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...

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!

🚨 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...

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.

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

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.

Anybody outside of the US looking for a #parasitologist? #postdoc #USacademic

Anybody around has experience with CibersortX? It has become my new nightmare!

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...

I'll say it again, thank your support staff, they are AWSOME!

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!

I don't wanna do a GO enrichment analysis EVER AGAIN!

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

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.

Never forget!

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

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...

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...

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)

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.

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

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.🧵

sadly #HolocostRemembranceDay resonates differently this year. We must remember more than ever and never accept resilience

I should not advertise this because it is really poor work/life balance but working in the lab on Sunday has perks

Don’t spend ages trying to fix something somebody has already fixed, go and ask first. It saves days

DoxyPEP—a dose of doxycycline after sex—helped reduce bacterial STIs in San Francisco & surrounding cities, according to real-world studies. Chlamydia & syphilis notably declined, though there was less effect on gonorrhea. My latest for @pozmagazine.bsky.social www.poz.com/article/doxy...

As we prepare to jump into a new year, I received an email from my scientific godmother. I admit I have been neglecting to send her regular updates this year. My only resolution is to communicate better with people that mean in lot to me. Happy New Year everybody and see you all in 2025

Just before leaving Baltimore for the holidays I got the fantastic news that my summer intern made it to MIT. This job is greatest when you can witness the growth of young people that deserve it. Happy holidays everybody

I just hate R

I am proud to share that the work from my time at the #BNITM is finally out in #Mbio today. Go check out the manuscript if you want to read about polycistronic transcription in #Leishmania parasites: journals.asm.org/doi/10.1128/...

Now I am fully here. I need to finish a paper and I will speak more here. See you very soon.

The magic of the scientific world is our diversity. We have 3 visiting scientists @genomescience.bsky.social from different African countries and it snows in #Baltimore today (very early in the season btw). They had their first experience with the snow, that was priceless to see #StrongerTogether

I guess it had to happen at least once. My computer crashed and I could save everything I knew wasn't on #OneDrive but apparently not all the folders in my OneDrive folder were synched so I lost 3 months of data analysis and paper writing 😭😭😭