silvoLab

@mike_schatz @benbfly @fiamh @coregenomics @nanopore @biorxivpreprint @DanTurnez @jldavies16 @GuardantHealth @GrailBio we try to use 20ng. But the important part to consider is the molarity of the sample (though with the new flow cells should be less important)

@benbfly @fiamh @coregenomics @nanopore @biorxivpreprint @DanTurnez @jldavies16 @GuardantHealth @GrailBio @silvoLab Our clinical samples were basically prep'ed for Illumina (Qiagen AllPrep DNA/RNA Mini Kit) and then ONT adapters ligated on. We started from about 50ng per sample. This was with blood for AML so was a relatively easy tissue to work with

@nanopore what's the current status of short fragment reads? The image on the website shows 20 or 200bp as the cutoffs. What do I need to ctDNA ie 166bp ish? Is there anything new online or @biorxivpreprint ? @DanTurnez @jldavies16

@bicidiario @kiki_la_bulla @marco_heffler @lucacozzuto @AurelianoStingi @dianacalibana @repubblica @Di_SPACE_Lauro Online (non trovo articoli) si indica un polimorfismo di APOBEC3A responsabile di questo nelle popolazioni dell’Asia (anche noi vi accennavamo nel nostro articolo). Questo polimorfismo è presente solo nel 20% di quelle popolazioni. Un po’ poco per avere un effetto sulla pandemia

@bicidiario @kiki_la_bulla @marco_heffler @lucacozzuto @AurelianoStingi @dianacalibana @repubblica @Di_SPACE_Lauro In realtà un evento selettivo del genere c’è già ed è il frutto del lavoro dei professionisti che combattono il virus (anche se non causa il collasso mutazionale) A naso direi che più degli APOBEC in Giappone sta funzionando il sistema sanitario: vaccini, prevenzione, etc.

E' vero che il Sars-CoV2 si è praticamente estinto da solo in Giappone? Ne parlo su @repubblica repubblica.it/salute/2021/11…

Our paper is out in @Nature! Extrachromosomal DNA molecules huddle together in cancer cells to activate oncogene expression (which we call ecDNA hubs). A great collaboration with @KatieEYost, @HowardYChang, @549nm, Zhe Liu, and others. (1/10) nature.com/articles/s4158…

Our study "Individualized VDJ recombination predisposes the available Ig sequence space" is now published in Genome Research 🥳 genome.cshlp.org/content/early/… Congrats @rlyhighvariance et al.!

@albertoxmartin @BernardoReinaSM @Nature @DerianoL @EviSoutoglou @Michel_CogneLab Great work @albertoxmartin! And the small differences between the two papers make it the more intriguing… It keeps fascinating me how B cells twist their repair capabilities to max out immunity nature.com/articles/s4158… nature.com/articles/s4158… and quite a long experience… 😀

@BernardoReinaSM @Nature @DerianoL @EviSoutoglou @silvoLab @Michel_CogneLab Congratulations Bernardo, it was great sharing this experience with your group.

Happy to share our paper on Fam72a, DNA repair and antibody diversification, which has just come out @nature. rdcu.be/cBYhU Thanks to all involved !! Especially to @DerianoL, @EviSoutoglou, @silvoLab, @Michel_CogneLab, Eric Pinaud and Karin Tarte.

@BernardoReinaSM @Nature @DerianoL @EviSoutoglou @Michel_CogneLab Who'd say that being better at repairing DNA damage could be problematic… (and viceversa) nature.com/articles/s4158… Thank you @BernardoReinaSM for starting it, and thanks to all others for making it so interesting. Glad to see plenty of good ol’ AID people gathered around 😀

1/Excited to share my first author publication where we create split-engineered base editors (seBEs). Here, we place base editors under the control of a small-molecule to regulate the timing of genome editing and decrease off-target effects. To achieve it: nature.com/articles/s4158…

Or if you know of other resources/books on the topic… Many thanks in advance :)

Aside from lamenting time and mental resources wasted when I forgot them, I need examples -possibly life-sciences related- to liven up the talk and convince them that choosing the right positive/negative controls is not magic.

I just volunteered to tell 1st year PhD students of the importance of controls in a scientist’s life. Question for scientists on twitter: can you tell me of egregious cases where the lack of a single control changed completely the story and doomed a published paper forever?

Hopefully, one step closer to the clinic… It was exciting working on it: methylation, fragmentomics, and all. Thanks @benbfly and all others! Just a teaser: the correlation of methylation and tumour fraction (healthy controls are the blue bubbles). biorxiv.org/content/10.110…

If you enjoy #RNA biology, #RNAediting, and all sort of RNA modifications (#m6A, etc.), join us next week for the Final EPITRAN Conference. Just a few hours every day, Mon to Wed. The registration is free and the discussions engaging… webmagazine.unitn.it/en/evento/cibi…

Accepted manuscript strongly suggesting that apparent SARS-CoV-2 reads that appear to be integrated in the human genome, are in fact an artefact of library preparation. frontiersin.org/articles/10.33…

@bealelab @TimFenton10 your paper is always the first one I cite when I write of APOBECs and cancer :) 2004 - should I start feeling old?

@TimFenton10 First paper from my PhD speculated this sort of thing would happen :-)

One of the most inspiring, as a person and as a scientist. A huge loss indeed. I will miss him

Do you want to explore basic research but also clinical practice? The IRCM's Master's degree in cellular and molecular medicine (MCM) is for you! ircm.qc.ca/en/studies-and…