Pablo Riesgo-Ferreiro

Predicting TCR-pMHC Binding by Reinforcement Learning https://www.biorxiv.org/content/10.64898/2026.01.05.697685v1

NetMHCIIphosPan: a machine learning tool for predictingHLA class II antigen presentation of phosphorylated peptides. https://www.biorxiv.org/content/10.64898/2026.01.05.697746v1

A public health perspective of SARS-CoV-2 evolution and surveillance strategies in Germany from 2020 to 2023 - Communications Medicine Oh, Hölzer et al., discuss the multidisciplinary approach used for monitoring the genomic and virological evolution of SARS-CoV-2 during the COVID-19 pandemic and its implications on public health in Germany. They emphasize the need for continuous surveillance and adaptation of public health strategies to address evolving viral threats.

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

Agree, but I'd add as a useful pattern introducing consecutive numbers into names as a clearer alternative than a timestamp. Also you can combine those with timestamps if you add a new version and you need to keep both.

00_data_collection_20251224.ipynb
01_preprocessing_20251224.ipynb
[...]

HLA export by melanoma cells decoys cytotoxic T cells to promote immune evasion Melanoma cells escape immune surveillance by releasing MHC-antigen-loaded large EVs, known as melanosomes, that directly engage and impair CD8+ T cell receptors.

#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...

Lymphodepleting chemotherapy potentiates neoantigen-directed T cell therapy by enhancing antigen presentation Sagie et al. identify a KRAS.G12V-specific TCR and show that lymphodepleting chemotherapy enhances antigen presentation via immunoproteasome activation and HLA-I upregulation. Together, these changes synergize to improve T cell-mediated tumor killing in multiple models and highlight the potential of optimized chemotherapy to augment adoptive cell therapy efficacy.

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

The Year in Biology | Quanta Magazine Take a jaunt through a jungle of strange neurons underlying your sense of touch, hundreds of millions of years of animal evolution and the dense neural networks of brains and AIs.

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

The Gene Ontology knowledgebase in 2026 Abstract. The Gene Ontology (GO) knowledgebase (https://geneontology.org) is a comprehensive resource describing the functions of genes. The GO knowledgeba

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 Today's AI narrative is anchored in scale, and models are far from textbook statistical modeling. And yet, the plague that are hallucination shows us th…

Uncertainty in the LLM era - Science, more than scale
speakerdeck.com/gaelvaroquau...

My #EurIPS keynote, on scale, uncertainty, and narratives in AI

The Open Notebook's 15th Anniversary - The Open Notebook For 15 years, The Open Notebook has been the trusted home for journalists worldwide who cover science. What started as an experiment to demystify the craft of science writing has grown into a vital, g...

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

Spatial transcriptomic clocks reveal cell proximity effects in brain ageing Nature - A spatially resolved single-cell transcriptomics map of the mouse brain at different ages reveals signatures of ageing, rejuvenation and disease, including ageing effects associated with T...

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!

Infamous paper that popularized unproven COVID-19 treatment finally retracted Study on hydroxychloroquine by Didier Raoult and colleagues gets pulled on ethical and scientific grounds

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...

Genome in a Bottle Consortium goals:The Genome in a Bottle Consortium is a public-private-academic consortium hosted by NIST to develop the technical infrastructure (reference standards, reference methods, and reference...

Maybe keep an eye on the genome in a bottle initiative www.nist.gov/programs-pro...

The RNA part is less mature than others but still you'll find there some public human samples which you can analyse and contrast results.

The 2025 EMBL Annual Poster, listing all of the courses and conferences taking place in 2025 at EMBL

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

Calling Bullshit: Data Reasoning in a Digital World The world is awash in bullshit. Politicians are unconstrained by facts. Science is conducted by press release. Higher education rewards bullshit over analytic thought. Startup culture elevates bullshi...

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.

«Científico», una palabra inventada por españoles que en primer lugar se usó para hablar de una mujer La palabra apareció en un libro de Juan de Mena en el siglo XVI y fue popularizada por William Whewell en el XIX. La primera persona descrita por ella fue Mary Somerville

Interesting! From what I find it was in a book by Juan de Mena, las Trezientas in 1566 and later on by Manuel Martin in 1788.

Or that says here:
www.abc.es/ciencia/abci...

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

EmbedGEM: a framework to evaluate the utility of embeddings for genetic discovery AbstractSummary. Machine learning-derived embeddings are a compressed representation of high content data modalities. Embeddings can capture detailed infor

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.

Imperfect wound healing sets the stage for chronic diseases Although the age of the genome gave us much insight about how our organs fail with disease, it also suggested that diseases do not arise from mutations alone; rather, they develop as we age. In this R...

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

The altmetric works for bluesky!