Computational biologist at @IARCWHO. Views are my own. co-PI of the Computational Cancer Genomics team: https://xitter.cf/t.co/kbwe5cCyjX / @CancersRare

France
Joined May 2011
Could some lung neuroendocrine tumours be in the wrong box? New research involving 319 lung NETs identified four distinct molecular groups, including a more aggressive supra-carcinoid group with biological links to small cell lung cancer. The findings could help refine how these rare lung cancers are classified and studied. link.springer.com/article/10… #LCSM
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Matthieu Foll retweeted
New #IARCpaper establishes existence of4⃣molecular groups of lung neuroendocrine tumours with unique etiology, clinical & epidemiological features... Potential implications for prevention, classification & clinical management. Published in Molecular Cancer iarc.who.int/news-events/dee…
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Matthieu Foll retweeted
This is a fascinating but dense paper on molecular profiling of lung NENs. A few take-home points: -- There arefour strikingly different molecular groups that vary in patient characteristics, genomic and transcriptomic profiles, microenvironment, and morphology. -- A new molecular group, enriched for highly aggressive supra‐carcinoids that displayed an immune‐rich microenvironment linked to tumour-macrophage crosstal -- There appears to be an undifferentiated cell population within supra-carcinoids showing the transcriptomic similarities between supra-carcinoids and the recently identified atypical small cell lung cancer tumours, further demonstrating their molecular link to high-grade lung neuroendocrine carcinomas -- There appear to be distinct evolutionary trajectories, suggesting that molecular groups are determined early in tumourigenesis by genomic events, and that transitions between groups, though infrequent, are possible for supra-carcinoids link.springer.com/article/10…
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ecDNA are rogue genetic material that amplify genes, contribute to treatment resistance and drive genomic heterogeneity. We report on the Origins and impact of extrachromosomal DNA today in @Nature nature.com/articles/s41586-0…
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'Emerging strategies to investigate the biology of early cancer' nature.com/articles/s41568-0…
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Semi-supervised Omics Factor Analysis (SOFA) disentangles known sources of variation from latent factors in multi-omics data biorxiv.org/cgi/content/shor… #biorxiv_bioinfo
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The Curated Cancer Cell Atlas: comprehensive characterisation of tumours at single-cell resolution biorxiv.org/cgi/content/shor… #biorxiv_cancer
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We are thrilled to welcome Yuliya Lim as a PhD student in the team, under the supervision of @nl_alcala, L. Fernandez-Cuesta, and @m_foll! Yuliya recieved a competitive PhD fellowship from @laliguecancer and will work on deciphering the mysteries of cancer ecosystem complexity.
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Very happy to share our opinion on the need for a naming convention for #peritumoral tissues (#PTT)! Great work by Dzenis Koca with Dr Behnoush Abedi-Ardekani and Dr Joël Le Maoult! nature.com/articles/s41416-0…
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Matthieu Foll retweeted
Can tumours be described as complex ecological systems? What is the mathematical description of their dynamics and treatments? Check our @iScience_CP paper with @AguadeGuim and @ara_anderson in cell.com/iscience/fulltext/S…
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New research from @katherlab on #computational #pathology: We benchmark pathology foundation models 👇 Several of these are publicly available under permissive licenses. arxiv.org/abs/2408.15823 Some takeaways: 1. The vision-language model CONCH (@AI4Pathology) outperforms vision-only models in many tasks. 2. Data diversity matters more than volume for improving pathology model performance. 3. Combining multiple models boosts accuracy, outperforming single models in most tasks.
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Assessment of methods to deconvolve cellular composition from bulk gene expression. #DREAM, #Immunotherapy, #deconvolution nature.com/articles/s41467-0…
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Matthieu Foll retweeted
Tumor heterogeneity is a major obstacle to effective cancer treatment. It is caused by multiple factors, including irreversible mutations and reversible phenotypic changes. But how can we model the interplay between both processes and what's their effect on cancer treatment? 1/
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Our opinion piece is out today, "The origin of novel traits in cancer"! Do the phenotypes come first and only later are they locked in by genetic or epigenetic changes? Insights from evolutionary biology are super useful for understanding cancer! cell.com/trends/cancer/abstr… #S_Frank
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Matthieu Foll retweeted
Are computational biologists the drivers of research? 7 years ago I co-wrote an editorial about how computational biologists are no longer just supportive, but are now running the show. Today I would write how every biologist should also be computational. genomebiology.biomedcentral.…
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Matthieu Foll retweeted
💬 “Making #data publicly available should no longer be a by-product but a recognised part of the #research process” 💡Our Executive Director @cdessimoz was at the @scnatCH symposium “Open Research Data (ORD) – are we on track?” last 31 May. more on👉 scnat.ch/en/uuid/i/6796a687-…
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