Félix de Carpentier

GitHub - lh3/longdust: Identify long STRs, VNTRs, satellite DNA and other low-complexity regions in a genome Identify long STRs, VNTRs, satellite DNA and other low-complexity regions in a genome - lh3/longdust

lh3/longdust: Identify long STRs, VNTRs, satellite DNA and other low-complexity regions in a genome github.com/lh3/longdust 🧬🖥️🧪

Ancient hybridization underlies tuberization and radiation of the potato lineage Genomic and functional analyses reveal that the potato lineage originated from a homoploid interspecific hybridization event between the Tomato and Etuberosum lineages 8–9 million years ago. The alter...

The hybrid origin of potato tuberization.

From: www.cell.com/cell/fulltex...

A New Detailed Mass Offset Search in MSFragger for Improved Interpretation of Complex PTMs https://www.biorxiv.org/content/10.1101/2025.07.28.667198v1

Fig. 1. Automated continuous chaotic bioprinting. a) Schematic illustration showing automated chaotic bioprinting of noodles with internally aligned lamellar microstructures, using the three-element KSM (Kenics static mixer) printhead, with highlighted lateral and transverse views. b) Schematics of various three-dimensional (3D) hybrid food items, produced by simultaneous chaotic bioprinting of microalgae and muscle cells. c) Schematic illustration showing bioink designs for microalga and muscle cell-bioprinting.

Fig. 6. 3D-bioprinted hybrid food. a) Photographs showing 3D hybrid drumsticks on day 0 and day 16, bioprinted with C2C12 cell- and Chlamydomonas cell-bioinks. b) Viability values of bioprinted C2C12 cells and Chlamydomonas cells within the hybrid drumsticks, assessed over the 15-day culture period at 37 °C. Data are presented as themean values ± SEMs (n = 3 independent samples, each obtained from a separate bioprinting run). c) Fluorescence confocal micrographs showing the expression of skeletal muscle myosin (green) by C2C12 cells and Chlamydomonas cells with red autofluorescence of chlorophyll on day 16, within bioprinted hybrid drumsticks. d) Photographs of bioprinted hybrid cuboids at day 0 and day 14, using C2C12 cell- and Chlamydomonas cell-bioinks. e) Photographs of cut pieces of bioprinted hybrid cuboids on day 21, used for cooking studies. f) Comparison of mechanical properties of hybrid food before and after cooking on day 21. Data are presented as the mean values ± SEMs (n = 4 independent samples, each obtained from a separate bioprinting run) and a two-tailed paired t-test was applied to measure p values.

Fig. 7. Chaotic-bioprinted chicken-microalga hybrid noodle. a) Photograph of hybrid chicken-microalga noodles on day 21, bioprinted with chicken cell- and Chlamydomonas cell-laden bioinks. b) Fluorescence micrograph showing live chicken cells (green) and Chlamydomonas cells with red autofluorescence of chlorophyll, within the bioprinted hybrid chicken-microalga noodles on day 21. c) Viability values of chicken cells and Chlamydomonas cells within bioprinted hybrid chicken-microalga noodles, assessed over the 21-day culture period at 37 °C. Data are presented as the mean values ± SEMs (n = 3 independent samples, each obtained from a separate bioprinting run). d) Fluorescence confocal micrographs showing the expressions of F-actin, MYH2, and skeletal muscle myosin (green) by chicken cells and Chlamydomonas cells with red autofluorescence of chlorophyll, within bioprinted chicken-microalga hybrid noodles on day 21.

Interesting work by Maharjan et al. (2025) on the 3D #bioprinting of plant- and animal cell-based hybrid foods, especially noodles that are made of 30–40% edible #microalgae ( #Chlamydomonas or Chlorella) and 60–70% muscle cells (C2C12 or chicken #myoblasts) 🍜🍗🧐.
🔗 www.nature.com/articles/s41...

