Alexandra Weisberg
@weisbergaj.bsky.social
Asst. Prof, Dept. of Botany and Plant Pathology at Oregon State University.
Reposted by Alexandra Weisberg
I’ve released a tool to sketch and edit phylogenetic trees!
yawak.jp/PhyloWeaver/
Load a Newick file and intuitively add/remove/resize branches.
Useful for quick conceptual trees, extracting subtrees, or turning ideas into Newick.
yawak.jp/PhyloWeaver/
Load a Newick file and intuitively add/remove/resize branches.
Useful for quick conceptual trees, extracting subtrees, or turning ideas into Newick.
PhyloWeaver – Interactive phylogenetic tree editor
Edit and visualize phylogenetic trees directly in your browser. PhyloWeaver lets you interactively rearrange tree topologies and export high-quality figures for publications and presentations.
yawak.jp
November 18, 2025 at 1:59 AM
I’ve released a tool to sketch and edit phylogenetic trees!
yawak.jp/PhyloWeaver/
Load a Newick file and intuitively add/remove/resize branches.
Useful for quick conceptual trees, extracting subtrees, or turning ideas into Newick.
yawak.jp/PhyloWeaver/
Load a Newick file and intuitively add/remove/resize branches.
Useful for quick conceptual trees, extracting subtrees, or turning ideas into Newick.
Reposted by Alexandra Weisberg
gggenomes: A Grammar of Graphics for Comparative Genomics thackl.github.io/gggenomes/ #Rstats
A Grammar of Graphics for Comparative Genomics
An extension of ggplot2 for creating complex genomic maps. It builds on the power of ggplot2 and tidyverse adding new ggplot2-style geoms & positions and dplyr-style verbs to manipulate the…
thackl.github.io
November 18, 2025 at 7:02 PM
gggenomes: A Grammar of Graphics for Comparative Genomics thackl.github.io/gggenomes/ #Rstats
Our manuscript comparing Nanopore vs. Illumina reads for population-level variant calling and genotyping is now out: journals.asm.org/doi/10.1128/... . This work was led by Andrea Schiffer and @arftrhmn.bsky.social.
A comparison of short- and long-read whole-genome sequencing for microbial pathogen epidemiology | mSystems
Genome assembly and variant calling are important steps in microbial population studies
and epidemiology. Most variant calling and genotyping pipelines are designed for Illumina
short sequencing reads...
journals.asm.org
November 13, 2025 at 9:31 PM
Our manuscript comparing Nanopore vs. Illumina reads for population-level variant calling and genotyping is now out: journals.asm.org/doi/10.1128/... . This work was led by Andrea Schiffer and @arftrhmn.bsky.social.
Reposted by Alexandra Weisberg
How do GWAS and rare variant burden tests rank gene signals?
In new work @nature.com with @hakha.bsky.social, @jkpritch.bsky.social, and our wonderful coauthors we find that the key factors are what we call Specificity, Length, and Luck!
🧬🧪🧵
www.nature.com/articles/s41...
In new work @nature.com with @hakha.bsky.social, @jkpritch.bsky.social, and our wonderful coauthors we find that the key factors are what we call Specificity, Length, and Luck!
🧬🧪🧵
www.nature.com/articles/s41...
Specificity, length and luck drive gene rankings in association studies - Nature
Genetic association tests prioritize candidate genes based on different criteria.
www.nature.com
November 7, 2025 at 12:05 AM
How do GWAS and rare variant burden tests rank gene signals?
In new work @nature.com with @hakha.bsky.social, @jkpritch.bsky.social, and our wonderful coauthors we find that the key factors are what we call Specificity, Length, and Luck!
🧬🧪🧵
www.nature.com/articles/s41...
In new work @nature.com with @hakha.bsky.social, @jkpritch.bsky.social, and our wonderful coauthors we find that the key factors are what we call Specificity, Length, and Luck!
🧬🧪🧵
www.nature.com/articles/s41...
