Cress Lab
@cresslab.bsky.social
The Cress Lab | Innovative Genomics Institute @ UC Berkeley | Microbiome Editing | Microbiome Delivery Technologies | Phage and MGE Functional Genomics | Hiring!
https://www.cresslab.bio/
https://www.cresslab.bio/
Pinned
Cress Lab
@cresslab.bsky.social
· Feb 26
CRISPRi-ART enables functional genomics of diverse bacteriophages using RNA-binding dCas13d - Nature Microbiology
Leveraging RNA-targeting dCas13d enables selective interference with phage protein translation and facilitates measurement of phage gene fitness at a transcriptome-wide scale.
doi.org
Dive into our lab’s first peer-reviewed publication—co-led with our friends @benadler.bsky.social and Muntathar Al-Shimary from the @doudna lab! If you’ve already read the preprint, don’t miss the new updates: doi.org/10.1038/s415... @naturemicrobiol.bsky.social
Reposted by Cress Lab
New paper out: An archaeal genetic code with all TAG codons as pyrrolysine: www.science.org/doi/10.1126/...
An archaeal genetic code with all TAG codons as pyrrolysine
Multiple genetic codes developed during the evolution of eukaryotes and bacteria, yet no alternative genetic code is known for archaea. We used proteomics to confirm our prediction that certain archae...
www.science.org
November 23, 2025 at 7:22 PM
New paper out: An archaeal genetic code with all TAG codons as pyrrolysine: www.science.org/doi/10.1126/...
Reposted by Cress Lab
Thrilled to share the core of my PhD work, now published in NAR!
This project was a true collaborative effort across multiple teams, and it was a joy to bring it to life.
Huge thanks to everyone involved, and especially to @fnobrega.bsky.social for the incredible support and guidance 🙏🏻
🧵1/5
This project was a true collaborative effort across multiple teams, and it was a joy to bring it to life.
Huge thanks to everyone involved, and especially to @fnobrega.bsky.social for the incredible support and guidance 🙏🏻
🧵1/5
⭐ NAR Breakthrough! ⭐
A community-driven collection uniting 52 phages, 74 Klebsiella isolates, and extensive genomic + phenotypic data — all freely available at klebphacol.org.
🧬 Learn more: doi.org/10.1093/nar/...
@fnobrega.bsky.social @danielarothschild.bsky.social #antimicrobialresistance
A community-driven collection uniting 52 phages, 74 Klebsiella isolates, and extensive genomic + phenotypic data — all freely available at klebphacol.org.
🧬 Learn more: doi.org/10.1093/nar/...
@fnobrega.bsky.social @danielarothschild.bsky.social #antimicrobialresistance
November 22, 2025 at 6:12 PM
Thrilled to share the core of my PhD work, now published in NAR!
This project was a true collaborative effort across multiple teams, and it was a joy to bring it to life.
Huge thanks to everyone involved, and especially to @fnobrega.bsky.social for the incredible support and guidance 🙏🏻
🧵1/5
This project was a true collaborative effort across multiple teams, and it was a joy to bring it to life.
Huge thanks to everyone involved, and especially to @fnobrega.bsky.social for the incredible support and guidance 🙏🏻
🧵1/5
Reposted by Cress Lab
⭐ NAR Breakthrough! ⭐
A community-driven collection uniting 52 phages, 74 Klebsiella isolates, and extensive genomic + phenotypic data — all freely available at klebphacol.org.
🧬 Learn more: doi.org/10.1093/nar/...
@fnobrega.bsky.social @danielarothschild.bsky.social #antimicrobialresistance
A community-driven collection uniting 52 phages, 74 Klebsiella isolates, and extensive genomic + phenotypic data — all freely available at klebphacol.org.
🧬 Learn more: doi.org/10.1093/nar/...
@fnobrega.bsky.social @danielarothschild.bsky.social #antimicrobialresistance
November 20, 2025 at 6:01 PM
⭐ NAR Breakthrough! ⭐
A community-driven collection uniting 52 phages, 74 Klebsiella isolates, and extensive genomic + phenotypic data — all freely available at klebphacol.org.
🧬 Learn more: doi.org/10.1093/nar/...
@fnobrega.bsky.social @danielarothschild.bsky.social #antimicrobialresistance
A community-driven collection uniting 52 phages, 74 Klebsiella isolates, and extensive genomic + phenotypic data — all freely available at klebphacol.org.
🧬 Learn more: doi.org/10.1093/nar/...
