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Sean Meaden

@seanmeaden.bsky.social
644 followers 523 following 19 posts

Microbial ecology / evolution / genomics @ University of York

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Reposted by Sean Meaden
Levayer Lab @levayerr.bsky.social · 28/09/2026
Here it is...by delegating decision to non transparent AI models we generate an incentive for grant applicants to use AI writing to tweak system and the vicious/absurd feedback loop is set (which all started by an overload of grant application driven by AI writing). www.science.org/content/arti...
science.org
U.K. funder uses ‘AI triage’ to reject grant proposals—leaving researchers dismayed
The AI-based assessment, which wasn’t explicitly described in the funding call, has raised privacy and fairness concerns
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Leah Smith @leahmsmith.bsky.social · 28/09/2026
Adapting the power of transposon sequencing to phages! Our final paper is out now👇 Our plasmids 🧬 are available on @addgene.bsky.social – try phage Tn-seq on your favorite phage!
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Ellie Jameson @elliejameson.bsky.social · 22/09/2026
MScRes bursary of £2000 available at Bangor University to study Bacteriophages as natural biocontrols for plant pathogens. Deadline is 19th October. Please contact me for more details #PhageSky #MicroSky
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JL Weissman @jlw-ecoevo.bsky.social · 10/09/2026
My lab is hiring two(!) postdocs interested in (1) building trait prediction models capable of resolving complex microbial traits from genomes and metagenomes, and/or (2) building mathematical models of microbial community dynamics www.microbialgamut.com/mGAMUT_postd...
microbialgamut.com
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Sean Meaden @seanmeaden.bsky.social · 08/09/2026
Standing room only for Sophie Dodds' Generation Research talk. Sophie has been doing brilliant work all summer charactering a novel phage- we're sad to see her go, but exciting data is incoming! Highly recommend the GenRes programme for students and ECR supervisors. @biologyatyork.bsky.social
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Tatiana Dimitriu @tatianadimitriu.bsky.social · 20/08/2026
New paper led by Liam Shaw, with Arancha Peñil Celis, @aresarroyom.bsky.social, @adalijuanluo.bsky.social & Fernando de la Cruz. academic.oup.com/nar/article/... This is very much Liam’s story, but I loved playing a small part in it 🧵
academic.oup.com
The leading region of many plasmids is adapted for translational efficiency
Abstract. To successfully transfer, conjugative plasmids must overcome a recipient cell’s defence mechanisms. The leading region of many plasmids—the first
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Malcolm White @mfwhite2.bsky.social · 11/08/2026
Tim Blower and I are guest editing a Biochemical Journal @biochemsoc.bsky.social themed collection on: The Prokaryotic Immune System It's now open for research submissions and we'd welcome submission of research and review articles. More info: portlandpress.com/biochemj/pag...
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Jamie Blaza @jnb-lab.bsky.social · 10/08/2026
Permanent academic position as a Lecturer in cryo-ET open at York. We are looking for someone to lead a research program making the most of the stunning advances occurring in cryo-ET. It's a research and teaching post but with a focus on research in the early years. jobs.york.ac.uk/vacancy/lect...
jobs.york.ac.uk
Jobs - The University of York
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Xena Dyball @xenadyball.bsky.social · 06/08/2026
I am excited to share that our manuscript titled 'Defining the ESKAPE pathogen prophage repertoire with PHORAGER' is now available online as a preprint in BioRxiv! 🤩 (doi.org/10.64898/202...) Here we present PHORAGER, a Nextflow pipeline for the identification and quality assessment of prophages 🧬
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Siobhán O'Brien @siderophile.bsky.social · 29/07/2026
We rely on healthy soil microbial communities to support ecosystem functioning and plant growth, but what happens when soils are exposed to multiple environmental stressors simultaneously? Spoiler: it's not good doi.org/10.1093/isme...
academic.oup.com
Fungicide and warming interact to reduce soil ecosystem functioning
Abstract. Soil microbial communities are essential to the functioning of their ecosystems, providing vital services such as plant growth promotion and bior
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Ville Friman @frimanscience.bsky.social · 12/06/2026
Very happy that this piece of research finally sees the daylight! Super nice collaboration between Nanjing, York and Helsinki. Fun fact: we started this work over 10 years ago when I was working as a fellow at Imperial College. Sometimes good things come to those who wait.
