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Franck Dumetz 🦠😻🏳️‍🌈

@franckdumetz.bsky.social
371 followers 227 following 75 posts

Research Associate @GenomeScience.bsky.social studying #parasites and #NTDs | #RNAbiology, #RNAstructures, G-quadruplex, Spliced-Leader enthusiast | #LGBTinSTEM 🏳️‍🌈 | 🇪🇺 | 😺lover

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Franck Dumetz 🦠😻🏳️‍🌈 @franckdumetz.bsky.social · 27/08/2026
Please consider a donation to help people in Nepal who suffered from the horrific unforeseeable flash flood www.globalgiving.org/projects/nep...
globalgiving.org
Nepal Flood Relief Fund
Catastrophic flash floods have swept through Nepal and communities along the Bhote Koshi river system, taking lives, destroying homes and critical infrastructure, and leaving hundreds of people unaccounted for. Floodwaters and debris have devastated remote communities across the Himalayan region as search-and-rescue efforts continue. Your donation to the Nepal Flood Relief Fund will provide urgent relief and long-term recovery support to communities impacted by this devastating disaster.
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Franck Dumetz 🦠😻🏳️‍🌈 @franckdumetz.bsky.social · 31/07/2026
I say that publicly, so maybe I stick to it this time: It is the last time I annotate a genome myself! But it was so fun to go through the entire genome manually and to observe things I never saw while working on Leishmania. #crithidia #blurredeyes
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Franck Dumetz 🦠😻🏳️‍🌈 @franckdumetz.bsky.social · 12/06/2026
🧬 New resource for the trans-splicing community! V7 of our curated Splice Leader (SL) sequence table 210 sequences across 11 eukaryotic phyla, newly added Arthropoda, Chaetognatha, Cryptista & Ctenophora. Free to use & cite 👇 doi.org/10.6084/m9.f... #RNAbiology #TransSplicing #Genomics #OpenData
doi.org
Splice Leader (SL) Sequences Across Eukaryotes – Curated Reference Table V7
This dataset compiles experimentally validated splice leader (SL) sequences from diverse eukaryotic taxa, providing a comparative reference for studies on trans-splicing and RNA processing. Version 7 represents a major update from v3 (January 2025), nearly doubling the number of entries from 112 to 210 sequences (+98 entries, +87%).Taxonomic coverage has been significantly expanded to now include 11 phyla: Euglenozoa, Nematoda, Platyhelminthes, Cnidaria, Rotifera, Chordata, Alveolata, and four newly added phyla — Arthropoda (Copepoda), Chaetognatha (Sagittoidea), Cryptista (Cryptomonada), and Ctenophora (Tentaculata/Nuda). The largest expansions were in Nematoda, Cnidaria, and Chaetognatha.The dataset schema was restructured to improve phylogenetic resolution, replacing the single "Family" field with a two-level "Phylum / Subgroup" classification. A formal SL sequence naming convention was introduced, with 170 of 210 entries carrying standardized identifiers. Each entry includes the SL sequence (5' to 3'), sequence length, primary literature reference (DOI and PMID), and contributor information.
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Franck Dumetz 🦠😻🏳️‍🌈 @franckdumetz.bsky.social · 11/05/2026
We collectively have to start recognizing support staff more. Our grant office is composed of three brilliant administrators who are fast-acting, knowledgeable, and they never say "it's not possible" when you come with something new. That truly changes everything.
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Franck Dumetz 🦠😻🏳️‍🌈 @franckdumetz.bsky.social · 08/05/2026
My R21 got scored!!! It's a non-fundable score, but I will have comments to work on. That is truly invigorating for me since I put a lot of time and effort into all the proposals; the "not discussed" comments were not very helpful. Thanks to everybody who read it, I'm very grateful
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Franck Dumetz 🦠😻🏳️‍🌈 @franckdumetz.bsky.social · 07/05/2026
There are milestones in an academic career, today is one: it is the first time in my academic life that I actually look for a human gene!!! I had to ask on what website to find that lol
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Franck Dumetz 🦠😻🏳️‍🌈 @franckdumetz.bsky.social · 14/04/2026
Proud to be part of the @genomescience.bsky.social delegation representing junior faculty members from Microbial Systems and what we have to offer in term of pandemic preparedness.
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Franck Dumetz 🦠😻🏳️‍🌈 @franckdumetz.bsky.social · 21/01/2026
Shoutout to Mike Humphrys from @MarylandGenomics @genomescience.bsky.social for his help earlier today. His comprehension of sequencing technologies and library preparation is close to encyclopedic, and it made the difference.
