Want to explore host-plasmid and plasmid-plasmid distributions in your dataset? Or any tree with a set of binary traits?
I’ve made a CLI for our model here:
github.com/wtmatlock/pl...
I’ve made a CLI for our model here:
github.com/wtmatlock/pl...
September 22, 2026 at 5:01 PM
Want to explore host-plasmid and plasmid-plasmid distributions in your dataset? Or any tree with a set of binary traits?
I’ve made a CLI for our model here:
github.com/wtmatlock/pl...
I’ve made a CLI for our model here:
github.com/wtmatlock/pl...
Doing the periodic cleaning of used plasmid miniprep columns and realized in honor of Earth Day it may be worth reminding you molecular biologists:
Plasmid miniprep columns can be cleaned and reused essentially indefinitely! Just add 1 M HCl, soak overnight and wash 3x w/ water. Save $ and plastic
Plasmid miniprep columns can be cleaned and reused essentially indefinitely! Just add 1 M HCl, soak overnight and wash 3x w/ water. Save $ and plastic
April 22, 2026 at 9:34 PM
Doing the periodic cleaning of used plasmid miniprep columns and realized in honor of Earth Day it may be worth reminding you molecular biologists:
Plasmid miniprep columns can be cleaned and reused essentially indefinitely! Just add 1 M HCl, soak overnight and wash 3x w/ water. Save $ and plastic
Plasmid miniprep columns can be cleaned and reused essentially indefinitely! Just add 1 M HCl, soak overnight and wash 3x w/ water. Save $ and plastic
I’m delighted to share our new pre-print:
Make it so: Rapid and affordable plasmid sequencing on ONT platforms with PICARD-seq
www.biorxiv.org/content/10.6...
I wanted to use a MinION to sequence my large repetitive plasmids in-house. Luckily @jwdebler.bsky.social was willing to help.
1/14
Make it so: Rapid and affordable plasmid sequencing on ONT platforms with PICARD-seq
www.biorxiv.org/content/10.6...
I wanted to use a MinION to sequence my large repetitive plasmids in-house. Luckily @jwdebler.bsky.social was willing to help.
1/14
Make it so: Rapid and affordable plasmid sequencing on ONT platforms with PICARD-seq
Plasmid construction underpins molecular biology and synthetic biology, yet validation is often limited to the inserted fragment rather than the whole plasmid, and around a third of laboratory-made pl...
www.biorxiv.org
September 25, 2026 at 2:12 AM
I’m delighted to share our new pre-print:
Make it so: Rapid and affordable plasmid sequencing on ONT platforms with PICARD-seq
www.biorxiv.org/content/10.6...
I wanted to use a MinION to sequence my large repetitive plasmids in-house. Luckily @jwdebler.bsky.social was willing to help.
1/14
Make it so: Rapid and affordable plasmid sequencing on ONT platforms with PICARD-seq
www.biorxiv.org/content/10.6...
I wanted to use a MinION to sequence my large repetitive plasmids in-house. Luckily @jwdebler.bsky.social was willing to help.
1/14
Plasmid-gate: Debunking the DNA contamination claims in mRNA vaccines.
www.globalvaccinedatanetwork.org/news/plasmid...
www.globalvaccinedatanetwork.org/news/plasmid...
Plasmid-gate: Debunking the DNA contamination claims in mRNA vaccines | Global Vaccine Data Network
In recent months, the internet has buzzed with a conspiracy theory dubbed "Plasmid-gate." The claim? COVID-19 mRNA vaccines are "contaminated" with residual DNA, which could integrate into human DNA a...
www.globalvaccinedatanetwork.org
November 28, 2024 at 7:01 AM
Plasmid-gate: Debunking the DNA contamination claims in mRNA vaccines.
www.globalvaccinedatanetwork.org/news/plasmid...
www.globalvaccinedatanetwork.org/news/plasmid...
www.nature.com/articles/s41...
New paper out!!
New paper out!!
