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Megan Phillips

@meganphillips.bsky.social
471 followers 392 following 2 posts

Staph aureus evolution + genomics | PhD candidate @ Emory University | Population Biology, Ecology, & Evolution | 🧬💻🦠🍄 | Mastodon 🦣 @meganphillips@mstdn.science | orcid.org/0000-0002-0781-3325

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Reposted by Megan Phillips
Sheyda Azimi @sazimi.bsky.social · 13/08/2026
New preprint of our work on effects of intra-strain diversity of Pseudomonas on modulating host response is out! Some variants of concern, flip the switch in host responses! www.biorxiv.org/content/10.6...
biorxiv.org
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The Rokas Lab at Vanderbilt University @rokaslab.bsky.social · 11/06/2026
Interested in how #fungi came about on this planet? If so, take a look at my new article that just came out in @annualreviews.bsky.social. doi.org/10.1146/annu...
doi.org
The Origin and Early Evolution of Fungi: Challenges, Inferences, and Principles
Fungi are widespread on our planet and essential for life as we know it, but how did they come about? Their last common ancestor lived hundreds of millions of years ago, but its characteristics, and t...
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Robert Petit @rpetit3.bsky.social · 30/04/2026
Howdy! Happy to announce that Bactopia v4 is finally out! 🥳 This release supports the latest from @seqera.io Nextflow v26 (strict syntax, static types, and records! oh my!) It also open's the doors to start doing some fun things with Bactopia. To learn more, check out: bactopia.io/blog/bactopi...
bactopia.io
Bactopia v4 Updates and Improvements | Bactopia
Learn about the new features and improvements in Bactopia version 4.
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Michael Brockhurst @brockhurstlab.bsky.social · 20/02/2026
How does treatment induced antibiotic resistance happen in real-world infections? We analysed 25k Pseudomonas isolates from 180 patients in a clinical trial to find out! TLDR: The ecological and evolutionary paths are surprisingly diverse & complex even in patients receiving identical treatment…
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TARGetAMR @target-amr.bsky.social · 02/02/2026
🚀 Happening this week! 🧬 Dive into the TyphiNET AMR surveillance dashboard with Dr Zoe Dyson, LSHTM 🦠 Discover how genomics data is powering public health insights ➕ Featuring an ECR talk from Dr Parul Sharma, Emory University 📅 Thurs 5 Feb @ 12pm GMT 🔗 Register: www.targetamr.org.uk/hdrevents/th...
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Xing-Xing Shen @xingxingshen.bsky.social · 29/01/2026
Excited to share a new piece of work in @embojournal.org Parasitoid wasps hijack a bacterial gene that governs venoms against host. Coauthors include @rokaslab.bsky.social and others. Read more from: link.springer.com/article/10.1...
link.springer.com
A bacterial gene acquired by parasitoid wasps contributes to venom secretion against host defence - The EMBO Journal
Horizontal gene transfer (HGT) is an important source of gene innovation in prokaryotic and eukaryotic organisms. Several genes acquired by hosts of parasitoid wasps via HGT have been reported to prot...
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Allison Lopatkin, PhD @ajlopatkin.bsky.social · 27/01/2026
Big week: welcomed a new baby boy Harris Lopatkin, AND our PlasAnn paper is finally out: academic.oup.com/nar/article/... (obviously the first more important than the second 🥰). Currently on leave but if anyone has the need to annotate large plasmids, go check it out!
academic.oup.com
PlasAnn: a curated plasmid-specific database and annotation pipeline for standardized gene and function analysis
Abstract. Conjugative plasmids are key drivers of bacterial adaptation, enabling the horizontal transfer of accessory genes within and across diverse micro
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Megan Hochstrasser @meganhoch.bsky.social · 29/09/2025
Free, professional illustrations of research organisms! 🎨🐁🪼🧪 We compiled original vector/raster graphics of 70+ organisms & viruses into a CC0 library. All by @arcadiascience.com's Audrey Bell Check it out & show us how you use them! research.arcadiascience.com/pub/resource... #SciArt #OpenScience
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bioRxiv Genomics @biorxiv-genomic.bsky.social · 16/09/2025
Transition of Staphylococcus aureus tetracycline resistance plasmid pT181 from independent multicopy replicon to predominantly integrated chromosomal element over 65 years www.biorxiv.org/content/10.1101/202…
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James Bonfield @jbonfield.bsky.social · 15/09/2025
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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Tim Read @timothyread.bsky.social · 10/09/2025
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...
elifesciences.org
Host and antibiotic jointly select for greater virulence in Staphylococcus aureus
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Richard Neher @neher.io · 23/08/2025
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...
phagesdb.org
The Actinobacteriophage Database | Home
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José Cerca @naturalselection.bsky.social · 19/08/2025
The 2025-26 Eco-Evo job list is out. Good luck to those applying! docs.google.com/spreadsheets...
docs.google.com
ecoevojobs.net 2025-26
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Annie Hatmaker, Ph.D. @annemakerofhats.bsky.social · 18/08/2025
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
rdcu.be
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...
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Claus Wilke @clauswilke.com · 15/08/2025