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Britt Koskella @bkoskella.bsky.social · 19/05/2026
Please share widely! Abstract submissions open for the 2026 Jacques Monod conference: Ecology and evolution of host-parasite interactions in a changing world! Held in beautiful Roscoff France from November 2- 6, 2026. Abstracts submission deadline : June 6 cjm.sb-roscoff.fr/en/conferenc...
cjm.sb-roscoff.fr
Ecology and evolution of host-parasite interactions in a changing world | CNRS - Conférences Jacques Monod (CJM)
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Kirsty Grainger @kirstygrainger.bsky.social · 14/05/2026
Two institutions putting in over 50 applications for a fellowship scheme that awards roughly 15 each years. If you don't know which two, guess them look at the data (my biases were not wrong this time)
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Branko Rihtman @cyanoney.bsky.social · 11/05/2026
New version of Inphared!!! With improved capabilities, such as defence and anti defence annotation in phage genomes, predicted lifestyle annotation, constantly expanding curated phage genome database and other improvements! Check out the preprint with all the numbers.
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Michael Brockhurst @brockhurstlab.bsky.social · 28/04/2026
We have a PhD studentship available to develop genome safeguarding technologies for synthetic phage therapeutics www.findaphd.com/phds/project... It is part of an exciting new @officialuom.bsky.social PhD by Enterprise programme www.bmh.manchester.ac.uk/study/resear...
findaphd.com
(PhD by Enterprise) Genome safeguarding technologies for synthetic phage therapeutics against multidrug resistant bacterial infections at The University of Manchester on FindAPhD.com
PhD Project - (PhD by Enterprise) Genome safeguarding technologies for synthetic phage therapeutics against multidrug resistant bacterial infections at The University of Manchester, listed on FindAPhD...
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Rachel M. Wheatley @rachelmwheatley.bsky.social · 30/03/2026
🔊 Looking for a Research Assistant in Bacterial Evolution to join my lab 🦠 🥼Main duties: Research (AMR + microbiome) + lab assistance. ⏲️ Post duration: 30 months 🗓️ Closing date for applications: 20th April 2026 💰 Salary: ~£35k Details and how to apply: tinyurl.com/2a3v66y7 Please share!
lnkd.in
LinkedIn
This link will take you to a page that’s not on LinkedIn
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Siobhán O'Brien @siderophile.bsky.social · 31/03/2026
Just a few weeks left to register - places are filling up fast!
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Daniel Padfield @padpadpadpad.bsky.social · 30/03/2026
PLEASE SHARE. PhD Opportunity with me, Ben Raymond and Jan Engelstaedter and Andrew Letten at University of Queensland. Experimentally testing mechanisms of how temperature may change selection and spread of AMR in E. coli. Coupled with some advanced modelling and sequencing. 🧪🦠 #microsky
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Paul Fogg @pcmfogg.bsky.social · 20/03/2026
It is a pleasure to announce the 4th UK MGE workshop will be in York on 23rd-24th June 2026! Registration is free and we are actively looking for contributors. Interested? If so, please register via the website and select the talk option www.ukmgeworkshop.org We look forward to seeing you in York!
ukmgeworkshop.org
MGE-UK-4
We are thrilled to invite you to the fourth edition of the MGE UK Workshop, hosted this year in the historic City of York. Mobile Genetic Elements (MGEs) are the ultimate architects of biology. MGEs i...
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Reposted by Sean Meaden
Jason Wilson @jasonwils.bsky.social · 02/02/2026
It was great to play a part in this study, using all of the work on alphaproteobacterial GTAs to help inform and identify key tell-tale patterns of GTAs in the human gut microbiome. I'm sure there will be many great followup studies on these fascinating particles. www.nature.com/articles/s41...
nature.com
Large-scale capsid-mediated mobilisation of bacterial genomic DNA in the gut microbiome - Nature Communications
Here, the authors show that packaging of bacterial DNA by phage-like particles is widespread in the gut microbiome, with activity of gene transfer agents being prominent in Oscillospiraceae and Rumino...