A plasmid-chromosome crosstalk in multidrug resistant enterobacteria - Nature Communications
The authors describe a new crosstalk between a globally disseminated carbapenem resistance plasmid and clinical enterobacteria clones. This crosstalk provides a fitness advantage to the plasmid-carryi...
www.nature.com
December 30, 2024 at 6:33 PM
www.nature.com/articles/s41...
New paper out!!
New paper out!!
Curious about plasmid biology? Our latest paper is out now in Nature Communications! 🚨
doi.org/10.1038/s414...
We analyzed thousands of diverse bacterial plasmids to shed light for the first time on a key aspect of plasmid biology: plasmid copy number. 1/7 👇
doi.org/10.1038/s414...
We analyzed thousands of diverse bacterial plasmids to shed light for the first time on a key aspect of plasmid biology: plasmid copy number. 1/7 👇
Universal rules govern plasmid copy number - Nature Communications
Plasmids exhibit a broad range of sizes and copies per cell, and these two parameters appear to be negatively correlated. Here, Ramiro-Martínez et al. analyse the copy number of thousands of diverse b...
doi.org
July 2, 2025 at 10:07 AM
Curious about plasmid biology? Our latest paper is out now in Nature Communications! 🚨
doi.org/10.1038/s414...
We analyzed thousands of diverse bacterial plasmids to shed light for the first time on a key aspect of plasmid biology: plasmid copy number. 1/7 👇
doi.org/10.1038/s414...
We analyzed thousands of diverse bacterial plasmids to shed light for the first time on a key aspect of plasmid biology: plasmid copy number. 1/7 👇
A huge, new resource for plasmid research - PlasmidScope is a database of 852,000 #plasmid sequences with a rich set of annotations, automated online analysis and interactive visualisation academic.oup.com/nar/article/...
PlasmidScope: a comprehensive plasmid database with rich annotations and online analytical tools
Abstract. Plasmids are extrachromosomal genetic molecules that replicate independent of chromosomes in bacteria, archaea, and eukaryotic organisms. They co
academic.oup.com
April 22, 2025 at 5:00 AM
A huge, new resource for plasmid research - PlasmidScope is a database of 852,000 #plasmid sequences with a rich set of annotations, automated online analysis and interactive visualisation academic.oup.com/nar/article/...
Here hold this for me
April 1, 2026 at 10:56 PM
Here hold this for me
🚨🚨New paper out in @natcomms.nature.com!!
Come for the first large-scale analysis of plasmid copy number across species,
stay for one of the most intriguing results of my lab: universal scaling laws in plasmid biology! 📈🧬
👉 www.nature.com/articles/s41...
Come for the first large-scale analysis of plasmid copy number across species,
stay for one of the most intriguing results of my lab: universal scaling laws in plasmid biology! 📈🧬
👉 www.nature.com/articles/s41...
Universal rules govern plasmid copy number - Nature Communications
Plasmids exhibit a broad range of sizes and copies per cell, and these two parameters appear to be negatively correlated. Here, Ramiro-Martínez et al. analyse the copy number of thousands of diverse b...
www.nature.com
July 2, 2025 at 11:08 AM
🚨🚨New paper out in @natcomms.nature.com!!
Come for the first large-scale analysis of plasmid copy number across species,
stay for one of the most intriguing results of my lab: universal scaling laws in plasmid biology! 📈🧬
👉 www.nature.com/articles/s41...
Come for the first large-scale analysis of plasmid copy number across species,
stay for one of the most intriguing results of my lab: universal scaling laws in plasmid biology! 📈🧬
👉 www.nature.com/articles/s41...
It works! Cut with EcoR1 for 1hr. Gel order is:
Ladder (NEB 1KB Plus)
Cut p100bp Plasmid
Uncut p100bp Plasmid
Ladder (NEB 1KB Plus)
Cut p100bp Plasmid
Uncut p100bp Plasmid
July 2, 2025 at 7:16 PM
It works! Cut with EcoR1 for 1hr. Gel order is:
Ladder (NEB 1KB Plus)
Cut p100bp Plasmid
Uncut p100bp Plasmid
Ladder (NEB 1KB Plus)
Cut p100bp Plasmid
Uncut p100bp Plasmid
I’ve started my SNSF Ambizione Group Leader position at the University of Zurich 🧬
We will study plasmid evolution, plasmid interactions, and CRISPR-Cas systems to better understand antibiotic resistance spread.
