fdecarpentier.bsky.social - Profile | ThreadSky | a Reddit-style client for Bluesky

New preprint! Deacon is a versatile tool for filtering FASTA/FASTQ files and streams at hundreds of megabases per second using minimizers, built with rapid metagenomic host depletion in mind, but equally useful for search. github.com/bede/deacon

submitted 2 hours ago • 4 comments

Joining the race to the bottom has never been cooler... www.biorxiv.org/node/4580343... www.biorxiv.org/content/10.1...

submitted 19 days ago • 0 comments

But why does an amoeba need horns on its shell? They're quite carefully made, with flat plates neatly glued around them (possibly scales from another organism). The spheres around the mouth are siliceous resting cysts of chrysophyte algae. #ProtistsonSky #MEvoSky #Amoebae #Peatlands

submitted 2 days ago • 1 comment

The FLC gene helps determine #FloweringTime variation in #Arabidopsis. Analysis of FLC mutants across 62 natural #genetic backgrounds by @plantevolution.bsky.social shows how #PanGenetics analysis of hub genes can reveal the extent of their broader genetic network @plosbiology.org 🧪 plos.io/3ZkZNvV

submitted 3 days ago • 0 comments

New tenure track assistant professor position in molecular microbiology in our department @dmf-unil.bsky.social @unil.bsky.social! We are casting a wide net for an experimental molecular microbiologist. Apply here: wwwfbm.unil.ch/releve/appli...

submitted 3 days ago • 0 comments

90% of you probably don’t need to read this. But maybe some of you are curious & 10% will feel seen. Or a little less alone. This isn’t about seeking sympathy. It’s about sharing something hard to say out loud; partly to heal, partly in case someone needs to hear it too. (1/3) tinyurl.com/DudinO

submitted 3 days ago • 9 comments

Last week I shared a preprint on tomtom-lite, a super fast re-implementation of Tomtom for annotating short genomic spans with the motifs they most resemble. Now, there's a convenient command line tool `ttl` that comes with the installation. You can get it with `pip instal memelite`

submitted 4 days ago • 1 comment

❗ We have an open post-doc position in our group! 🌱🥔🧬 Are you interested in novel crop breeding techniques and potatoes? If yes, the CRISPS project (in collaboration with Wageningen University and SLU Sweden) may be something for you! You can apply here: jobs.admin.ch/job-vacancie... #NBTs

submitted 4 days ago • 0 comments

Excellent job opportunity at @unihohenheim.bsky.social: build your own team in Experimental Plant Biodiversity Research (within @plantecology.bsky.social, group of Frank Schurr). Great environment (also b/c of new @greenrobust.de and #TERRA @dfg.de clusters of excellence), and great people!

submitted 5 days ago • 1 comment

NEW PAPER, NEW THREAD! 👀 We collected insects in creeks polluted with raw sewage. 🤢 Microplastics in caddisflies were once rare. But now, in some creeks, more than half of all cases include artificial material! 🤯 A shitty thread on plastics and poop, thankfully, without the smell of it 💩 1/x 🧵👇

submitted 14 days ago • 6 comments

Why are there intronic reads in your bulk RNA-seq data? You're not alone—it's common, and the reasons are more layered than you think. Let’s break it down. 🧵

submitted 7 days ago • 2 comments

20 years of research on giant viruses www.nature.com/articles/s44...

submitted 8 days ago • 0 comments

I wrote a quick application note on Tomtom-lite, a Python implementation of the Tomtom algorithm for comparing PWMs against each other. This implementation can be 10-1000x faster and, as a Python function, can be integrated into your workflows easier. www.biorxiv.org/content/10.1...

submitted 9 days ago • 2 comments

The Modern R Stack for Production AI: doi.org/10.59350/z9f... Python isn't the only game in town anymore: R can interact with local and cloud LLM APIs, inspect and modify your local R environment and files, implement RAG, computer vision, NLP, evals, & much more #Rstats

submitted 11 days ago • 3 comments

Super excited to release a huge evolution project on the works for many years: Evolution experiments synchronized across climates to understand rapid adaptation Preprint: doi.org/10.1101/2025... All data available: www.grene-net.org/data #MOILAB @ucberkeleyofficial.bsky.social @hhmi.org 🧵👇

submitted 13 days ago • 9 comments

Kinetic Insights into Photoinduced Monomer-Dimer Conversion and Activation of Orange Carotenoid Protein www.biorxiv.org/content/10.1...