Empowering bioinformatics communities with Nextflow and nf-core genomebiology.biomedcentral.com/articles/10.... 🧬🖥️🧪

nf-core is the standard by which "community" should be measured, and the countless hours by contributors has truly transformed the practice of bioinformatics over the past few years

Check out our new preprint all about Pirsonia, a tiny killer of bloom-forming Coscinodiscus diatoms!
www.biorxiv.org/content/10.1...
#protistsonsky #marinemicrobes 🌊🔬

A dinoflagellate-infecting giant virus with a micron-length tail www.biorxiv.org/content/10.1...

FAMSA2 enables accurate multiple sequence alignment at protein-universe scale We introduce FAMSA2, an algorithm that produces high-accuracy multiple protein sequence alignments with unprecedented speed. Across structural, phylogenetic, and functional benchmarks, FAMSA2 matches ...

Interested in a tool that aligns millions of proteins in minutes with quality similar to or better than the state-of-the-art utilities? Please take a look at our FAMSA2 paper: www.biorxiv.org/content/10.1...
and GH repo: github.com/refresh-bio/...

A two year post-doctoral position at the BacterialGenome Plasticity Unit starting October 1st - Research

Postdoc position to work at the Institut Pasteur with Alex Kaminski and Didier Mazel on Z-DNA phages ! research.pasteur.fr/en/job/a-two...

Global hotspots of mycorrhizal fungal richness are poorly protected - Nature Machine-learning algorithms trained on 25,000 geolocated soil samples are used to create high-resolution global maps of mycorrhizal fungi, revealing that less than 10% of their biodiversity hotspots a...

The first high-resolution, predictive biodiversity map of Earth’s underground mycorrhizal fungal communities shows over 90% of underground mycorrhizal fungal ecosystems are unprotected, threatening carbon drawdown and ecosystem resilience to climate extremes.

www.nature.com/articles/s41...

🧬Latent-X is our first frontier model for protein design.

For mini-binders, our AI model achieved picomolar binding affinities — the strongest reported vs prior methods in head-to-head lab validation.

Explore our best binders here: platform.latentlabs.com

More details on the breakthrough in this🧵

CRISPR-Cas9 genome editing in Corallochytrium limacisporum,a key species for understanding animal origins | Open Biology Microbial holozoans are the closest unicellular relatives of animals. They share a substantial gene repertoire with animals and exhibit complex life cycles. Studying these organisms is crucial for und...

Very happy to share our new paper where we develop CRISPR-Cas9 genome editing in our favorite unicellular relative of animals, Corallochytrium limacisporum! With @sebasn1.bsky.social @multicellgenome.bsky.social Elena and Claudio.

Check it out:
royalsocietypublishing.org/doi/10.1098/...

Promethea = PROvora + MEteora + HEmimastigophora. The new supergroup, unifying previously “orphan” lineages with gene-rich mitogenomes. Position of #telonemids is still uncertain. #protistsonsky tinyurl.com/yk9xkt49

Very pleased to say we have an Assistant Professor job opening (tenure track) in the Department of Genetics at Trinity College Dublin! 😀
www.jobs.ac.uk/job/DOA399/a... - deadline is August 19th! Please repost!

Complete biosynthesis of salicylic acid from phenylalanine in plants - Nature Characterization of four SALICYLIC ACID-DEFICIENT GENEs in rice identifies an ancestral pathway for biosynthesis of salicylic acid from phenylalanine and provides genetic targets for engineering disea...

Complete biosynthesis of salicylic acid from phenylalanine in plants www.nature.com/articles/s41... @nature.com

📢 For all HaloTag lovers💙💚💛❤️💜🩶 we are excited to share that our work, in which we developed a new biotin-HaloTag ligand, is now published in @jcb.org! Full link here: rupress.org/jcb/article-...

Check out our paper to explore how the evolutionary history of SELMA supports or challenges various hypotheses on the origin of red complex plastids.

academic.oup.com/mbe/article/...

