Our new preprint is out! Using AI-guided design (RFdiffusion + ProteinMPNN), we engineered a plant immune receptor to recognise non-cognate pathogen effectors. Huge thanks to our amazing co-authors for making this possible! doi.org/10.64898/202...

Computational design of de novo integrated domains enables rational control of pathogen effector recognition in plant NLR immune receptors.

The rapid evolution of plant pathogens poses a persistent threat to global agricultural sustainability, often outpacing the discovery and deployment of natural disease resistance genes. While bioengin...

doi.org

From my time with @jbdsf.bsky.social: Our latest CBASS story is now published! ‘CBASS’ is the ancestral origin of anti-viral cGAS immunity and encoded in diverse bacteria. For the first time, we show that CBASS enables cell survival (vs cell death) to protect bacteria from phage infection. More ⬇️

Cell Host & Microbe@cp-cellhostmicrobe.bsky.social · 2mo ago

CBASS limits phage at no expense A CBASS type encoding a phospholipase (CapV) effector limits the late stage of phage replication while maintaining Pseudomonas aeruginosa cell viability. CBASS limits packaged phage DNA, reducing virion production www.cell.com/cell-host-mi...

I’m honored to be a part of the 2026 Leading Edge community, especially in memory of the incredible person and scientist Dr. Zara Weinberg. I was lucky enough to know Zara during my time at UCSF, and I will strive to continue her legacy empowering scientists for generations to come!

Leading Edge Fellows Program@leadingedgeprogram.bsky.social · 2mo ago

We are thrilled to announce the 2026 Zara Weinberg Leading Edge Fellows! 40 remarkable postdocs pursuing transformative research in biological/biomedical sciences. This is the 7th Leading Edge cohort and we are so excited to welcome them! www.leadingedgesymposium.org/fellows/

Can CRISPR edits enable precise tuning of plant gene expression? We think: yes. In our newest manuscript, we measured the effects of >30,000 CRISPR-like promoter mutations in sorghum protoplasts.

Cell death is a fundamental mechanism of antiviral immunity across diverse organisms, including bacteria. As my final PhD project with @jbdsf.bsky.social, I was curious whether cell death is required for successful immunity with the ancient cGAS pathway known as ‘CBASS.’ Spoiler – the answer is no!

bioRxiv Microbiology@biorxiv-microbiol.bsky.social · 6mo ago

CBASS limits bacteriophage production while maintaining cell viability in Pseudomonas aeruginosa https://www.biorxiv.org/content/10.64898/2026.02.24.707611v1

How can we understand the earliest events in evolution of eukaryotic immunity? @yao-li.bsky.social reports incredible molecular fossils of complete bacterial-like operons in eukaryotes that illuminate how animal immunity was first acquired from anti-phage defense www.biorxiv.org/content/10.1...

Really excited to join Stanford ChemE this September! We'll engineer proteins in plant immune and hormone pathways, combining high-throughput directed evolution with ML. Our goal is to enhance climate stress resilience and disease resistance in crops: rim.stanford.edu

Harnessing synthetic biology to engineer resilient crops

rim.stanford.edu

Must read for all who use Nicotiana benthamiana as a platform: “Causes and consequences of experimental variation in Nicotiana benthamiana transient expression” #plantscience www.biorxiv.org/content/10.1...

We've identified a group of nucleases that can target multiple phages with hypermodified DNA, using a sensor domain present across many domains of life. We’ve even used this as a tool to find phages with hypermodified DNA! Really thankful to all the co-authors who have been such great help!

END nucleases: Antiphage defense systems targeting multiple hypermodified phage genomes

Prokaryotes carry clusters of phage defense systems in defense islands that have been extensively exploited bioinformatically and experimentally for discovery of immune functions. However, little effo...

biorxiv.org

Excited to share that my work from the @aaronwhiteley.bsky.social lab is now on bioRxiv! With @benmorehouse.bsky.social, we discovered that the Panoptes defense system—named after the all-seeing watchman of Hera—uses decoy nucleotides to detect phage anti-defense proteins.

A minimal CRISPR polymerase produces decoy cyclic nucleotides to detect phage anti-defense proteins

Bacteria use antiphage systems to combat phages, their ubiquitous competitors, and evolve new defenses through repeated reshuffling of basic functional units into novel reformulations. A common theme ...

biorxiv.org

First post on Bluesky!! ☀️ Very happy to share that my main postdoc work ‘Systematic Discovery and Design of Synthetic Immune Receptors in Plants’ is finally out on Biorxiv! www.biorxiv.org/content/10.1... The full story is summarized here:

Systematic Discovery and Design of Synthetic Immune Receptors in Plants

Plants deploy a diverse array of pattern recognition receptors (PRRs) that perceive microbe-associated molecular patterns (MAMPs) to activate immune responses. Leucine-rich repeat receptor-like kinase...

biorxiv.org

This is excellent

Dr. Rebecca Calisi-Rodríguez@rebeccacalisi.bsky.social · last yr.

I emailed university faculty/staff/administrators a roadmap to support DEI through legal challenges, collective resistance, and institutional protections for faculty. The question isn’t whether institutions will comply—it’s who will fight back, and how! greencarelab.ucdavis.edu/how-universi...

In our latest review, we explore 12 deep-learning tools for metagenomic analysis, covering their strengths, limitations, and key applications. We hope it serves as both a resource and inspiration for new ways to analyze metagenomic data. Great work by Eli Levy Karin! 📄 doi.org/10.1093/nsr/...

New version of DefenseFinder available defensefinder.mdmlab.fr (& cli) Now encompassing 263 systems (+111 this year..!). Thanks @ftesson.bsky.social, DefenseFinder grandmaster. Full list of systems here: defense-finder-models/List_system_article.md at master · mdmparis/defense-finder-models

Nature research paper: Multi-interface licensing of protein import into a phage nucleus https://go.nature.com/3QdP5SJ

Multi-interface licensing of protein import into a phage nucleus - Nature

This study uncovers a highly conserved jumbo phage protein, Imp1, that possesses multiple interfaces to license protein import into a proteinaceous nucleus-like compartment, using a genetic selection that forces the phage to decrease or abolish the import of specific proteins.

go.nature.com

REVIEW: Design and regulation of engineered bacteria for environmental release by Chris Voigt & co #microsky www.nature.com/articles/s41...

Design and regulation of engineered bacteria for environmental release - Nature Microbiology

Chemla et al. review the release of bacteria into the environment and propose engineering strategies to help improve performance and reduce risk.

nature.com

I'm very excited to share my first graduate research project! Check out our preprint which describes how data generated with directed evolution can be used to model the phenotypic effects of naturally-evolved sequence variants. (1/11) www.biorxiv.org/content/10.1...

Combining Directed Evolution with Machine Learning Enables Accurate Genotype-to-Phenotype Predictions

Linking sequence variation to phenotypic effects is critical for efficient exploitation of large genomic datasets. Here we present a novel approach combining directed evolution with protein language m...

biorxiv.org

I'm thrilled to announce our latest work is now published in Cell! Viruses encode numerous proteins that inhibit host defenses, but identifying immune-modulatory proteins among millions of viral sequences has been nearly impossible - until now! www.cell.com/cell/fulltex...