Reposted by Alexandra Weisberg
The 5th of 6 faculty positions in UNC Biology is posted. We're working with the @ncbg.bsky.social to fill a joint position as Director of the UNC Herbarium at @ncbg.bsky.social and as Associate Professor within the Department of Biology (BIOL). Please share 1/n
unc.peopleadmin.com/postings/308...
unc.peopleadmin.com/postings/308...
Associate Professor & Director of NCBG Herbarium
This is a research, teaching, and public service position at the University of North Carolina at Chapel Hill, serving jointly as Herbarium Director at the North Carolina Botanical Garden (NCBG) and as...
unc.peopleadmin.com
November 6, 2025 at 11:36 AM
The 5th of 6 faculty positions in UNC Biology is posted. We're working with the @ncbg.bsky.social to fill a joint position as Director of the UNC Herbarium at @ncbg.bsky.social and as Associate Professor within the Department of Biology (BIOL). Please share 1/n
unc.peopleadmin.com/postings/308...
unc.peopleadmin.com/postings/308...
Reposted by Alexandra Weisberg
Widespread horizontal transfer and strong selection enhance microbial adaptation in Antarctic soils www.biorxiv.org/content/10.1... #jcampubs
November 5, 2025 at 4:25 PM
Widespread horizontal transfer and strong selection enhance microbial adaptation in Antarctic soils www.biorxiv.org/content/10.1... #jcampubs
Reposted by Alexandra Weisberg
@prczhaoyansong.bsky.social’s deep dive into the dark matter of compost communities is now out 🎉 Genomic islands hijack jumbo phages—whose capsids enable transfer of large tracts of DNA—shedding new light on the scale & scope of phage-mediated gene flow 😎
www.pnas.org/doi/10.1073/...
www.pnas.org/doi/10.1073/...
Jumbo phage–mediated transduction of genomic islands | PNAS
Bacteria acquire new genes by horizontal gene transfer, typically mediated by mobile
genetic elements (MGEs). While plasmids, bacteriophages, and c...
www.pnas.org
October 28, 2025 at 6:36 PM
@prczhaoyansong.bsky.social’s deep dive into the dark matter of compost communities is now out 🎉 Genomic islands hijack jumbo phages—whose capsids enable transfer of large tracts of DNA—shedding new light on the scale & scope of phage-mediated gene flow 😎
www.pnas.org/doi/10.1073/...
www.pnas.org/doi/10.1073/...
Reposted by Alexandra Weisberg
If you admix barcodes in your Illumina library, use Demulticoder: An R Package for the Simultaneous Analysis of Multiplexed Metabarcodes | Phytopathology® apsjournals.apsnet.org/doi/10.1094/...
Demulticoder: An R Package for the Simultaneous Analysis of Multiplexed Metabarcodes | Phytopathology®
Metabarcoding is a widely used approach relying on short DNA sequences to identify organisms present in a community. Although established workflows exist for analysis of single metabarcodes, these are...
apsjournals.apsnet.org
October 22, 2025 at 8:43 PM
If you admix barcodes in your Illumina library, use Demulticoder: An R Package for the Simultaneous Analysis of Multiplexed Metabarcodes | Phytopathology® apsjournals.apsnet.org/doi/10.1094/...
Reposted by Alexandra Weisberg
A one-of-a-kind repeated natural experiment. Population Genomic Analysis of Two Independent Clonal Invasions of the Sudden Oak Death Pathogen into One Forest | Phytopathology® apsjournals.apsnet.org/doi/10.1094/...
Population Genomic Analysis of Two Independent Clonal Invasions of the Sudden Oak Death Pathogen into One Forest | Phytopathology®
Upon introduction, clonal pathogen populations are expected to go through a genetic bottleneck followed by gradual clonal divergence. Two distinct and purely clonal lineages of the sudden oak death pa...
apsjournals.apsnet.org
October 23, 2025 at 3:22 PM
A one-of-a-kind repeated natural experiment. Population Genomic Analysis of Two Independent Clonal Invasions of the Sudden Oak Death Pathogen into One Forest | Phytopathology® apsjournals.apsnet.org/doi/10.1094/...
