Cress Lab

Protease-Controlled Prophage Activation in Staphylococcus aureus: New Mechanisms Driving Antimicrobial Resistance and Virulence at University of St Andrews on FindAPhD.com PhD Project - Protease-Controlled Prophage Activation in Staphylococcus aureus: New Mechanisms Driving Antimicrobial Resistance and Virulence at University of St Andrews, listed on FindAPhD.com

📢 Funded PhD in molecular microbiology & phage biology

How do bacterial stress responses control prophage activation and horizontal gene transfer?

Join us at St Andrews to dissect Clp protease–mediated regulation in Staphylococcus aureus.

Apply:
www.findaphd.com/phds/project...

Early-bird registration discounts for CRISPR 2026 expire Feb 28. CRISPR 2026, held at Yale University, June 10 - 12, is the continuation of the original CRISPR meeting established in 2008.

Register here: web.cvent.com/event/ac20b6...

Excited to share a preprint from my postdoc work in
Shipman’s lab!

We developed Detectrons — programmable biosensors that convert RNA signals into stable DNA barcodes inside living cells, enabling multiplexed RNA sensing. 🧵👇

biorxiv.org/content/10.6...

New preprint on Detectrons from @jihoon-han.bsky.social! These are programmable biosensors for RNA that produce DNA barcodes in the presence of their target RNA. Check out Jihoon's quoted thread and the preprint for more:
www.biorxiv.org/content/10.6...

Ancient co-option of LTR retrotransposons as yeast centromeres - Nature Evolutionarily related ‘proto-point’ centromeres providing resolution to the evolutionary origins of point centromeres are identified in yeast, and comparison shows they evolved in an ancestor with re...

Our paper is now out in Nature:

“Ancient co-option of LTR retrotransposons as yeast centromeres”

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

A short thread on how retrotransposons helped give rise to yeast point centromeres.

1/14

📣new preprint from the phagefoundry.org team 🎉 Jessica Trinh and Catherine Mageeney (Sandia National Laboratories)!!

Systematic analysis of prophages from ~1000 Acinetobacter baumannii isolates, induction & screening. We found this 😎 looking phage with bunch of 💍💍

The Bart Lab at UC Berkeley is looking for a postdoc. Please share!

🧬 New preprint alert!
Protein language models have transformed biology - but what about the tokens they read?
In our new preprint, 👑@EllaRannon👑 studies how tokenization choices shape pLM performance and efficiency. 🧵 (1/5)
www.biorxiv.org/content/10.6...

PlasAnn: a curated plasmid-specific database and annotation pipeline for standardized gene and function analysis Abstract. Conjugative plasmids are key drivers of bacterial adaptation, enabling the horizontal transfer of accessory genes within and across diverse micro

Big week: welcomed a new baby boy Harris Lopatkin, AND our PlasAnn paper is finally out: academic.oup.com/nar/article/... (obviously the first more important than the second 🥰). Currently on leave but if anyone has the need to annotate large plasmids, go check it out!

Postdoctoral position - Synthetic Biology / Bacterial Immunity - Research The Bikard lab at Institut Pasteur in Paris is seeking to hire postdoctoral researchers. We are investigating bacteria / bacteriophages interactions, and the genetic innovation that happens at this in...

🚨 Hiring Alert! 🚨My lab at Institut Pasteur is recruiting several Postdocs! We have exciting open projects in: 🦠 Synthetic Biology and🛡️ Bacterial Immunity. Come do great science with us in the middle of Paris! 🇫🇷🥐 research.pasteur.fr/en/job/postd...

Check out our latest preprint from @jnvmartinson.bsky.social and @leosong.bsky.social! 🌟🦠

We found that conjugative plasmids can actively eliminate recipient bacteria that resist plasmid acquisition. 🧵

Plasmids weaponize conjugation to eliminate non-permissive recipients https://www.biorxiv.org/content/10.64898/2026.02.10.705089v1

We're honored and grateful to have a project accepted by @nsfexfab.bsky.social BioFoundry, spearheaded by our amazing postdoctoral researcher Dr. Madeline Hayes @chucksbiscuit.bsky.social (co-advised by @cresslab.bsky.social and Dr. Michelle O'Malley from UCSB)! 🦠🔍🤩

The visualization of two bacterial genomes, of 50 and 52kb, representing independent instances of extreme genomic reduction in ancient heritable endosymbionts of planthoppers.

Our new paper in @natcomms.nature.com is now online-early!

We describe independent evolution of bacterial genomes of only ~50–52 kb — the smallest known outside cellular organelles — revealing striking convergence toward minimal gene sets.

