Benoît Aliaga
@benoit3166.bsky.social
25 followers 28 following 16 posts
Postdoc at Toulouse Cancer Research Center #aging #cancer #epigenetics #evolution #bioinformatics
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Reposted by Benoît Aliaga
Reposted by Benoît Aliaga
steffenfuchs.bsky.social
We're very happy to invite you to the 𝟑𝐫𝐝 𝐘𝐨𝐮𝐧𝐠 𝐒𝐜𝐢𝐞𝐧𝐭𝐢𝐬𝐭 𝐂𝐚𝐧𝐜𝐞𝐫 𝐂𝐨𝐧𝐠𝐫𝐞𝐬𝐬 𝐚𝐭 𝐭𝐡𝐞 𝐅𝐫𝐞𝐧𝐜𝐡 𝐄𝐦𝐛𝐚𝐬𝐬𝐲 𝐢𝐧 𝐁𝐞𝐫𝐥𝐢𝐧 𝐨𝐧 𝐎𝐜𝐭𝐨𝐛𝐞𝐫 𝟗 &𝟏𝟎.

Visit our website ys2c.org for further information.
benoit3166.bsky.social
🚀 Calling all young cancer researchers!
Abstract submission is NOW OPEN for the 3rd #YS2C Congress!
📍 Berlin | 🗓️ Oct 9–10, 2025
Showcase your work, connect, and inspire the future of cancer research.
👉 Submit today: ys2c.org
#CancerResearch #Postdoc #Clinician
benoit3166.bsky.social
Come check out my poster (#4) at the Persister Cells Conference! I’ll be presenting our latest publication from 1:00 to 2:30 PM—happy to discuss and answer questions. See you there!

📍 Poster #4
🕐 1:00 - 2:30 PM

More details here: t.co/stm6WyvOYR

@helloeacr.bsky.social @verapancaldi.bsky.social
https://academic.oup.com/nar/article-abstract/doi/10.1093/nar/gkaf084/8020235?utm_source=etoc&utm_campaign=nar&utm_medium=email
t.co
benoit3166.bsky.social
Thanks to David Juan, Daniel Rico, and Enrique Carrillo for the initial ChAs framework and for discussions on this project, to Emanuele Raineri for co-developing ChAseR and to Simone Ecker for fundamental discussions on gene expression variability that led to this.
benoit3166.bsky.social
But does this have any relevance in solid tumours? Hard to say due to lack of data, but some of our findings might hold (see supplementary material).
benoit3166.bsky.social
In brief, we reveal distinct genome spatial patterns associated with gene evolutionary ages. We suggest that RNA PolII facilitates old UC genes’ preferential interactions. Polycomb regulation of EM genes is largely lost in cancer, where MM genes may cluster at the periphery.
benoit3166.bsky.social
Old UC genes have preferential interactions in all 3 cell states. EM genes have reduced preferential interactions in cancer. New genes acquire some preferential interactions only in cancer, potentially mediated by the lamina at the nuclear periphery.
benoit3166.bsky.social
We used chromatin assortativity (ChAs) analysis to quantify clustering patterns of genes with specific characteristics. Read this paper to know more about the ChAseR tool to perform this analysis (Madrid-Mencia et al. 2020 shorturl.at/Ax73E).
benoit3166.bsky.social
Polycomb is key for 3D chromatin structure (Pancaldi et al. 2016 shorturl.at/YEOQr). So we looked at spatial organisation of genes of specific evolutionary ages finding preferential interactions on 3D promoter-centred chromatin networks.
benoit3166.bsky.social
We analysed differentiation and oncogenesis with 3 cell types: stem, differentiated, and cancer (hESC, B cells, and CLL, a B-cell lymphoma). RNA PolII Pausing regulates primarily old UC genes, especially in normal B cells, in which Polycomb targets the highest gene percentage.
benoit3166.bsky.social
Combining ChIP-seq and DNA methylation datasets in monocytes we see different regulation: Polycombs preferentially regulates intermediate EM genes, and DNA methylation regulates mainly recent MM genes.
benoit3166.bsky.social
Second: in monocytes the Polycomb, H3K27me3 repressive mark shows a higher enrichment around intermediate EM genes, than around old UC and young MM genes.
benoit3166.bsky.social
First: gene expression and expression variability across individuals are strongly associated with evolutionary ages in 3 immune cell types, old UC genes - low variability, recent EM genes - high variability
benoit3166.bsky.social
We studied gene regulation and 3D organisation across 16 evolutionary ages, further grouped into three classes: UC (Unicellular genes), EM (Early metazoan genes), and MM (Mammalian-specific genes) as in Trigos et al. 2017 tinyurl.com/yvwwja2s
PNAS
Proceedings of the National Academy of Sciences (PNAS), a peer reviewed journal of the National Academy of Sciences (NAS) - an authoritative source of high-impact, original research that broadly spans...
tinyurl.com
benoit3166.bsky.social
Old genes are often highly expressed in cancer, while newer genes tend to be repressed. However, the underlying mechanisms were never explored.
Reposted by Benoît Aliaga
ryanelliott.bsky.social
💊 Chemotherapy: disrupting cancer cell cell growth and survival at multiple levels.

This handy diagram summarizes chemotherapy classes and where they fit according to their mechanism of action ⚙️

#oncsky #hemeonc #hemesky #pharmsky #medsky #IMsky #cancer #chemo
(Falzone et al., 2023. Cell)
Reposted by Benoît Aliaga
training.ebi.embl.org
The @events.embl.org 2025 Courses and Conferences poster has had an update!

If you're especially interested in training in #datascience #AIinScience #omics and #bioinformatics, you can find a list of the EMBL-EBI courses here: www.ebi.ac.uk/training/liv...

🧪🖥️🧬
Reposted by Benoît Aliaga
robertife.bsky.social
Please RS/RT. #GordonConference on "Histone and DNA Modifications" #epigenetics #chromatin 20-25. July 2025. Il Ciocco, Italy. Great speaker lineup.
➡️Register now www.grc.org/histone-and-...