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Franck Dumetz 🦠😻🏳️‍🌈 @franckdumetz.bsky.social · 10/12/2025
I wish everybody had a boss like @DavidSerre. That's it! I'm leaving that here for future reference
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Franck Dumetz 🦠😻🏳️‍🌈 @franckdumetz.bsky.social · 10/12/2025
Who do we have to lobby to be able to submit pod5 files from @nanoporetech.com to SRA? The actual only way is to use guppy-4.2.2 basecalling fast5 files and that makes very little sense and it is very unpractical! #sequencing #ONT #SRA #NCBI #reproducibility #OpenScience
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Sam Bagenstos @sbagen.bsky.social · 08/12/2025
The best reading of this article: Trump is going to use FDA to restrict medication abortion, but he wants to wait until after the midterms so the Republicans don't experience blowback. But that just makes the midterms more important. www.bloomberg.com/news/article...
bloomberg.com
FDA Slow Walking a Long-Awaited Abortion Pill Safety Study
The Food and Drug Administration has delayed a promised review of safety data for the abortion drug mifepristone at Commissioner Marty Makary’s request to put it off until after the midterm elections,...
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Gabriel da Silva @gabriel93dasilva.bsky.social · 08/12/2025
I am trilled to share my latest publication where we contribute to the knowledge of how ATR kinase, a DNA damage response factor, modulates DNA replication timing during stress in Leishmania major. Huge thanks to @rmc9z.bsky.social, @LuizTosi and the collaborators for the support and guidance!
dx.plos.org
ATR, a DNA damage kinase, modulates DNA replication timing in Leishmania major
Author summary A series of protein kinases act at the pinnacle of eukaryotic cells’ DNA damage response, organising and guiding repair. One such kinase is ATR, which recognises single-stranded DNA for...
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Reposted by Franck Dumetz 🦠😻🏳️‍🌈
Krutika Kuppalli, MD FIDSA @krutikakuppalli.bsky.social · 09/12/2025
🚨 Scientists detected a recombinant monkeypox virus combining Clade Ib & Clade IIb in a traveler from Asia to the UK. The virus continues to surprise us — this is what happens when transmission continues unchecked. Surveillance + data sharing matter more than ever. virological.org/t/inter-clad...
virological.org
Inter-Clade Recombinant Mpox Virus Detected in England in a Traveller Recently Returned from Asia
Inter-Clade Recombinant Mpox Virus Detected in England in a Traveller Recently Returned from Asia Authors: Steven T. Pullan1, Isobel Everall1, Rebecca Doherty1, Lucy Crossman1, Emma Wise1, Hassan Ha...
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Franck Dumetz 🦠😻🏳️‍🌈 @franckdumetz.bsky.social · 03/12/2025
The indirect cost crisis is following its journey where ever it is now. No matter the outcome, we should stay thankful to work with talented administrators and IT staff. @genomescience.bsky.social has a fantastic team of IT specialists. They are essential for our day-to-day life here, thanks guys!
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Institute for Genome Sciences @genomescience.bsky.social · 02/12/2025
It's been a tough year for everyone in #science, and the cuts have hit students hard. On this #GivingTuesday please consider a gift to: The Claire M. Fraser Fund for Graduate Education Give here: bit.ly/CMFGradEd
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Franck Dumetz 🦠😻🏳️‍🌈 @franckdumetz.bsky.social · 30/11/2025
I’m not a medical doctor but I have been working on Neglected Tropical Disease and parasitic disease for my entire career and this has been what has been driving me this whole time.
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Franck Dumetz 🦠😻🏳️‍🌈 @franckdumetz.bsky.social · 14/11/2025
Please people please, once your paper is published, go back on SRA and release it publicly!
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Franck Dumetz 🦠😻🏳️‍🌈 @franckdumetz.bsky.social · 27/10/2025
Find that collaborator that makes you look at the data in a different way and kiss them (or just say thank you) and spend the rest of the day (and night) revisit everything you have done in a year!
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Franck Dumetz 🦠😻🏳️‍🌈 @franckdumetz.bsky.social · 02/10/2025
Saying thank you to someone and truly meaning it is heartwarming. Just putting that here #thankyou
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Franck Dumetz 🦠😻🏳️‍🌈 @franckdumetz.bsky.social · 28/09/2025
After a great week for me and my student, I decided to capitalize on the luck to use MEGA for a tree and cibersort to deconvolute my data. There is no amount of luck that can make those 2 things happen or I used too much of it for everything good that happened earlier this week #sundayscience #fail
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Gabriel Negreira @gnegreira.bsky.social · 11/09/2025
Happy to share our latest preprint, where we present a novel high-throughput #single-cell DNA method that resolves genomic heterogeneity in #Leishmania, from #aneuploidy, #CNVs to #drug-resistance mutations. 🧵... Link here: www.biorxiv.org/content/10.1...
