Replication Crisis xkcd.com/3117/

Check out my editorial about immune exclusion in hepatoblastoma and a possible role of beta-catenin: www.sciencedirect.com/science/arti...

Thank you @easlnews.bsky.social for giving me the opportunity to present our work on hepatoblastoma genomics and future therapeuties in Amsterdam, together with my mentor @zucmanrossi.bsky.social @crcordeliers.bsky.social

🔙 on our Hepatology and Liver Transplantation Days! 🤝 We had the pleasure of welcoming @tz-hirsch.bsky.social for a presentation titled: Evolution of Hepatoblastoma: From #Liver Development to Chemoresistance. 🧫 His talk sparked dynamic discussions during the session on #hepatic #pathogenesis.

Thank you @ihuhepatolyon.bsky.social for the invitation and the opportunity to present our team work on hepatoblastoma evolution, in a nice castle in Lyon! #FunGeST @crcordeliers.bsky.social

🚀 C'est parti pour le Young Investigators Mentoring Symposium au CRC, organisé par le consortium GENIAL en collaboration avec le laboratoire de @zucmanrossi.bsky.social. Une occasion de favoriser l'échange, la collaboration et la visibilité des talents émergents dans le monde de la recherche!

Great scientific day about mosaicism 👾 at @institutimagine.bsky.social including inspiring talks from Serge Romana and Peter Campbell

Thrilled to reconnect with colleagues from around the globe at the SIOPEL meeting in Cardiff! Working together to better understand and treat childhood liver cancer. 🌍 @crcordeliers.bsky.social

Tools like our Single-cell #PediatricCancer Atlas (ScPCA) Portal make data widely available and easier for researchers to use for their own experiments. Currently, you can explore and download data from 700 samples across 55 cancer types at scpca.alexslemonade.org!

Re-upping these two #CancerResearch 🧪 starter packs for any new arrivals go.bsky.app/FEoaJMc go.bsky.app/6EcjWNA Together they include PIs, oncologists, students, postdocs, journals, patient advocates, and organizations supporting cancer research 🧪🔬⚕️ Both are full - sorry I can't add any more 😅

Excited to share our lab's first preprint: we used spatial transcriptomics to dissect how aging disrupts the cycling ovary! 🧵 This was an incredible team effort w/ @jennifergarrison.bsky.social #TammyLan @davidsebfischer.bsky.social #AlisonKochersberger #RuthRaichur #SophiaSzady

Try out SpatialLeiden for identifying spatial domains/clusters in your #SpatialTranscriptomics data: www.biorxiv.org/content/10.1... github.com/HiDiHlabs/sp... It's as easy as Leiden, but as performant as the best in class. Give it a try and let us know if it works for you!

My first post on Bluesky ! I officially announce that after 15 years at the PARCC HEGP, the Favier Lab has moved today to the Centre de Recherche des Cordeliers. We are very exited to be part of such a prestigious institute ! A new era begins!🤩

Only a subset of patients respond to immunotherapy Why? Which ones? We conducted an unbiased analysis of response biomarkers and found that hundreds of possible biomarkers collapse into five latent, orthogonal factors that underlie immunotherapy response. www.nature.com/articles/s41...

Women are under-represented at senior levels in #academia globally, & across all #science 🧪 disciplines, as shown by these "scissor-shaped curves" ✂️ So how can we ever achieve #gender #equality? We discuss various strategies in this #Cell Commentary #WomeninSTEM www.cell.com/cell/fulltex... 🧵 1/

Children who develop two independent tumors during childhood are extremely rare We wanted to see if our genomic technologies could shed light into those exceptional cases. Read about it in this recent paper: tinyurl.com/yt9m584d

A paradigm-shifting concept 😮 When there’s no mutated target for your CAR-T cells, why not target the wild-type and mutate all non-cancer cells to protect them? www.science.org/doi/10.1126/...

We recently announced a dual new release of intOGen and boostDM Computational analysis of 33,218 tumor genomes to identify cancer genes and driver mutations ➡️ Compendium of Cancer Driver Genes - www.intogen.org ➡️ In Silico Saturation Mutagenesis of Cancer Genes - www.intogen.org/boostdm

Happy to be here & share our work on hepatoblastoma - using transcriptomics and patient-derived tumoroids to identify embryonic biliary transcription factor SOX4 as a modifier of Wnt activation & proliferation - published today in #NatComms @natureportfolio.bsky.social www.nature.com/articles/s41...

Evolving cell states and oncogenic drivers during the progression of IDH-mutant gliomas - Nature Cancer 🧪 www.nature.com/articles/s43...

Let's build a starter pack for childhood cancer research. Please send a message to be added! 🎗️ go.bsky.app/Tpd9QnM

NOTCH1 Drives Sexually Dimorphic Immune Responses in Hepatocellular Carcinoma - by Katherine Lindblad1, @amaialujambio.bsky.social and colleagues doi.org/10.1158/2159...

Resharing here a recent X post. In this preprint, we introduce an improved version of NanoSeq, a duplex sequencing protocol with <5 errors per billion bp in single DNA molecules, and use it to study the somatic mutation landscape of oral epithelium in >1000 people. 1/ www.medrxiv.org/content/10.1...

1/ 🧬 Single-cell genomics reveals biological variations beyond cell types. Unveiling these in separate latent dim’s is known as disentanglement. Led by @AmirAliMoinfar, we develop DRVI to learn nonlinear, disentangled & interpretable latent spaces. biorxiv.org/content/10.1101/2024.11.06.622266v1

—Please give me an A.I. that automatically detects, interprets all types of medical. images (scans, retina, endoscopy, skin) that I can interact with, can integrate data from other sources, saves a lot of time, and improves accuracy —Sure, here it is www.nature.com/articles/s41...

Visited my old high school today to talk to students about fundamental research🧪 I must have convinced them that I’m passionate about my job because they asked me if I was paid during my post-doc :)

With the deluge of new friends - if you are or know someone who is a looking for a position as computational scientist (any level) in #pancreaticcancer, #macrophages #spatialbiology #singlecell... we might have something for you. Will also consider wet lab ppl, send email if interested. pls repost!

Cancer cells often harbor oncogenes outside chromosomes on extrachromosomal DNA (ecDNA), which is unevenly inherited by dividing cells. We reported in Nature last week that collectives of ecDNAs are inherited together by dividing cancer cells. 1/ www.nature.com/articles/s41...

More data highlighting how cell of origin and lineage plasticity may alter lung cancer phenotype. Elegant story exploring basal cells in SCLC www.biorxiv.org/content/10.1...

A gentle introduction to pangenomics https://academic.oup.com/bib/article/25/6/bbae588/7902219

Cancer cell states: Lessons from ten years of single-cell RNA-sequencing of human tumors. Itay Tirosh & Mario L. Suva www.sciencedirect.com/science/arti...

Intravenous and intracranial GD2-CAR T cells for H3K27M+ diffuse midline gliomas Incredible study now out in Nature, with long-term remission for pediatric glioma Michelle Monje, Crystal Mackall et al Well done to all the authors for this true tour de force! 🧪⚕️🩺 www.nature.com/articles/s41...

PhD student: "please don't be excited yet, these are just preliminary results, I still need to repeat the experiment multiple times" PI:

Qingli has been sleuthing through cancer genomes... she realised that long indels in mismatch repair deficient (MMRd) tumours are totally distinct from sequencing noise, so enable exquisitely sensitive and robust detection of MMRd even in the poorest quality data & ultra-low tumour content