Yann Moalic

Frontiers | On the origins and variation of nucleotide skews of archaeal genomes We have used nucleotide skews as the proxy to understand the evolution of archaeal genomes. Our genome-wide studies using substantial datasets suggest that t...

www.frontiersin.org/journals/mic...

a figure from the linked paper which shows A) a world map and B) a schematic representation of various natural and artificial habitats, both annotated with information about which sulfur disproportionating bacteria have been found in the specific regions and environments

New paper from my 2nd PostDoc is now published in The ISME Journal by @isme-microbes.bsky.social!

#Sulfur disproportionation occurs globally across anoxic habitats & has multiple mechanisms of independent evolutionary origin academic.oup.com/ismej/advanc...

#Bacteria #Microbes #Evolution #DeepSea

Genome modelling and design across all domains of life with Evo 2 - Nature Evo 2 is an artificial intelligence-based biological foundation model trained on 9 trillion DNA base pairs spanning all domains of life that predicts functional properties from genomic sequences and p...

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

Final version @nature.com of our paper describing unconventional multicellular development in a choanoflagellate inhabiting an extreme environment. A ton of new data since the first @biorxivpreprint.bsky.social preprint (which we've kept updating).

A brief 🧵 (carried over from the old place)

CRISPR spacers reveal diverse and abundant Thermococcales viruses in hydrothermal vents www.researchsquare.com/article/rs-8...

Genome Editing Technologies and Synthetic Biology of Hyperthermophilic Archaea Hyperthermophilic archaea are characterized with robust metabolic capability and outstanding enzyme stability. Since their discovery, great efforts have been devoted into the development of genetic to...

link.springer.com/chapter/10.1...

Rapid directed evolution guided by protein language models and epistatic interactions Protein engineering is limited by the inefficient search through a high-dimensional sequence space to find combinations of synergistic mutations. Traditional approaches use stepwise mutation stacking,...

www.science.org/doi/10.1126/...

Openness means more than access. That's why we encourage submissions of Replication Studies.

Learn about publishing your replication study with us in our author guide: buff.ly/rcI0oAY

www.nature.com/nbt/volumes/...

A pilot in a submersible vehicle collecting sediments samples in 30 meters of water looking for Asgards (microbial relatives of eukaryotes)

One of the biggest questions in biology is how complex cells evolved about 2 billion years ago. Here's my new story on how scientists are solving the mystery of eukaryotes like us. Gift link: nyti.ms/4qMbo22

‘What are we doing here?’ The polymaths who searched for the meaning of life An ambitious book unravels the common themes driving people’s thirst for knowledge — matters that still resonate today.

Nice review by Urmila Chadayammuri of Maria Popova's new book Traversal. I have reviewed it for @science.org (coming soon) and my take has a lot of overlap with Urmila's. In short, it is a strange beast and all the better for that.
www.nature.com/articles/d41...

Integration of ploidy, Orc1/Cdc6 homolog function, and lysine acetylation with phosphate limitation and UV stress responses of Haloferax volcanii - Extremophiles Haloarchaea thrive in extreme environments where hypersalinity, DNA damage, and nutrient scarcity pose significant stresses. Here, we provide insight into how defined phosphate levels, UV stress, and ...

link.springer.com/article/10.1...

The Future of Bioinformatics Belongs to Those Who Speak Both Languages | Via Scientific AI is reshaping bioinformatics. Learn why hybrid thinkers with both computational depth and biological intuition will become the field’s essential leaders.

www.viascientific.com/blogs/the-fu...

Substrate specificity and action mechanism of the HerA-NurA nuclease from the hyperthermophilic archaeon Thermococcus kodakarensis | mBio To understand the specific function of the HerA-NurA complex, which is believed to function in the end resection process to create a 3′-overhanging DNA for the following strand invasion in homologous ...

journals.asm.org/doi/10.1128/...

Evolution and diversity of oxidoreductases involved in redox balance and energy conservation - Nature Ecology & Evolution HORBEC are protein complexes involved in the regulation of redox balance and energy conservation. The authors develop a bioinformatic tool for HORBEC annotation in bacterial and archaeal genomes and r...

