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Manolis Maragkakis

@manolis-maragkakis.bsky.social
3.1K followers 2.4K following 49 posts

Stadtman Principal Investigator @NIH / NIA. Computational Genomics, RNA, Aging, Stress Response, Senescence. Posts are my own. maragkakislab.com

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Manolis Maragkakis @manolis-maragkakis.bsky.social · 21/07/2026
NCBI/NLM is hosting a symposium on #epitranscriptomics data and database standards on September 14, 2026 #RNA [Free registration] ncbiinsights.ncbi.nlm.nih.gov/event/epitra...
ncbiinsights.ncbi.nlm.nih.gov
Epitranscriptomics Data Symposium 2026 - NCBI Insights
Research and Standards for a Growing Field We are excited to announce that NCBI/NLM is hosting a symposium on epitranscriptomics data and database standards on September 14, 2026 from 9:00 am – 3:00 p...
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Manolis Maragkakis @manolis-maragkakis.bsky.social · 15/05/2026
Congrats Michael! Best of luck in your new chapter
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Junyue Cao @junyuecao.bsky.social · 26/02/2026
New paper alert 🚀 Our organism-wide single-cell ATAC-seq atlas of mammalian aging is now out in @science.org, led by our fantastic graduate student Ziyu Lu from @rockefeller.edu! www.science.org/doi/10.1126/...
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Gan Lab @liganlab.bsky.social · 26/02/2026
Excited to share our new preprint showing cGAS mediates innate immune activity in TDP-43 proteinopathy. Pharmacological inhibition of cGAS restores microglial function, corrects RNA mis-splicing, & protects motor neurons across human iPSC & mouse models of ALS www.biorxiv.org/content/10.6...
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Manolis Maragkakis @manolis-maragkakis.bsky.social · 09/06/2025
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
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Nature Neuroscience @natneuro.nature.com · 06/06/2025
Neuronal aging leads to widespread dysregulation of RNA biology, including mislocalization of splicing proteins like TDP-43, chronic cellular stress, and reduced resiliency @kevinrhine.bsky.social www.nature.com/articles/s41...
nature.com
Neuronal aging causes mislocalization of splicing proteins and unchecked cellular stress - Nature Neuroscience
Rhine et al. find that neuronal aging leads to widespread dysregulation of RNA biology, including mislocalization of splicing proteins like TDP-43, chronic cellular stress and reduced resiliency.
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Manolis Maragkakis @manolis-maragkakis.bsky.social · 04/06/2025
🚨 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
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Nature Chemical Biology @natchembio.nature.com · 03/06/2025
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...
nature.com
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...
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Olivier Duss @olivierduss.bsky.social · 29/04/2025
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...
biorxiv.org
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...
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Manolis Maragkakis @manolis-maragkakis.bsky.social · 10/04/2025
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.
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Manolis Maragkakis @manolis-maragkakis.bsky.social · 10/04/2025
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.
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Manolis Maragkakis @manolis-maragkakis.bsky.social · 10/04/2025
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.
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Molecular Cell @cp-molcell.bsky.social · 10/04/2025
Online Now: A nuclear RNA degradation code is recognized by PAXT for eukaryotic transcriptome surveillance Online now:
dlvr.it
A nuclear RNA degradation code is recognized by PAXT for eukaryotic transcriptome surveillance
Soles et al. demonstrate that the combination of a 5′ splice site and a poly(A) junction constitutes a nuclear RNA degradation code that targets RNAs for degradation by the PAXT adaptor and the RNA exosome. This study provides fundamental insight into how the RNA exosome specifically recognizes misprocessed RNAs.
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Manolis Maragkakis @manolis-maragkakis.bsky.social · 10/04/2025
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
sciencedirect.com
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…
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Manolis Maragkakis @manolis-maragkakis.bsky.social · 08/04/2025
Wonderful collaboration with Payel Sen's group. Spatial transcriptomics reveal #inflammation origins in the white matter of the #aging mouse #brain
nature.com
Spatial transcriptomics of the aging mouse brain reveals origins of inflammation in the white matter - Nature Communications
This study profiles the spatial transcriptomic landscape of mouse brain coronal sections across three age groups and both sexes. Here, authors show a strong female-biased pro-inflammatory gene signatu...
