Alexandra Weisberg
@weisbergaj.bsky.social
Asst. Prof, Dept. of Botany and Plant Pathology at Oregon State University.
Reposted by Alexandra Weisberg
Two back-to-back publications about transcriptional regulations of SA-mediated activation of plant immunity from Nin Zheng’s lab and Yuelin Zhang’s lab
www.nature.com/articles/s41...
www.nature.com/articles/s41...
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Transcriptional activation of plant immunity by salicylic acid - Nature
A mechanistic basis for how the hormone salicylic acid promotes transcriptional activation during plant immune responses is described.
www.nature.com
September 17, 2026 at 6:22 AM
Two back-to-back publications about transcriptional regulations of SA-mediated activation of plant immunity from Nin Zheng’s lab and Yuelin Zhang’s lab
www.nature.com/articles/s41...
www.nature.com/articles/s41...
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Reposted by Alexandra Weisberg
My department, Evolution and Ecology at UC Davis is hiring a plant evolution position! I am biased, but it's a great department 😃 apply here: recruit.ucdavis.edu/JPF07777
recruit.ucdavis.edu
August 13, 2026 at 10:27 PM
My department, Evolution and Ecology at UC Davis is hiring a plant evolution position! I am biased, but it's a great department 😃 apply here: recruit.ucdavis.edu/JPF07777
Reposted by Alexandra Weisberg
Our study on giant transposons Starship 🚀🧬 in the genome of the lichen fungus Xanthoria is now out in @pnas.org! What did we find out about Starships in #lichen fungi? 👇Updated thread below 🖥️ 🧪 🦠 🧫 #SymbioSky 1/6
www.pnas.org/doi/10.1073/...
www.pnas.org/doi/10.1073/...
August 11, 2026 at 7:31 PM
Our study on giant transposons Starship 🚀🧬 in the genome of the lichen fungus Xanthoria is now out in @pnas.org! What did we find out about Starships in #lichen fungi? 👇Updated thread below 🖥️ 🧪 🦠 🧫 #SymbioSky 1/6
www.pnas.org/doi/10.1073/...
www.pnas.org/doi/10.1073/...
Reposted by Alexandra Weisberg
🚨 New paper with @bramvandijk.bsky.social, out now in Genome Biology and Evolution!
Why do accessory genes so often hitch a ride on temperate phages? We show that spatial structure alone can tip selection toward a prophage locus over a chromosomal one.
doi.org/10.1093/gbe/...
🧵 Two mechanisms:
Why do accessory genes so often hitch a ride on temperate phages? We show that spatial structure alone can tip selection toward a prophage locus over a chromosomal one.
doi.org/10.1093/gbe/...
🧵 Two mechanisms:
Viral Lifecycle Dynamics and Spatial Structure Explain Why Accessory Genes Are Associated With Temperate Phages
Abstract. Genes encoding for virulence factors are frequently found on prophages, yet the evolutionary forces driving this association remain unclear. The
doi.org
August 7, 2026 at 1:01 PM
🚨 New paper with @bramvandijk.bsky.social, out now in Genome Biology and Evolution!
Why do accessory genes so often hitch a ride on temperate phages? We show that spatial structure alone can tip selection toward a prophage locus over a chromosomal one.
doi.org/10.1093/gbe/...
🧵 Two mechanisms:
Why do accessory genes so often hitch a ride on temperate phages? We show that spatial structure alone can tip selection toward a prophage locus over a chromosomal one.
doi.org/10.1093/gbe/...
🧵 Two mechanisms:
Reposted by Alexandra Weisberg
Major #Botany2026 FOMO, but the drive MA->OR starts this week. So, sharing from afar: I’m recruiting grad students for my new lab at OSU! Info: www.mckenzie-lab.org . We're going to have FUN with systematics, speciation genomics, methods, natural history, and more in North Am angiosperms. Reach out!