Very grateful to everyone who supported me along the way.
We will study plasmid evolution, plasmid interactions, and CRISPR-Cas systems to better understand antibiotic resistance spread.
Very grateful to everyone who supported me along the way.
May 12, 2026 at 8:33 AM
I’ve started my SNSF Ambizione Group Leader position at the University of Zurich 🧬
We will study plasmid evolution, plasmid interactions, and CRISPR-Cas systems to better understand antibiotic resistance spread.
Very grateful to everyone who supported me along the way.
We will study plasmid evolution, plasmid interactions, and CRISPR-Cas systems to better understand antibiotic resistance spread.
Very grateful to everyone who supported me along the way.
Accurate plasmid reconstruction from metagenomics data using assembly–alignment graphs and contrastive learning www.nature.com/articles/s41... #jcampubs
Accurate plasmid reconstruction from metagenomics data using assembly–alignment graphs and contrastive learning - Nature Biotechnology
PlasMAAG uses cross-sample information to improve plasmid reconstruction from metagenomic samples.
www.nature.com
February 4, 2026 at 8:20 PM
Accurate plasmid reconstruction from metagenomics data using assembly–alignment graphs and contrastive learning www.nature.com/articles/s41... #jcampubs
New paper out in PNAS!!! 🎉
Do more plasmid copies mean faster evolution?
🧵 Dive into the story
www.pnas.org/doi/10.1073/...
Do more plasmid copies mean faster evolution?
🧵 Dive into the story
www.pnas.org/doi/10.1073/...
Plasmid mutation rates scale with copy number | PNAS
Plasmids are extrachromosomal DNA molecules that spread by horizontal transfer and
shape bacterial evolution. Plasmids are typically present at mul...
www.pnas.org
January 27, 2026 at 12:02 PM
New paper out in PNAS!!! 🎉
Do more plasmid copies mean faster evolution?
🧵 Dive into the story
www.pnas.org/doi/10.1073/...
Do more plasmid copies mean faster evolution?
🧵 Dive into the story
www.pnas.org/doi/10.1073/...
FUTURE. EPISODE.
August 1, 2026 at 10:45 AM
FUTURE. EPISODE.
🆕Read my short perspective on @daganlab.bsky.social's intriguing @currentbiology.bsky.social paper that examined plasmid-mediated gene mobilisation by comparing plasmid cargoes with chromosomal sequences across almost 2000 isolates, now in Trends in Microbiology 💻💫🧬 #MicroSky
Loading and unloading plasmid cargoes
Plasmids are vehicles for horizontal gene transfer between cells, but they also exchange
genes with associated chromosomes in a process termed 'intracellular mobility'. I
discuss a recent article by K...
www.cell.com
December 3, 2024 at 10:30 PM
🆕Read my short perspective on @daganlab.bsky.social's intriguing @currentbiology.bsky.social paper that examined plasmid-mediated gene mobilisation by comparing plasmid cargoes with chromosomal sequences across almost 2000 isolates, now in Trends in Microbiology 💻💫🧬 #MicroSky
Very happy to see this work published! We unveil a plasmid-chromosome crosstalk by showing that pOXA-48 encodes for a regulator that mediates the transcription of an enterobacterial chromosomal operon, resulting in a growth benefit for the plasmid-carrying bacteria!
www.nature.com/articles/s41...
www.nature.com/articles/s41...
