🚨 Fresh from the press! We created and analyzed over 100 in vitro cyanobacterial consortia using well-characterized model cyanobacterial hosts to better understand how cyanobacteria recruit and interact with their microbiomes. Check it out: doi.org/10.1093/isme...

Many of you gave me so much encouragement when I posted here earlier about my 10 year long passion project to make a microbial map of the ocean. Pinch me because I can't believe I get to update you that today that research was published in the journal SCIENCE! @science.org

Happy to share our recent work on rRNA processing and conformation: www.biorxiv.org/content/10.1... Huge thanks to @ppenev.bsky.social @Amos Nissley @Dipti Nayak @Rohan Sachdeva @jhdcate.bsky.social @Jill Banfield @banfieldlab.bsky.social !!

I’m very excited to finally share the results of a passion project that has been on my mind for nearly a decade. You can find the pre-print below, but what follows is the saga of how this project came to be:

After 24 years of work, I’m thrilled to announce the TYMEFLIES dataset, which comprises metagenomes from Lake Mendota (Madison, WI), collected roughly every 10 days (471 samples) for 20 years! @quendi.bsky.social @robinrohwer.bsky.social rdcu.be/d5put A thread…

#PhD #position #alert 2 bioinfo PhD positions @ProbstLab @RESIST_CRC #1 on microbial & epigenetic stress response in rivers tinyurl.com/bdf8eu5a #2 on virus-host stress response in rivers tinyurl.com/43cjd6es (supervision Moraru) Please share!

the tool of the elite bioinformatician

📰 Hot off the press at @naturecomms.bsky.social: RNA language models predict mutations that improve RNA function www.nature.com/articles/s41... Congrats to @kshulgina.bsky.social @jhdcate.bsky.social and coauthors on a great C-GEM + @innovativegenomics.bsky.social collaboration! #NSFfunded #RNAsky

Excited to have our review 'Archaea and the origin of eukaryotes' in the @NatureRevMicro special issue celebrating the 40th anniversary of Woese and Fox's paper! With @anjspa1 @cstairs J. Lombard and @Ettema_lab https://www.nature.com/articles/nrmicro.2017.133

Hello 🦋 #protein / #microbio / #BioML community! We are excited to release Gaia🌎, a context-aware protein search tool, extending protein search and discovery capabilities beyond sequence and structure, to include *genomic context*. Search your favorite protein sequences with on gaia.tatta.bio

Great job opportunity in my hometown! Pgh is a fantastic city.

And then there was one… Celebrating the final ‘cosm harvest from our 7th/last 13CO2 experiment of 2024. We’re studying how the psY gene affects CH4 fluxes and soil C cycles. Much gratitude to Rina Estera, Flor Ercoli, Pam Ronald Lab, Dave Savage Lab & many others @innovativegenomics.bsky.social

Fully Funded PhD Opportunity in Evolutionary Biology at the U of Rhode Island. Join us to explore the origin and early evolution of eukaryotes using cutting-edge comparative (meta)genomics and molecular evolution approaches. Applications are due December 15th. Contact me ASAP at [email protected]

We are searching for a postdoc to join our team, focused on anaerobic ciliate-methanogen symbiosis. Please share widely!

New paper out! We found evidence of sporadic domain insertion events that affected protein-coding genes hundreds of million years ago. These insertions were retained by the DNA-dependent RNA polymerase in bacteria and by ribosomal protein uL10 in archaea. onlinelibrary.wiley.com/doi/full/10....

Reposting this here: Two years ago we published the discovery of hotspots of novel anti-phage defense systems in the genome of P4 phage satellites, including a mysterious Phage Anti-Restriction Induced System (PARIS). We have now published the mechanism in @Nature www.nature.com/articles/s41...

Many years in the making, our new paper in collaboration with the Banfield lab. - Autotrophic biofilms sustained by deeply sourced groundwater host diverse bacteria implicated in sulfur and hydrogen metabolism microbiomejournal.biomedcentral.com/articles/10....

first post on ~here~ to highlight the work of former Banfield lab undergrad @jettliu.bsky.social out today in mBio, examining the genetic characteristics of phages of CPR bacteria: journals.asm.org/doi/10.1128/...

Hey, we have a new paper out! In collaboration with Brian Hammer's group, we examine how E. coli evolves to *resist* being killed by the Type 6 Secretion System (basically a microbial poison-tipped spear attack). www.cell.com/iscience/ful...

The father of Archaea examines Asgards! www.hindawi.com/journals/arc...

Our latest work on bacterial methane clathrate proteins in collaboration with @raquellieberman.bsky.social is featured in this article ! research.gatech.edu/seafloor-spa...

I’m really excited to share our new pre-print “Genome-wide Characterization of Diverse Bacteriophages Enabled by RNA-Binding CRISPRi”, with co-first author Muntathar Al-Shimary  from the Doudna and the newly-minted Cress labs! www.biorxiv.org/content/10.1...

Our work on clustering the 214M AlphaFold protein structure was published in @Nature. We identified 2.3M clusters using our fast structure cluster algorithm and analysed its annotations, evolution and novel domains. Work with Pedro Beltrao. 1/n 📄 www.nature.com/articles/s41... 💾 cluster.foldseek.com

Excited for my first Blue Skye post! 🚀 Our latest paper from the Baker lab is out today in mBio! Interested in ocean hydrocarbon degradation & SIP-metagenomics? Check this out! 👇 journals.asm.org/doi/10.1128/... @archaeal.bsky.social

Made it over! 🥳