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Franck Dumetz 🦠😻🏳️‍🌈 @franckdumetz.bsky.social · 22/09/2025
My very first fully bioinformatic paper! I did everything myself and now I'm off to do a PCR. I'm grateful to David Serre for teaching me. I hope this will bring new insight to the community and people will enjoy reading it. More to come very soon about Trypanosomatid's genome annotation
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Franck Dumetz 🦠😻🏳️‍🌈 @franckdumetz.bsky.social · 01/09/2025
No MPM for me this year, I have way too much on my plate BUT it doesn't I won't be there. Look for my name and see the great job my very talented student Anushka Shome has done in collaboration with the Hovel-Miner lab on T. brucei
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Franck Dumetz 🦠😻🏳️‍🌈 @franckdumetz.bsky.social · 17/07/2025
Sonny is helping to download some Toxoplasma gondii sequences to analyse. He is fascinated by the idea, as everybody can see 😻😏🙃
Sonny and Toxoplasma sequences
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Franck Dumetz 🦠😻🏳️‍🌈 @franckdumetz.bsky.social · 11/07/2025
Join me at BUGSS on Sat August 9th for a approachable and interactive "lecture" on the theory of Nanopore Sequencing, discuss pros and cons, potential applications, answer your questions, and more. See you there! #ONTsequencing #CitizenScience @genomescience.bsky.social @nanoporetech.com
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Franck Dumetz 🦠😻🏳️‍🌈 @franckdumetz.bsky.social · 11/07/2025
Don't give away fantastic news like "remember what I told you didn't work? well it worked and it looks great but I can't find the file where the description is" just 90min before a progress meeting cause now I want to know for in 90min and not next week Friday #teachingmoment #fantasticintern
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Franck Dumetz 🦠😻🏳️‍🌈 @franckdumetz.bsky.social · 29/06/2025
Making meaningful bioproject/biosample/SRA entry for the entire community to reuse the data is a tedious process but it is worth it. Thank you to my dear colleague and friend @robincubed.bsky.social you taught me the best practices and keeps on advising me.
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Franck Dumetz 🦠😻🏳️‍🌈 @franckdumetz.bsky.social · 27/06/2025
I'm doing the stupid research security training mandated if you apply or get federal funds. Nothing there is new if you do academic research for the right reasons. I wonder if all people in government atm have done and passed it... No, don't tell me, i know
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Franck Dumetz 🦠😻🏳️‍🌈 @franckdumetz.bsky.social · 02/06/2025
Urgent family business made me fly back to France for some time. I have a summer student starting today and I can only say thank you to all my colleagues that are actually helping to make it work! I don't think I could have make it work without them. #appreciateyourcolleagues
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Franck Dumetz 🦠😻🏳️‍🌈 @franckdumetz.bsky.social · 28/05/2025
@nanoporetech.com the customer service is... abysmal these days
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Franck Dumetz 🦠😻🏳️‍🌈 @franckdumetz.bsky.social · 21/05/2025
In our liberal echo chamber that we created here posting this article is probably less impacting but I'm doing it anyway. #NTD are/will be on the rise soon, #billions were spent in elimination efforts that are now totally wasted.
science.org
Crippling tropical diseases threaten to surge after U.S. funding cuts
Closing of programs that fought neglected diseases imperils drug donation and distribution efforts in 26 countries
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Franck Dumetz 🦠😻🏳️‍🌈 @franckdumetz.bsky.social · 05/05/2025
Anybody outside of the US looking for a #parasitologist? #postdoc #USacademic
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Franck Dumetz 🦠😻🏳️‍🌈 @franckdumetz.bsky.social · 04/04/2025
Anybody around has experience with CibersortX? It has become my new nightmare!
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Reposted by Franck Dumetz 🦠😻🏳️‍🌈
Bungo Akiyoshi @bungoakiyoshi.bsky.social · 24/03/2025
I am happy to share a preprint on the marine plankton project I started one year ago (thanks to Julius and Drahomira's help) www.biorxiv.org/content/10.1...
biorxiv.org
Discovery of unique mitotic mechanisms in Paradiplonema papillatum
Diplonemids are highly diverse and abundant marine plankton with significant ecological importance. However, little is known about their biology, even in the model diplonemid Paradiplonema papillatum ...
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Franck Dumetz 🦠😻🏳️‍🌈 @franckdumetz.bsky.social · 24/03/2025
I'll say it again, thank your support staff, they are AWSOME!