Reposted by Alexandra Weisberg
New paper with my (amazing) friend and mentor @jrpenades.bsky.social
Really looking forward to see what plasmid aficionados think of this one!!
With @asantoslopez.bsky.social @wfigueroac3.bsky.social Akshay Sabins and others
www.cell.com/cell-reports...
Really looking forward to see what plasmid aficionados think of this one!!
With @asantoslopez.bsky.social @wfigueroac3.bsky.social Akshay Sabins and others
www.cell.com/cell-reports...
Non-conjugative plasmids limit their mobility to persist in nature
Sabnis et al. explain why non-conjugative plasmids move at a low rate in nature. While
increased mobility can easily evolve by incorporating phage DNA into plasmids, this
is disadvantageous because it...
www.cell.com
October 22, 2025 at 1:12 PM
New paper with my (amazing) friend and mentor @jrpenades.bsky.social
Really looking forward to see what plasmid aficionados think of this one!!
With @asantoslopez.bsky.social @wfigueroac3.bsky.social Akshay Sabins and others
www.cell.com/cell-reports...
Really looking forward to see what plasmid aficionados think of this one!!
With @asantoslopez.bsky.social @wfigueroac3.bsky.social Akshay Sabins and others
www.cell.com/cell-reports...
Reposted by Alexandra Weisberg
Still a couple of formatting things that need fixing (this is a "pre-proof") but our genomes paper is now available online! www.sciencedirect.com/science/arti...
Really happy to see it out there, I hope people find it useful/interesting!
Really happy to see it out there, I hope people find it useful/interesting!
Completed genomes from Variovorax provide insight into genome diversification through horizontal gene transfer
Approximately 10% of all bacterial genomes sequenced thus far contain a secondary replicon. This property of bacterial populations vastly increases ge…
www.sciencedirect.com
October 22, 2025 at 3:33 PM
Still a couple of formatting things that need fixing (this is a "pre-proof") but our genomes paper is now available online! www.sciencedirect.com/science/arti...
Really happy to see it out there, I hope people find it useful/interesting!
Really happy to see it out there, I hope people find it useful/interesting!
Reposted by Alexandra Weisberg
job alert: UC Davis is looking to hire a 9 month tenure-track Assistant Professor of Mycology in the Department of Plant Pathology. More details below, for full consideration submit by 1 December 2025
recruit.ucdavis.edu/JPF07339
recruit.ucdavis.edu/JPF07339
Assistant Professor of Plant Pathology
University of California, Davis is hiring. Apply now!
recruit.ucdavis.edu
October 16, 2025 at 7:59 PM
job alert: UC Davis is looking to hire a 9 month tenure-track Assistant Professor of Mycology in the Department of Plant Pathology. More details below, for full consideration submit by 1 December 2025
recruit.ucdavis.edu/JPF07339
recruit.ucdavis.edu/JPF07339
Reposted by Alexandra Weisberg
This is first paper from a new line of research in my lab, with more to come soon. If interested in PDPs I highly recommend this @baym.lol paper www.nature.com/articles/s41... and this classic from Matti Jalasvuori royalsocietypublishing.org/doi/10.1098/...
Diverse and abundant phages exploit conjugative plasmids - Nature Communications
Some phages use plasmid-encoded conjugation proteins as receptors to infect their bacterial hosts, making their host range dependent on horizontal transfer of the plasmid. Here, the authors present a method for identification of new plasmid-dependent phages, and find that they are common and abundant in wastewater and their genetic diversity is largely unexplored.
www.nature.com
October 9, 2025 at 10:07 AM
This is first paper from a new line of research in my lab, with more to come soon. If interested in PDPs I highly recommend this @baym.lol paper www.nature.com/articles/s41... and this classic from Matti Jalasvuori royalsocietypublishing.org/doi/10.1098/...
