Allison Lopatkin, PhD

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

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!

AI slop and the destruction of knowledge This week I was looking for info on what cognitive scientists mean when they speak of ‘domain-general’ cognition. I was curious, because the nuances are relevant for something I am researching at t…

AI slop and the destruction of knowledge irisvanrooijcogsci.com/2025/08/12/a...

How sad. Losing public trust in mRNA vaccines should spark massive education efforts to rebuild understanding - not abandonment of genuinely good technology.

Of course! I should have said recent and in areas with high antibiotic likelihood (ie hospital or student wastewater in some cases)

Plasmid prevalence is independent of antibiotic resistance in environmental Enterobacteriaceae The rapid rise of antibiotic-resistant pathogens poses a critical threat to the treatment of infectious diseases. While the spread of antibiotic resistance genes (ARGs) via plasmid conjugation has bee...

If you ever find yourself needing evidence for ‘Plasmids are just as common in microbes without resistance genes,’ we’ve got you covered! Check our new paper, out today:

www.microbiologyresearch.org/content/jour...

Why does ppt always refuse to let me draw a straight line at the times I need it most 😞

First official Master from the lab 🥰 congrats Yuchang!!!!

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...

🚨🚨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...

Very excited for my first microbial population biology GRC!!

Experimental evolution of evolvability Evolvability—the capacity to generate adaptive variation—is a trait that can itself evolve through natural selection. However, the idea that mutation can become biased toward adaptive outcomes remains...

Experimental evolution of evolvability | Science www.science.org/doi/10.1126/...

The role of bacterial metabolism in antimicrobial resistance Nature Reviews Microbiology - In this Review, Ahmad et al. examine how antibiotics influence bacterial metabolism and how metabolism, in turn, affects drug efficacy and the emergence and evolution...

New review out in @NatureRevMicro on the complex rltnshp btween metabolism & AMR! A true labor of love from previous postbac Mehrose, grad students Varun & Zirui, and collaborator @drrobsmith.bsky.social (plus figures I'll likely use for many talks to come 😊) rdcu.be/eaES2

It’s official. Twitter is (mostly) a cesspool of bots.

Great idea 🙏🏻

Favorite 3D printer cad software for the lab?

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...

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...

Incredible graphic - the myriad of ways that bacteria defend themselves against antibiotics.

14 resistance mechanisms, summarised by Idan Yelin & Roy Kishony in Cell

www.sciencedirect.com/science/arti...

Can someone please standardize graduate school recommendation letter submission portals so I don’t need to make 5 different accounts and give slightly different answers to very similar questions

Please add me 😊🙏🏻

We should’ve moved here years ago

Please consider attending the 2025 ASM Microbe meeting! I will be talking about Tn7 and Tn7-like elements as a "Track Hub" talk and it would be great to see you there! asm.org/events/asm-m...

Mobile Elements Starter Pack on BlueSky!

Interested in plasmids, phages, ICEs, transposons, integrons, and all things accessory genome? Follow this curated list of researchers and labs doing exciting work in mobile elements.

elmo from sesame street is surrounded by flames ALT: elmo from sesame street is surrounded by flames

Thank you for the continued support of my lab through purchasing my rainbow plasmids! Just paid for primers to isolate a putative blue gene from our #BlueSoup microbe. Excited to get some cloning done with @bielleogy.bsky.social If anyone wants 🌈🦠, fresh stabs at atinygreencell.com

And here I was about to ask again since I forgot I already asked once 😂😅😭 still getting the hang of this app 😁 thank you!!!

Thank you!! I hope you enjoy 😊

On our website here!! lopatkinlab.com/assets/PDFs/...

Directed evolution of engineered virus-like particles with improved production and transduction efficiencies https://www.nature.com/articles/s41587-024-02467-x 🧬🖥️🧪

Please add me! 🙏🏻😊

Addgene reposting our review feels like a real milestone for me in a very nerdy niche way 😅😊

The metabolic burden associated with plasmid acquisition: An assessment of the unrecognized benefits to host cells The environment bacteria are in dictates whether carrying a plasmid is ultimately a benefit or a burden. On the left, environment A shows one condition that made bearing this plasmid beneficial, wher...

Plasmids are commonly viewed as burdensome. But maybe this burden can be advantageous? Check out this new review paper from the lab that investigates this further!!

onlinelibrary.wiley.com/doi/10.1002/...

Agreed and also: For a PhD student, choosing a good lab also matters more than the school name 🫣