August 3, 2026 at 3:12 PM
Major #Botany2026 FOMO, but the drive MA->OR starts this week. So, sharing from afar: I’m recruiting grad students for my new lab at OSU! Info: www.mckenzie-lab.org . We're going to have FUN with systematics, speciation genomics, methods, natural history, and more in North Am angiosperms. Reach out!
Reposted by Alexandra Weisberg
Just posted: a group paper describing major updates to my software pixy, for population genetic summary statistics.
www.biorxiv.org/content/10.6...
New since 2021: arbitrary ploidy, multiallelic sites, missingness-aware Watterson's θ and Tajima's D, Hudson's FST, multicore execution!
www.biorxiv.org/content/10.6...
New since 2021: arbitrary ploidy, multiallelic sites, missingness-aware Watterson's θ and Tajima's D, Hudson's FST, multicore execution!
August 3, 2026 at 4:43 PM
Just posted: a group paper describing major updates to my software pixy, for population genetic summary statistics.
www.biorxiv.org/content/10.6...
New since 2021: arbitrary ploidy, multiallelic sites, missingness-aware Watterson's θ and Tajima's D, Hudson's FST, multicore execution!
www.biorxiv.org/content/10.6...
New since 2021: arbitrary ploidy, multiallelic sites, missingness-aware Watterson's θ and Tajima's D, Hudson's FST, multicore execution!
Reposted by Alexandra Weisberg
Nature research paper: Diverse bacterial pattern recognition receptors sense the core phage proteome
go.nature.com/45fpXCZ
go.nature.com/45fpXCZ
Diverse bacterial pattern recognition receptors sense the core phage proteome - Nature
Systematic analysis of prokaryotic STAND NTPases — relatives of animal and plant immune receptors — uncovers diverse antiviral sensors that detect most of the core structural and replicative proteins of bacteriophages.
go.nature.com
July 29, 2026 at 6:12 PM
Nature research paper: Diverse bacterial pattern recognition receptors sense the core phage proteome
go.nature.com/45fpXCZ
go.nature.com/45fpXCZ
Reposted by Alexandra Weisberg
cnsplots: Publication-Ready Scientific Plots for Cell, Nature, and Science Journals github.com/faridrashidi... really cool work here from a postdoc at NIH.
GitHub - faridrashidi/cnsplots: 🎨 Toolkit for generating publication-quality plots for Cell, Nature and Science journals
🎨 Toolkit for generating publication-quality plots for Cell, Nature and Science journals - faridrashidi/cnsplots
github.com
July 29, 2026 at 10:20 AM
cnsplots: Publication-Ready Scientific Plots for Cell, Nature, and Science Journals github.com/faridrashidi... really cool work here from a postdoc at NIH.
Reposted by Alexandra Weisberg
We just published: Why you should sequence your plasmids (and how to do it for free)
Through @GetGenome scientists in 100 countries can access free whole-plasmid sequencing —giving researchers the confidence to move their experiments forward.
medium.com/p/why-you-sh...
Through @GetGenome scientists in 100 countries can access free whole-plasmid sequencing —giving researchers the confidence to move their experiments forward.
medium.com/p/why-you-sh...
Why you should sequence your plasmids (and how to do it for free)
Through GetGenome, scientists in 100 countries can access free whole-plasmid sequencing — removing barriers, improving quality control…
medium.com
August 11, 2025 at 12:14 PM
We just published: Why you should sequence your plasmids (and how to do it for free)
Through @GetGenome scientists in 100 countries can access free whole-plasmid sequencing —giving researchers the confidence to move their experiments forward.
medium.com/p/why-you-sh...
Through @GetGenome scientists in 100 countries can access free whole-plasmid sequencing —giving researchers the confidence to move their experiments forward.
medium.com/p/why-you-sh...
Reposted by Alexandra Weisberg
Oregon State University's Department of Integrative Biology is currently hiring up to three tenure-track faculty members, with an emphasis on organismal biology.