Reposted by Alexandra Weisberg
UNC Chapel Hill is hiring an Assistant Professor in Plant Molecular Biology. Per Jeff
Dangl MPMI candidates are also highly desired in the search. unc.peopleadmin.com/postings/307...
Dangl MPMI candidates are also highly desired in the search. unc.peopleadmin.com/postings/307...
Assistant Professor
The Department of Biology at UNC Chapel Hill (https://bio.unc.edu/) is searching to hire a tenure track Assistant Professor to study critical questions in Plant Molecular Biology.We seek candidates wh...
unc.peopleadmin.com
October 6, 2025 at 10:27 PM
UNC Chapel Hill is hiring an Assistant Professor in Plant Molecular Biology. Per Jeff
Dangl MPMI candidates are also highly desired in the search. unc.peopleadmin.com/postings/307...
Dangl MPMI candidates are also highly desired in the search. unc.peopleadmin.com/postings/307...
Reposted by Alexandra Weisberg
Here’s published version of our manuscript using GWAS to investigate tailocin sensitivity in Pseudomonas syringae. TL:DR pretty clear LPS is tailocin receptor but also that P.syringae often completely swaps out its entire O antigen biosynth pathway w/ recombination
academic.oup.com/g3journal/ad...
academic.oup.com/g3journal/ad...
Genomic correlates of tailocin sensitivity in Pseudomonas syringae
Abstract. Phage-derived bacteriocins, also referred to as tailocins, are structures encoded by bacterial genomes and deployed into the extracellular enviro
academic.oup.com
October 6, 2025 at 6:57 PM
Here’s published version of our manuscript using GWAS to investigate tailocin sensitivity in Pseudomonas syringae. TL:DR pretty clear LPS is tailocin receptor but also that P.syringae often completely swaps out its entire O antigen biosynth pathway w/ recombination
academic.oup.com/g3journal/ad...
academic.oup.com/g3journal/ad...
Reposted by Alexandra Weisberg
Chromosome architecture affects virulence and competitiveness in Agrobacterium tumefaciens C58 | Science Advances www.science.org/doi/10.1126/...
Chromosome architecture affects virulence and competitiveness in Agrobacterium tumefaciens C58
Chromosome architecture influences Agrobacterium fitness, competitiveness, and virulence, shaping its adaptation and evolution.
www.science.org
October 5, 2025 at 3:20 AM
Chromosome architecture affects virulence and competitiveness in Agrobacterium tumefaciens C58 | Science Advances www.science.org/doi/10.1126/...
Reposted by Alexandra Weisberg
Our story describing the Panoptes bacterial immune defense system is now finally peer-reviewed and published today! www.nature.com/articles/s41...
The Panoptes system uses decoy cyclic nucleotides to defend against phage - Nature
The Panoptes antiphage system defends bacteria by detecting phage-encoded counter-defences that sequester cyclic nucleotide signals, triggering membrane disruption and highlighting a broader strategy of sensing immune evasion through second-messenger surveillance.
www.nature.com
October 1, 2025 at 4:05 PM
Our story describing the Panoptes bacterial immune defense system is now finally peer-reviewed and published today! www.nature.com/articles/s41...
Reposted by Alexandra Weisberg
First publication from our lab!
The role of mobile genetic elements in adaptation of the microbiota to the dynamic human gut ecosystem
#CurrOpinMicrobiol from @lgbacteria.bsky.social
www.sciencedirect.com/science/arti...
#CurrOpinMicrobiol from @lgbacteria.bsky.social
www.sciencedirect.com/science/arti...
September 29, 2025 at 4:56 PM
First publication from our lab!
