Félix de Carpentier
@fdecarpentier.bsky.social
410 followers 930 following 53 posts
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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Reposted by Félix de Carpentier
robp.bsky.social
Have you recently completed (or finishing soon) a PhD in CS or a related discipline? Do you want to do research advancing the theory & practice of algorithmic genomics & build tools that people love to use? I'll be looking to hire a postdoc! Official ad coming soon:
docs.google.com/document/d/1...
Postdoc Description.docx
Title: Postdoctoral Associate Summary statement: The postdoctoral research associate is responsible for developing novel computational methodology for high-throughput sequence genomics tasks, as well ...
docs.google.com
Reposted by Félix de Carpentier
biorxivpreprint.bsky.social
Structural Insights into RubisCO Dynamics and Pyrenoid Architecture in Chlamydomonas reinhardtii https://www.biorxiv.org/content/10.1101/2025.09.18.677200v1
Reposted by Félix de Carpentier
godi.bsky.social
🌊🔬 Looking for a postdoc to join our team!
Cocco-Channel project ➡️ studying coccolithophore phycospheres and their role in ocean carbon cycling.
✔️ Plus if you bring experience in microbial ecology, molecular/microscopy tools & fieldwork
👉 More info: euraxess.ec.europa.eu/jobs/375178
#protistsonsky
Reposted by Félix de Carpentier
filiphusnik.bsky.social
OIST is seeking up to four tenure-track or tenured faculty in Ecology, Environmental Science, Earth Science, and Oceanography. Application deadline: Oct 15. Please share. Thx!
www.oist.jp/careers/facu...
Reposted by Félix de Carpentier
annizlab.bsky.social
X-Mapper 🦠🧬🧪 - a sequence aligner developed for microbes, now on Bioconda! 🚀
• 11–24× fewer suboptimal alignments (same for human genome)
• 3–579× lower inconsistency
• improves on ~30% of reads aligned to non-target species
github.com/mathjeff/map...
bioconda.github.io/recipes/x-ma...
#microsky
Alignment algorithms represent a balance between speed and accuracy. We evaluated this balance across aligners, with accuracy measured by suboptimal alignments. We found that the relationship between alignment time (with 30 threads) and suboptimal alignment rates exhibits diminishing returns, where X-Mapper stands out as an outlier, offering the highest accuracy with competitive speed.
Reposted by Félix de Carpentier
thibautbrunet.bsky.social
Latest from ours: www.cell.com/cell-reports...

This is two stories in one: a case study/cautionary tale on developing genetic tools in new organisms, and the first hint at a gene regulatory network for choanoflagellate multicellular development (which turn out to involve a Hippo/YAP/ECM loop!) A 🧵
Reposted by Félix de Carpentier
biorxiv-bioinfo.bsky.social
Ragnarok: a flexible and RApid GeNe Annotation (ROcKs) pipeline deployed through Nextflow https://www.biorxiv.org/content/10.1101/2025.10.03.680343v1
Reposted by Félix de Carpentier
kevinjkircher.com
Sometimes I think about how from 1935-1975ish, Bell Labs produced an insane amount of revolutionary science and technology, including 11 Nobel Prizes, the transistor, UNIX, C, the laser, the solar cell, information theory, etc. The secret? Provide scientists with ample, steady, no-strings funding.
sites.stat.columbia.edu
Reposted by Félix de Carpentier
brsoucek.bsky.social
Strong statement today from UC's Academic Senate:
Reposted by Félix de Carpentier
camplantsci.bsky.social
Russell R. Geiger Professorship of Crop Science

Dept. of Plant Sciences | Permanent | Closes on Monday 17 November 2025

www.cam.ac.uk/jobs/russell...

#plantsciences #plantscijobs #academicjobs
Reposted by Félix de Carpentier
jamesdinneen.bsky.social
I joined a team of ecologists wading through the muck of the Carolina coast in search of "ghost forests" killed by rising seas for @science.org. We were guided by a a new map that reveals millions of dead trees standing along the East Coast, marking an overlooked consequence of climate change...
AI reveals vast ‘ghost forests’ along U.S. coast
Machine learning method counts nearly 12 million dead trees, many likely killed by rising seas
www.science.org
Reposted by Félix de Carpentier
dportik.bsky.social
New pre-print from the Banfield lab, highlighting an interesting case of 1.5Mb megaplasmids found in human gut.

Plasmid genomes were resolved using #PacBio HiFi sequencing with hifiasm-meta for #metagenome assembly. Host association was detected using epigenetic signals.

doi.org/10.1101/2025...
Megaplasmids associate with Escherichia coli and other Enterobacteriaceae
Humans and animals are ubiquitously colonized by Enterobacteriaceae , a bacterial family that contains both commensals and clinically significant pathogens. Here, we report Enterobacteriaceae megaplas...
doi.org
Reposted by Félix de Carpentier
kranzuschlab.bsky.social
>18,000 new genomes of giant DNA viruses! An incredible trove of new genes and insights into evolution of host-virus interactions from @fmschu.bsky.social and @jgi.doe.gov

www.biorxiv.org/content/10.1...
Reposted by Félix de Carpentier
pacyc184.bsky.social
Giant DNA viruses encode a hallmark translation initiation complex of eukaryotic life | bioRxiv https://www.biorxiv.org/content/10.1101/2025.09.30.678621v1?rss=1
Giant DNA viruses encode a hallmark translation initiation complex of eukaryotic life
In contrast to living organisms, viruses were long thought to lack protein synthesis machinery and instead depend on host factors to translate viral transcripts. Here, we discover that giant DNA viruses encode a distinct and functional IF4F translation initiation complex to drive protein synthesis, thereby blurring the line between cellular and acellular biology. During infection, eukaryotic IF4F on host ribosomes is replaced by an essential viral IF4F that regulates viral translation, virion formation, and replication plasticity during altered host states. Structural dissection of viral IF4F reveals that the mRNA cap-binding subunit mediates exclusive interactions with viral mRNAs, constituting a molecular switch from translating host to viral proteins. Thus, our study establishes that viruses express a eukaryotic translation initiation complex for protein synthesis, illuminating a series of evolutionary innovations to a core process of life. ### Competing Interest Statement The authors have declared no competing interest. Pew Biomedical Scholars Program G. Harold & Leila Y. Mathers Foundation, https://ror.org/02a7hjv13 National Institutes of Health, 1R35GM142527, 1DP2GM146250, F31NS132412 Parker Institute for Cancer Immunotherapy, https://ror.org/0184qbg02 European Research Council, 832601, 101160452 Branco Weiss Fellowship Moderna Therapeutics (United States), https://ror.org/01xm4wg91
www.biorxiv.org
Reposted by Félix de Carpentier
biorxiv-plants.bsky.social
A Key Role for S-Nitrosylation in Immune Regulation and Development in the Liverwort Marchantia polymorpha https://www.biorxiv.org/content/10.1101/2025.09.29.679193v1
Reposted by Félix de Carpentier
tobiaswarnecke.bsky.social
Become my colleague @oxfordbiochemistry.bsky.social !
2 Associate Professorships in the areas of
- prokaryotic/eukaryotic microbiology
- metabolism

my.corehr.com/pls/uoxrecru...
Job Details
my.corehr.com
Reposted by Félix de Carpentier
jsantoyo.bsky.social
TEtrimmer: a tool to automate the manual curation of transposable elements. #TransposableElements #ManualCuration #Genomics #Bioinformatics @natcomms.nature.com 🧬 🖥️
www.nature.com/articles/s41...