Thanks @nature.com, C. Ro, & J. Leening for this feature about my work!
The article is here: nature.com/articles/d41... and mentions two of our papers (researchintegrityjournal.biomedcentral.com/articles/10.... & bmcmedresmethodol.biomedcentral.com/articles/10....)

🙏 amazing co-authors and friends!

A red algal polysaccharide influences the multicellular development of the choanoflagellate Salpingoeca rosetta Perotti et al. find that polysaccharides from algae promote multicellular development in the choanoflagellate S. rosetta. Because algal polysaccharides are abundant in the aquatic environments where S...

A red algal polysaccharide influences the multicellular development of the choanoflagellate Salpingoeca rosetta

in @currentbiology.bsky.social

www.cell.com/current-biol...

We are looking for new colleagues to come join us in Galway as group leaders (Junior and Senior). The Centre for Chromosome Biology is a great place and it is a good time to join. Please reach out if you want to chat about the opportunity!
www.nature.com/naturecareer...

Spread the word! We are looking for a lab technician to join our emerging group at @cbgpmadrid.bsky.social. Please check here: tinyurl.com/bdev9y6t. Essential to have a FP/technical degree diploma, regardless of having higher degrees.

A roadmap to developing unified streptophyte algal model systems Carrillo-Carrasco and colleagues highlight the importance of the establishment of streptophyte algal model systems and the community efforts towards this goal.

We've tried to gather and unite the streptophyte algae community all around the world to join forces and develop tools and methods for these critters. Learn more about it on @currentbiology.bsky.social!
With @jandevries.bsky.social, @dolfweijers.bsky.social, and (many) others!

tinyurl.com/29n4zwen

Multiple sequence alignments are so wicked fast with FAMSA2! What's the catch?
www.biorxiv.org/content/10.1...

I don't know much about phylogeny. Is the purpose/principle of WitChi different from tools like trimAl or ClipKit?

WitChi: Efficient Detection and Pruning of Compositional Bias in Phylogenomic Alignments Using Empirical Chi-Squared Testing Convergent evolution, where unrelated taxa independently evolve similar nucleotide or amino acid compositions, can introduce compositional bias into biological sequence data. Such biases distort phylo...

1.
🧵 New preprint out!
WitChi: a fast, open-source Python tool to detect, quantify & prune compositional bias in MSAs.
Lightweight, tree-free, scalable to 5k+ taxa... so we applied it to the GTDB archaea MSA.
#ArchaeaSky #MEvoSky #MicroSky
🔗 doi.org/10.1101/2025...
💻 github.com/stephkoest/w...

Disorder meets its match Designed protein pockets recognize intrinsically disordered protein regions

Designed protein pockets recognize intrinsically disordered protein regions @science.org
www.science.org/doi/10.1126/...
www.science.org/doi/10.1126/...
www.statnews.com/2025/07/17/n...

Hitting ‘undruggable’ disease targets – Institute for Protein Design Custom proteins made with AI bind disordered proteins and peptides with atomic precision.

The Baker lab @uwproteindesign.bsky.social did it again 😱

Protein design of IDPs binders

www.ipd.uw.edu/2025/07/hitt...

Conservation and divergence of UVR8-COP1/SPA-HY5 signaling in UV-B responses of Marchantia polymorpha Ultraviolet-B radiation (UV-B) poses a major challenge to all forms of plant life. The liverwort Marchantia polymorpha (Marchantia) serves as a key model organism to study signaling pathways and to in...

Happy to share this work we did together with @yuankeliang.bsky.social in @romanulm.bsky.social lab. We looked in detail at UVR8-mediated UV-B signaling in Marchantia and found some conserved functions but also a few surprises! #plantscience #marchantia #UVR8

ASTER: A Package for Large-scale Phylogenomic Reconstructions https://pubmed.ncbi.nlm.nih.gov/40668947/

OrthoFinder just dropped a major update

It’s faster, more accurate, and ready for thousands of genomes

Let’s break it down (1/10)

github.com/OrthoFinder/...
www.biorxiv.org/content/10.1...