Megan Phillips
@meganphillips.bsky.social
Staph aureus evolution + genomics | PhD candidate @ Emory University | Population Biology, Ecology, & Evolution | 🧬💻🦠🍄 | Mastodon 🦣 @[email protected] | https://orcid.org/0000-0002-0781-3325
Reposted by Megan Phillips
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
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
September 29, 2025 at 6:45 PM
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
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
Reposted by Megan Phillips
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
September 16, 2025 at 3:34 AM
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
Reposted by Megan Phillips
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
Ie: it's not us (Samtools team)! Be warned
September 15, 2025 at 8:40 AM
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
Ie: it's not us (Samtools team)! Be warned
Reposted by Megan Phillips
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/reviewed-pre...
Host and antibiotic jointly select for greater virulence in Staphylococcus aureus
elifesciences.org
September 10, 2025 at 4:39 PM
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/reviewed-pre...
Reposted by Megan Phillips
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...
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
August 23, 2025 at 4:21 PM
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...
We analyzed data collected by the fantastic SEA-PHAGES program in phagesdb.org.
[1/6]
www.biorxiv.org/content/10.1...
Reposted by Megan Phillips
Reposted by Megan Phillips
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
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
August 18, 2025 at 9:48 PM
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
Read it to find out how population structure impacts pathogenicity in Aspergillus flavus, a fungus that infects humans 🧪
rdcu.be/eAToj
Reposted by Megan Phillips
A simple design framework that will massively improve your slides and your public speaking
clauswilke.substack.com/p/slides-tha...
clauswilke.substack.com/p/slides-tha...
Slide designs that present themselves: The assertion–evidence template
Your slides are not your talk.
clauswilke.substack.com
August 15, 2025 at 11:10 AM
A simple design framework that will massively improve your slides and your public speaking
clauswilke.substack.com/p/slides-tha...
clauswilke.substack.com/p/slides-tha...
Reposted by Megan Phillips
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-...
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-...
August 11, 2025 at 11:54 AM
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-...
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-...
Reposted by Megan Phillips
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/...
July 23, 2025 at 7:35 AM
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/...
Reposted by Megan Phillips
Looking forward to seeing everyone, new and old, at the Microbial Population Biology GRS + GRC in just a couple days!
go.bsky.app/GGxRjzC
go.bsky.app/GGxRjzC
July 3, 2025 at 8:25 PM
Looking forward to seeing everyone, new and old, at the Microbial Population Biology GRS + GRC in just a couple days!
go.bsky.app/GGxRjzC
go.bsky.app/GGxRjzC
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)
June 18, 2025 at 8:10 PM
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)
Reposted by Megan Phillips
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!
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!
May 29, 2025 at 2:50 PM
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!
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!
Reposted by Megan Phillips
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]
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]
May 1, 2025 at 6:41 PM
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]
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]
Reposted by Megan Phillips
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.
- 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.
March 20, 2025 at 8:52 PM
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.
- 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.
Reposted by Megan Phillips
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
March 19, 2025 at 1:34 PM
Proud to be part of this group! journals.asm.org/doi/10.1128/...
Reposted by Megan Phillips
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
February 25, 2025 at 7:27 AM
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...
Reposted by Megan Phillips
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
February 24, 2025 at 4:17 PM
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...
Reposted by Megan Phillips
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
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
June 3, 2024 at 8:05 PM
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
www.micropublication.org/journals/bio...
Short papers, one figure. And we peer review! Please RT
Reposted by Megan Phillips
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
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
April 19, 2024 at 4:03 PM
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
bmcgenomics.biomedcentral.com/articles/10....
Reposted by Megan Phillips
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...
www.biorxiv.org/content/10.1...
March 18, 2024 at 3:10 PM
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...
www.biorxiv.org/content/10.1...
Reposted by Megan Phillips
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!!
March 19, 2024 at 1:30 AM
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!!
Reposted by Megan Phillips
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...
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...
March 14, 2024 at 6:54 PM
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...
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...
Reposted by Megan Phillips
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...
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
March 2, 2024 at 7:53 PM
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...
www.biorxiv.org/content/10.1...
Reposted by Megan Phillips
How to validate a Bayesian evolutionary model https://www.biorxiv.org/content/10.1101/2024.02.11.579856v1
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
February 12, 2024 at 5:38 PM
How to validate a Bayesian evolutionary model https://www.biorxiv.org/content/10.1101/2024.02.11.579856v1