Pablo Riesgo-Ferreiro
@priesgo.bsky.social
Bioinformatics Scientist @ BioNTech #bioinformatics #AI #immunology #cancer #vaccines Opinions my own, if you don't like them I have others
Google is requiring all Android developers to register centrally, pay a fee, and submit government ID. Apps from unregistered developers will be silently blocked. over 67 organizations oppose this. @keepandroidopen.bsky.social keepandroidopen.org
Keep Android Open
Your phone is about to stop being yours. In 2027, Google will block every Android app whose developer hasn't registered with them.
keepandroidopen.org
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
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
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.
doi.org
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...
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.
cell.com
Online now: Lymphodepleting chemotherapy potentiates neoantigen-directed T cell therapy by enhancing antigen presentation
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.
dlvr.it
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/...
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
doi.org
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...
His lab was humming with discovery. After one year under Trump, it’s almost silent
John Quackenbush built a lab that is at the forefront of human genetics research and bioinformatics. Trump administration cuts have put it in danger of collapse.
statnews.com
anil oza@aniloza.bsky.social · 9mo agoStay tuned for further installments of American Science, Shattered (and catch up on any of the stories you have missed so far!) www.statnews.com/american-sci...
Uncertainty in the LLM era - Science, more than scale speakerdeck.com/gaelvaroquau... My #EurIPS keynote, on scale, uncertainty, and narratives in AI
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…
speakerdeck.com
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 ... 🧵
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...
theopennotebook.com
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 🧵
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...
rdcu.be
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...
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
science.org
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.
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...
callingbullshit.org
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/)
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
academic.oup.com
This is possibly the last thing I was missing from R in python. Thanks for that!
Gregor Sturm@grst.bsky.social · 2y agoFormulaic is the go-to way to specify design formulas in Python, e.g. ~treatment + timepoint. To compare sth, one needs to specify a contrast, e.g "on treatment vs baseline". To make this easier, we developed "formulaic-contrasts": formulaic-contrasts.readthedocs.io/en/latest/
🎉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/...
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...
science.org
www.frontiersin.org/journals/imm... An approach to stratify AML patients in two immune groups based on expression profiles. #paper #immunology
Frontiers | Immune-based subgroups uncover diverse tumor immunogenicity and implications for prognosis and precision therapy in acute myeloid leukemia
BackgroundAlthough a considerable proportion of acute myeloid leukemia (AML) patients achieve remission through chemotherapy, relapse remains a recurring and...
frontiersin.org
This is so arbitrary it's laughable in retrospective
Natalia (娜塔莉)@wrycritic.bsky.social · 2y agoCW: Scientific racism You see, Haeckel has interpreted paleontology to be a constant road to higher development, a goal-driven “perfection” of the organisms over time. Lending itself to hierarchy, in which he had seen Mittellanderm (Germanics) as evolutionary superior to others.
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🧵