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Franck Dumetz 🦠😻🏳️‍🌈 @franckdumetz.bsky.social · 14/03/2025
Remember when I said I didn't want to do a GO analysis ever again, well I still think that however it is the first time it gave something interesting and something I can talk about in the discussion of my paper!
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Franck Dumetz 🦠😻🏳️‍🌈 @franckdumetz.bsky.social · 12/03/2025
I don't wanna do a GO enrichment analysis EVER AGAIN!
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Franck Dumetz 🦠😻🏳️‍🌈 @franckdumetz.bsky.social · 10/03/2025
Today wasn’t a great day. Anybody with some cat pictures or some hydatid cyst to help with my mood? Any other parasite would work
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Franck Dumetz 🦠😻🏳️‍🌈 @franckdumetz.bsky.social · 05/03/2025
Don't forget to tell your support staff that you appreciate the hard work they do and that they matter to what we do. Research would be so much harder without them.
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Franck Dumetz 🦠😻🏳️‍🌈 @franckdumetz.bsky.social · 05/03/2025
Never forget!
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Franck Dumetz 🦠😻🏳️‍🌈 @franckdumetz.bsky.social · 03/03/2025
Version 2 of the splice leader table is available doi.org/10.6084/m9.f... This time I published the pdf and excel table for easier manipulation. A big thank you to @jamesacotton.bsky.social for the info on Trichinella and correcting the on Schistosoma. Keep it coming! #openscience #SpliceLeader
doi.org
SL_table_list_v2-030325.xlsx
Version 2This table summarizes all splice leader sequences I, and other contributors, could find in the literature. The doi and PMID of the reference where the sequences were found serves as reference.This is table will be updated with new sequences if they are made available. Contact me if you want to add data to this, a new column will be added to give credit the person giving the data. This table was done on my free time and can not be associated to any funding.
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Reposted by Franck Dumetz 🦠😻🏳️‍🌈
Middle East Monitor @middleeastmonitor.bsky.social · 22/02/2025
A large-scale polio vaccination campaign was launched in Gaza on Saturday aiming to immunize approximately 600,000 Palestinian children under the age of 10, Anadolu Agency reports. Read: www.middleeastmonitor.com/20250222-gaz...
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Franck Dumetz 🦠😻🏳️‍🌈 @franckdumetz.bsky.social · 26/02/2025
Here is the table of splice leader sequences I created. Use it freely and if some are missing and you want the info on it, let me know in PM, I'll add it with the ref and the name of the contributor #scienceforall #openscience doi.org/10.6084/m9.f...
doi.org
Splice Leader sequences
This table summarizes all splice leader sequences I could find in the literature. The doi of the reference where the sequence was found serves as reference. This is table will be updated with new sequ...
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Franck Dumetz 🦠😻🏳️‍🌈 @franckdumetz.bsky.social · 23/02/2025
I generated a non-exhaustive review-style table of Splice Leader sequences. Reviews exist but the sequence info itself isn't easy to find. How to make it easily accessible for the community? (I don't want to write review, I just want to be helpful)
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Kamphorst LAB @kamphorstlab.bsky.social · 13/02/2025
March is still a long time from now. We need to stop the bleeding. Talk to your patients. Reach out to your patient advocates and community scientist - call your representatives! Make some noise.
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Reposted by Franck Dumetz 🦠😻🏳️‍🌈
BK. Titanji @boghuma.bsky.social · 06/02/2025
The #PEPFAR tracker is following the real time impact of each passing day of the funding suspensions spurred by the USAID funding freeze. Although there is a waiver to allow dispersion of ART, this is not happening because clinic workers have been laid off. People are dying. pepfarimpact.vercel.app
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Reposted by Franck Dumetz 🦠😻🏳️‍🌈
WHO @who.int · 03/02/2025
In a global first, Uganda’s Ministry of Health, the World Health Organization (WHO) and other partners today launched a first-ever vaccine trial for Ebola from the Sudan species of the virus, and at an unprecedented speed for a randomized vaccine trial in an emergency.🧵
Groundbreaking Ebola vaccination trial launches today in Uganda
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Franck Dumetz 🦠😻🏳️‍🌈 @franckdumetz.bsky.social · 27/01/2025
sadly #HolocostRemembranceDay resonates differently this year. We must remember more than ever and never accept resilience
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Franck Dumetz 🦠😻🏳️‍🌈 @franckdumetz.bsky.social · 26/01/2025
I should not advertise this because it is really poor work/life balance but working in the lab on Sunday has perks
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Franck Dumetz 🦠😻🏳️‍🌈 @franckdumetz.bsky.social · 13/01/2025
Don’t spend ages trying to fix something somebody has already fixed, go and ask first. It saves days
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