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Bas E. Dutilh @bedutilh.bsky.social · 29/01/2026
We have an open position for a bioinformatics/theoretical microbial ecology PhD student to study viral strategies in the global Microverse! Join us at the @microverse.bsky.social at @uni-jena.de, please apply through this link: jobs.uni-jena.de/jobposting/9...
jobs.uni-jena.de
PhD student bioinformatics: Viral strategies in the global Microverse
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Siobhán O'Brien @siderophile.bsky.social · 19/01/2026
Combined anthropogenic stressors (warming and fungicide) synergistically reduce soil microbial ecosystem functioning (respiration, metabolic capacity, plant performance, fungicide resistance). A tour-de-force by @kelbrick.bsky.social! www.biorxiv.org/content/10.6...
biorxiv.org
Fungicide and warming interact to reduce soil ecosystem functioning
Soil microbial communities are essential to the functioning of their ecosystems, providing vital services such as plant growth promotion and bioremediation. However, intensively managed environments such as agricultural soils are increasingly challenged with multiple harsh environmental stressors from the compounding effects of climate change and conventional agricultural practices. Understanding how soil communities will respond to environmental stress along multiple axes is key for predicting how environmental change will impact terrestrial soil ecosystems. We combine experimental evolution with community phenotyping, 16s rRNA metabarcoding, fungicide resistance assays and plant experiments, to show that fungicide and warming temperatures together drive a synergistic reduction in soil community respiration rates, metabolic capacity and plant growth promotion (Hordeum vulgare), which would have been missed by looking at stressor effects independently. Dual stressors caused widespread loss of metabolic activity, particularly for carbohydrates and carboxylic acids, highlighting impairment of community function. Fungicide-evolved soil isolates had a 16-fold increase in fungicide resistance, but only in the absence of warming, suggesting that the dual stressor treatment constrained fungicide adaptation. Together, our findings suggest that the number of stressors (rather than the nuances of individual stressors) may be key for predicting soil microbial community responses to environmental change across multiple axes. ### Competing Interest Statement The authors have declared no competing interest. BBSRC, BB/T009446/1 IRC New Foundations and Community Foundation Ireland, NF/2022/39250777 NERC, NE/S00713X/1
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Rodrigo Sánchez Martínez @rodrisanchez95.bsky.social · 09/01/2026
Two fantastic papers published back-to-back in @natmicrobiol.nature.com show that strictly lytic phages can persist intracellularly for long periods of time. Very much in line with ideas we had suggested in a recent study. Highly recommended reads 👇 www.nature.com/articles/s41...
nature.com
Client Challenge
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Paul Fogg @pcmfogg.bsky.social · 03/01/2026
Still time to apply for an exciting #BBSRC #PhD opportunity I am offering @biologyatyork.bsky.social with @seanmeaden.bsky.social & Hong Gao (Tees). Join an interdisciplinary team to study how viruses shape bacterial evolution and the spread of antibiotic resistance. Apply by 7th Jan bit.ly/4jfv9wx
bit.ly
Agents of Change: An exploration of how viruses and viriforms shape bacterial evolution, fitness, and antibiotic resistance (York YBDTP Project) at University of York on FindAPhD.com
PhD Project - Agents of Change: An exploration of how viruses and viriforms shape bacterial evolution, fitness, and antibiotic resistance (York YBDTP Project) at University of York, listed on FindAPhD...
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Tatiana Dimitriu @tatianadimitriu.bsky.social · 12/12/2025
Our story on plasmid streamlining is now published in PLoS Biology! With @andrewmatthews.bsky.social and @sonjalehtinen.bsky.social #MicroSky #Mevosky journals.plos.org/plosbiology/...
journals.plos.org
Plasmid streamlining drives the extinction of antibiotic resistance plasmids under selection for horizontal transmission
Conjugative plasmids play an important role in the spread of antimicrobial resistance (AMR) genes among pathogenic bacteria. This study shows that AMR loss in evolving populations is associated with t...
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Luke Hillary @lukehillary.bsky.social · 27/11/2025
📢 New preprint is out on bioRxiv 📢: How much does virome prep influence our view of the human gut virome? Short answer: a lot. Long answer: doi.org/10.1101/2025... Different methods lead to distinct community structures, richness, and major virus-host abundance patterns. 🧵 1/5
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Paul Hoskisson 🧫 🦠🐸 @paulhoskisson.bsky.social · 27/11/2025
Super meeting, and @microbiologysociety.org staff organisation was incredible as always! This meeting really fills a niche in evolutionary microbiology, let make sure it runs again! Great to see old friends and make new ones @gmknght.bsky.social
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Sean Meaden @seanmeaden.bsky.social · 27/11/2025
Two fully-funded PhD openings in my research group at the University of York. If you’re excited about viromes, phage biology, Nanopore sequencing, soils and the odd bit of alpine or agricultural field sampling, we’d love to hear from you! 🌱🦠🏔️ tiny.cc/c4pv001 tiny.cc/e4pv001
tiny.cc
A Farewell to Arms: The Trade-off Between Growth and Defence in Bacteria (York YBDTP Project) at University of York on FindAPhD.com
PhD Project - A Farewell to Arms: The Trade-off Between Growth and Defence in Bacteria (York YBDTP Project) at University of York, listed on FindAPhD.com
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Dave Baltrus 🦦 @surtlab.bsky.social · 19/11/2025
Whoever you are out there...apply for this. Jamie's awesome and the question is exactly where I think this kind of research is going in the next decade
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Ville Friman @frimanscience.bsky.social · 14/11/2025
Interested in doing a PhD in phage biology? See below a super cool project on megaphage ecology and evolution available at the University of Jyväskylä (FIN) in Elina Laanto's lab (Project no. 4). Co-supervision provided by yours truly.
