Alexandra Weisberg
@weisbergaj.bsky.social
📤 786
📥 739
📝 27
Asst. Prof, Dept. of Botany and Plant Pathology at Oregon State University.
reposted by
Alexandra Weisberg
Jeff Spence
5 days ago
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...
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Specificity, length and luck drive gene rankings in association studies - Nature
Genetic association tests prioritize candidate genes based on different criteria.
https://www.nature.com/articles/s41586-025-09703-7
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Alexandra Weisberg
Mark Peifer (He, him)
5 days ago
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...
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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...
https://unc.peopleadmin.com/postings/308835
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Alexandra Weisberg
Cameron Thrash
6 days ago
Widespread horizontal transfer and strong selection enhance microbial adaptation in Antarctic soils
www.biorxiv.org/content/10.1...
#jcampubs
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Alexandra Weisberg
Paul Rainey
14 days ago
@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/...
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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...
https://www.pnas.org/doi/10.1073/pnas.2512465122
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Alexandra Weisberg
Niklaus Grunwald
20 days ago
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/...
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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...
https://apsjournals.apsnet.org/doi/10.1094/PHYTO-02-25-0043-FI
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Alexandra Weisberg
Niklaus Grunwald
19 days ago
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/...
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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...
https://apsjournals.apsnet.org/doi/10.1094/PHYTO-10-24-0329-FI
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Alexandra Weisberg
Alvaro San Millan
20 days ago
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...
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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...
https://www.cell.com/cell-reports/fulltext/S2211-1247(25)01227-6
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Alexandra Weisberg
Paul Orwin
20 days ago
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!
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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…
https://www.sciencedirect.com/science/article/pii/S2666517425001580
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Alexandra Weisberg
Uehling lab
26 days ago
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
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Assistant Professor of Plant Pathology
University of California, Davis is hiring. Apply now!
https://recruit.ucdavis.edu/JPF07339
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Alexandra Weisberg
Craig MacLean
about 1 month ago
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/...
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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.
https://www.nature.com/articles/s41467-024-47416-z
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reposted by
Alexandra Weisberg
Gitta Coaker
about 1 month ago
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...
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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...
https://unc.peopleadmin.com/postings/307414
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Alexandra Weisberg
Dave Baltrus 🦦
about 1 month ago
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...
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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
https://academic.oup.com/g3journal/advance-article/doi/10.1093/g3journal/jkaf203/8243713?login=true
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Alexandra Weisberg
Gang Yu
about 1 month ago
Chromosome architecture affects virulence and competitiveness in Agrobacterium tumefaciens C58 | Science Advances
www.science.org/doi/10.1126/...
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Chromosome architecture affects virulence and competitiveness in Agrobacterium tumefaciens C58
Chromosome architecture influences Agrobacterium fitness, competitiveness, and virulence, shaping its adaptation and evolution.
https://www.science.org/doi/10.1126/sciadv.adx7408
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Alexandra Weisberg
Ben Morehouse
about 1 month ago
Our story describing the Panoptes bacterial immune defense system is now finally peer-reviewed and published today!
www.nature.com/articles/s41...
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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.
https://www.nature.com/articles/s41586-025-09557-z
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Alexandra Weisberg
Leonor García-Bayona
about 1 month ago
First publication from our lab!
add a skeleton here at some point
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Alexandra Weisberg
Molecular Plant & Plant Communications
about 2 months ago
ZmHSCF1 enhances Agrobacterium-mediated transformation frequency in commercial maize inbred lines by promoting embryogenic callus proliferation
#correspondence
#PlantCommunications
cell.com/plant-commun...
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Alexandra Weisberg
Drug Monkey
about 2 months ago
The NSF GRFP is now limited to undergrads and first-year grads
drugmonkey.wordpress.com/2025/09/26/t...
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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…
https://drugmonkey.wordpress.com/2025/09/26/the-nsf-grfp-is-now-limited-to-undergrads-and-first-year-grads/
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Alexandra Weisberg
Sarah Svensson
about 2 months ago
Dual transposon sequencing profiles the genetic interaction landscape in bacteria | Science
www.science.org/doi/10.1126/...