@fnobrega.bsky.social @danielarothschild.bsky.social #antimicrobialresistance
Reposted by Cress Lab
Calling all rising juniors & seniors: Interested in biological or biomedical research? Applications for our ’26 Summer Undergraduate Research Experience Program are now open! Nine weeks, hands-on research, & mentorship from some of the nation’s top scientists — learn more: bit.ly/CechFellows
Summer Undergraduate Research Experience | HHMI
The Cech Fellows Program is a paid, nine-week summer research experience empowering the next generation of scientific leaders.
bit.ly
November 18, 2025 at 2:44 PM
Calling all rising juniors & seniors: Interested in biological or biomedical research? Applications for our ’26 Summer Undergraduate Research Experience Program are now open! Nine weeks, hands-on research, & mentorship from some of the nation’s top scientists — learn more: bit.ly/CechFellows
Reposted by Cress Lab
What is the best strategy to win any contest?
Eliminate your opponents of course.
Recently, my friend @fernpizza.bsky.social showed how plasmids compete intracellularly (check out his paper published in Science today!). With @baym.lol, we now know they can fight.
www.biorxiv.org/content/10.1...
Eliminate your opponents of course.
Recently, my friend @fernpizza.bsky.social showed how plasmids compete intracellularly (check out his paper published in Science today!). With @baym.lol, we now know they can fight.
www.biorxiv.org/content/10.1...
November 20, 2025 at 10:12 PM
What is the best strategy to win any contest?
Eliminate your opponents of course.
Recently, my friend @fernpizza.bsky.social showed how plasmids compete intracellularly (check out his paper published in Science today!). With @baym.lol, we now know they can fight.
www.biorxiv.org/content/10.1...
Eliminate your opponents of course.
Recently, my friend @fernpizza.bsky.social showed how plasmids compete intracellularly (check out his paper published in Science today!). With @baym.lol, we now know they can fight.
www.biorxiv.org/content/10.1...
Reposted by Cress Lab
When different kinds of mobile genetic elements get together, they become even more powerful catalysts for microbial evolution! In this work we discovered a mechanism by which Insertion Sequences drive their spread across Plasmids, which helps explain this evolutionary potential!
What is the best strategy to win any contest?
Eliminate your opponents of course.
Recently, my friend @fernpizza.bsky.social showed how plasmids compete intracellularly (check out his paper published in Science today!). With @baym.lol, we now know they can fight.
www.biorxiv.org/content/10.1...
Eliminate your opponents of course.
Recently, my friend @fernpizza.bsky.social showed how plasmids compete intracellularly (check out his paper published in Science today!). With @baym.lol, we now know they can fight.
www.biorxiv.org/content/10.1...
November 21, 2025 at 7:35 PM
When different kinds of mobile genetic elements get together, they become even more powerful catalysts for microbial evolution! In this work we discovered a mechanism by which Insertion Sequences drive their spread across Plasmids, which helps explain this evolutionary potential!
Reposted by Cress Lab
Hot off the press! Our latest paper led by @fernpizza.bsky.social, understanding how plasmids evolve inside cells. These small, self-replicating DNA circles live inside bacteria and carry antibiotic resistance genes, but also compete with one another to replicate. 1/
www.science.org/doi/10.1126/...
www.science.org/doi/10.1126/...
Intracellular competition shapes plasmid population dynamics
From populations of multicellular organisms to selfish genetic elements, conflicts between levels of biological organization are central to evolution. Plasmids are extrachromosomal, self-replicating g...
www.science.org
November 20, 2025 at 9:42 PM
Hot off the press! Our latest paper led by @fernpizza.bsky.social, understanding how plasmids evolve inside cells. These small, self-replicating DNA circles live inside bacteria and carry antibiotic resistance genes, but also compete with one another to replicate. 1/
www.science.org/doi/10.1126/...
www.science.org/doi/10.1126/...
Reposted by Cress Lab
🚀New preprint from our lab!
I am very excited to finally share what has been the main focus of my PhD for the past almost 3 years! It is about viral dark matter and a powerful tool we built to shed light on it. 🧬💡
Continue reading (🧵)
I am very excited to finally share what has been the main focus of my PhD for the past almost 3 years! It is about viral dark matter and a powerful tool we built to shed light on it. 🧬💡
Continue reading (🧵)
November 20, 2025 at 6:52 PM
🚀New preprint from our lab!
