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

🧬 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

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.

doi.org

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.

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

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

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.

Institute for Genome Sciences@genomescience.bsky.social · 4mo ago

Join us for lunch and a timely dialogue on Pandemic Preparedness in a Changing Global Economy. Washington DC - Wednesday April 15th 12-2pm Click here to RSVP today! lnkd.in/esBbHdUe

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.

I wish everybody had a boss like @DavidSerre. That's it! I'm leaving that here for future reference

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

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...

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,...

bloomberg.com

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!

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...

dx.plos.org

🚨 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...

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...

virological.org

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!

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

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.

Jeremy Berg@jeremymberg.bsky.social · 8mo ago

My quote of the day I will offer those who suffer all my attention, my science and my love. Never will I betray them or risk their wellbeing to satisfy my vanity. The Oath of Hippocrates (Amelia Arenas translation)

Please people please, once your paper is published, go back on SRA and release it publicly!

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!

Saying thank you to someone and truly meaning it is heartwarming. Just putting that here #thankyou

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

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...

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

bioRxiv Genomics@biorxiv-genomic.bsky.social · 11mo ago

The UTRs of Leishmania donovani vary in length and are enriched in potential regulatory structures https://www.biorxiv.org/content/10.1101/2025.09.22.677690v1

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

Sonny is helping to download some Toxoplasma gondii sequences to analyse. He is fascinated by the idea, as everybody can see 😻😏🙃

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

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

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.

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

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

@nanoporetech.com the customer service is... abysmal these days

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.

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

science.org