Reposted by Alexandra Weisberg
ZmHSCF1 enhances Agrobacterium-mediated transformation frequency in commercial maize inbred lines by promoting embryogenic callus proliferation #correspondence #PlantCommunications cell.com/plant-commun...
September 26, 2025 at 4:40 PM
ZmHSCF1 enhances Agrobacterium-mediated transformation frequency in commercial maize inbred lines by promoting embryogenic callus proliferation #correspondence #PlantCommunications cell.com/plant-commun...
Reposted by Alexandra Weisberg
The NSF GRFP is now limited to undergrads and first-year grads drugmonkey.wordpress.com/2025/09/26/t...
The NSF GRFP is now limited to undergrads and first-year grads
The solicitation for the 2025 submission dates for the NSF Graduate Research Fellowship Program is out, with the first deadline of November 10 for life-sciences disciplines. The big news is that el…
drugmonkey.wordpress.com
September 26, 2025 at 7:36 PM
The NSF GRFP is now limited to undergrads and first-year grads drugmonkey.wordpress.com/2025/09/26/t...
Reposted by Alexandra Weisberg
Dual transposon sequencing profiles the genetic interaction landscape in bacteria | Science www.science.org/doi/10.1126/...
Dual transposon sequencing profiles the genetic interaction landscape in bacteria
Gene redundancy complicates systematic characterization of gene function as single-gene deletions may not produce discernible phenotypes. We report dual transposon sequencing (dual Tn-seq), a platform...
www.science.org
September 25, 2025 at 11:19 PM
Dual transposon sequencing profiles the genetic interaction landscape in bacteria | Science www.science.org/doi/10.1126/...
Reposted by Alexandra Weisberg
Delighted to see our paper studying the evolution of plasmids over the last 100 years, now out! Years of work by Adrian Cazares, also Nick Thomson @sangerinstitute.bsky.social - this version much improved over the preprint. Final version should be open access, apols.
Thread 1/n
Thread 1/n
September 25, 2025 at 9:29 PM
Delighted to see our paper studying the evolution of plasmids over the last 100 years, now out! Years of work by Adrian Cazares, also Nick Thomson @sangerinstitute.bsky.social - this version much improved over the preprint. Final version should be open access, apols.
Thread 1/n
Thread 1/n
Reposted by Alexandra Weisberg
Interested in #virulence? Not sure what it is - or how to explain it? Just curious? 🧐🦠🧬🦋
@kayla-king.bsky.social and I just wrote a Primer for @currentbiology.bsky.social on the ecology and evolution of virulence!
Check it below and share :)
#MicroSky #EvoSky #pathogens
@kayla-king.bsky.social and I just wrote a Primer for @currentbiology.bsky.social on the ecology and evolution of virulence!
Check it below and share :)
#MicroSky #EvoSky #pathogens
Ecology and evolution of virulence
Silva and King discuss the concept of virulence and the ecological and evolutionary
factors that shape it.
www.cell.com
September 22, 2025 at 3:22 PM
Interested in #virulence? Not sure what it is - or how to explain it? Just curious? 🧐🦠🧬🦋
@kayla-king.bsky.social and I just wrote a Primer for @currentbiology.bsky.social on the ecology and evolution of virulence!
Check it below and share :)
#MicroSky #EvoSky #pathogens
@kayla-king.bsky.social and I just wrote a Primer for @currentbiology.bsky.social on the ecology and evolution of virulence!
Check it below and share :)
#MicroSky #EvoSky #pathogens
Reposted by Alexandra Weisberg
Reposted by Alexandra Weisberg
My department at UC Davis is hiring a mycologist, broadly interpreted. Please repost, share, and consider applying. recruit.ucdavis.edu/JPF07339
Assistant Professor of Plant Pathology
University of California, Davis is hiring. Apply now!
recruit.ucdavis.edu
September 22, 2025 at 5:36 PM
My department at UC Davis is hiring a mycologist, broadly interpreted. Please repost, share, and consider applying. recruit.ucdavis.edu/JPF07339