I am very excited to finally share what has been the main focus of my PhD for the past almost 3 years! It is about viral dark matter and a powerful tool we built to shed light on it. 🧬💡
Continue reading (🧵)
I am very excited to finally share what has been the main focus of my PhD for the past almost 3 years! It is about viral dark matter and a powerful tool we built to shed light on it. 🧬💡
Continue reading (🧵)
Reposted by Cress Lab
🚨Preprint alert - this is a big one! We transfer the revolutionary power of TnSeq to bacteriophages.
Our HIDEN-SEQ links the "dark matter" genes of your favorite phage to any selectable phenotype, guiding the path from fun observations to molecular mechanisms.
A thread 1/8
Our HIDEN-SEQ links the "dark matter" genes of your favorite phage to any selectable phenotype, guiding the path from fun observations to molecular mechanisms.
A thread 1/8
November 20, 2025 at 8:40 PM
🚨Preprint alert - this is a big one! We transfer the revolutionary power of TnSeq to bacteriophages.
Our HIDEN-SEQ links the "dark matter" genes of your favorite phage to any selectable phenotype, guiding the path from fun observations to molecular mechanisms.
A thread 1/8
Our HIDEN-SEQ links the "dark matter" genes of your favorite phage to any selectable phenotype, guiding the path from fun observations to molecular mechanisms.
A thread 1/8
Reposted by Cress Lab
The best group of lab Minions out there 🥸🧪
We’re a bit late, but better late than never (bi do)! Happy Belated Halloween from the Cress and @therubinlab.bsky.social Labs!
November 19, 2025 at 12:41 AM
The best group of lab Minions out there 🥸🧪
Reposted by Cress Lab
We built GenoPHI: a machine learning workflow that predicts phage-host interactions at strain level. This could help rapidly select phages to treat drug-resistant bacterial infections or for microbiome engineering without exhaustive lab testing.
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
www.biorxiv.org
November 16, 2025 at 11:16 PM
We built GenoPHI: a machine learning workflow that predicts phage-host interactions at strain level. This could help rapidly select phages to treat drug-resistant bacterial infections or for microbiome engineering without exhaustive lab testing.
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Reposted by Cress Lab
📣 New preprint from us at phagefoundry.org 📣
A solid machine learning framework & to predict strain-level phage-host interactions across diverse bacterial genera from genome sequences alone. Avery Noonan from the Arkin Lab led this massive effort
www.biorxiv.org/content/10.1...
A solid machine learning framework & to predict strain-level phage-host interactions across diverse bacterial genera from genome sequences alone. Avery Noonan from the Arkin Lab led this massive effort
www.biorxiv.org/content/10.1...
Phage Foundry
phagefoundry.org
November 16, 2025 at 5:58 PM
📣 New preprint from us at phagefoundry.org 📣
A solid machine learning framework & to predict strain-level phage-host interactions across diverse bacterial genera from genome sequences alone. Avery Noonan from the Arkin Lab led this massive effort
www.biorxiv.org/content/10.1...
A solid machine learning framework & to predict strain-level phage-host interactions across diverse bacterial genera from genome sequences alone. Avery Noonan from the Arkin Lab led this massive effort
www.biorxiv.org/content/10.1...
Reposted by Cress Lab
#microsky #phagesky
Predicting host- #phage interactions from genomics.
www.biorxiv.org/content/10.1...
Predicting host- #phage interactions from genomics.
www.biorxiv.org/content/10.1...
Phylogeny-agnostic strain-level prediction of phage-host interactions from genomes
Bacteriophages offer promising alternatives to antibiotics for treating drug-resistant infections and engineering microbiomes, but applications are limited by inability to select phages infecting spec...
www.biorxiv.org
November 16, 2025 at 9:53 AM
#microsky #phagesky
Predicting host- #phage interactions from genomics.
www.biorxiv.org/content/10.1...
Predicting host- #phage interactions from genomics.
www.biorxiv.org/content/10.1...
Reposted by Cress Lab
I’m excited to share my recent postdoc work. Here, we interrogate how different phage infection outcomes (productive vs. restrictive) affect the expression of phage defense systems. We find that a restricted infection not only inhibits the phage but also induces increased immune protein abundance.
Surviving phage attack dynamically regulates bacterial immunity to defeat counterdefenses https://www.biorxiv.org/content/10.1101/2025.11.13.688357v1
November 15, 2025 at 6:10 PM
I’m excited to share my recent postdoc work. Here, we interrogate how different phage infection outcomes (productive vs. restrictive) affect the expression of phage defense systems. We find that a restricted infection not only inhibits the phage but also induces increased immune protein abundance.
Reposted by Cress Lab
Beautiful preprint from Simone Evans et al. in Alex Gao's group looking at MBL/nuclease and other cool zymogens (pepco, EACC1) in antiphage defense systems. Great to see this paradigm extended - probably many more proteolytically activated effectors out there...