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Liam Faller @liamfaller.bsky.social · 06/03/2025
New review from the lab looking at high throughput methods of identifying ribosome heterogeneity. Great work from @ferhatalkan.bsky.social, Edwin Kyei-Baffour, and Qi Chang Lin! royalsocietypublishing.org/doi/10.1098/...
royalsocietypublishing.org
High-throughput approaches for the identification of ribosome heterogeneity | Philosophical Transactions of the Royal Society B: Biological Sciences
Recent advances in the fields of RNA translation and ribosome biology have demonstrated the heterogeneous nature of ribosomes. This manifests not only across different cellular contexts but also withi...
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Eugene Valkov @eugenevalkov.bsky.social · 12/02/2025
Latest work from our next door neighbors! #RNAsky #RNAbiology
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Altmetric @altmetric.com · 06/02/2025
Here's Twitter's descent since 2022
2022-2025 X Twitter mention data
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Manolis Maragkakis @manolis-maragkakis.bsky.social · 22/12/2024
Thanks Eugene!
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Manolis Maragkakis @manolis-maragkakis.bsky.social · 21/12/2024
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
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Manolis Maragkakis @manolis-maragkakis.bsky.social · 17/12/2024
If you want to hear me rant about #RNA, #stress, #aging, #senescence come join me at the RNA collaborative seminar tomorrow Wed 4pm (EST) #RNAsociety #RNAsky #RNAbiology
us02web.zoom.us
Welcome! You are invited to join a webinar: RNA Collaborative - NCI RNA Biology Initiative. After registering, you will receive a confirmation email about joining the webinar.
Featuring: “Genome-Scale Exon Deletion Screens Reveal Exons Critical for Cell Fitness and Gene Expression” Thomas Gonatopoulos-Pournatzis, PhD NIH Stadtman Investigator, Functional Transcriptomics S...
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Manolis Maragkakis @manolis-maragkakis.bsky.social · 12/12/2024
circRNAs as tools for gene silencing, similar to microRNA-mediated gene silencing. Do we also need circRNA target prediction software? Circular RNAs trigger nonsense-mediated mRNA decay: Molecular Cell
cell.com
Circular RNAs trigger nonsense-mediated mRNA decay
Boo and Shin et al. uncover that the EJC deposited onto circRNAs after back-splicing is spatially located near the 3′ UTR of mRNA through circRNA-mRNA interaction. The EJC on circRNA triggers NMD of the mRNA. Mechanistic studies reveal the roles of circNMD in apoptosis and its therapeutic potential for mRNA downregulation.
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Altmetric @altmetric.com · 11/12/2024
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
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Ruben Gonzalez @rubenlgonzalez.bsky.social · 11/12/2024
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...
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Manolis Maragkakis @manolis-maragkakis.bsky.social · 12/12/2024
Thanks. 👀 seems I'm the most permanent staff. Coming from snakemake, maybe time to dive into nextflow as well 😅
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Manolis Maragkakis @manolis-maragkakis.bsky.social · 12/12/2024
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.
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Manolis Maragkakis @manolis-maragkakis.bsky.social · 11/12/2024
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
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Ricard Solé @ricardsole.bsky.social · 07/12/2024
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....
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Pablo Gómez Barreiro @pagomba.bsky.social · 07/12/2024
🎄🧪 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
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Manolis Maragkakis @manolis-maragkakis.bsky.social · 05/12/2024
G3BP1 promotes intermolecular RNA-RNA interactions during #RNA condensation #RNAsky www.cell.com/molecular-ce...
cell.com
G3BP1 promotes intermolecular RNA-RNA interactions during RNA condensation
Parker et al. demonstrate that some proteins responsible for organizing ribonucleoprotein granules can chaperone intermolecular RNA-RNA interactions in addition to their role in scaffolding. These findings cement RNA-RNA interaction networks as a key component of granules, highlighting the need to further explore the regulation of RNA dynamics within granules.
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Tae Gyun Kim @taegyunkim.bsky.social · 05/12/2024
A chimeric peptide promotes immune surveillance of senescent cells in injury, fibrosis, tumorigenesis and aging www.nature.com/articles/s43...
nature.com
A chimeric peptide promotes immune surveillance of senescent cells in injury, fibrosis, tumorigenesis and aging - Nature Aging
Ming, Yang, Huang et al. design a chimeric matchmaker peptide, which targets a senescent cell-specific surface marker and modifies the cell surface with polyglutamic acid. This promotes interactions w...
