Matthieu Foll

5 relative abundance plots arranged to have increasing compositional variability (variability across relative abundance samples, here vertical bars)

1/ Hey y'all, I'm excited to share my latest paper, which is out now in PNAS! We introduce FAVA, a statistical framework to measure compositional variability across microbiome samples. If you want to measure variability across a stacked bar plot, FAVA is for you! Paper: doi.org/10.1073/pnas...

Cooperative nutrient scavenging is an evolutionary advantage in cancer - Nature Nutrient-starved tumour cells cooperate by secreting aminopeptidases that digest oligopeptides in the microenvironment, creating a shared pool of free amino acids.

Tumor cells help each other out when amino acids are scarce www.nature.com/articles/s41...

Inspiring talk from @matthieufoll.bsky.social and Lynnette Fernandez-Cuesta about the future of #lung #neuroendocrine #tumor classification and clinical management, and how to use #AI to learn simple morphological features to recognize molecular subtypes #CRCL25

@lisemangiante.bsky.social from @stanfordpress.bsky.social : breast #cancer adopt specific ecological strategies to adapt to their microenvironment 🤯 #CRCL25

How do lung #neuroendocrine #tumors and their microenvironment coevolve ? Great talk by Alexandra Sexton Oates at #CRCL25 #LungNETs #lungcancer

Thrilled to introduce our Cell Reports @cellreports.bsky.social article, showing how the iconic 'Hallmarks of Cancer' are located in the space of real human primary tumors. A team effort co-led by Eduard Porta, Matthew H. Bailey, and yours truly #SpatialBiology #Visium
www.cell.com/cell-reports...

Genetic background sets the trajectory of cancer evolution Human cancers are heterogeneous. Their genomes evolve from genetically diverse germlines in complex and dynamic environments, including exposure to potential carcinogens. This heterogeneity of humans,...

🌟NEW PREPRINT ALERT!🌟

We are very pleased to introduce #StrainDifferences: “Genetic background sets the trajectory of cancer evolution”

www.biorxiv.org/content/10.1...

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Cell type-specific interaction analysis using doublets in scRNA-seq AbstractSummary. Doublets are usually considered an unwanted artifact of single-cell RNA-sequencing (scRNA-seq) and are only identified in datasets for the

Cell type-specific interaction analysis using doublets in scRNA-seq

🚨 Very proud of this commentary led by @rijazaidi.bsky.social reasoning on the impact of methods and experimental design on cancer evolution understanding, motivated by the outstanding work of @TheBoutros, @VanLooLab, @kellrott et al

Original work 👉 doi.org/10.1038/s415...

Our Commentary 👇

Recommendations for Bioinformatics in Clinical Practice www.biorxiv.org/content/10.... "Key recommendations include adopting the hg38 genome build as the reference and a standard set of recommended analyses, including the use of multiple tools for structural variant (SV) calling"

High content of nuclei-free low-quality cells in reference single-cell atlases: a call for more stringent quality control using nuclear fraction - BMC Genomics The advent of droplet-based single-cell RNA-sequencing (scRNA-seq) has dramatically increased data throughput, enabling the release of a diverse array of tissue cell atlases to the public. However, we...

Not checking nuclear markers like MALAT1 or intronic reads in your scRNA-seq data?🚨
We show their power to flag low-quality cells—even in top public datasets. It’s time to prioritize better QC for cleaner, more reliable genomics research!
Read more: bmcgenomics.biomedcentral.com/articles/10....
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Congratulations @EMathian! So well deserved! https://x.com/CancersRare/status/1738201813545848991

Still looking for a postdoc? Yes, we have a second position to join our team and work with @nl_alcala @FCLynnette and myself! https://rarecancersgenomics.com/vacancies/
#PostdocJobs https://x.com/CancersRare/status/1726698337007776217

Looking for a postdoc? Join our team to work with @nl_alcala @FCLynnette and myself! https://rarecancersgenomics.com/vacancies/
#PostdocJobs https://x.com/CancersRare/status/1726697028372348929

https://x.com/cancersrare/status/1636469351212634112

So happy to see this paper published and feeling lucky to lead the #MESOMICS project together with @FCLynnette and a fantastic team @CancersRare. Cancers associated with asbestos exposure are deadly and rising, despite its classification as a carcinogen by @IARCWHO 50 years ago https://t.co/FId6...

Proton and alpha radiation-induced mutational profiles in human cells Ionizing radiation (IR) is known to be DNA damaging and mutagenic, however less is known about which mutational footprints result from exposures of human cells to different types of IR. We were interested in the mutagenic effects of particle radiation exposures on genomes of various human cell types, in order to gauge the genotoxic risks of space travel, and of certain types of tumor radiotherapy. To this end, we exposed cultured cell lines from the blood, breast and lung to intermittent proton and alpha particle (helium nuclei) beams at doses sufficient to affect cell survival. Whole-genome sequencing revealed that mutation rates were not overall markedly increased upon proton and alpha exposures. However, there were changes in mutation spectra and distributions, such as the increases in clustered mutations and of certain types of indels and structural variants. The spectrum of mutagenic effects of particle beams may often be cell-type and/or genetic background specific. Overall, the mutational effects of recurrent exposures to proton and alpha radiation on human cells appear subtle, however further work is warranted to understand effects of chronic, long-term exposures on various human tissues. ### Competing Interest Statement The authors have declared no competing interest.

