Francesc Castro-Giner

Universität Basel: Bioinformatician (100%) The Department of Biomedicine (DBM) is a joint effort between the University of Basel and the University Hospitals Basel. It unites basic and clinical scientists to advance our understanding of health...

We have a 3-years position open in our facility. Come join us to do great science in a nice team!
jobs.unibas.ch/offene-stell...

A genetically encoded device for transcriptome storage in mammalian cells Understanding how cells make decisions over time requires the ability to link past molecular states to future phenotypic outcomes. We present TimeVault, a genetically encoded system that records and s...

🧬🔬@science.org A genetically encoded device for #transcriptome storage in mammalian cells | Science www.science.org/doi/10.1126/... @broadinstitute.org

Bulk RNA-seq to the rescue of differential expression analysis i... Due to the costs of single-cell sequencing, sample sizes are often relatively limited, sometimes leading to poorly reproducible results. In many contexts, however, larger bulk RNAseq data is…

"Bulk RNA-seq to the rescue of differential expression analysis in single-cell transcriptomics" 🧫 📑 A new PCI Genomics recommendation by @mireyaplass.bsky.social: doi.org/10.24072/pci...

Many people hours, calls and messages later: OSTA is now “in (pre)print”, though the real thing lives at bioconductor.org/books/OSTA.

Check it out, get in touch. We welcome any feedback, suggestions, wishes (& contributions).

It’s been a joy working with you @estellayixingdong.bsky.social!

The CRISPR gene scissors are only of limited use to detect cancer-causing genes in animals because the method interferes with their immune system. Researchers, however, have now shown that a few tricks can be pulled to render the gene scissors invisible to immune cells.

ethz.ch/en/news-and-...

SARS-CoV-2 mRNA vaccines sensitize tumours to immune checkpoint blockade - Nature mRNA vaccines targeting SARS-CoV-2 also sensitize tumours to immune checkpoint inhibitors.

I've been asked about this paper (www.nature.com/articles/s41...) enough times that I finally had to read it.

The basic claim is that mRNA vaccines had huge synergistic benefit with checkpoint blockade against lung cancer melanoma.

tl;dr it's glam-slop & everyone involved should be embarrassed

Applications now open for CRUK Clinical Academic PhD Training Programme. Join us @icr.ac.uk and The Royal Marsden NHS Foundation Trust.
We are offering a super exciting project to investigate cytoskeletal dynamics in Circulating Tumour Cells from Breast Cancer Patients.

AI "peer" review - the impact on scientific publishing It is the first time, in the second half of this year, that I am not trying to urgently deal with something. So, instead of working on some ...

New blog post - AI "peer" review - the impact on scientific publishing. Some thoughts on AI manuscript assessments and potential impacts on scientific publishing www.evocellnet.com/2025/11/ai-p...

ISEEC

The International Society for Evolution, Ecology and Cancer #ISEEC has now a #YouTube channel: www.youtube.com/channel/UCrC...

posit::conf(2025) - YouTube Welcome to the official playlist for posit::conf(2025)! Dive into the latest innovations, cutting-edge techniques, and inspiring insights from the premier op...

Recordings from posit::conf(2025) now on YouTube: www.youtube.com/playlist?lis... #Rstats

Excited to share our latest publication. I'm happy to have contributed to this work — most of the credit goes to Dr. Massimo Saini.

StealTHY: An immunogen-free CRISPR platform to expose concealed metastasis regulators in immunocompetent models By sidestepping Cas9 immunogenicity, the StealTHY CRISPR platform enables immune-compatible in vivo genetic screens, directly translatable to humanized cancer models. Using this immune-stealth strategy allows for the discovery of metastatic drivers and reveals the AMH-AMHR2 axis as a clinically actionable pathway for dampening carcinoma metastasis.

Now online! StealTHY: An immunogen-free CRISPR platform to expose concealed metastasis regulators in immunocompetent models

Our own Tatiana Miti describing work where an agent-based model captures metastatic dynamics in TNBC and the resulting emerging behaviour shows how tumor cells self-organize to drive the metastasis

Tumor infiltration of major blood vessels, not metastasis, may be primary cause of cancer death The ultimate cause of death from cancer may not be metastatic disease, as researchers have long surmised, but an infiltration of tumors into major blood vessels that cause blood clots and multiorgan failure, a one-of-a-kind clinical study led by UT Southwestern Medical Center suggests.

Evidence suggests that tumor infiltration into major blood vessels, rather than metastasis alone, may be a primary driver of fatal outcomes in advanced cancer due to blood clots and organ failure. doi.org/g9649b

Macarena Toll-Riera (IBE): a lifetime studying evolution - El·lipse In this interview, Macarena Toll-Riera, head of the evolutionary microbiology group (IBE: CSIC-UPF), explains her path to the field of evolution.

