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fdecarpentier.bsky.social
Postdoctoral researcher at UC Berkeley | Microalgae, environmental stress, molecular and synthetic biology | Formerly @ Université Paris Sud, Sorbonne Université, AgroParisTech, and ISA Lille. https://scholar.google.com/citations?user=f5eOF_YAAAAJ
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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

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

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...

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

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`

❗ 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

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!

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 🧵👇

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. 🧵

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

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...

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

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 🧵👇

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

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.

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...

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

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.

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

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

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

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/...

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

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...

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...

🚨 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 🧵👇🏽

🆕 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

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...

#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

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

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

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!

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...

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 🧵👇

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

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

“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...

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

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/...

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/...

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

📣 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

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

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

Evolution of far-red light photoacclimation in cyanobacteria: Current Biology https://www.cell.com/current-biology/fulltext/S0960-9822(25)00502-0?rss=yes

Thrilled to have won @nature.com 2025 #ScientistAtWork photo competition! 🧪🐳📷 www.nature.com/immersive/d4...