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

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

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)

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...

Are you a long-time fan of Archaea, an extremophile-phile, or are you simply curious? Either way, we have good news. We’re delighted to announce the 2026 EMBO Workshop on Archaea, 6–10 July. Sign up: meetings.embo.org/event/26-arc... We look forward to seeing you in Cambridge, UK. Please repost!

🚨 What if evolution is the ”law”… and networks are the machines that do the work? In this paper (just published) I try to formalize how living systems are non-equilibrium, information-processing, adaptive matter. With a great biological flavor! 🧪🌐🌍🧬🦠 👉 iopscience.iop.org/article/10.1... 🧵 1/

The scikit-bio paper in online in Nature Methods! Many thanks to our collaborators, community contributors and reviewers! We couldn’t have done it without you. www.nature.com/articles/s41... #Bioinformatics #OpenSource

Now published. Thank you very much to our collaborative team, and very supportive editors and reviewers!!! www.pnas.org/doi/10.1073/...

Our study on ribonucleotides incorporation the genomes of Haloferax volcanii and Thermococcus barophilus is new published in #NAR #ribonucleasesH academic.oup.com/nar/article/...

Nature research paper: Ribonucleotide incorporation into mitochondrial DNA drives inflammation go.nature.com/3KBRg2W

A high-resolution genome mapping technique now enables detailed study of transposons, offering new insights into genetic evolution, disease mechanisms, and potential agricultural advancements. doi.org/hbb5vk

How do cells activate or silence genes? Read about the #LaskerAward winners who devised ingenious experimental methods, leveraged offbeat model organisms, & capitalized on underappreciated observations to understand how organisms carefully control gene activity. #LaskerLaureate 🧪

Academia is plagued by not-fit-for-purpose metrics that are then used ranking individuals and institutions Will we ever move away from these? - there is a lot of talk but not a great deal of action? The comment ⬇️ is a refreshing look at the problem. www.nature.com/articles/d41...

The Thermococcales as a model system: historical perspectives and emerging tools | Journal of Bacteriology journals.asm.org/doi/10.1128/...

Methanobrevibacter smithii: Trends in Microbiology www.cell.com/trends/micro...

AI is not just another research tool; it is redefining what research is, how it is done and what counts as an original contribution go.nature.com/47Uh6sf

Artificial intelligence has enabled the complete mapping of Phage G, the largest cultivated bacteriophage, providing a new model for studying megaphages and potential antimicrobial applications. doi.org/g98g28

Big pharma seduced by transcription factors again. What has changed? www.nature.com/articles/s41...

Cross-species “xenotransplants”, as the well-worn joke goes, are the future—and always will be. But that punchline is starting to sound out of touch econ.st/4qvPMIf Illustration: Allie Sullberg

One transcript, two functions: the emerging roles of dual-function RNAs microLIFE review by @lizmarialuke.bsky.social and Kai Papenfort at @uni-jena.de academic.oup.com/microlife/ad...

Here's the link to the system, try it! qedscience.com @qedscience.bsky.social

Check out our paper on intricate nested interactions between viruses and virus satellites of haloarchaea and their nanosized DPANN symbionts. Excellent collaboration with @deemteam.bsky.social, @anagtz.bsky.social and Michail Yakimov Free access link: rdcu.be/eLtCH 🧵 by @yifanzhou.bsky.social 👇

Controlled environment agriculture enables year-round indoor crop production with higher yields and reduced resource use, offering a resilient supplement to traditional farming amid increasing climate challenges. doi.org/g95j6g

(p)ppGpp-dependent activation of gene expression during nutrient limitation #mBio from Jonathan Dworkin journals.asm.org/doi/10.1128/...

Language models reveal a complex sequence basis for adaptive convergent evolution of protein functions | PNAS www.pnas.org/doi/10.1073/...

🥳Excited to share our latest collaborative work using whole-cell models and #AI to design genomes!🦠🧬 What a time to be alive! Project led by Ioana Gherman, with Kieren Sharma, Joshua Rees-Garbutt, Claire Grierson, Lucia Marucci, Wei Pang & Zahraa Abdallah #synbio authors.elsevier.com/sd/article/S...

Phenomenal. In my 10 year update of A Brief History, I make the point that in the first edition, not one disease had been successfully treated using gene therapy. Today that number is at least 7.

Sucrose-driven carbon redox rebalancing eliminates the Crabtree effect and boosts energy metabolism in yeast www.nature.com/articles/s41...

Archaea thrive in harsh niches that challenge DNA integrity. 🧬 In H. volcanii, Sailer et al. revealed Cas1 & Hel308a as new Microhomology-Mediated End Joining (MMEJ) players, expanding the toolkit for archaeal genomes repair. buff.ly/lnyY7JF

Holy cow - hyperspectral detection of bacteria at long distance.... "The bacteria were detectable outdoors under ambient light from up to 90 m in a single 4,000-m2 hyperspectral image taken using fixed and unmanned aerial vehicle-mounted cameras." 🤯 www.nature.com/articles/s41...

L'étude croise plusieurs bases collectées indépendamment sur plusieurs thématiques. Autre fait intéressant : quelques centaines de comptes sont quasiment de toutes les polémiques depuis plusieurs années. De vrais leaders dans l'art de la décohésion sociale.