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Reposted by Megan Phillips

bioRxiv Genomics @biorxiv-genomic.bsky.social · 23d

Transition of Staphylococcus aureus tetracycline resistance plasmid pT181 from independent multicopy replicon to predominantly integrated chromosomal element over 65 years https://www.biorxiv.org/content/10.1101/2025.09.14.675889v1

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Reposted by Megan Phillips

James Bonfield @jbonfield.bsky.social · 24d

Heads up: ignore samtools dot org, similarly minimap2 dot com and likely others. It's owned by a known phishing site and while the binaries they offer look valid currently (but note they may be serving us different binaries to others), that could change.

Ie: it's not us (Samtools team)! Be warned

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Reposted by Megan Phillips

Tim Read @timothyread.bsky.social · 28d

Delighted to see the first version of our new ELife paper. A collaboration with Levi Morran, we show how an intact antibiotic resistance gene (mecA) changes the course of S. aureus evolution on a new host. Kudos to Michelle Su and Kim Hoang for making this happen.

elifesciences.org/reviewed-pre...

Host and antibiotic jointly select for greater virulence in Staphylococcus aureus

elifesciences.org

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Reposted by Megan Phillips

Richard Neher @neher.io · Aug 23

It was a great pleasure to contribute to this work by Jemma Fendley, @mmolari.bsky.social, and Boris Shraiman on pan-genomes, linkage, and recombination in phage genomes.

We analyzed data collected by the fantastic SEA-PHAGES program in phagesdb.org.

[1/6]

www.biorxiv.org/content/10.1...

The Actinobacteriophage Database | Home

phagesdb.org

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Reposted by Megan Phillips

José Cerca @naturalselection.bsky.social · Aug 19

The 2025-26 Eco-Evo job list is out. Good luck to those applying!

docs.google.com/spreadsheets...

ecoevojobs.net 2025-26

docs.google.com

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Reposted by Megan Phillips

Annie Hatmaker, Ph.D. @annemakerofhats.bsky.social · Aug 18

Thrilled to share that the final chapter of my PhD with @rokaslab.bsky.social is now out in @natcomms.nature.com 🎉
Read it to find out how population structure impacts pathogenicity in Aspergillus flavus, a fungus that infects humans 🧪
rdcu.be/eAToj

Population structure in a fungal human pathogen is potentially linked to pathogenicity

Nature Communications - Genetic diversity between clinical and environmental fungal isolates of Aspergillus flavus is poorly studied. Here, the authors analysed genomic data from a global set of...

rdcu.be

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Reposted by Megan Phillips

Claus Wilke @clauswilke.com · Aug 15

A simple design framework that will massively improve your slides and your public speaking
clauswilke.substack.com/p/slides-tha...

Slide designs that present themselves: The assertion–evidence template

Your slides are not your talk.

clauswilke.substack.com

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Reposted by Megan Phillips

Denis Wirtz @deniswirtz.bsky.social · Aug 11

These are the most challenging times for early-career scientists and engineers.

My team is doing its bit to help by maintaining and even expanding our database of funding opportunities for early-career researchers.

We found 437 of them.

Download it freely here: research.jhu.edu/rdt/funding-...

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Reposted by Megan Phillips

Eduardo Rocha @epcrocha.bsky.social · Jul 23

Here's our new broad review on the extended mobility of plasmids, about all mechanisms driving and limiting their transfer. From conjugation to conduction, phage-plasmids to hitchers, molecular to evolutionary dynamics, ecology to biotech. The state of affairs. 1/9 academic.oup.com/nar/article/...

graphical abstract of the article the extended mobility of plasmids

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Mike Blazanin @mikeblazanin.bsky.social · Jul 3

Looking forward to seeing everyone, new and old, at the Microbial Population Biology GRS + GRC in just a couple days!

go.bsky.app/GGxRjzC

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Megan Phillips @meganphillips.bsky.social · Jun 18

I’m excited to present my work on mobile genetic element evolution at #Evol2025 on Tuesday, June 24! Come by the Bioinformatics & Molecular Evolution session at 9:45am for my talk, “The little plasmid that could: evolution of a small antimicrobial resistance element” (room Athena F)

Title slide for June 24, 2025 talk "The little plasmid that could: evolution of a small antimicrobial resistance element," in the Bioinformatics & Molecular Evolution Session. Orange slide background with white circular outline around talk information. Presenting/1st author is Megan Phillips (at Emory University), other authors are Robert Petit, Daniel Weissman, & Timothy Read.

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Reposted by Megan Phillips

LaBella Lab @lablabella.bsky.social · May 29

Our very first Wild Yeast Sampling day!!

From garden to genome - this summer our group is going to learn how to find and sequence wild yeast

Awesome collab with @morgancarterphd.bsky.social

My hope is that we can bring this to the classroom very soon!

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Reposted by Megan Phillips

Tami Lieberman @contaminatedsci.bsky.social · May 1

Do people in the same household share strains when they have the same species?

How many cells transmit when a strain is shared?
Can strain composition be dynamic when species composition is stable?

We answer these and related questions for the facial skin microbiome in our latest paper.

