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Alexandra Weisberg

@weisbergaj.bsky.social
906 followers 760 following 32 posts

Asst. Prof, Dept. of Botany and Plant Pathology at Oregon State University.

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Reposted by Alexandra Weisberg
Tiffany Lowe-Power stands with Minnesota @tlowepower.bsky.social · 24/09/2026
Please repost/share We're hiring! UC Davis Plant Pathology seeks a tenure-track Assistant Professor in plant health & microbiomes. recruit.ucdavis.edu/JPF07904 My department is full of great colleagues, and we look forward to recruiting our new colleague!
recruit.ucdavis.edu
Assistant Professor of Plant Pathology
University of California, Davis is hiring. Apply now!
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Will Matlock @wtmatlock.bsky.social · 20/02/2026
🚨 New preprint 🚨 How promiscuous really are conjugative plasmids, and what does that mean for plasmid co-occurrence? A pleasure to collaborate with @craigmaclean.bsky.social on the first paper of my fellowship! www.biorxiv.org/content/10.6...
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Joe Hanly @hanliconius.bsky.social · 22/09/2026
I hate to do this with real data, but this is a persistent data vis issue in chromosome synteny riparian plots that we Need to get better at. Left, a synteny plot published today. Right, a rearranged version with exactly the same gross arrangement but with reordered chromosomes:
chromosome synteny riparian plot in which every chromosome has crossing lineschromosome synteny plot in which no chromosomes have crossing lines. The underlying structure is identical.
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Pingtao Ding (he/him) @dinglab.bsky.social · 17/09/2026
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...
nature.com
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.
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Rachael Bay @rachaelabay.bsky.social · 13/08/2026
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
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Gulnara Tagirdzhanova @metalichen.bsky.social · 11/08/2026
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/...
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Sultan Nazir @sultannazir.bsky.social · 07/08/2026
🚨 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:
doi.org
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
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Patrick McKenzie @patrickmckenzie.bsky.social · 03/08/2026
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!
lab logo with a cartoon of white-flowering beebalm and the following text: "McKenzie Lab, Plant Evolution, Oregon State"
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Kieran Samuk @ksamuk.bsky.social · 03/08/2026
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!
Alt text: Schematic of the pixy workflow. Left, inputs: a bgzipped, tabix- or CSI-indexed VCF with callable sites supplied as an all-sites VCF or gVCF blocks, a populations file, and optional BED and sites files. Centre, core: windowing by fixed width, BED or region; statistic selection; options for Hudson's FST, multiallelic SNPs, automatic ploidy detection and multicore execution. Right, outputs: one TSV per statistic for pi, dxy, FST, Watterson's theta and Tajima's D, with raw count columns for exact aggregation. Bottom, development: GitHub fork and pull request, local checks with ruff, mypy and pytest, continuous integration across Python 3.10 to 3.14, and distribution through conda-forge. Features new since the 2021 release are badged "new".
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Nature @nature.com · 29/07/2026
Nature research paper: Diverse bacterial pattern recognition receptors sense the core phage proteome go.nature.com/45fpXCZ
go.nature.com
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.
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Stephen Turner @stephenturner.us · 29/07/2026
cnsplots: Publication-Ready Scientific Plots for Cell, Nature, and Science Journals github.com/faridrashidi... really cool work here from a postdoc at NIH.
github.com
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
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Sophien Kamoun @kamounlab.bsky.social · 11/08/2025
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...
medium.com
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…
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Mark Phillips @maphillips.bsky.social · 15/07/2026
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_...
oregonstate.wd501.myworkdayjobs.com
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...
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Sorek Lab @soreklab.bsky.social · 09/07/2026
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!
science.org
Bacteria sense virus-induced genome degradation via methylated mononucleotides
Phages often degrade the genome of their bacterial host to individual nucleotides. Here we describe Metis, a bacterial defense system that directly senses phage-mediated host genome degradation. Metis...