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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...
https://www.science.org/doi/10.1126/science.adt7685
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Alexandra Weisberg
Zamin Iqbal
about 2 months ago
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
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Alexandra Weisberg
Luís M. Silva
about 2 months ago
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
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Ecology and evolution of virulence
Silva and King discuss the concept of virulence and the ecological and evolutionary factors that shape it.
https://www.cell.com/current-biology/fulltext/S0960-9822%2825%2901095-4
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Alexandra Weisberg
Charikleia Karageorgiou (Clio)
about 2 months ago
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The formation and propagation of human Robertsonian chromosomes
Nature - Analysis of human Robertsonian chromosomes originating from 13, 14 and 21 reveal that they result from breaks at the SST1 macrosatellite DNA array and recombination between homologous...
https://rdcu.be/eH1VP
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Alexandra Weisberg
Gitta Coaker
about 2 months ago
My department at UC Davis is hiring a mycologist, broadly interpreted. Please repost, share, and consider applying.
recruit.ucdavis.edu/JPF07339
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Assistant Professor of Plant Pathology
University of California, Davis is hiring. Apply now!
https://recruit.ucdavis.edu/JPF07339
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Alexandra Weisberg
Olaya Rendueles
about 2 months ago
This promises to be a great read! “the pathogenicity island was horizontally transferred from Yersinia pestis to E. coli and other Enterobacterales approximatively 4,800 years ago” ⏩️ it then spread to Klebsiella and positively selected over the last 100 yrs ago
add a skeleton here at some point
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reposted by
Alexandra Weisberg
about 2 months ago
Call for a tenure-track position at our Department of Plant Molecular Biology in Lausanne! We are searching for promising early-career researchers in the broad field of plant-organismal interactions. Deadline: November 30, 2025 - Please re-post!
career5.successfactors.eu/career?caree...
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Career Opportunities: DBMV: Tenure Track Assistant Professor towards Associate Professor in the field of Plant-organism (22484)
https://career5.successfactors.eu/career?career%5fns=job%5flisting&company=universitdP&navBarLevel=JOB%5fSEARCH&rcm%5fsite%5flocale=en%5fUS&career_job_req_id=22484&selected_lang=en_US&jobAlertController_jobAlertId=&jobAlertController_jobAlertName=&browserTimeZone=Europe/Zurich&_s.crb=kX%2flqloffOMPUSNmJBKig4RwtuZbfADI8MRbx13TBC8%3d
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Alexandra Weisberg
Charlotte Wright
2 months ago
How many chromosomes can an animal have? In our paper out now in
@currentbiology.bsky.social
we show that the Atlas blue butterfly has 229 chromosome pairs- the highest in diploid Metazoa! These arose by rapid autosome fragmentation while sex chromosomes stayed intact.
www.cell.com/current-biol...
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Constraints on chromosome evolution revealed by the 229 chromosome pairs of the Atlas blue butterfly
The genome of the Atlas blue butterfly contains ten times more chromosomes than most butterflies, and more than any other known diploid animal. Wright et al. show that this extraordinary karyotype is ...
https://tinyurl.com/atlasbluebutterfly
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reposted by
Alexandra Weisberg
Dan Sloan
2 months ago
The Department of Biology at Colorado State University is hiring an Assistant Professor in the area of plant-microbe interactions! Please spread the word!
jobs.colostate.edu/postings/165...
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Assistant Professor Plant-Microbe Interactions
We seek a creative, collaborative, and visionary plant biologist to establish an internationally recognized research program at the forefront of plant-microbe interactions aimed at understanding how t...
https://jobs.colostate.edu/postings/165524
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Alexandra Weisberg
David Lowry
2 months ago
Super excited about this new Open Rank tenure-track faculty search for the MSU Plant Resilience Institute. We successfully hired two excellent new faculty in our last search and we are hoping to build on that success with this search.
careers.msu.edu/jobs/assista...
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Assistant/Associate/Full Professor Tenure System - East Lansing, Michigan, United States
Working/Functional Title Assistant/Associate/Full Professor Tenure System Position Summary The Plant Resilience Institute (PRI) at Michigan State University invites applications for multiple tenure-st...
https://careers.msu.edu/jobs/assistant-associate-full-professor-tenure-system-east-lansing-michigan-united-states-7b2f3962-aab0-432f-b689-d44e35a8813b
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Alexandra Weisberg
James T. Stroud
2 months ago
Feel free to reach out to any of us here at GT if you have questions! On bluesky: me,
@wcratcliff.bsky.social
,
@benjaminfreeman.bsky.social
,
@sepl.bsky.social
,
@seananderson.bsky.social
,
@digglelab.bsky.social
, and everyone else here:
biosciences.gatech.edu/people
add a skeleton here at some point
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Alexandra Weisberg
Zamin Iqbal
2 months ago
For anyone who has used pling for comparing plasmids using rearrangement distances ("how many structural events apart are these plasmids"), here's how to tweak parameters, and integrate it with typing info, and the host phylogeny
www.biorxiv.org/content/10.1...
github.com/iqbal-lab-or...