Note: Previous links are no longer active due to a change in our hiring system.
oregonstate.wd501.myworkdayjobs.com/OSU_Careers_...
Note: Previous links are no longer active due to a change in our hiring system.
oregonstate.wd501.myworkdayjobs.com/OSU_Careers_...
Assistant Professor
Department: Special Instructions to Applicants: To ensure full consideration, applications must be received by 10/1/26. Applications will continue to be accepted after the full consideration date, unt...
oregonstate.wd501.myworkdayjobs.com
July 15, 2026 at 12:02 AM
Oregon State University's Department of Integrative Biology is currently hiring up to three tenure-track faculty members, with an emphasis on organismal biology.
Note: Previous links are no longer active due to a change in our hiring system.
oregonstate.wd501.myworkdayjobs.com/OSU_Careers_...
Note: Previous links are no longer active due to a change in our hiring system.
oregonstate.wd501.myworkdayjobs.com/OSU_Careers_...
Reposted by Alexandra Weisberg
Our paper out in Science today:
The Metis defense system senses molecular byproducts released when a phage degrades the bacterial genome, and then prevents replication of the phage in the infected cell
Congratulations @ostermanilya.bsky.social and co-authors!
The Metis defense system senses molecular byproducts released when a phage degrades the bacterial genome, and then prevents replication of the phage in the infected cell
Congratulations @ostermanilya.bsky.social and co-authors!
July 9, 2026 at 7:14 PM
Our paper out in Science today:
The Metis defense system senses molecular byproducts released when a phage degrades the bacterial genome, and then prevents replication of the phage in the infected cell
Congratulations @ostermanilya.bsky.social and co-authors!
The Metis defense system senses molecular byproducts released when a phage degrades the bacterial genome, and then prevents replication of the phage in the infected cell
Congratulations @ostermanilya.bsky.social and co-authors!
Reposted by Alexandra Weisberg
#microsky
New preprint from the lab!
Widespread immune systems protect bacteria against conjugative plasmids
www.biorxiv.org/content/10.6...
Kudos to the extremely talented lead author Ludovic Poiré! Key contributions by @francoisrousset.bsky.social and also help from C. Lesterlin/TacC lab.
🧵⬇️
New preprint from the lab!
Widespread immune systems protect bacteria against conjugative plasmids
www.biorxiv.org/content/10.6...
Kudos to the extremely talented lead author Ludovic Poiré! Key contributions by @francoisrousset.bsky.social and also help from C. Lesterlin/TacC lab.
🧵⬇️
Widespread immune systems protect bacteria against conjugative plasmids
Conjugative plasmids are a class of mobile genetic elements capable of efficient transfer between bacterial cells. Although they can introduce beneficial traits such as antibiotic resistance to recipi...
www.biorxiv.org
July 7, 2026 at 7:58 AM
#microsky
New preprint from the lab!
Widespread immune systems protect bacteria against conjugative plasmids
www.biorxiv.org/content/10.6...
Kudos to the extremely talented lead author Ludovic Poiré! Key contributions by @francoisrousset.bsky.social and also help from C. Lesterlin/TacC lab.
🧵⬇️
New preprint from the lab!
Widespread immune systems protect bacteria against conjugative plasmids
www.biorxiv.org/content/10.6...
Kudos to the extremely talented lead author Ludovic Poiré! Key contributions by @francoisrousset.bsky.social and also help from C. Lesterlin/TacC lab.
🧵⬇️
Reposted by Alexandra Weisberg
We’re happy to introduce phageFACTor (Functional Annotation and Curation Tool)
👩💻Developed by Tanaïs Moreau, our most recent PhD candidate, and building on Phold, we were able to improve annotation of prophage genes by as much as 50% 🧬
You should check it out github.com/TMs-code/pha...