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Anne Chevallereau @annechevallereau.bsky.social · 22/10/2025
JOB OFFER #PhageSky We have a postdoc position opening in my group to investigate phage-MGE interactions ! We're based in the very nice city of Lyon, France @mmsb-lyon.bsky.social Contact me for more info ! >> Apply on the CNRS webpage emploi.cnrs.fr/Offres/CDD/U...
emploi.cnrs.fr
Portail Emploi CNRS - Offre d'emploi - Postdoctoral researcher Microbiology (M/F)
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Ashish Malik @ashish-malik.bsky.social · 17/10/2025
PhD opportunity with me at University of Edinburgh linked with Forest Research, funded by E5 DTP. On the microbial mechanisms of soil carbon cycling in tree-planted upland soils. Apply before 14th Dec. Please share with your network. Pic: one of our Scottish sites. e5-dtp.ed.ac.uk/project?item...
An upland landscape in Scotland with trees and open areas.
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Gavin Thomas (he/him) @gavinhthomas.bsky.social · 10/10/2025
I'll be writing more about this soon, but Reyme's developed a very cool culturomics workflow to enable us to understand and recreated real microbiomes from the human underarm. Corynebacterium focus in this paper. journals.asm.org/doi/full/10....
journals.asm.org
Revealing the diversity of commensal corynebacteria from a single human skin site | mSystems
This study uncovers the hidden diversity of Corynebacterium, an important yet often overlooked group of bacteria inhabiting human skin. Focusing on the underarm and using advanced sequencing technique...
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Giusy Mariano @giusym1990.bsky.social · 01/10/2025
🚨PhD Opportunity Alert🚨 Join me, @suzieh.bsky.social and @walllabuoglasgow.bsky.social to investigate how environment shapes anti-phage defences & prophage–prophage conflict in Pseudomonas aeruginosa. Apply here: www.gla.ac.uk/postgraduate...
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Paul Fogg @pcmfogg.bsky.social · 23/09/2025
🚨Exciting #Postdoc opportunity in the Fogg & Antson labs: 3-year post based @biologyatyork.bsky.social to explore the #StructuralBiology & mechanism of viral DNA-packaging motors using cutting-edge #Cryo-EM, biophysical and molecular approaches. Apply by 9th Oct at bit.ly/3Iz3bOu #ScienceJobs
bit.ly
Jobs - The University of York
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Daniel Padfield @padpadpadpad.bsky.social · 16/09/2025
I have an MRC-funded PhD project available (www.exeter.ac.uk/study/fundin...) on how warming will change the problem of AMR. Join a small and friendly group (padpadpadpad.netlify.app/about) in (sometimes) sunny Cornwall. 🧪🦠 #microsky Please share the ad below with anyone who may be interested.
A teal flyer for a PhD opportunity to investigate how warming may change antimicrobial resistance. The project will use experiments on Klebsiella bacteria to answer questions about how temperature affects their response to antibiotics, plasmid transfer, and fitness costs. The research involves microbiology lab work, bioinformatics, and mathematical modeling. The flyer includes contact details for Dr. Daniel Padfield and the logos of the sponsoring institutions.
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Daniel Padfield @padpadpadpad.bsky.social · 15/09/2025
Today in the AI hellscape we are building for ourselves, people are easily creating "official looking" websites of popular bioinformatics software that are not at all linked to the developers.