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Clustering of plasmid genomes for genomic epidemiology by using rearrangement distances, with pling
Integration of plasmids into genomic epidemiology is challenging, because there are no clearly defined evolving-units (equivalent to species), and because plasmids appear to evolve as much by structur...
https://www.biorxiv.org/content/10.1101/2025.09.02.673752v1
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Alexandra Weisberg
Max Telford
3 months ago
This true also of figure legends. "The Sky is Blue" not " "Graph showing principal colours of things above your head"
add a skeleton here at some point
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Alexandra Weisberg
Kai Kupferschmidt
2 months ago
Sequence data from the new Ebola outbreak in DRC suggests it is indeed a new spillover. And just incredible to see the virus sequenced and the data publicly shared less than 24 hours after confirmation of the outbreak.
#IDsky
🧪
virological.org/t/the-16th-e...
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The 16th Ebola Virus Disease Outbreak in Bulape Health Zone, Kasai, Democratic Republic of the Congo: A new spillover event from an unknown reservoir host
Background The Democratic Republic of the Congo (DRC) is currently facing concurrent outbreaks including mpox, cholera and malaria (1-4). The Ministry of Public Health, DRC has declared the 16th Ebola...
https://virological.org/t/the-16th-ebola-virus-disease-outbreak-in-bulape-health-zone-kasai-democratic-republic-of-the-congo-a-new-spillover-event-from-an-unknown-reservoir-host/1003
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Alexandra Weisberg
Bruno Ngou
2 months ago
Very happy to share our latest work “Systematic discovery and engineering of synthetic immune receptors in plants” out in
@science.org
!
www.science.org/doi/10.1126/...
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Systematic discovery and engineering of synthetic immune receptors in plants
Plants deploy a diverse array of pattern recognition receptors (PRRs), which perceive microbe-associated molecular patterns to activate immune responses. Leucine-rich repeat receptor-like kinase subgr...
https://www.science.org/doi/10.1126/science.adx2508
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Alexandra Weisberg
闵娅(Min Ya; Minya) PhD
2 months ago
My department is hiring a Plant-Fungal Assist Prof!! As the newest
#NewPI
here, don't get me started on how wonderful my colleagues, how smooth my onboarding has been, how supportive the school and the department are, how nice my brand new lab is, and how convenient living in Champaign Urbana is!
add a skeleton here at some point
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Alexandra Weisberg
Judith Behnsen
2 months ago
Excited to share our new publication, out today in Nature!
www.nature.com/articles/s41...
.
@kanchanj.bsky.social
led this fascinating fungal-bacterial interaction project. We are grateful for our wonderful collaborators Brian Peters and David Underhill.
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Commensal yeast promotes Salmonella Typhimurium virulence - Nature
Commensal Candida albicans enhances the virulence and dissemination of Salmonella enterica subsp. enterica serovar Typhimurium.
https://www.nature.com/articles/s41586-025-09415-y
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Alexandra Weisberg
PlantEvolution 🌱🌾
2 months ago
Biology never ceases to amaze!
add a skeleton here at some point
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The Weisberg Lab at Oregon State University is recruiting a postdoctoral scholar in molecular microbiology to study mobile genetic element host range and transmission in microbial communities. Please see the full job description here:
files-dev.cqls.oregonstate.edu/Weisberg_Lab...
3 months ago
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Alexandra Weisberg
Matt Bracken
3 months ago
Multiple ecology faculty positions at
@notredame.bsky.social
. Apply at
apply.interfolio.com/171650
. (1/2). 🌎🌐🧪
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Alexandra Weisberg
Emily Josephs
3 months ago
MSU Plant Bio is hiring a new herbarium director! Our herbarium is a wonderful resource on campus and I'm excited to have the opportunity to make it even better by bringing in a new director. Details here:
plantbiology.natsci.msu.edu/job-postings...
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https://plantbiology.natsci.msu.edu/job-postings/index.aspx
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Alexandra Weisberg
Anny Chung (鍾彥儀)
3 months ago
🍄 UGA Plant Pathology is hiring TT faculty in Mycology/Fungal Biology/Fungal Ecology at the Asst/Assc level! Please pass along this opportunity to anyone you know who may be interested. I'm on the search committee and happy to answer questions. 🍄
www.ugajobsearch.com/postings/445...