Hesitating between being proud or jealous that former PhD student @tm_delhomme’s latest preprint very first sentence mentions “extraterrestrial colonization”… Sorry I missed it during summer! I https://www.biorxiv.org/content/10.1101/2022.07.29.501997v1

Disentangling heterogeneity of Malignant Pleural Mesothelioma through deep integrative omics analyses Malignant Pleural Mesothelioma (MPM) is an aggressive cancer with rising incidence and challenging clinical management. Using the largest series of whole-genome sequencing data integrated with transcriptomic and epigenomic data using multi-omic factor analysis, we demonstrate that MPM heterogeneity arises from four sources of variation: tumor cell morphology, ploidy, adaptive immune response, and CpG island methylator phenotype. Previous genomic studies focused on describing only the tumor cell morphology factor, although we robustly find the three other sources in all publicly available cohorts. We prove how these sources of variation explain the biological functions performed by the cancer cells, and how genomic events shape MPM molecular profiles. We show how these new sources of variation help understand the heterogeneity of the clinical behavior of MPM and drug responses measured in cell lines. These findings unearth the interplay between MPM functional biology and its genomic history, and ultimately, inform classification, prognostication and treatment. ![Figure][1]</img> ### Competing Interest Statement Where authors are identified as personnel of the International Agency for Research on Cancer/World Health Organisation, the authors alone are responsible for the views expressed in this article and they do not necessarily represent the decisions, policy or views of the International Agency for Research on Cancer/World Health Organisation. Where authors are identified as personnel of the Centre de Recherche en Cancerologie de Lyon (CRCL), the authors declare no conflict of interests. A.S. participated in expert boards and clinical trials with Astra-Zeneca, BMS, MSD, Roche. N.G. declares consultancy, research support from BMS, Astra-Zeneca, Roche, and MSD. All the other authors declare no conflict of interests. [1]: pending:yes

So proud of this preprint https://biorxiv.org/cgi/content/short/2021.09.27.461908v1, read this thread to know more: https://x.com/CancersRare/status/1443249588261949440

Great work from the @CancersRare team: @gabriel_aurelie @LiseMangiante @nl_alcala and @FCLynnette

Open science = open access + open data + open code + open peer review. Thanks @GigaScience for allowing all this and the great publication experience. Cc @usenextjournal https://x.com/GigaScience/status/1324079575878557697

Playing with ⁦@github⁩ #Codespaces beta. First thing tried is of course running ⁦@nextflowio⁩!

Model-based joint visualization of multiple compositional omics datasets Abstract. The integration of multiple omics datasets measured on the same samples is a challenging task: data come from heterogeneous sources and vary in s

Model-based joint visualization of multiple compositional omics datasets https://academic.oup.com/nargab/article/2/3/lqaa050/5874365

Pr H. Chneiweiss presenting ongoing @WHO efforts for a global governance for human genome editing at the 1st International symposium on Human Genomics organized by @fr_genomics #FG_ISHG2020

Somatic mutations and clonal dynamics in healthy and cirrhotic human liver - Nature Whole-genome sequencing of liver microdissections from five healthy individuals and nine with cirrhosis demonstrates the effects of liver disease on the genome, including increased rates of mutation, complex structural variation and different mutational signatures.

Somatic mutations and clonal dynamics in healthy and cirrhotic human liver | Nature https://www.nature.com/articles/s41586-019-1670-9

The landscape of somatic mutation in normal colorectal epithelial cells - Nature Genome sequencing of hundreds of normal colonic crypts from 42 individuals sheds light on mutational processes and driver mutations in normal colorectal epithelial cells.

The landscape of somatic mutation in normal colorectal epithelial cells | Nature https://www.nature.com/articles/s41586-019-1672-7

nextflow hello

Running @nextflowio in @usenextjournal in a snap of a finger: https://nextjournal.com/mfoll/nextflow-hello

Great place, great project, great mentoring, speaking from experience! https://t.co/o8iY8MFuCN

The three technologies bioinformaticians need to be using right now http://www.opiniomics.org/the-three-technologies-bioinformaticians-need-to-be-using-right-now/

We are organising a @nextflowio training in September at @IARCWHO in #Lyon together with @canceroCLARA, please RT. #HPC #Bioinformatics https://t.co/cQa9gUdiyv cc @LyonDataScience @grenobledata @JeBiF @IFB_Bioinfo @SfbiFr @BioinfoFr

One reference genome is not enough - Genome Biology A recent study on human structural variation indicates insufficiencies and errors in the human reference genome, GRCh38, and argues for the construction of a human pan-genome.

One reference genome is not enough https://genomebiology.biomedcentral.com/articles/10.1186/s13059-019-1717-0