🧵[1/10]

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𝖬𝖺𝗁𝖽𝗂 𝖢𝗁𝖾𝗋𝖺𝗀𝗁𝖼𝗁𝗂 @mahdi.ch · Mar 20

It's NOT safe for non-citizens to cross the US border at this time.
- Academic conferences in the US must recognize the right of authors abroad who'd prefer not to travel.
- Those outside the US must recognize the right of non-citizen authors in the US who'd prefer not to travel.
NO QUESTIONS ASKED.

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Reposted by Megan Phillips

Paul J Planet @pjplanet.bsky.social · Mar 19

Proud to be part of this group! journals.asm.org/doi/10.1128/...

Geographic divergence of methicillin-resistant Staphylococcus aureus ST5-SCCmecI in the aftermath of a major earthquake and tsunami: impact of a plasmid harboring heavy metal resistance genes | mBio

Methicillin-resistant Staphylococcus aureus (MRSA) is a major cause of life-threatening infections worldwide and a growing public health concern. The rise of antibiotic-resistant bacteria, such as MRSA, is often linked to genetic adaptations that enhance ...

journals.asm.org

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Reposted by Megan Phillips

Gemma C. Atkinson @gemmaatkinson.bsky.social · Feb 25

Excited to share that our paper on locus visualisation tool LoVis4u is out! Entirely driven by fantastic PhD student Artyom Egorov @egorov.bsky.social academic.oup.com/nargab/artic...

LoVis4u: a locus visualization tool for comparative genomics and coverage profiles

Abstract. Comparative genomic analysis often involves visualization of alignments of genomic loci. While several software tools are available for this task

academic.oup.com

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Reposted by Megan Phillips

Annika Barber @annikabarber.bsky.social · Feb 24

Wondering if your study section cancelled? I update this sheet daily. As of today, 56/124 study sections that should have met since Jan 2, 2025 have "not met as scheduled." docs.google.com/spreadsheets...

2025 Study section tracking

docs.google.com

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Reposted by Megan Phillips

Stacy Farina @stacyfarina.bsky.social · Jun 3

Do you work in ecology/evolution? Did you do a study that is too small to publish as a full manuscript? Negative results? Part of a larger effort? Consider publishing in microPublication Biology: EEB!

www.micropublication.org/journals/bio...

Short papers, one figure. And we peer review! Please RT

microPublication - Get Your Data Out, Be Cited

www.micropublication.org

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Paul Hoskisson 🧫 🦠🐸 @paulhoskisson.bsky.social · Apr 19

This is very intriguing -

Many purported pseudogenes in bacterial genomes are bona fide genes

bmcgenomics.biomedcentral.com/articles/10....

Many purported pseudogenes in bacterial genomes are bona fide genes - BMC Genomics

Background Microbial genomes are largely comprised of protein coding sequences, yet some genomes contain many pseudogenes caused by frameshifts or internal stop codons. These pseudogenes are believed ...

bmcgenomics.biomedcentral.com

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Reposted by Megan Phillips

Zamin Iqbal @zaminiqbal.bsky.social · Mar 18

Mandatory reading and surprising results from Michael Hall and colleagues - much better bacterial SNP/indel calling results from latest nanopore (beating illumina), and deep learning methods really doing well. Extremely thorough work
www.biorxiv.org/content/10.1...

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Reposted by Megan Phillips

Britt Koskella @bkoskella.bsky.social · Mar 19

Please share: Our 2024-25 RaMP postbac scholars program is now open for applications. If you (or anyone you know) recently graduated and are interested in microbiome research but didn’t have the opportunity to engage in meaningful research during your degree, check us out!!

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Reposted by Megan Phillips

Will Matlock @wtmatlock.bsky.social · Mar 14

Very excited to announce our transdisciplinary AMR workshop 🎉

Join us to hear perspectives and discussion from patient activists, journalists, philosophers, microbiologists, historians, clinicians, policy makers, and artists. More info: www.torch.ox.ac.uk/event/commun...

A poster for a workshop called “Communication, Narratives, and Antimicrobial Resistance”. 9am to 6pm 16th May 2024. Merton College, University of Oxford.

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Alvaro San Millan @sanmillan.bsky.social · Mar 2

New preprint in collaboration with @asantoslopez.bsky.social lab and led by Jorge Sastre. Combining experimental evolution and analyses of longitudinal samples from hospitalised patients, we unveiled a new mechanism of plasmid-mediated evolution beyond HGT 1/8
www.biorxiv.org/content/10.1...

Plasmid-encoded insertion sequences promote rapid adaptation in clinical enterobacteria

bioRxiv - the preprint server for biology, operated by Cold Spring Harbor Laboratory, a research and educational institution

www.biorxiv.org

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bioRxiv Evolutionary Biology @biorxiv-evobio.bsky.social · Feb 12

How to validate a Bayesian evolutionary model https://www.biorxiv.org/content/10.1101/2024.02.11.579856v1

Biology has become a highly mathematical discipline in which probabilistic models play a central rol

www.biorxiv.org

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Tomer Ullman @tomerullman.bsky.social · Feb 7

my hopes for gen z taking over the academic process is that it will be matched for harshness, but at least more efficient

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