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Dr Katherine Duncan @kateduncan.bsky.social · 10/09/2025
Really looking forward to sharing our science with Yorkshire Philosophical Society at Tempest Anderson Hall on Oct 14th - thank you to @gavinhthomas.bsky.social for the invite www.ypsyork.org/events/antib...
ypsyork.org
Antibiotics from the Abyss | Yorkshire Philosophical Society
promoting the understanding of science since 1822
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Kat Coyte @coytelab.bsky.social · 08/09/2025
closing at the end of this week!
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Sean Meaden @seanmeaden.bsky.social · 03/09/2025
"the assemblage used a peak of 2.18 million CPU cores" Fair enough 🤯
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Rayan Chikhi @rayanchikhi.bsky.social · 03/09/2025
🌎👩‍🔬 For 15+ years biology has accumulated petabytes (million gigabytes) of🧬DNA sequencing data🧬 from the far reaches of our planet.🦠🍄🌵 Logan now democratizes efficient access to the world’s most comprehensive genetics dataset. Free and open. doi.org/10.1101/2024...
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Kat Coyte @coytelab.bsky.social · 12/08/2025
A new 4 year PostDoc position in our lab! Modeling + experiments to explore dynamics of carbon fixing hot-spring microbiomes. Part of an exciting multidisciplinary team with Sophie Nixon, @brockhurstlab.bsky.social & others Please share & get in touch if interested! tinyurl.com/e7j7bha3
jobs.manchester.ac.uk
Research Associate in Microbiome Ecology:Oxford Road
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Michael Brockhurst @brockhurstlab.bsky.social · 13/08/2025
We are also hiring a 4-year postdoc to study the dynamics and evolution of mobile genetic elements in the C-fixing Icelandic host-spring microbiomes Join our exciting multidisciplinary team funded by @ukri.org BBSRC sLoLa www.jobs.manchester.ac.uk/Job/JobDetai...
jobs.manchester.ac.uk
Research Associate in Microbial Evolution:Oxford Road
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Ellinor Alseth @ellinoralseth.bsky.social · 08/08/2025
Feels surreal to say but: I'm hiring! If you are or know anyone interested in looking at the evolution of phage resistance using A. baumannii and natural transformation, then this might be for you www.jobbnorge.no/en/available...
jobbnorge.no
Research position in Microbial Pharmacology and Population Biology (282139) | UiT The Arctic University of Norway
Job title: Research position in Microbial Pharmacology and Population Biology (282139), Employer: UiT The Arctic University of Norway, Deadline: Wednesday, August 27, 2025
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Meaghan Castledine @mcastd.bsky.social · 05/08/2025
Want to name a real virus? I have recently discovered 9 new phages which now need names! To enter, you simply need to donate to the Cystic Fibrosis Trust on my JustGiving page (£2 = 1 entry) and share your email with me on donation (see link info). Please share 💚 www.justgiving.com/page/meaghan-c-1
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Ryan Cook @ryancook94.bsky.social · 17/06/2025
New pre-print alert! 🚨🫁 COPD affects millions worldwide. While we know bacterial dysbiosis drives disease, the role of bacteriophages remains unexplored. We re-analysed 135 COPD metagenomes to characterise the lung virome for the first time 🫁 1/9 www.biorxiv.org/content/10.1...
biorxiv.org
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Asaf Levy @asaflevylab.bsky.social · 11/06/2025
Our new paper is online in Genome Biology: "Plasmids, prophages, and defense systems are depleted from plant microbiota genomes" genomebiology.biomedcentral.com/articles/10....
genomebiology.biomedcentral.com
Plasmids, prophages, and defense systems are depleted from plant microbiota genomes - Genome Biology
Plant-associated bacteria significantly impact plant growth and health. Understanding how bacterial genomes adapt to plants can provide insights into their growth promotion and virulence functions. He...
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Alex Crits-Christoph @acritschristoph.bsky.social · 28/05/2025
HMMER is the bedrock of genomic annotation globally, and now its funding is terminated for no reason. @cryptogenomicon.bsky.social is now on bsky:
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David Sünderhauf @davvi36.bsky.social · 12/05/2025
I *finally* get to share our work on plasmid competition– super proud to now have this on bioRxiv: CRISPR-Cas is beneficial in plasmid competition, but limited by competitor toxin-antitoxin activity when horizontally transferred www.biorxiv.org/content/10.1... 1/6 👇
pKJK5 vs RP4 cartoon sketch on plasmid competition
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Fiona J Whelan @whelanfj.bsky.social · 28/03/2025
Come join us! Next week marks my 1 year anniversary at @uniofmanchester.bsky.social and I've never looked back!
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