Meet Macarena Toll-Riera, group leader at @ibe-barcelona.bsky.social , whose passion for #evolution led her from Zürich back to @prbb.org 

👉In our interview she shares insights on #WomenInScience, #Sustainability & research challenges

Have a read!👇 
https://tuit.cat/pbPgm

#PRBBcommunity

🔥Trio Fatale: Neutrophils, NETs and Necrosis
👉 authors.elsevier.com/a/1lk-k3qNrU...

We summarized for @cp-immunity.bsky.social
"Neutrophils drive vascular occlusion, tumour necrosis and metastasis" published in @nature.com by @megeblad.bsky.social @adrover.bsky.social rdcu.be/eFdau

Congrats!

We are hiring a PhD student! Are you fascinated by microbes and evolution? Come join us in Barcelona!

Phylogenetic inference reveals clonal heterogeneity in circulating tumor cell clusters - Nature Genetics Phylogenetic analyses in patients with cancer and xenograft models highlight heterogeneity within individual CTC clusters, providing insights into clonal dynamics during metastasis.

We are excited to share our latest research published in Nature Genetics, where we could detect genetic heterogeneity within circulating tumor cell clusters that can seed metastases. To do so, we tailor-made a new phylogenetic algorithm "CTC-SCITE": www.nature.com/articles/s41...

Two children at school in uniforms and it looks like Japan, both of them look like girls or femmes. One is holding a giant tuba so that it's stuffed over the face of the other one that's pinned up against the wall. The one holding the tuba is labeled every company. The tuba is labeled unwanted AI And the one against the wall is labeled me

BIRS Recap: Machine learning for model parameterization mathematical-oncology.org

Machine learning for model parameterization:
mathematical-oncology.org/blog/machine...

@hamiscalculated.bsky.social @jmetzcar.bsky.social @stolzbernadette.bsky.social
#MathOnco #MachineLearning

Nociceptive neurons promote gastric tumour progression via a CGRP–RAMP1 axis - Nature Functional connectivity between gastric cancer cells and sensory neurons offers a potential therapeutic target.

new out in #Nature: two cancer neuroscience papers. Number one: www.nature.com/articles/s41...

oops, actually three cancer neuroscience papers, number three, very cool combination of retrograde tracing and single cell analyses: www.nature.com/articles/s41...

Digoxin for reduction of circulating tumor cell cluster size in metastatic breast cancer: a proof-of-concept trial - Nature Medicine This proof-of-concept phase 1 trial shows that the size of circulating tumor cell clusters (which can promote metastatic spread) can be reduced by treatment with the Na+/K+ ATPase inhibitor digoxin in...

New out in #NatureMedicine: A phase 1 trial shows that the size of #CTC clusters (which can promote metastatic spread) can be reduced by treatment with the Na+/K+ ATPase inhibitor #digoxin in patients with metastatic #BreastCancer. By Nicola Aceto et al.
www.nature.com/articles/s41...

How a heart medication—digoxin—might help prevent cancer spread by dissolving clusters of circulating tumor cells
www.nature.com/articles/s41...

Dissolving clusters of cancer cells to prevent metastases Successful test in breast cancer patients: the active agent digoxin, a cardiac medication, dissolves clusters of circulating breast cancer cells in the blood, thus reducing the risk of metastases form...

Successful test in #Breast #Cancer patients: the active agent digoxin, a cardiac #Medication, dissolves clusters of circulating breast cancer cells in the blood, thus reducing the risk of #Metastases formation. ethz.ch/en/news-and-...

A few weeks ago, a client asked me for advice on how to make use of his new colour palette within spaghetti plots. What seemed like a simple question morphed into a full blog post!
www.cararthompson.com/posts/2025-0...

Colour can be used to emphasise different stories - pick the approach you need!

So pleased to have the paper out, available here: www.nature.com/articles/s41586-024-08423-8
For me this was discovery science as I had always hoped it would be. A lot of fun, and some proper detective work with plenty of twists & turns on the way. Brief thread below

H4K20me3-Mediated Repression of Inflammatory Genes Is a Characteristic and Targetable Vulnerability of Persister Cancer Cells Cell persistence and senescence are distinct states of proliferative arrest induced by cancer therapy, with persister cells being characterized by the silencing of inflammatory genes through the heter...

I am thrilled to finally share our work on persister cancer cells: we identify distinctive features and actionable #vulnerabilities ⚡️of persister cancer cells (#DTP), and provide mechanistic insight into their low #inflammatory activity:
aacrjournals.org/cancerres/ar...

I have now also ported the color vision deficiency simulation app to Shiny live. Advantage is this runs entirely in your browser, even though you "upload" the image it never leaves your computer.

Biologist, stop putting UMAP plots in papers!

Blogpost here: simplystatistics.org/posts/2024-1...