Manolis Maragkakis
@manolis-maragkakis.bsky.social
2.8K followers 2.3K following 47 posts
Stadtman Principal Investigator @NIH / NIA. Computational Genomics, RNA, Aging, Stress Response, Senescence. Posts are my own.
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manolis-maragkakis.bsky.social
RNAkinet identifies nascent RNA by predicting 5EU metabolically labeled #RNA from raw #nanopore electrical signal. Should allow association of RNA metabolism dynamics with isoform usage, poly(A) tails and native RNA mods. academic.oup.com/nargab/artic...
manolis-maragkakis.bsky.social
Excited to share our work with @markrcookson.bsky.social and Payel Sen labs. We combine #SingleCell and #Nanopore sequencing to profile #RNA isoforms from young to geriatric mouse brains. We uncover #aging changes in transcription, processing, and splicing that also impact coding potential.

#RNAsky
manolis-maragkakis.bsky.social
🚨 We’re looking for a curious mind to join our lab at the NIH!
Passionate about #RNA biology, #MachineLearning, and the #genomics of #aging?

Interested in a postdoc or a PhD research visit at NIH? Let’s connect.
📩 DM or email for details!

#Bioinformatics #AI #ComputationalBiology
Reposted by Manolis Maragkakis
natchembio.nature.com
A programmable RNA acetylation system using dCas13-eNAT10 is developed to install N4-acetylcytidine on target RNAs in cells and in vivo, enabling functional studies of RNA acetylation and revealing the unique role of RNA acetylation in transcript localization

www.nature.com/articles/s41...
Programmable RNA acetylation with CRISPR–Cas13 - Nature Chemical Biology
Yu et al. developed a programmable RNA acetylation system using dCas13–eNAT10 to specifically install N4-acetylcytidine on target RNAs in cells and in vivo, enabling functional studies of RNA acetylat...
www.nature.com
Reposted by Manolis Maragkakis
olivierduss.bsky.social
The timeline of co-transcriptional #mRNA processing and #modification may have to be revised: cleavage, termination, and #m6A deposition may occur earlier than most #splicing! Potential textbook changing study in bioRxiv by edueyras.bsky.social & Rippei Hayashi labs!
www.biorxiv.org/content/10.1...
Single-molecule multimodal timing of in vivo mRNA synthesis
mRNA synthesis requires extensive pre-mRNA maturation, the organisation of which remains unclear. Here, we directly sequence pre-mRNA without metabolic labelling or amplification to resolve transcript...
www.biorxiv.org
manolis-maragkakis.bsky.social
Yeah almost all pop up when I allow the word mRNA. Also cleaning up some myself. Hopefully it doesn't get too much out of hand.
manolis-maragkakis.bsky.social
It is based on regular expressions, not tags, so anything (with some filters :) ) with the word RNA in some context will make it to the feed. If signal to noise ratio gets lower, then stricter filters may be needed.
manolis-maragkakis.bsky.social
I've built an #RNA feed for personal use to capture RNA biology posts across the entire network. Some arbitrary filters used to hopefully increase signal to noise ratio but otherwise not moderated. Feel free to follow if you find useful.
manolis-maragkakis.bsky.social
An interesting perspective and framework: #RNA condensates-not individual RNAs-may have acted as replicative units in early life. RNAs in condensate recruit similar RNAs, then the condensate divides once it reaches a critical size.

#RNAsky
An RNA condensate model for the origin of life
The RNA World hypothesis predicts that self-replicating RNAs evolved before DNA genomes and coded proteins. Despite widespread support for the RNA Wor…
www.sciencedirect.com
Reposted by Manolis Maragkakis
altmetric.com
Here's Twitter's descent since 2022
2022-2025 X Twitter mention data
manolis-maragkakis.bsky.social
Our paper out in eLife. Full-length direct RNA #nanopore sequencing uncovers 5' #RNA shortening upon cellular #stress that depends on ✅ stress-granules and #XRN1 but ❌ not poly(A) or cap removal elifesciences.org/articles/96284

🤔 useful to further reduce translational load during #ISR?

#RNAbiology
Reposted by Manolis Maragkakis
altmetric.com
SERVICE UPDATE

We normally don't ask you to "share like and subscribe" but please distribute this.

You are now able to delete the link after it embeds on your post so you can get those precious extra characters, and we will catch your post mentioning research.

#AcademicSky #Medsky #HigherEd
Reposted by Manolis Maragkakis
rubenlgonzalez.bsky.social
Our latest work is out in Nature today! Using smFRET, we directly visualized recruitment of the eIF4F complex to the 5' cap of eukaryotic mRNAs and formation of an activated mRNA. Our findings reveal new and surprising roles for each eIF4F component. 1/3 www.nature.com/articles/s41...
manolis-maragkakis.bsky.social
Thanks. 👀 seems I'm the most permanent staff. Coming from snakemake, maybe time to dive into nextflow as well 😅
manolis-maragkakis.bsky.social
Yes I do use snakemake regularly but that's only because I found it a bit easier for my workflow several years back. Mostly HPC.
manolis-maragkakis.bsky.social
Not looking to start a debate on #nextflow vs. #snakemake, but curious about their ease of adoption in a typical lab setting with ~4-year PhD/postdoc turnover. How do you feel newcomers adapt to each? Would you recommend one for easier onboarding? Feedback appreciated!
#genomics #bioinformatics
Reposted by Manolis Maragkakis
ricardsole.bsky.social
How can physics define universal laws for computation, from cells and chips to brains? In this @pnas.org Perspective, led by @sfiscience.bsky.social David Wolpert and Jan Korbel, they suggest how Stochastic Thermodynamics can provide the proper framework pnas.org/doi/epub/10....
Reposted by Manolis Maragkakis
pagomba.bsky.social
🎄🧪 Racing to submit your manuscript before the holidays? Check out our ShinyApp for editorial insights on publishers & journals—submission-to-acceptance times and more! Based on data from: doi.org/10.1162/qss_...

Check the app here 👉 pagoba.shinyapps.io/strain_explo...

#AcademicSky
#Science
pagoba.shinyapps.io