My co-first author paper was out. Cancer-specific innate and adaptive immune rewiring drives resistance to PD-1 blockade in classic Hodgkin lymphoma nature.com/articles/s4146…

String manipulation in Bash is a game-changer for bioinformatics & data processing. Rename files, extract substrings, and replace text—without external tools. Here’s how to do it efficiently 🧵👇

Some people today are discouraging others from learning programming on the grounds AI will automate it. This advice will be seen as some of the worst career advice ever given. I disagree with the Turing Award and Nobel prize winner who wrote, “It is far more likely that the

(1/n) The first preprint from our lab is now out in Nature Genetics! We tried to tackle a key challenge in spatial biology to quantitatively characterizing cellular niches by learning spatial gene programs using NicheCompas led by Sebastian Birk. Paper: shorturl.at/b4Hjk

scRepertoire now has a function to remove TCR/BCR VDJ genes from the variable features used for dimensional reduction. Friends don't let friends bias their clusters with indirect measures of clonal expansion. borch.dev/uploads/screpe…

🥳🔥Our study is out in Genome Biology! Conventional filtering out high-mtRNA cells depletes key malignant populations in cancer single-cell studies. Read it here 👉 genomebiology.biomedcentral.com/articles/10.11… Thanks to the dream team: Josephine Yates Agnieszka Kraft

Science Seminar on APr 17th 1pm GMT by Prof. Santiago Carmona titled Discovering the #cancer cell #transcriptional programs underpinning local invasion in basal cell #carcinoma. Please register at eventbrite.co.uk/e/cardiff-univ… Santiago Carmona 🧬 🖥️ carmonation.bsky.social UNIGE_en SIB Medical Education

Let's build together! 🛠️ We're open-sourcing C2S-Scale to empower the community: • Code: Replicate, adapt, extend! 💻 • Model Weights: Access models up to 27B params! 🧠 Models up to 1B parameters are already available on Huggingface, and models up to 27B parameters will be

Evaluating the practical aspects and performance of commercial single-cell RNA sequencing technologies | bioRxiv biorxiv.org/content/10.110…

Our work on "Evaluating the representational power of pre-trained DNA language models for regulatory genomics" led by Amber Tang with help from Nirali Somia & Steven Yu is finally published in Genome Biology! Check it out! genomebiology.biomedcentral.com/articles/10.11…

💥 A gut microbe metabolite that drives #atherosclerosis? Yes—Imidazole propionate (ImP) triggers vascular inflammation without changing cholesterol. 🧪 We show the pathway—and how to block it. nature.com/articles/s4158… #OpenAccess at nature CNIC #microbiome #CVD

📢 We have an open position at University of Geneva UNIGE_en for a PhD student with CS/Math/Physics background to study adaptive immune responses using deep learning. If interested please contact me directly!

Identifying malignant cells in single-cell transcriptomics data – from first principles to computational solutions, framed around the hallmarks of cancer. New review from the lab! nature.com/articles/s4200…

A new review on the challenges of identifying cancer cells in single-cell data, summarizing current computational solutions as well as underexplored features of malignancy. From scientists SIB nature.com/articles/s4200…

[1/5] ✨ Conoce a los ponentes confirmados del VI Congreso Internacional de la Sociedad Peruana de Bioinformática y Biología Computacional✨ #SPBBC #rsg_peru #BigMind #UPCH #ISCB #Bioinformática #CongresoInternacional #DelQuiipuAlCodigo

🎉 Registration is now OPEN for the GCIR Annual Symposium 2025! 📅 2 Oct | 9:30 - 5 pm 📍 Jeantet, Geneva Join us for a day of talks on #infection, #autoimmunity, #cancer immunology & tissue immunity Register 👉bit.ly/4603uJI #GCIR2025 #Inflammation UNIGE_en

The 3rd edition of my book Deep Learning with Python is being printed right now, and will be in bookstores within 2 weeks. You can order it now from Amazon or from Manning. This time, we're also releasing the whole thing as a 100% free website. I don't care if it reduces book

Excited to share our new study: Single-cell multiomics reveals archetypal regulatory programs shared across CD4 and CD8 T cell subsets in viral infection bioRxiv: doi.org/10.1101/2025.0… 🧵 Key findings below 👇