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Assistant or Associate Professor - Fungal Biology/Mycology
The Department of Plant Pathology in the College of Agricultural and Environmental Sciences (CAES) at the University of Georgia is recruiting for the position of Assistant or Associate Professor in Fu...
https://www.ugajobsearch.com/postings/445304
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Alexandra Weisberg
Alicia Calvo-Villamañán
3 months ago
This work is finally published! 🥳🧬 Plasmids are associated with very variable fitness costs in their different bacterial hosts. But, what is the contribution of each of the plasmid-genes in these host-specific effects? Study led by
@jorgesastred.bsky.social
,
@sanmillan.bsky.social
and myself! 1/14
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Dissecting pOXA-48 fitness effects in clinical Enterobacterales using plasmid-wide CRISPRi screens
Nature Communications - This study investigates the effects of the carbapenem resistance plasmid pOXA-48 in clinical enterobacteria. Using CRISPRi screens, the authors revealed that the...
https://rdcu.be/eBhe3
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Alexandra Weisberg
Silas Tittes
3 months ago
Super cool! Love the gif highlighting marginal trees along the arg!
add a skeleton here at some point
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Alexandra Weisberg
Nicky Whiffin
3 months ago
Isn't genetics cool??? Within only 145 nucleotides(!) of a non-coding RNA (RNU4-2) - different variants in distinct regions / structures cause three distinct disorders!!! (all discovered within the last 18 months) 🤯🤓🧬❤️
add a skeleton here at some point
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Alexandra Weisberg
Cedric Feschotte
7 months ago
💥🥳 At long last, our latest paper is out! Gag proteins of endogenous retroviruses are required for zebrafish development
www.pnas.org/doi/10.1073/...
Led heroically by Sylvia Chang &
@jonowells.bsky.social
A study which has changed the way I think of
#transposons
! No less! 🧵 1/n
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Gag proteins encoded by endogenous retroviruses are required for zebrafish development | PNAS
Transposable elements (TEs) make up the bulk of eukaryotic genomes and examples abound of TE-derived sequences repurposed for organismal function. ...
https://www.pnas.org/doi/10.1073/pnas.2411446122
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Allison Lopatkin, PhD
3 months ago
If you ever find yourself needing evidence for ‘Plasmids are just as common in microbes without resistance genes,’ we’ve got you covered! Check our new paper, out today:
www.microbiologyresearch.org/content/jour...
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Plasmid prevalence is independent of antibiotic resistance in environmental Enterobacteriaceae
The rapid rise of antibiotic-resistant pathogens poses a critical threat to the treatment of infectious diseases. While the spread of antibiotic resistance genes (ARGs) via plasmid conjugation has bee...
https://www.microbiologyresearch.org/content/journal/mgen/10.1099/mgen.0.001453?originator=authorOffprint&identity=211348&ts=20260812142018&signature=1514bc96dc33e787a3789cee4ed43266
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Alexandra Weisberg
Matthew Hahn
3 months ago
This looks like an amazing tool
www.biorxiv.org/content/10.1...
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Phyling: phylogenetic inference from annotated genomes
Phyling is a fast, scalable, and user-friendly tool supporting phylogenomic reconstruction of species phylogenies directly from protein-encoded genomic data. It identifies orthologous genes by searchi...
https://www.biorxiv.org/content/10.1101/2025.07.30.666921v1
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Come join our department, it is a great place to be and work! See the quoted thread for more details.
add a skeleton here at some point
3 months ago
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Come be our colleague! See the thread for more details on the position.
add a skeleton here at some point
3 months ago
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Alexandra Weisberg
Jeffrey Ross-Ibarra
3 months ago
Day 2 of Popgen is also where I say “Please look at your kinship matrix.”Probably the best summary of pop structure there is, identifies problems or weird stuff in the data, and avoids pitfalls of structure-like plots and PCA.
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Alexandra Weisberg
Itai Yanai
5 months ago
90% of doing science is being open to new ideas.
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Alexandra Weisberg
Morgan Carter
3 months ago
Reported in this
@newphyt.bsky.social
study:
nph.onlinelibrary.wiley.com/doi/full/10....
Two plasmid‐borne virulence genomic islands of Clavibacter michiganensis are genetically diverse and determine the development of wilt symptoms in host plants - Hwang - New Phytologist - Wiley Online Library
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Two plasmid‐borne virulence genomic islands of Clavibacter michiganensis are genetically diverse and determine the development of wilt symptoms in host plants
Plasmids contribute to the efficient adaptation of bacteria to specific niches in nature. The gram-positive bacterium Clavibacter michiganensis carries two plasmid-borne important virulence genes, c.....
https://nph.onlinelibrary.wiley.com/doi/full/10.1111/nph.70329
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