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

Bipartite network of ncORF-CDS co-translation in mice

🧬 A major data reanalysis in December's most-read Genetics paper uncovers thousands of previously hidden protein-coding regions in human and mouse genomes: buff.ly/6TsX3ct

Archaeal G-quadruplexes: a novel model for understanding unusual DNA/RNA structures across the tree of life Abstract. Archaea, a domain of microorganisms found in diverse environments, including the human microbiome, represent the closest known prokaryotic relati

Archaeal G-quadruplexes: a novel model for understanding unusual DNA/RNA structures across the tree of life url: academic.oup.com/nar/article/...

A web-based atlas for exploring post-transcriptional regulation in the archaeon Sulfolobus acidocaldarius | mSystems Post‑transcriptional regulation is a key control layer in gene expression. Yet, resources integrating antisense RNAs (asRNAs), RNA processing sites, and RNA-protein interactions are scarce for archaea...

A web-based atlas for exploring post-transcriptional regulation in the archaeon Sulfolobus acidocaldarius
#microbiology #archaea #MicroSky #ArchaeaSky
@asm.org
journals.asm.org/doi/10.1128/...

Iron Sulfides Produced by Thermococcales: An Iron Detoxification Mechanism Thermococcales, archaea from hydrothermal vents, promote iron sulfide precipitation, enabling survival in iron-rich environments. Some cells become encrusted in pyrite and do not survive mineralizati...

enviromicro-journals.onlinelibrary.wiley.com/doi/10.1111/...

Advancing regulatory variant effect prediction with AlphaGenome - Nature AlphaGenome, a deep learning model that inputs 1-Mb DNA sequence to predict functional genomic tracks at single-base resolution across diverse modalities, outperforms existing models in variant effect...

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

How the ocean’s hydrothermal systems made the first life on Earth possible Researchers have discovered that chemical reactions in underwater hydrothermal vents could have produced the necessary ingredients for life on Earth.

How the ocean’s hydrothermal systems made the first life on Earth possible

Predicting protein interfaces in the age of AlphaFold: Why dynamics and disorder remain a challenge Two recent studies in Cell Systems show why protein dynamics matter for prediction. By moving beyond static structures and embracing the dynamic “jigglings and wigglings” that Richard Feynman famously...

www.cell.com/cell-systems...

Effects of ribonucleotides on telomeric G4 formation, dynamics, and initiation of ribonucleotide excision repair by RNase H2 Abstract. Human telomeres are composed of TTAGGG repeats that can fold into G-quadruplexes (G4s). G4s can form several different conformations, including p

academic.oup.com/nar/article/...

New preprint from my lab (with Arya Kaul, @fernpizza.bsky.social, and @brinda.eu), in which we explore new genes hitchhiking on the beneficial deletion that fused them together, and find them in the LTEE, M. Tb/bovis, and across the bacterial tree of life

Now published in Nature Biotechnology:
go.nature.com/44P7nSm
If you missed it, the TL;DR is in my April thread below

Rescuing the bacterial replisome at a nick requires recombinational repair and helicase reloading - Nature Communications DNA damage can lead to cell death. Here, the authors show that a simple cut on either strand of DNA can inactivate bacterial chromosome replication. Surprisingly, only a core set of recombination prot...

A cool genetic system to study site-pecific replication fork collapse and repair from the brilliant @winterhalterlab.bsky.social

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

Out today in @cp-cell.bsky.social! We studied how environmental stresses like high-fat diets today can prime tumorigenesis months to years in the future (1/n)

FYI: New online! Detecting transcription factor binding sites with PADIT-seq

Dynamic protrusions mediate unique crawling motility in Asgard Archaea (Promethearchaeota) Crawling motility is a hallmark of eukaryotic cells and requires a dynamic actin cytoskeleton, regulated adhesion, and spatially organized signalling pathways1–3. Asgard archaea (phylum Promethearchae...

1. As we recently joined BlueSky, we want to repost this story for all newcomers!

We sat down with @radler92.bsky.social to get more insight into the unique videos from his recent preprint on Promethearchaeota (formerly Asgard archaea).

doi.org/10.1101/2025...

(Videos and info below)

Quantitative profiling of millions of nucleotides reveals sequence-encoded interactions that govern plasmid propagation Plasmids are central to modern biotechnology, especially therapeutic development, yet their propagation in Escherichia coli remains difficult to predict. Although expression-induced burden is well und...

So you think your mammalian plasmids have nothing to fear from cloning and propagation in E.coli?
Quantitative profiling of millions of nucleotides by Tom Copeman will prove you wrong! Supervised with the amazing @proftomellis.bsky.social and AZ, now on BioRxiv:
doi.org/10.64898/202...