submitted 14 days ago • 0 comments

My father worked in a tire factory in Appalachia. Friends and family in the military. Used to vote Republican. Got into college on a diversity program for the underprivileged. Ended up a Harvard professor. And now my funding is terminated because we're trying to stick it to the elites.

submitted 16 days ago • 4 comments

I am happy to introduce to you our new paper on pelagic #Asgard archaea that use #rhodopsins with carotenoid antennas to harvest light energy in the oceans. Structural insights into light-harvesting by antenna-containing rhodopsins in marine Asgard archaea www.nature.com/articles/s41...

submitted 15 days ago • 4 comments

Announcing myloasm, a new long-read (ONT R10/PacBio) metagenome assembler that I've been working on during my postdoc in the Heng Li lab (@lh3lh3.bsky.social). myloasm-docs.github.io

submitted 15 days ago • 5 comments

NIH funding supporting the HMMER and Infernal software projects has been terminated. NIH states that our work, as well as all other federally funded research at Harvard, is of no benefit to the US.

submitted 22 days ago • 35 comments

Deep-learning-based single-domain and multidomain protein structure prediction with D-I-TASSER www.nature.com/articles/s41... #jcampubs

submitted 17 days ago • 0 comments

Cool videos from our new paper applying Diversity Search to Flow-Lenia to explore a vast space of eco-evolutionary dynamics. Preprint paper, dataset and online visualization tool soon available, stay tuned! I'll present this and other Lenia experiments on May 27 at www.dem.eco #ALife #Open-endedness

submitted 30 days ago • 0 comments

Penguin poop gives off ammonia, which enhances cloud formation and cools coastal Antarctica, allowing more penguins to poop there, probably. 🐧🧪

submitted 20 days ago • 16 comments

Now published! Big congrats to first author @gginell.bsky.social We are actively working improving/updating various aspects of FINCHES; don't hesitate to reach out if you run into issues, have questions. www.science.org/doi/10.1126/...

submitted 21 days ago • 8 comments

The Trump administration has just revoked Harvard's SEVIS certification www.bbc.co.uk/news/article...

submitted 21 days ago • 1 comment

Delighted to see our work now published in @currentbiology.bsky.social. A great place for Bostrychia to stake its claim as an emerging red algal model system. Check it out here: www.cell.com/current-biol...

submitted 34 days ago • 4 comments

Very excited to present the Great Barrier Reef Microbial Genomes Database (GBR-MGD), a comprehensive DB of 1000s of high-quality prokaryote, virus, plasmid, and chromosome-level eukaryote MAGs using Nanopore long reads. Subthreads incoming. Please share widely. 🙂 www.biorxiv.org/content/10.1...

submitted 23 days ago • 2 comments

🚨 preprint 2️⃣ this month: our (purely experimental🧪) venture into #ChemBio We prouldy present: ADD-tagging of proteins (or "ADDing") —a super convenient enzymatic technique to install click chemistry handles on proteins. Led by superstar @wahyuwidodo.bsky.social www.biorxiv.org/content/10.1... A 🧵👇🏽

submitted 24 days ago • 4 comments

🆕 Out now in JEM (@jeukmicro.bsky.social‬)! Using rrn gene and organelle phylogenies from recovered cysts, we describe 𝘈𝘱𝘰𝘴𝘵𝘪𝘤𝘩𝘰𝘤𝘺𝘴𝘵𝘪𝘴 𝘨𝘶𝘥𝘦𝘵𝘢𝘮𝘢, an apicomplexan parasite found in the ovaries of the Japanese sea cucumber 🥚 🥒 🇯🇵 dx.doi.org/10.1111/jeu.... #ProtistsOnSky

submitted 24 days ago • 2 comments

I'm looking for a postdoc in computational evolutionary phage genomics, with the goal to better understand how protein innovation arises in viruses, at @jagiellonskiuni.bsky.social in Krakow (Poland). Drop me a line if it sounds cool! Deadline: 20.06. Link here: mcb.uj.edu.pl/documents/15...