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Xavier Charpentier @labxc.bsky.social · 07/07/2026
#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. 🧵⬇️
biorxiv.org
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...
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Bacteriophage Lab of Institut Pasteur @phagepasteur.bsky.social · 01/07/2026
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...
In this example, we're showing the improvement in the percentage of annotated genes from prophage "Maintenon" from Clostridium innocuum (doi: 10.1186/s40168-023-01541-x) using the phageFACTor pipeline
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Sebastian S. Cocioba @atinygreencell.bsky.social · 25/06/2026
Mary-Dell Chilton died today. She should have won a Nobel for creating modern plant bioengineering. youtube.com/watch?v=AXc9677PvEA
youtube.com
Moments of Discovery: The Mary-Dell Chilton Story
YouTube video by National Inventors Hall of Fame - NIHF
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Elinne Becket, PhD @bielleogy.bsky.social · 25/06/2026
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...
biorxiv.org
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Dave Baltrus 🦦 @surtlab.bsky.social · 23/06/2026
🤯
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Heng Li @lh3lh3.bsky.social · 16/06/2026
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
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Sofya Garushyants @garushyants.bsky.social · 12/06/2026
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...
sciencedirect.com
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…
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Ákos T Kovács @evolvedbiofilm.bsky.social · 12/06/2026
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...
nature.com
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...
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Mauricio Contreras @mpcontreras.bsky.social · 04/06/2026
Molecular mimicry of a pathogen virulence target by a plant immune receptor | Science www.science.org/doi/10.1126/...
science.org
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...
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Patrick McKenzie @patrickmckenzie.bsky.social · 22/05/2026
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!
Picture of a person (me) holding a stuffed beaver toy and a laptop that reads “McKenzie Lab at Oregon State University”
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In Preparation @inprep.bsky.social · 03/04/2026
open.substack.com
PI Nostalgic For Era When One Person's Music Taste Was Inflicted On Entire Lab
MADISON, WI—Expressing a wistfulness he could not fully articulate, professor of biochemistry Dr.
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Needhi Bhalla 💅🏽 @needhibhalla.bsky.social · 02/04/2026
The two papers: www.science.org/doi/10.1126/... and www.science.org/doi/10.1126/...
science.org
DefensePredictor: A machine learning model to discover prokaryotic immune systems
Antiphage defense systems protect bacteria from viral infection and have inspired important biotechnologies such as CRISPR-Cas9 while also revealing the evolutionary roots of eukaryotic innate immunit...
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Alexandra Weisberg @weisbergaj.bsky.social · 31/03/2026
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!
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Michael Habig @michaelhabig.bsky.social · 25/03/2026
Now out! We show that TEs can be horizontally transferred between fungal species via Starships. Once transferred, these TEs can become active, changing the genome organization and affecting the lifestyle of the recipient fungus. www.nature.com/articles/s41... @oggenfussursula.bsky.social #TEsky
nature.com
Transposable elements hitchhike on Starships across fungal genomes - Nature Communications
Large mobile genetic elements known as Starships act as vehicles for transferring transposable elements (TEs) between fungi. Here, Griem-Krey et al. show that these ‘hitchhiking’ TEs can drive rapid e...
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Natalie Cooper @nhcooper123.bsky.social · 25/03/2026
Hi all. I am very excited that after 6 years I finally got my phylogenetic comparative methods book and online exercises online. Feel free to use and share. The book is here: nhcooper123.github.io/pcm-primer/. Note that it is not finished, we had to abandon it before the sunk costs fallacy broke us
nhcooper123.github.io
Phylogenetic Comparative Methods
Phylogenetic Comparative Methods
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Shu-Sin Chng @figlegend.bsky.social · 23/03/2026
Here is it! Super new science from us on horizontal gene transfer & bact defense systems! Liyana OW YONG discovered the first-of-its-kind defense factor AbjA that triggers 'abortive conjugation' as a defense mechanism, by targeting the T4SS! How neat?! #MicroSky 1/7 www.biorxiv.org/content/10.6...