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Olivier Borkowski @oborkowski.bsky.social · 04/12/2024
Tracking transcription–translation coupling in real time doi.org/10.1038/s415...
doi.org
Tracking transcription–translation coupling in real time - Nature
Single-molecule fluorescence microscopy experiments with a recombinant Escherichia coli transcription–translation system provides insights into the coordination of the transcription and translation ma...
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Eugene Valkov @eugenevalkov.bsky.social · 04/12/2024
#RNAsky #RNAbiology
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Carolyn Bertozzi @carolynbertozzi.bskyverified.social · 03/12/2024
Cool new work from Jenn Prescher and coworkers @ucirvine.bsky.social, “RNA lantern” technology for bioluminescence imaging of RNA transcripts www.nature.com/articles/s41...
nature.com
A modular platform for bioluminescent RNA tracking - Nature Communications
Studying RNA dynamics in vivo often relies on fluorogenic approaches, but these can be hampered by factors such as limited sensitivity and sample autofluorescence. Here, the authors describe an ultras...
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Melike Dönertaş @mdonertas.bsky.social · 29/11/2024
A panoramic view of cell population dynamics in mammalian aging www.science.org/doi/10.1126/...
science.org
A panoramic view of cell population dynamics in mammalian aging
To elucidate aging-associated cellular population dynamics, we present PanSci, a single-cell transcriptome atlas profiling over 20 million cells from 623 mouse tissues across different life stages, se...
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Manolis Maragkakis @manolis-maragkakis.bsky.social · 28/11/2024
Can I join 🙋‍♂️? Thanks!
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Manolis Maragkakis @manolis-maragkakis.bsky.social · 27/11/2024
Tips for scientist that are joining bsky. Super helpful to fill out your profile *before* you follow anyone. Listing interests and what you do helps a lot. At least one post, also helps to set the tone. Then starter packs will help you find accounts. Also ask to be added when within your expertise.
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Manolis Maragkakis @manolis-maragkakis.bsky.social · 27/11/2024
Yes anyone can add. afaik that’s the reason paperpile was developed in the first place i.e. facilitate collaboration
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Manolis Maragkakis @manolis-maragkakis.bsky.social · 26/11/2024
@paperpile.bsky.social is excellent for collaboration. Works with google docs and MS Word.
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Manolis Maragkakis @manolis-maragkakis.bsky.social · 26/11/2024
Thanks. Could you please add me 🙋‍♂️?
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Manolis Maragkakis @manolis-maragkakis.bsky.social · 26/11/2024
Maybe machine learning in aging research. I also second post-transcriptional regulation.
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Manolis Maragkakis @manolis-maragkakis.bsky.social · 26/11/2024
img: Sci-Illustrate.com. Dichotomy of stress response in senescent and cycling cells. Low #ribosome content in #senescence (right) reduces upstream ORF bypass (gold line) on ATF4 #RNA, despite high eIF2α-P (green). ➡️ Prevents #ISR activation and remodels the secretome (red). #aging #cancer #GeroSky
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Manolis Maragkakis @manolis-maragkakis.bsky.social · 26/11/2024
🙋‍♂️ Could I please join? Thanks
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Manolis Maragkakis @manolis-maragkakis.bsky.social · 26/11/2024
Can I please join? Thanks
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Sandra McAllister, PhD @sandramcallister.bsky.social · 25/11/2024
I hope you'll find this helpful in building our community around #CancerandAging go.bsky.app/AfLLSfN
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Manolis Maragkakis @manolis-maragkakis.bsky.social · 26/11/2024
🙋‍♂️ can I join? thanks
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Manolis Maragkakis @manolis-maragkakis.bsky.social · 26/11/2024
Given the stochasticity, the true benefit of a postdoc is to have fun doing something you like and care about. So I always advise my trainees to make sure they have fun along the way. And certainly, from day one, constantly evaluate their chances of landing an academic job.
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Jalees Rehman @jalees.bsky.social · 25/11/2024
Mitochondrial fatty acid oxidation drives senescence www.science.org/doi/10.1126/...
science.org
Mitochondrial fatty acid oxidation drives senescence
Nuclear DNA damage activates fatty acid–fueled mitochondrial energy metabolism to induce cellular senescence, a hallmark of aging.
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Manolis Maragkakis @manolis-maragkakis.bsky.social · 26/11/2024
🙋‍♂️ me too. Thanks!
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Manolis Maragkakis @manolis-maragkakis.bsky.social · 26/11/2024
Very nice work!
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