Alexandra Weisberg

What this technology is going to do is not end higher education, but it is going to undo so much of the baseline work on accessibility by pushing overworked professors to take things back to offline modalities, in person timed exams, keeping tech out of the classroom, etc.

Koonin's lab in NIH is looking for postdocs. If you know someone who is interested, please spread the word. The details about the position are below: www.training.nih.gov/jobs/pdf-ecb...

Check out our latest preprint from @jnvmartinson.bsky.social and @leosong.bsky.social! 🌟🦠

We found that conjugative plasmids can actively eliminate recipient bacteria that resist plasmid acquisition. 🧵

Addressing pandemic-wide systematic errors in the SARS-CoV-2 phylogeny - Nature Methods This Resource paper presents a global SARS-CoV-2 phylogenetic tree of 4,471,579 high-quality genomes consistently constructed by Viridian, an efficient amplicon-aware assembler.

A long time ago in a galaxy far away, there was a SARS-CoV-2 pandemic. Our paper, led by @martibartfast.bsky.social
a) correcting errors in 4.5 million genomes & their phylogeny
b) improving representation of the Global South in public data
www.nature.com/articles/s41...
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1/2 Want to become up to date with pangenomes and genome graphs and their history? Check out this fantastic review by @zbao.bsky.social!

Complexity welcome: Pangenome graphs for comprehensive population genomics
#pangenomes #plantscience #genomegraphs
www.cambridge.org/core/journal...

USDA postdoctoral fellowships are open. If you’re interested in writing a postdoc fellowship with me in plant immunity, spatial defense, or vector-borne disease, please reach out.
(US citizens, nationals, permanent residents only; PhD awarded Jan 2023–Jan 2027.) www.nifa.usda.gov/grants/progr...

www.pnas.org/doi/10.1073/...

Excited to share that PNAS published our research article focused on "Why are Ralstonia goofy?"

This position is still open. The Weisberg lab is recruiting a postdoc or Ph.D. student to study horizontal gene transfer in plant-associated microbial communities. Please see the job ad for more information and feel free to contact me if you have any questions!

Three male side-blotched lizard with three neck colors: orange, blue, and yellow

Lizards have evolved their own version of rock-paper-scissors. Here's my story on the genetics behind nature's games. Gift link: nyti.ms/493KGMI

Identifying Effective Cryoprotectant Agents for Emerging Bacterial Model Species Host-associated bacteria live amongst eukaryotes within varied niches and form relationships ranging from facultative to obligate. With advancement in studies of such symbiotic associations, fastidiou...

After years of struggling with how to cryopreserve one of our endosymbiotic bacteria, we found something that worked!
🦠☃️
We crowd-sourced suggestions and then @ruthwright.bsky.social tried the most common ones (like 🥛...). Want to do the same? Here is how we did it:
www.biorxiv.org/content/10.6...

Cell wall patterning regulates plant stem cell dynamics The plant cell wall regulates development through spatiotemporal modulation of its chemical and mechanical properties. Pectin methylesterification is recognized as a rheological switch controlling wal...

Thrilled to have our paper out in @science.org. Cell division guides plant cell wall formation. Does the reverse hold? We show that bimodal pectin methylesterification, via PME5 mRNA nuclear sequestration, influences plant cell division and cell plate orientation. www.science.org/doi/10.1126/...

A wheat resistosome defines common principles of immune receptor channels - Nature Evolutionary conservation of plant receptor structure allowed for generation of new variants of wheat and barley nucleotide-binding leucine-rich repeat receptors (NLRs) that recognize AvrSr35 of the w...

"Common principles of immune receptor channels..." #ThingsThatMakeYouGoHmm 🤔 www.nature.com/articles/s41...

We are thrilled to announce the first official release (v0.1.8) of #𝗯𝗲𝗱𝗱𝗲𝗿, the successor to one of our flagship tool, #𝗯𝗲𝗱𝘁𝗼𝗼𝗹𝘀! Based on ideas we conceived of long ago (!), this was achieved thanks to the dedication of Brent Pedersen.

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How does the arms race between #bacterial defense systems and mobile genetic elements contribute to #microbiome community structure?

Read below for an insightful exploration of this issue! It will not disappoint
@plosbiology.org 🧪
#bacteria #immune #phage #ecology

GitHub - alanrogers/popgen: A course on population genetics A course on population genetics. Contribute to alanrogers/popgen development by creating an account on GitHub.

I taught (and co-taught) a course on human population genetics from 2000-2024. Having retired, I'm now making all the course materials public: github.com/alanrogers/p... #popgen #evbio

New preprint: 🚀🧬 Starship in the genome of the lichen fungus Xanthoria. Discovery of giant transposons Starships challenged what we thought we knew about fungal genomes. But what about Starships in #lichen fungi? Let us present Tangerine! 🖥️ 🧪 🦠 🧫 #SymbioSky doi.org/10.1101/2025...

Cellular energy sensor SnRK1 suppresses salicylic acid–dependent and –independent defenses and bacterial resistance in Arabidopsis | PNAS In nature, plants cope with various pathogens that compete for cellular resources during infection. It has long been suggested that plant defense a...

Cellular energy sensor SnRK1 suppresses salicylic acid–dependent and –independent defenses and bacterial resistance in Arabidopsis

www.pnas.org/doi/abs/10.1...

🧬🛡️How are new immune mechanisms created?

We show how Lamassu antiphage system, originated from a DNA-repair complex and evolved into a compact and modular immune machine, wt Dinshaw Patel lab in @pnas.org.
👏 @matthieu-haudiquet.bsky.social, Arpita Chakravarti & all authors!

doi.org/10.1073/pnas...

I tried an even harder example on Gemini Pro image generation and this is quite scary/amazing. I asked for a microscopy image of around 20 HeLa cells, GFP tagged 20% nuclear, 10% membrane, +1 nuclear staining, + overlap. Image below and prompt in the following post.

Our new collaborative work led by @taliamycota.bsky.social
Jiajun Cui & Emma Caullireau between my lab @ucllifesciences.bsky.social @cloeucl.bsky.social & the Karasov Lab (tkarasovlab.org) @uofubiology.bsky.social
and collaborators: @plantricia.bsky.social et al.

tinyurl.com/5yx2wmz5

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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...

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/...

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.

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.

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…

gggenomes: A Grammar of Graphics for Comparative Genomics thackl.github.io/gggenomes/ #Rstats

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...

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.

Gotcha, thanks! We do SPRI cleanups at different ratios to size select, but maybe this will assist even more.

Is there a specific benefit to doing the SPRI cleanup with LFB instead of ethanol?

Specificity, length and luck drive gene rankings in association studies - Nature Genetic association tests prioritize candidate genes based on different criteria.

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...

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...

Widespread horizontal transfer and strong selection enhance microbial adaptation in Antarctic soils www.biorxiv.org/content/10.1... #jcampubs

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...

@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/...