biorxiv.org
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Nature Astronomy @natastron.nature.com · 16/03/2026
Samples returned from the asteroid Ryugu contain all five canonical nucleobases (A, G, C, T, U). Their presence in Ryugu and Bennu supports the hypothesis that carbonaceous asteroids contributed to the prebiotic chemical inventory of early Earth. dlvr.it/TRWtVp ☄️
dlvr.it
A complete set of canonical nucleobases in the carbonaceous asteroid (162173) Ryugu - Nature Astronomy
Samples returned from the asteroid Ryugu contain all five canonical nucleobases (A, G, C, T and U). Their presence in Ryugu and Bennu supports the hypothesis that carbonaceous asteroids contributed to the prebiotic chemical inventory of early Earth.
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Alvaro San Millan @sanmillan.bsky.social · 13/03/2026
Final version of our last paper is out! www.nature.com/articles/s41...
nature.com
Plasmids promote antimicrobial resistance through insertion sequence-mediated gene inactivation - Nature Microbiology
Inactivation of chromosomal genes through plasmid-encoded IS elements is an extended mechanism of antimicrobial resistance evolution in bacteria.
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bioRxiv Plant Bio @biorxiv-plants.bsky.social · 11/03/2026
Effector-triggered stomatal immunity prevents leaf invasion by bacterial pathogens www.biorxiv.org/content/10.64898/20…
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Thomas Lecaque @tlecaque.bsky.social · 23/02/2026
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.
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Sofya Garushyants @garushyants.bsky.social · 17/02/2026
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...
training.nih.gov
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Rubin Lab @therubinlab.bsky.social · 12/02/2026
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. 🧵
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Zamin Iqbal @zaminiqbal.bsky.social · 09/02/2026
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... (thread 1/n)
nature.com
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.
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PlantEvolution 🌱🌾 @plantevolution.bsky.social · 27/10/2025
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...
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Gitta Coaker @gittacoaker.bsky.social · 23/01/2026
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...
nifa.usda.gov
AFRI Education and Workforce Development
The AFRI Education and Workforce Development Program focuses on developing the next generation of research, education, and extension professionals.
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Tiffany Lowe-Power stands with Minnesota @tlowepower.bsky.social · 23/01/2026
www.pnas.org/doi/10.1073/... Excited to share that PNAS published our research article focused on "Why are Ralstonia goofy?"
pnas.org
The EPS-I exopolysaccharide transforms Ralstonia wilt pathogen biofilms into viscoelastic fluids for rapid dissemination in planta | PNAS
Ralstonia solanacearum species complex (RSSC) pathogens cause destructive plant wilt diseases of a wide variety of crops, leading to significant ag...
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Alexandra Weisberg @weisbergaj.bsky.social · 14/01/2026
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!
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Carl Zimmer @carlzimmer.com · 06/01/2026
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
Three male side-blotched lizard with three neck colors: orange, blue, and yellow
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Morgan Carter @morgancarterphd.bsky.social · 08/12/2025
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...
biorxiv.org
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...
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Weibing Yang @weibingyang.bsky.social · 06/12/2025
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/...
science.org
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...
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Sophien Kamoun @kamounlab.bsky.social · 04/12/2025
"Common principles of immune receptor channels..." #ThingsThatMakeYouGoHmm 🤔 www.nature.com/articles/s41...
nature.com
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...
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Aaron Quinlan (he/him) @aaronquinlan.bsky.social · 02/12/2025
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. 1/n
quinlanlab.org
Intro to Bedder – The Quinlan Lab
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Nonia Pariente @npariente.bsky.social · 28/11/2025
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
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Alan Rogers @alanrogers.bsky.social · 27/11/2025
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
github.com
GitHub - alanrogers/popgen: A course on population genetics
A course on population genetics. Contribute to alanrogers/popgen development by creating an account on GitHub.
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Gulnara Tagirdzhanova @metalichen.bsky.social · 28/11/2025
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...
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