A plasmid-chromosome crosstalk in multidrug resistant enterobacteria - Nature Communications
The authors describe a new crosstalk between a globally disseminated carbapenem resistance plasmid and clinical enterobacteria clones. This crosstalk provides a fitness advantage to the plasmid-carryi...
www.nature.com
January 2, 2025 at 11:20 AM
Very happy to see this work published! We unveil a plasmid-chromosome crosstalk by showing that pOXA-48 encodes for a regulator that mediates the transcription of an enterobacterial chromosomal operon, resulting in a growth benefit for the plasmid-carrying bacteria!
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Beautiful work - isolation of a crassphage, and turns out it is a phage-plasmid!
March 21, 2024 at 3:50 AM
Beautiful work - isolation of a crassphage, and turns out it is a phage-plasmid!
Remembering my character Dwerp today from our last DnD campaign. What a fun little fella he was to play.
November 30, 2025 at 3:47 PM
Remembering my character Dwerp today from our last DnD campaign. What a fun little fella he was to play.
New pre-print: Plasmid dependent phage effectively eliminate AMR bacteria and block plasmid transmission in the chicken gut microbiome
Fun collaboration with Tao He lab (JAAS) and @brockhurstlab.bsky.social lab (Manchester)
#phagesky#microsky
www.biorxiv.org/content/10.1...
Fun collaboration with Tao He lab (JAAS) and @brockhurstlab.bsky.social lab (Manchester)
#phagesky#microsky
www.biorxiv.org/content/10.1...
Plasmid dependent phage eliminate pathogenic bacteria and antibiotic resistance plasmids from the chicken gut microbiome
Conjugative plasmids are a key reservoir of antimicrobial resistance (AMR) in commensal and pathogenic bacteria within the gut microbiome. Plasmid-dependent phage (PDPs) are a promising therapeutic op...
www.biorxiv.org
October 27, 2025 at 8:19 AM
New pre-print: Plasmid dependent phage effectively eliminate AMR bacteria and block plasmid transmission in the chicken gut microbiome
Fun collaboration with Tao He lab (JAAS) and @brockhurstlab.bsky.social lab (Manchester)
#phagesky#microsky
www.biorxiv.org/content/10.1...
Fun collaboration with Tao He lab (JAAS) and @brockhurstlab.bsky.social lab (Manchester)
#phagesky#microsky
www.biorxiv.org/content/10.1...
Plasmid-encoded host reprogramming promotes plasmid dissemination https://www.biorxiv.org/content/10.64898/2026.07.07.736705v1
July 8, 2026 at 7:16 AM
Plasmid-encoded host reprogramming promotes plasmid dissemination https://www.biorxiv.org/content/10.64898/2026.07.07.736705v1
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 👇
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 👇
May 12, 2025 at 5:11 AM
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 👇
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 👇
New pre-print www.biorxiv.org/content/10.1...
Plasmid-dependent phage (PDPs) are ubiquitous, but the selective pressures that they impose on plasmids are not well understood. Project led by Daniel Cazares in collaboration with @brockhurstlab.bsky.social!
#phagesky#microsky
Plasmid-dependent phage (PDPs) are ubiquitous, but the selective pressures that they impose on plasmids are not well understood. Project led by Daniel Cazares in collaboration with @brockhurstlab.bsky.social!
#phagesky#microsky
Trade-offs between phage resistance and conjugative ability shape the ecological and evolutionary response of a multidrug resistance plasmid to plasmid-dependent phage
Phage therapy is a promising alternative to antibiotics to treat multidrug resistant infections. Plasmid dependent phages (PDPs) are particularly attractive as therapeutics because they can both kill ...
www.biorxiv.org
October 9, 2025 at 10:07 AM
New pre-print www.biorxiv.org/content/10.1...
Plasmid-dependent phage (PDPs) are ubiquitous, but the selective pressures that they impose on plasmids are not well understood. Project led by Daniel Cazares in collaboration with @brockhurstlab.bsky.social!
#phagesky#microsky
Plasmid-dependent phage (PDPs) are ubiquitous, but the selective pressures that they impose on plasmids are not well understood. Project led by Daniel Cazares in collaboration with @brockhurstlab.bsky.social!
#phagesky#microsky