🔗 doi.org/10.1038/s414...

A phage protein screen identifies triggers of the bacterial innate immune system - Nature Microbiology A library of 400 phage protein-coding genes is used to find a trove of antiphage systems, revealing systems that target tail fibre and major capsid proteins.

I’m thrilled to share our work on phage triggers of the bacterial immune system in its final form @natmicrobiol.nature.com www.nature.com/articles/s41...

Also a big thanks to @cresslab.bsky.social and @therubinlab.bsky.social who came up with the idea to start this meeting and were instrumental in making it happen! And congratulations to @therubinlab.bsky.social and @paulwilmes.bsky.social for their elections as vice-chairs for the next one!

It was a true privilege to co-chair the inaugural GRC meeting on Microbiome Editing together with @jenniferdoudna.bsky.social . The positive energy and quality of the Science presented were truly inspiring. I look forward to the next one chaired by KC Huang and @omalleylab.bsky.social !!!

A phage protein screen identifies triggers of the bacterial innate immune system Nature Microbiology, Published online: 16 January 2026; doi:10.1038/s41564-025-02239-6A library of 400 phage protein-coding genes is used to find a trove of antiphage systems, revealing systems that target tail fibre and major capsid proteins.

Out Now! A phage protein screen identifies triggers of the bacterial innate immune system #MicroSky

illustration of petri dishes growing different microbes

We're excited to help launch the inaugural Gordon research conference on #microbiome editing, coming up in January in Pomona, CA! Learn more and register here: https://ow.ly/a6Am50X9XkE

This is shaping up to be one of the top conferences on microbiome editing!!

Conference poster on microbiome editing

Such a privilege to share the Phage Foundry (phagefoundry.org) team’s work at the inaugural GRC meeting on Microbiome Editing 🎉🎊.

On my way to two *awesome* back-to-back conferences:

First, GRC on Microbiome Editing in Pomona, CA
www.grc.org/microbiome-e...

Then, Keystone Conference on Human Microbiomes in Banff (co-organizing)
www.keystonesymposia.org/conferences/...

I get ~100 emails a day, but such an email is rare:
"Dr. Moon,
On behalf of Chairs Jennifer Doudna and David Bikard..."

So excited to see the Nobel laureate again, chair a session & give a talk at #microbiome editing GRC! See you all!
@dbikard.bsky.social

www.grc.org/microbiome-e...

Bioengineering the coral holobiont: Evidence, hurdles, and pathways for rebuilding reefs At the frontline of climate impacts, coral reef ecosystems now increasingly depend on active intervention for their functional survival. Bioengineering the coral holobiont, comprising the host, algal ...

Feeling grateful to end this year by contributing to a commentary on bioengineering the coral holobiont. This is my first manuscript as a professor and a dream come true to team up with leaders in coral probiotics, Raquel Peixoto and @reefgenomics.bsky.social. 🪸🧪🧬🦠

www.cell.com/one-earth/ab...

Stepwise DNA unwinding gates TnpB genome-editing activity https://www.biorxiv.org/content/10.64898/2026.01.09.698545v1

DDLS Research School Postdoc call 2026 Call for Academic and Industrial Postdoctoral Fellowships in Data-Driven Life Science 2026 Generic Description of the DDLS Postdoc Program The SciLifeLab and Wallenberg National Program for Data-Drive...

I’m looking to host a postdoc in our lab to use proteomics to discover and characterize phage receptors.
Strong fit if you have experience in MS based proteomics and an interest in infection biology.
Call info: www.scilifelab.se/data-driven/...
#postdoc #proteomics #phage #infectionbiology

Last call to secure your spot at Microbes in Wastewater Symposium!

Connect with experts across wastewater research, environmental microbiology, and public health. Plus, enjoy an exclusive dinner cruise on the beautiful Newport Beach Harbor!

Register now: www.wastewateramr.com

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

If you are looking to integrate your latest genetic creation into the genome of your favourite bug, you might find our latest review now out in OUP Synthetic Biology useful. 🧬⚒️ Work led by Riesa Rohmat with input from Thea Irvine and Shivang Joshi. #genome #synbio doi.org/10.1093/synb...

Diverse bacterial pattern recognition receptors sense the conserved phage proteome Recognition of foreign molecules inside cells is critical for immunity in all domains of life. Proteins of the STAND NTPase superfamily, including eukaryotic nucleotide-binding oligomerization domain ...

🧫 🧪 We’re so excited to share our new preprint, where we tackle the wealth of structural and functional diversity across antiviral STAND NTPases in bacteria.

www.biorxiv.org/content/10.6...