A simple design framework that will massively improve your slides and your public speaking clauswilke.substack.com/p/slides-tha...
clauswilke.substack.com
Slide designs that present themselves: The assertion–evidence template
Your slides are not your talk.
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Denis Wirtz @deniswirtz.bsky.social · 11/08/2025
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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Eduardo Rocha @epcrocha.bsky.social · 23/07/2025
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 · 03/07/2025
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 · 18/06/2025
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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LaBella Lab @lablabella.bsky.social · 29/05/2025
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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Tami Lieberman @contaminatedsci.bsky.social · 01/05/2025
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 · 20/03/2025
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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Paul J Planet @pjplanet.bsky.social · 19/03/2025
Proud to be part of this group! journals.asm.org/doi/10.1128/...
journals.asm.org
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 ...
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Gemma C. Atkinson @gemmaatkinson.bsky.social · 25/02/2025
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...
academic.oup.com
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
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Annika Barber @annikabarber.bsky.social · 24/02/2025
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...
docs.google.com
2025 Study section tracking
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Stacy Farina @stacyfarina.bsky.social · 03/06/2024
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.org
microPublication - Get Your Data Out, Be Cited
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Paul Hoskisson 🧫 🦠🐸 @paulhoskisson.bsky.social · 19/04/2024
This is very intriguing - Many purported pseudogenes in bacterial genomes are bona fide genes bmcgenomics.biomedcentral.com/articles/10....
bmcgenomics.biomedcentral.com
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 ...
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Zamin Iqbal @zaminiqbal.bsky.social · 18/03/2024
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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Britt Koskella @bkoskella.bsky.social · 19/03/2024
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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Will Matlock @wtmatlock.bsky.social · 14/03/2024
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 · 02/03/2024
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...
biorxiv.org
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
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bioRxiv Evolutionary Biology @biorxiv-evobio.bsky.social · 12/02/2024
How to validate a Bayesian evolutionary model www.biorxiv.org/content/10.1101/202…
biorxiv.org
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
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Tomer Ullman @tomerullman.bsky.social · 07/02/2024
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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Megan Phillips @meganphillips.bsky.social · 11/01/2024
Atlanta @meehubs.bsky.social participants, join us at 2:15pm in the main room for the ggtricks() workshop! Hone your ggplot and data manipulation R skills by exploring a dataset of Pokémon stats 📊 github.com/veganm/MEEHu...
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Danna Gifford @dannagifford.bsky.social · 02/11/2023
📣 Paper: We show that mutators can drive the evolution of multi-resistance to antibiotics, in cases where purely wild type populations can't This came out earlier this year while the other place was imploding But it's a story I'm proud of for many reasons... 1/n journals.plos.org/plosgenetics...
journals.plos.org
Mutators can drive the evolution of multi-resistance to antibiotics
Author summary The global rise in antimicrobial resistance means we urgently need new approaches that halt its spread. Combination therapy, using multiple antibiotics as one treatment, proposes to do ...
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🧬Jacob L Steenwyk @jlsteenwyk.bsky.social · 02/11/2023
#R Package Update: There are ~2x as many colorblind-friendly color palettes🎨 in ggpubfigs, which can help make your #figures📊 accessible to as many people as possible Link to GitHub: github.com/JLSteenwyk/g... Link to Publication: journals.asm.org/doi/10.1128/...
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Nina Molin Høyland-Kroghsbo @ninamolinhk.bsky.social · 31/10/2023
Happy halloween 🦠
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MEEhubs @meehubs.bsky.social · 26/09/2023
Join us for 3 days of amazing science - submit your abstract now to MEEhubs2024, our free (!) conference on microbial ecology and evolution (Jan 9-11 2024). Submission deadline extended to October 9th 2023! More info on www.meehubs.org
meehubs.org
OA Virtual conferences
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Mark Rubin @markrubin.bsky.social · 19/09/2023
Scientist? New to BlueSky? Here's a list of over 80 science-related feeds you might want to follow and contribute to! #AcademicSky #WomenInSTEM 🧪
docs.google.com
BlueSky Science-Related Feeds
Sheet1 Likes,Name (Click to visit feed),Tags,Contact to ask to be added to contributor list 2,<a href="https://bsky.app/profile/did:plc:ftnzzw4cnon2pzpw7i5m2xu7/feed/aaaiqnkwsgsz6">#AI&HCI</a>,#HCI, ...
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