles #melanosomes decorated with MHC-I & high affinity tumor associated antigens which subvert cytotoxic T cells! www.cell.com/cell/fulltex...

Online now: Lymphodepleting chemotherapy potentiates neoantigen-directed T cell therapy by enhancing antigen presentation

AI is nothing like the brain. And that’s okay.

As a final nod to 2025, #GeneOntology announces our latest paper in @narjournal.bsky.social! Updates include expanded #Ontology & annotations in #Metabolism, multi-org interactions, #chromatin remodeling, & more. Also ft. #Functionome v2 and 1500+ GO-CAM pathway models! 🧬🧪 doi.org/10.1093/nar/...

Interesting approach for a neoantigen score.

A Falsifiable Framework for Testing Neutralityin T-Cell Receptor Repertoire Databases https://www.biorxiv.org/content/10.64898/2025.12.04.692300v1

This piece on the Quackenbush lab felt close. www.statnews.com/2025/12/05/r...

Uncertainty in the LLM era - Science, more than scale speakerdeck.com/gaelvaroquau... My #EurIPS keynote, on scale, uncertainty, and narratives in AI

During the past 15 years, The Open Notebooks has: ✍️Published more than 600 articles—over 1.5 million words!—on the craft of science writing 🌐Translated more than 100 of these stories into Spanish 📚Published 2 books! 🎓Produced 7 free, online science journalism master classes ... 🧵

Evaluating the effects of CD8/CD4 on T cell function in terms of TCR-pMHC-coreceptor catch and slip bonds https://www.biorxiv.org/content/10.64898/2025.12.01.691627v1

Protein language models excel at generating functional yet remarkably diverse artificial sequences. They however fail to naturally sample rare datapoints, like very high activities. In our new preprint, we show that RL can solve this without the need for additional data: arxiv.org/abs/2412.12979

Thrilled to see this paper out!! 🧪 Spatial transcriptomics of brain aging and 'spatial aging clocks' identify cells that have pro-aging or pro-rejuvenating effects on their neighbors! Huge CONGRATS to Eric Sun and all authors! Fantastic collaboration with @jameszou.bsky.social! rdcu.be/d33uQ 🧵

Cell is happy to connect (and re-connect) with scientists across all areas of biology on Bluesky! We aim to start posting in 2025. Until then, we'll be keeping an eye out for your exciting and interesting findings... 🔬👀

One of the biggest questions we get is when will our journals be here. We thank you for your patience. You can now follow our journals with this starter pack!

It took four days from submission to publication, and nearly five years from publication to retraction. After campaigning by many, many scientists, and an investigation by Elsevier, an infamous paper on hydroxychloroquine as a COVID-19 treatment has been retracted. 🧪 www.science.org/content/arti...

Hi Bluesky community! 👋 Are you looking forward to 2025 as much as we are? 👀 We just updated our 2025 Annual Poster to include even more events for you to join, so go and have a look! ➡️ s.embl.org/poster-bl #EMBLEvents #molecularbiology #lifesciencetraining

As I mentioned three weeks ago, Jevin West and I are developing a sort of followup course to Calling Bullshit. We've got the basic scrollytelling tech worked out and now need to choose a design. We're not designers and would like to simply buy an HTML5 template if only for the colors and fonts.

What if Eroom's law, the decreasing productivity of drug discovery, is a result of aggressive accounting whereby pharma companies consider as much stuff as possible as R&D to avoid taxes? I bet eroom's law holds in movies too - where losses are built to equal move revenue

In our work (EmbedGEM: doi.org/10.1093/bioa...) we developed the first formal evaluation framework for multivariate phenotypes that reports metrics for both heritability as well as disease relevance. The way we evaluate heritability is using several simple proxies: number of associations, (6/)

This is possibly the last thing I was missing from R in python. Thanks for that!

🎉Thrilled that #GenePT is published! We show how to create #ChatGPT embeddings of genes and #singlecell --> improve gene function prediction + cell annotation/analyses🧬 📰 www.nature.com/articles/s41... 🌐 github.com/yiqunchen/Ge... Great job Yiqun Chen! #LLM for bio.

Out in time for the #ASCB meeting an @science.org Review from Jody Rosenblatt and friends www.science.org/doi/10.1126/...

www.frontiersin.org/journals/imm... An approach to stratify AML patients in two immune groups based on expression profiles. #paper #immunology

This is so arbitrary it's laughable in retrospective

Imagine your notebook surviving for centuries to be studied by historians. This happened to transcriptions by Nicholai Miklouho-Maclay, Russian of Ukrainian Cossack descent, of a palaeontology class delivered by Ernst Haeckel (1866) This unlikely record, captures the rise of race science in Germany🧵

What are shapley interactions and why should you care about them? This is a guest post by Julia, Max, Fabian and Hubert on my newsletter Mindful Modeler. I also learned a lot from this post and definitely recommend checking out the shapiq package. mindfulmodeler.substack.com/p/what-are-s...

Timescales in Cell Biology #Cell PDF download: www.cell.com/cell/pdf/S00...

A nice analysis of different tokenization strategies (BPE, wordpiece, sentencepiece) on protein sequences. arxiv.org/abs/2411.17669

In case some mentors may want to read this. #Nature #PhD #scisky #student #mentor Source: www.researchgate.net/publication/...

Design of high specificity binders for peptide-MHC-I complexes https://www.biorxiv.org/content/10.1101/2024.11.28.625793v1

Our Herpesfolds paper is out in Nature Communications! rdcu.be/d1uM7 Congrats to Timothy Soh, @sofiaaognibene , Saskia Sanders, Robin Schaeper and Benedikt Kaufer! Have a look at our database at herpesfolds.org by Malte Kansy

Immune cells change in proportions with age - naive go down, effector go up. www.science.org/doi/10.1126/...

The danger theory of immunity strikes back... rdcu.be/d1uQN