Allison Lopatkin, PhD
@ajlopatkin.bsky.social
Assistant prof at University of Rochester engineering genetic communication in microbial populations. Mountain enthusiast, passionate teacher
Reposted by Allison Lopatkin, PhD
AI slop and the destruction of knowledge irisvanrooijcogsci.com/2025/08/12/a...
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…
irisvanrooijcogsci.com
August 12, 2025 at 10:12 PM
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.
Jay Bhattacharya, the NIH Director, thinks that if science isn’t popular it should be abandoned.
“No matter how elegant the science, a platform that lacks credibility among the people it seeks to protect cannot fulfill its public health mission”.
He is unfit for his job in every imaginable way.
“No matter how elegant the science, a platform that lacks credibility among the people it seeks to protect cannot fulfill its public health mission”.
He is unfit for his job in every imaginable way.
August 14, 2025 at 9:50 AM
How sad. Losing public trust in mRNA vaccines should spark massive education efforts to rebuild understanding - not abandonment of genuinely good technology.
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...
www.microbiologyresearch.org/content/jour...
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...
www.microbiologyresearch.org
August 12, 2025 at 5:14 PM
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...
www.microbiologyresearch.org/content/jour...
Why does ppt always refuse to let me draw a straight line at the times I need it most 😞
August 8, 2025 at 8:25 PM
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!!!!
July 23, 2025 at 2:14 AM
First official Master from the lab 🥰 congrats Yuchang!!!!
Reposted by Allison Lopatkin, PhD
🚨🚨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...
Very excited for my first microbial population biology GRC!!
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 4, 2025 at 10:23 AM
Very excited for my first microbial population biology GRC!!
Reposted by Allison Lopatkin, PhD
Experimental evolution of evolvability | Science www.science.org/doi/10.1126/...
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...
www.science.org
February 20, 2025 at 9:16 PM
Experimental evolution of evolvability | Science www.science.org/doi/10.1126/...
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
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...
rdcu.be
February 20, 2025 at 10:37 PM
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.
January 30, 2025 at 2:57 AM
It’s official. Twitter is (mostly) a cesspool of bots.
Favorite 3D printer cad software for the lab?
January 4, 2025 at 10:34 PM
Favorite 3D printer cad software for the lab?
Reposted by Allison Lopatkin, PhD
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...
Reposted by Allison Lopatkin, PhD
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...
14 resistance mechanisms, summarised by Idan Yelin & Roy Kishony in Cell
www.sciencedirect.com/science/arti...
November 13, 2024 at 12:46 PM
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...
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
November 21, 2024 at 9:37 PM
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
We should’ve moved here years ago
November 18, 2024 at 10:31 AM
We should’ve moved here years ago
Reposted by Allison Lopatkin, PhD
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...
ASM Microbe | Abstracts
ASM Microbe 2025 showcases the best microbial sciences in the world and provides a one-of-a-kind forum to explore everything from basic microbiology to translation and application.
asm.org
November 16, 2024 at 5:03 PM
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...
Reposted by Allison Lopatkin, PhD
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.
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.
November 10, 2024 at 8:45 AM
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.
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.
Reposted by Allison Lopatkin, PhD
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
elmo from sesame street is surrounded by flames
ALT: elmo from sesame street is surrounded by flames
media.tenor.com
November 16, 2024 at 1:35 AM
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
Reposted by Allison Lopatkin, PhD
Directed evolution of engineered virus-like particles with improved production and transduction efficiencies https://www.nature.com/articles/s41587-024-02467-x 🧬🖥️🧪
November 14, 2024 at 9:45 AM
Directed evolution of engineered virus-like particles with improved production and transduction efficiencies https://www.nature.com/articles/s41587-024-02467-x 🧬🖥️🧪
Addgene reposting our review feels like a real milestone for me in a very nerdy niche way 😅😊
We certainly think the burden of plasmids is ADDvantageous!
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/...
onlinelibrary.wiley.com/doi/10.1002/...
November 12, 2024 at 11:25 PM
Addgene reposting our review feels like a real milestone for me in a very nerdy niche way 😅😊
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/...
onlinelibrary.wiley.com/doi/10.1002/...
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...
onlinelibrary.wiley.com
November 12, 2024 at 6:19 PM
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/...
onlinelibrary.wiley.com/doi/10.1002/...
Agreed and also: For a PhD student, choosing a good lab also matters more than the school name 🫣
For a PhD student, choosing a good lab is 10 times more important than choosing a particular topic to study
November 12, 2024 at 11:36 AM
Agreed and also: For a PhD student, choosing a good lab also matters more than the school name 🫣
Any starter packs on syn bio (for bacteria) on here per chance?
November 12, 2024 at 1:00 AM
Any starter packs on syn bio (for bacteria) on here per chance?
Plus side of the impending AI overlord takeover - you no longer have to manually collect google scholar citations.
Our amazing masters student Abhishek created a bot to do it for you!
We're using it for an ongoing project and you should too:
github.com/ajlopatkin/G...
Our amazing masters student Abhishek created a bot to do it for you!
We're using it for an ongoing project and you should too:
github.com/ajlopatkin/G...
November 30, 2023 at 12:42 AM
Plus side of the impending AI overlord takeover - you no longer have to manually collect google scholar citations.
Our amazing masters student Abhishek created a bot to do it for you!
We're using it for an ongoing project and you should too:
github.com/ajlopatkin/G...
Our amazing masters student Abhishek created a bot to do it for you!
We're using it for an ongoing project and you should too:
github.com/ajlopatkin/G...
I check this app once every ~6 days when I remember and each time I remind myself to start using it more regularly
October 19, 2023 at 1:08 AM
I check this app once every ~6 days when I remember and each time I remind myself to start using it more regularly