Erin Huiting
@erinhuiting.bsky.social
Investigating host-pathogen interactions across all domains of life 🌱🦠. Current focus is plants within @pcronald.bsky.social lab at @ucdavis.bsky.social. PhD in Joe Bondy-Denomy’s lab at UCSF. Website: https://erin.phd. Schmidt Science Fellow.
Reposted by Erin Huiting
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...
www.biorxiv.org/content/10.1...
September 5, 2025 at 10:13 AM
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...
www.biorxiv.org/content/10.1...
Reposted by Erin Huiting
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
August 20, 2025 at 4:37 PM
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
Reposted by Erin Huiting
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...
transient expression”
#plantscience
www.biorxiv.org/content/10.1...
June 17, 2025 at 4:51 AM
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...
transient expression”
#plantscience
www.biorxiv.org/content/10.1...
Reposted by Erin Huiting
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...
www.biorxiv.org
April 2, 2025 at 4:39 PM
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!
Reposted by Erin Huiting
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 ...
www.biorxiv.org
March 31, 2025 at 10:00 PM
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.
Reposted by Erin Huiting
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:
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...
www.biorxiv.org
March 18, 2025 at 2:01 AM
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:
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:
Reposted by Erin Huiting
This is excellent
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...
This Is Not a Drill: How Universities Can Save DEI
By now, many of us have read the headlines: the U.S. Department of Education has ruled that race-based scholarships, cultural centers, and Diversity, Equity, and Inclusion (DEI) programs violate...
greencarelab.ucdavis.edu
February 23, 2025 at 12:43 AM
This is excellent
Reposted by Erin Huiting
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/...
📄 doi.org/10.1093/nsr/...
February 22, 2025 at 5:47 AM
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/...
📄 doi.org/10.1093/nsr/...
Reposted by Erin Huiting
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
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
Webservice | DefenseFinder webservice and knowledge base
On this site, you can freely use (without any login) the DefenseFinder webservice (see below) and get help to navigate the ever expanding world of defense systems.There is a collaborative knowledge ba...
defensefinder.mdmlab.fr
February 19, 2025 at 4:28 AM
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
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
Reposted by Erin Huiting
Nature research paper: Multi-interface licensing of protein import into a phage nucleus
https://go.nature.com/3QdP5SJ
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
February 6, 2025 at 5:48 PM
Nature research paper: Multi-interface licensing of protein import into a phage nucleus
https://go.nature.com/3QdP5SJ
https://go.nature.com/3QdP5SJ
Reposted by Erin Huiting
REVIEW: Design and regulation of engineered bacteria for environmental release
by Chris Voigt & co
#microsky
www.nature.com/articles/s41...
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.
www.nature.com
February 4, 2025 at 4:06 PM
REVIEW: Design and regulation of engineered bacteria for environmental release
by Chris Voigt & co
#microsky
www.nature.com/articles/s41...
by Chris Voigt & co
#microsky
www.nature.com/articles/s41...
Reposted by Erin Huiting
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...
www.biorxiv.org
January 29, 2025 at 10:23 PM
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...
Reposted by Erin Huiting
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...
January 23, 2025 at 3:35 PM
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...