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
www.biorxiv.org
November 15, 2025 at 10:21 PM
Beautiful preprint from Simone Evans et al. in Alex Gao's group looking at MBL/nuclease and other cool zymogens (pepco, EACC1) in antiphage defense systems. Great to see this paradigm extended - probably many more proteolytically activated effectors out there...
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Reposted by Cress Lab
also, an excellent perspective by @dbikard.bsky.social summarizing the work! 🙏
www.science.org/doi/10.1126/...
www.science.org/doi/10.1126/...
Programmable DNA insertion in native gut bacteria
A gene-editing approach enables modification of bacteria within the mouse gut
www.science.org
November 13, 2025 at 9:39 PM
also, an excellent perspective by @dbikard.bsky.social summarizing the work! 🙏
www.science.org/doi/10.1126/...
www.science.org/doi/10.1126/...
Reposted by Cress Lab
We are hiring PhD & Postdocs in this space so please reach out if interested. Also check out the Gordon Research Conference on Microbiome Editing in Jan 11-16, 2026.
www.grc.org/microbiome-e...
www.grc.org/microbiome-e...
2026 Microbiome Editing Conference GRC
The 2026 Gordon Research Conference on Microbiome Editing will be held in Pomona, California. Apply today to reserve your spot.
www.grc.org
November 13, 2025 at 8:53 PM
We are hiring PhD & Postdocs in this space so please reach out if interested. Also check out the Gordon Research Conference on Microbiome Editing in Jan 11-16, 2026.
www.grc.org/microbiome-e...
www.grc.org/microbiome-e...
Reposted by Cress Lab
Very excited to share our latest work in Science on metagenomic editing (MetaEdit) of the gut microbiome in vivo & directly modifying unculturable immune-modulatory SFB bug in the small intestine. 🦠🧬🛠️
www.science.org/doi/10.1126/...
www.science.org/doi/10.1126/...
Metagenomic editing of commensal bacteria in vivo using CRISPR-associated transposases
Although metagenomic sequencing has revealed a rich microbial biodiversity in the mammalian gut, methods to genetically alter specific species in the microbiome are highly limited. Here, we introduce ...
www.science.org
November 13, 2025 at 8:53 PM
Very excited to share our latest work in Science on metagenomic editing (MetaEdit) of the gut microbiome in vivo & directly modifying unculturable immune-modulatory SFB bug in the small intestine. 🦠🧬🛠️
www.science.org/doi/10.1126/...
www.science.org/doi/10.1126/...
Reposted by Cress Lab
🚀 PhD opportunity
The Dept of Biological and Environmental Science, University of Jyväskylä, is recruiting 1–4 new PhD candidates.
One of the positions is potentially in my lab, focusing on megaphages and their hosts.
Details and apply here 👇
bit.ly/48eqYNB
#phage
The Dept of Biological and Environmental Science, University of Jyväskylä, is recruiting 1–4 new PhD candidates.
One of the positions is potentially in my lab, focusing on megaphages and their hosts.
Details and apply here 👇
bit.ly/48eqYNB
#phage
Doctoral Researcher positions, Biological and Environmental Sciences
The Department of Biological and Environmental Sciences is seeking applicants for 1–4 fully funded doctoral researcher positions. The positions will begin on August 1, 2026, or as agreed, for a maximu...
ats.talentadore.com
November 14, 2025 at 7:35 AM
🚀 PhD opportunity
The Dept of Biological and Environmental Science, University of Jyväskylä, is recruiting 1–4 new PhD candidates.
One of the positions is potentially in my lab, focusing on megaphages and their hosts.
Details and apply here 👇
bit.ly/48eqYNB
#phage
The Dept of Biological and Environmental Science, University of Jyväskylä, is recruiting 1–4 new PhD candidates.
One of the positions is potentially in my lab, focusing on megaphages and their hosts.
Details and apply here 👇
bit.ly/48eqYNB
#phage
Reposted by Cress Lab
1/9 Metagenomics lets us read microbiomes in nature without cultivation, but writing (editing) them in their native context is still a major challenge.
Meet MetaEdit: a platform for pathway-scale metagenomic editing inside the gut microbiome. science.org/doi/10.1126/...
Meet MetaEdit: a platform for pathway-scale metagenomic editing inside the gut microbiome. science.org/doi/10.1126/...