submitted 24 days ago • 2 comments

#MicrobiologyMonday: Some female leaf beetles place a fecal string on top of each egg they lay. Why? The fecal string, which is eaten by hatching larvae, facilitates vertical transfer of gut bacteria between host insect generations. #mSystems: asm.social/2q8

submitted 25 days ago • 1 comment

Enhanced cell aggregation in the Chlamydomonas reinhardtii rbo1 mutant in response to multifactorial stress combination https://www.biorxiv.org/content/10.1101/2025.05.16.654601v1

submitted 25 days ago • 0 comments

teeny tiny victories: 1st & only time my beasties on the cover of Science - take them when they come! #protistsonsky

submitted 25 days ago • 0 comments

I will be recruiting new postdocs with start dates end 2025 - early 2026. If you'd like to work at the Pasteur Institute in the heart of Paris surrounded by amazing scientists, reach out to discuss possible projects on SynBio / Bacterial Immunity!

submitted 26 days ago • 3 comments

Bioinformatics folks: check out our @biorxivpreprint on a new, very efficient and accurate system for automated genome annotation, EviAnn, led by my colleague Aleksey Zimin: www.biorxiv.org/content/10.1...

submitted 30 days ago • 1 comment

Do you know who Douglas Prasher is? Many don't, even though he is the person who cloned the original #GFP gene in the late 1980s. In my short history of plant light #microscopy I also cover a bit of his story - & why he is relatively unknown today, despite the importance of his work. See this 🧵👇

submitted 389 days ago • 3 comments

A colony of ciliates Zoothamnium sp. in timelapse. Jump, jump, jump! 🦑 #plankton

submitted 26 days ago • 3 comments

New vacancy in my team! PhD student position on microbial genome evolution, focusing on the evolutionary principles underlying bacterial genome architecture. Please repost and share with talented MSc students in #evobio, bioinformatics or related :) www.uu.nl/en/organisat... #MEvoSky #MicroSky

submitted 30 days ago • 3 comments

“Americans die earlier and are sicker than people in other high-income countries. This has been true for a long time, and the trend is getting worse.” gift link www.wsj.com/health/welln...

submitted 28 days ago • 39 comments

Research from last year marked the first documented case of an ape using a plant with scientifically proven medicinal properties to treat a fresh wound. #ScienceMagArchives scim.ag/43wWq7n

submitted 27 days ago • 8 comments

Wow: check it out; these fungi distribute their chromosomes across different nuclei! Normally each nucleus has a complete set of all chromosomes. Distribution of haploid chromosomes into separate nuclei in two pathogenic fungi | Science www.science.org/doi/10.1126/...

submitted 28 days ago • 0 comments

RAxML-NG v2.0 beta is here github.com/amkozlov/rax... Features 1. Difficulty prediction academic.oup.com/mbe/article/... 2. Adaptive search academic.oup.com/mbe/article/... 3. Early Stop www.biorxiv.org/content/10.1... 4. Model selection 5. Rapid bootstrapping academic.oup.com/mbe/article/...

submitted 29 days ago • 0 comments

Catch & Release - rapid cost-effective protein purification from plants using a DIY GFP-Trap-protease approach https://www.biorxiv.org/content/10.1101/2025.05.15.654187v1

submitted 29 days ago • 0 comments

📣 The @multicellgenome.bsky.social of @ibe-barcelona.bsky.social hosts the @embo.org‬ Workshop "Evolution and origins of multicellularity across the tree of life"🧬🦠✨ 📆 9-11 October 2025 📍 Auditorium @prbb.org‬ ⌛ Abstract submission: 1st June 👉https://meetings.embo.org/event/25-multicellularity

submitted 30 days ago • 0 comments

Apply now for the first conference joining the study of all multicellularity events! 👇

submitted 29 days ago • 1 comment

Our recent paper is out where we propose kmer-based phylogenetics for fungal Starship TEs (which are unalignable as highly variable). We think it could help with spotting bonafide HGT events (and suggest direction of transfer?) doi.org/10.1093/g3jo... @mcmullan0.bsky.social @norwichmicro.bsky.social

submitted 30 days ago • 2 comments