Luis E. Valentin-Alvarado

Recurrent acquisition of nuclease-protease pairs in antiviral immunity Antiviral immune systems diversify by integrating new genes into existing pathways, creating new mechanisms of viral resistance. We identified genes encoding a predicted nuclease paired with a trypsin...

Excited to finally share this work!
We noticed a pair of genes - a nuclease and a protease - shuffles between antiviral systems. We show how proteolysis activates the nuclease, triggering defense in known and unknown immune contexts.
tinyurl.com/2uwwy4ty

‼️ New pre-print from co-leads @owentuck.bsky.social and Jason Hu! Check out this fascinating example of how coevolution enables defense system innovation.

Very proud to have our lab’s first work published in @cp-cellhostmicrobe.bsky.social!

In this work, we use functional metagenomics to find phage defenses from human and soil microbiomes!

Congrats to first author @luis840alberto.bsky.social !

www.cell.com/cell-host-mi...

(1/3)

if i were a better person i would do a tweetorial on our recent paper - but, hey, read the paper. its right there, waiting for you. #Giantvirus #histones are cool! their #nucleosomes are cool. check it out.! thats the tweetorial.
rdcu.be/exXBX

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...

Our latest work, driven by the fabulous @stephkoe.bsky.social! WitChi takes care of compositional bias in large phylogenomic datasets! WitChi is fast, efficient and free, try it out!

With @kassipan.bsky.social and @danieltamarit.bsky.social

#Archaea #GRC folks, be sure to catch work by @oceancait.bsky.social representing our group this week in Switzerland.

She'll talk about new Asgard archaea enrichments form the Oregon coast. Talk on Sunday, Poster during the week.

A cartoon depiction of the Asgard archaeon Skadiarchaeum sp., named after the Norse goddess of skiing and hunting, Skadi.

In a couple of days, my grad student Stavros Trimmer will present his new Asgard archaea culture at the GRC Archaea. He named it Skadiarchaeum after Skadi, the Norse goddess of skiing and hunting. Cartoon of Skadi based on cryoET, which was performed together with with @florianwollweber.bsky.social

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...

This #WorldZoonosesDay, learn five key facts about #zoonotic diseases and how we can prevent future outbreaks.
Check out our infographic: onehealthtrust.org/publications...

🚨 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...

Structural motif search across the protein-universe with Folddisco www.biorxiv.org/content/10.1...
Code: github.com/steineggerla...
Web app: search.foldseek.com/folddisco

Franklin W. Stahl, 95, Dies; Helped Create a ‘Beautiful’ DNA Experiment

Franklin W. Stahl, 95, Dies; Helped Create a ‘Beautiful’ DNA Experiment. Gift article:
www.nytimes.com/2025/07/07/s...

Lots of other fun Antarctic-themed things happening all week for the Family Fiesta too!
www.monash.edu/performing-a...

📑 Programs? Printed.
🏛️ Venue? Looking amazing.
🧪 Energy? Building fast.

We're almost ready to welcome the HFSP community to Melbourne for an unforgettable week of science and connection!
Who's coming to the 24th HFSP Awardees Meeting?

#HFSP #HFSPmtg2025

@science.org Zincore-coregulator dedicated to zinc🖐️ TFs essential in development www.science.org/doi/10.1126/...
@rborza.bsky.social @sgregoricchio.bsky.social @amazouzi.bsky.social @zwartlab.bsky.social @lindersimon.bsky.social @tassosperrakis.bsky.social @thijnbrummel.bsky.social + al.

Beautiful work by Pam et al. !!

Congrats @sgribaldo.bsky.social !!

Bay Area friends! I’ll be around for the next few weeks. If you’re nearby and want to catch up - science chats, hikes, coffee, or just vibes — send me a message. Would love to reconnect

Our new consensus statement on reducing and reporting contamination in microbiome studies is the cover image of this month's Nature Microbiology: www.nature.com/articles/s41... In the cover photo, you can see our postdoc Sophie Holland in fully PPE sampling the atmosphere of terrestrial Antarctica.

Happy #WorldMicrobiomeDay!

#PacBio is honoring the tiny microbial communities making a big impact on discovery. HiFi sequencing empowers researchers to explore the #microbiome with exceptional accuracy, strain-level ID, complete genomes, and deep functional insights. (1/2)

DAFNEE is a great resource for #Biology #Evolution #Ecology and genuinely most Life Science disciplines. Choose journals run by the community and that invest back into the community. The journals in DAFNEE also include multidisciplinary journals that would take #Genetics #MolBiol etc...

Enrichment cultivation and visualization of Ca. Methanonezhaarchaeum fastidiosum

Preprint🚨 #microsky 🦠 “Cultivation of Methanonezhaarchaeia, the third class of methanogens within the phylum Thermoproteota”, authored by @kohtzarchaeota.bsky.social & Sylvia Nupp, expands the diversity of methanogens! 90% enriched, methylotrophic culture from a hot spring. A 🧵 tinyurl.com/yw8ku2bj

🧵🦠🖥️🧬🧪
Please RePost 🙏

We just released reference genomes for another 250 strains to the ATCC Genome Portal (genomes.ATCC.org)! We now have assemblies for

_5,750 microbial genomes_

AND

all assemblies w/ @nanoporetech.com data will include DNA methylation profiles too (details👇)

#genomics 1/

List of 30 CloneFISH cultures available for free (requester is asked to pay shipping fees).

Manuscript/resource alert #microsky 🦠 My lab offers the community a collection of 30 E. coli (CloneFISH) cultures, each carrying a plasmid for the heterologous expression of a (near) full-length 16S rRNA gene from one of 30 lineages of archaea, including 19 yet uncultured ones.

What a vibrant community! I had so much fun.

We’re happy to share our preprint where applied phages to Microbiomes to test microbial interaction hypotheses - without losing the relevance of the community.

Bonus: using SNPs we studied how our targeted organism recovers from infection, and find how the community likely influences this process.

Dan Portik (@dportik.bsky.social) from #PacBio is live at #ASMicrobe sharing insights on oral microbiome assembly using HiFi long-read sequencing until 11:30 AM.

Catch him at poster 974 in section HMB in the exhibit hall. He’ll be back again from 3 to 4 PM!

Excited to share our new paper in @cellreports.bsky.social that reshapes our understanding of chromosome organization's deep evolutionary roots! Our work dives into the origins of the machinery that structures our very genomes.

🔗: doi.org/10.1016/j.ce...

#Genomics #Evolution #CellBiology #LECA

A short preprint describing the GlobDB is now on arXiv: arxiv.org/abs/2506.11896

If you find the resource useful, please also check globdb.org for info on how to cite the underlying resources and tools.