Metagenomic editing of commensal bacteria in vivo using CRISPR-associated transposases
Although metagenomic sequencing has revealed a rich microbial biodiversity in the mammalian gut, methods to genetically alter specific species in the microbiome are highly limited. Here, we introduce ...
science.org
November 14, 2025 at 2:25 PM
1/9 Metagenomics lets us read microbiomes in nature without cultivation, but writing (editing) them in their native context is still a major challenge.
Meet MetaEdit: a platform for pathway-scale metagenomic editing inside the gut microbiome. science.org/doi/10.1126/...
Meet MetaEdit: a platform for pathway-scale metagenomic editing inside the gut microbiome. science.org/doi/10.1126/...
Reposted by Cress Lab
🔬 Interested in bacterial immune systems & AMR, or how antibiotics affect phage infectivity?
Three SWBio DTP PhD project opportunities linked to the MultiDefence consortium are now open (1/4)
#PhD #DoctoralTraining #ResearchCarrers #LifeSciences #phagesky #AMR #microsky #PhDPositions
Three SWBio DTP PhD project opportunities linked to the MultiDefence consortium are now open (1/4)
#PhD #DoctoralTraining #ResearchCarrers #LifeSciences #phagesky #AMR #microsky #PhDPositions
November 14, 2025 at 5:21 PM
🔬 Interested in bacterial immune systems & AMR, or how antibiotics affect phage infectivity?
Three SWBio DTP PhD project opportunities linked to the MultiDefence consortium are now open (1/4)
#PhD #DoctoralTraining #ResearchCarrers #LifeSciences #phagesky #AMR #microsky #PhDPositions
Three SWBio DTP PhD project opportunities linked to the MultiDefence consortium are now open (1/4)
#PhD #DoctoralTraining #ResearchCarrers #LifeSciences #phagesky #AMR #microsky #PhDPositions
We’re a bit late, but better late than never (bi do)! Happy Belated Halloween from the Cress and @therubinlab.bsky.social Labs!
November 14, 2025 at 6:20 PM
We’re a bit late, but better late than never (bi do)! Happy Belated Halloween from the Cress and @therubinlab.bsky.social Labs!
Reposted by Cress Lab
Huge congrats to Owen, Jason, and team! Such a fun story
Our nuclease-protease story is out! We explored a fascinating case of coevolution and modularity in prokaryotic immune systems: www.science.org/doi/10.1126/...
Thanks to wonderful coauthors/collaborators/friends, the whole @doudna-lab.bsky.social and everyone at @innovativegenomics.bsky.social
Thanks to wonderful coauthors/collaborators/friends, the whole @doudna-lab.bsky.social and everyone at @innovativegenomics.bsky.social
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...
www.science.org
November 14, 2025 at 7:27 AM
Huge congrats to Owen, Jason, and team! Such a fun story
Reposted by Cress Lab
Our nuclease-protease story is out! We explored a fascinating case of coevolution and modularity in prokaryotic immune systems: www.science.org/doi/10.1126/...
Thanks to wonderful coauthors/collaborators/friends, the whole @doudna-lab.bsky.social and everyone at @innovativegenomics.bsky.social
Thanks to wonderful coauthors/collaborators/friends, the whole @doudna-lab.bsky.social and everyone at @innovativegenomics.bsky.social
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...
www.science.org
November 13, 2025 at 10:15 PM
Our nuclease-protease story is out! We explored a fascinating case of coevolution and modularity in prokaryotic immune systems: www.science.org/doi/10.1126/...
Thanks to wonderful coauthors/collaborators/friends, the whole @doudna-lab.bsky.social and everyone at @innovativegenomics.bsky.social
Thanks to wonderful coauthors/collaborators/friends, the whole @doudna-lab.bsky.social and everyone at @innovativegenomics.bsky.social
Reposted by Cress Lab
Very happy to share our recent work @cultivarium.bsky.social on genetic tools for Ideonella sakaiensis, a (Betaproteo-)bacterium that degrades PET plastic.
We identified a plasmid vector for the strain and generated a large RB-TnSeq library, screening for genes impacting plastic degradation.
We identified a plasmid vector for the strain and generated a large RB-TnSeq library, screening for genes impacting plastic degradation.
November 12, 2025 at 7:05 PM
Very happy to share our recent work @cultivarium.bsky.social on genetic tools for Ideonella sakaiensis, a (Betaproteo-)bacterium that degrades PET plastic.
We identified a plasmid vector for the strain and generated a large RB-TnSeq library, screening for genes impacting plastic degradation.
We identified a plasmid vector for the strain and generated a large RB-TnSeq library, screening for genes impacting plastic degradation.