👩💻Developed by Tanaïs Moreau, our most recent PhD candidate, and building on Phold, we were able to improve annotation of prophage genes by as much as 50% 🧬
You should check it out github.com/TMs-code/pha...
July 1, 2026 at 5:24 PM
We’re happy to introduce phageFACTor (Functional Annotation and Curation Tool)
👩💻Developed by Tanaïs Moreau, our most recent PhD candidate, and building on Phold, we were able to improve annotation of prophage genes by as much as 50% 🧬
You should check it out github.com/TMs-code/pha...
👩💻Developed by Tanaïs Moreau, our most recent PhD candidate, and building on Phold, we were able to improve annotation of prophage genes by as much as 50% 🧬
You should check it out github.com/TMs-code/pha...
Reposted by Alexandra Weisberg
Mary-Dell Chilton died today. She should have won a Nobel for creating modern plant bioengineering.
youtube.com/watch?v=AXc9677PvEA
youtube.com/watch?v=AXc9677PvEA
Moments of Discovery: The Mary-Dell Chilton Story
YouTube video by National Inventors Hall of Fame - NIHF
youtube.com
June 25, 2026 at 1:18 PM
Mary-Dell Chilton died today. She should have won a Nobel for creating modern plant bioengineering.
youtube.com/watch?v=AXc9677PvEA
youtube.com/watch?v=AXc9677PvEA
Reposted by Alexandra Weisberg
So I'm finally thoroughly parsing through this preprint from @bjesseshapiro.bsky.social & Patrick Lypaczewski where they homebrewed targeted ONT library prep, and it's even more brilliant than at first glance. Plus they've been so generous in answering my questions.
www.biorxiv.org/content/10.6...
www.biorxiv.org/content/10.6...
www.biorxiv.org
June 25, 2026 at 6:43 PM
So I'm finally thoroughly parsing through this preprint from @bjesseshapiro.bsky.social & Patrick Lypaczewski where they homebrewed targeted ONT library prep, and it's even more brilliant than at first glance. Plus they've been so generous in answering my questions.
www.biorxiv.org/content/10.6...
www.biorxiv.org/content/10.6...
Reposted by Alexandra Weisberg
🤯
Are restriction/modification modules only used for host defense?
@selmamhm.bsky.social shows an alternative use. "Restriction-modification systems are required for Neisseria gonorrhoeae pilin antigenic variation" www.pnas.org/doi/10.1073/pnas.2602688123 #Microd
#Microsky. #Microbiology
@selmamhm.bsky.social shows an alternative use. "Restriction-modification systems are required for Neisseria gonorrhoeae pilin antigenic variation" www.pnas.org/doi/10.1073/pnas.2602688123 #Microd
#Microsky. #Microbiology
PNAS
Proceedings of the National Academy of Sciences (PNAS), a peer reviewed journal of the National Academy of Sciences (NAS) - an authoritative source of high-impact, original research that broadly spans...
www.pnas.org
June 23, 2026 at 10:11 PM
🤯
Reposted by Alexandra Weisberg
Minibwa is a hybrid of bwa-mem and minimap2 and the successor of bwa-mem for short-read mapping. ~4X/2.5X as fast as bwa-mem/bwa-mem2 for WGS reads at comparable accuracy. Native support of directional bisulfite-seq. Applicable to long reads. Preprint at arxiv.org/abs/2606.15357
June 16, 2026 at 4:13 PM
Minibwa is a hybrid of bwa-mem and minimap2 and the successor of bwa-mem for short-read mapping. ~4X/2.5X as fast as bwa-mem/bwa-mem2 for WGS reads at comparable accuracy. Native support of directional bisulfite-seq. Applicable to long reads. Preprint at arxiv.org/abs/2606.15357
Reposted by Alexandra Weisberg
Our paper on the YprA family of helicases and their roles in bacterial defence is now out!
We describe ARMADA, a defence system synergise with Druantia and show that both systems spread horizontally on a novel type of mobile genetic element that we call SPIDERs
www.sciencedirect.com/science/arti...
We describe ARMADA, a defence system synergise with Druantia and show that both systems spread horizontally on a novel type of mobile genetic element that we call SPIDERs
www.sciencedirect.com/science/arti...
YprA-family helicases provide the missing link between diverse prokaryotic immune systems
Bacteria and archaea possess an enormous variety of antiviral immune systems that often share homologous proteins and domains. YprA-family helicases a…
www.sciencedirect.com
June 12, 2026 at 2:34 PM
Our paper on the YprA family of helicases and their roles in bacterial defence is now out!
We describe ARMADA, a defence system synergise with Druantia and show that both systems spread horizontally on a novel type of mobile genetic element that we call SPIDERs
www.sciencedirect.com/science/arti...
We describe ARMADA, a defence system synergise with Druantia and show that both systems spread horizontally on a novel type of mobile genetic element that we call SPIDERs
www.sciencedirect.com/science/arti...
Reposted by Alexandra Weisberg
Bacterial cell division protein FtsZ complexes with a phage protein to activate bacterial immunity
@natmicrobiol.nature.com from Michael Laub & Abel Garcia-Pino
www.nature.com/articles/s41...
@natmicrobiol.nature.com from Michael Laub & Abel Garcia-Pino
www.nature.com/articles/s41...
Bacterial cell division protein FtsZ complexes with a phage protein to activate bacterial immunity - Nature Microbiology
The activation of an antiphage defence system relies on host factors targeted by phages, a mechanism analogous to the way that eukaryotic innate immune systems detect pathogen-induced perturbations of...
www.nature.com
June 12, 2026 at 10:27 AM
Bacterial cell division protein FtsZ complexes with a phage protein to activate bacterial immunity
@natmicrobiol.nature.com from Michael Laub & Abel Garcia-Pino
www.nature.com/articles/s41...
@natmicrobiol.nature.com from Michael Laub & Abel Garcia-Pino
www.nature.com/articles/s41...
Reposted by Alexandra Weisberg
Molecular mimicry of a pathogen virulence target by a plant immune receptor | Science www.science.org/doi/10.1126/...
Molecular mimicry of a pathogen virulence target by a plant immune receptor
Plants and animals respond to pathogen attack by mounting innate immune responses that require intracellular nucleotide-binding leucine-rich repeat (NLR) proteins. These immune receptors detect pathog...
www.science.org
June 4, 2026 at 6:15 PM
Molecular mimicry of a pathogen virulence target by a plant immune receptor | Science www.science.org/doi/10.1126/...
Reposted by Alexandra Weisberg
I’m starting at Oregon State University this September as Herbarium Director and Assistant Professor in the Department of Botany and Plant Pathology. An absolute dream job and I am so grateful!
Looking to grow the lab soon and will update here. In the meantime please don’t hesitate to reach out!
Looking to grow the lab soon and will update here. In the meantime please don’t hesitate to reach out!
May 22, 2026 at 5:16 PM
I’m starting at Oregon State University this September as Herbarium Director and Assistant Professor in the Department of Botany and Plant Pathology. An absolute dream job and I am so grateful!
Looking to grow the lab soon and will update here. In the meantime please don’t hesitate to reach out!
Looking to grow the lab soon and will update here. In the meantime please don’t hesitate to reach out!
Reposted by Alexandra Weisberg
Reposted by Alexandra Weisberg
April 2, 2026 at 8:49 PM
Weisberg Lab PhD student Boluwatife Giwa presented her research on Botrytis genomics at the 2026 APS Pacific Division Meeting and was awarded the 1st place poster award and a travel award. Congrats!
March 31, 2026 at 4:44 PM
Weisberg Lab PhD student Boluwatife Giwa presented her research on Botrytis genomics at the 2026 APS Pacific Division Meeting and was awarded the 1st place poster award and a travel award. Congrats!