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Amir Mitchell

@amitchell.bsky.social
695 followers 267 following 399 posts

Systems biologist trying to disentangle host-drug-microbiome interactions | PI at UMass medical school | hoping to keep the BS to a minimum (not always successful) mitchell-lab.umassmed.edu

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Amir Mitchell @amitchell.bsky.social · 28/09/2026
Congratulations, beautiful work!
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Reposted by Amir Mitchell
Hyun Youk @youklab.bsky.social · 24/09/2026
Trying Bluesky for the 1st time — a somewhat belated first post. A paper from my lab on how predictability can emerge over time in a non-chaotic deterministic system, and an Illinois Physics story about it: www.nature.com/articles/s41... physics.illinois.edu/news/hyun-yo...
nature.com
Predictability can be dynamically constructed in deterministic systems - Nature Communications
In a deterministic, non-chaotic system, the initial state fixes the future completely, yet that future may be impossible to forecast from it. Using a cellular automaton of communicating cells, this st...
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Amir Mitchell @amitchell.bsky.social · 25/08/2026
Doubt everything (the senior postdoc or detached PI told you) 🤯😱💯 journals.asm.org/doi/10.1128/...
journals.asm.org
As a component of aseptic technique, Bunsen burners do not universally decrease deposition of microbe-containing particles | Microbiology Spectrum
The ability to manipulate and control microbial presence in built environments is imperative to research and medicine. The lack of documented evidence relating Bunsen burner use and airborne contamination led us to conclude that this element of aseptic technique has until now been supported primarily by lore and tradition rather than experimental data. Given that laboratory open flame use has financial, temporal, and safety implications for research institutions across the globe, we sought to determine whether it is a worthwhile investment of resources. Ultimately, our data suggest that this practice is not evidence-based and that, except in a specific subset of circumstances, Bunsen burners can be removed from classroom and laboratory practice without compromising research integrity.
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Amir Mitchell @amitchell.bsky.social · 06/08/2026
Our recent mBio paper (3rd paper for @carmenli.bsky.social 🥂). We mapped evo resistance adaptations in 40 antibiotic + non-antibiotic drugs to evaluate the risk of multi-drug resistance (in vitro) ... we're now studying this in vivo (more to come). 🦠🧪 journals.asm.org/doi/10.1128/...
Genomic position of adaptive mutations identified in E. coli strains adapted against 40 antibiotic and non antibiotic drug in vitro. Repeated mutations in regulator of the acrA/B efflux pump are common to multi-drug resistant strains.
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Amir Mitchell @amitchell.bsky.social · 30/07/2026
Beautiful work (Petrungaro, Bollenbach lab) on evo trajectories toward abx resistance (E. coli). Goes beyond many other studies in its attention to the experimental setup (identical selective pressure across all lines). I strongly recommend reading the entire paper! www.nature.com/articles/s41...
nature.com
Function-specific epistasis shapes evolutionary trajectories towards antibiotic resistance - Nature Communications
Antibiotic resistance can evolve through the combination of factors but the predictability of this is unclear. Here, the authors used high-throughput evolution experiments to reveal that antibiotic re...
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Amir Mitchell @amitchell.bsky.social · 17/04/2026
Funding agencies should impose application funnels that maintain ~25% success rates (very low rates, with the same pool of money, are only seemingly kind to the applicants and are detrimental to collective productivity)
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Amir Mitchell @amitchell.bsky.social · 17/04/2026
IMO, the real cost of low success rates is not the time wasted on reviews but the time researchers collectively waste developing grant proposals that will not be funded. 1/2
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Amir Mitchell @amitchell.bsky.social · 17/03/2026
It's an important piece (provocative, yes, even triggering). It surfaces one the biggest challenges research universities will soon face. The current incentive model in (US) academia awards progress more than anything which only compounds the problem
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Amir Mitchell @amitchell.bsky.social · 13/03/2026
Absolutely, what can be more fitting 😉
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Amir Mitchell @amitchell.bsky.social · 04/03/2026
Our latest paper was just published. Will prepare a full thread very soon 🦠🧪🤖
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Amir Mitchell @amitchell.bsky.social · 13/02/2026
🎯
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Amir Mitchell @amitchell.bsky.social · 13/02/2026
I'm developing an #AI bot name HAL to assist with our research. Here's our first conversation with it over Slack (didn't tell the lab before deploying it) 😂
A screenshot of our first conversation with an AI bot over slack
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Amir Mitchell @amitchell.bsky.social · 10/02/2026
I tip my hat at the authors putting in all the efforts for these follow-up experiments
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Amir Mitchell @amitchell.bsky.social · 31/01/2026
Just concluded a 2-week coding spree with a student using VS+codex. The x5-10 gain in productivity blew my mind 🤯. BUT, I'm also sure that for inexperienced coders AI-coding makes garbage-in-gargbe-out pitfall inescapable.
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Amir Mitchell @amitchell.bsky.social · 19/01/2026
Beautiful “full arc” story on abx response with impressive level of mechanistic detail (could be a class example for undergrad microbiology lesson)
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Amir Mitchell @amitchell.bsky.social · 16/01/2026
Congrats on publishing this beautiful work! I'm still mind-blown that: (1) there's a 7th RND pump in E. coli and (2) that its somewhat unclear what it actually pumps out IRL
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Amir Mitchell @amitchell.bsky.social · 16/01/2026
It's a beautiful approach! But it's very disappointing that there is actually NO phenotypic characterization of the rearranged strains in the manuscript ... hoping it's an evolving manuscript that they'll keep updating
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Amir Mitchell @amitchell.bsky.social · 31/12/2025
Totally agree. Fail early, fail often (and aim high) is something more scientists need to live by.
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Amir Mitchell @amitchell.bsky.social · 22/12/2025
Huge credit to @carmenli.bsky.social for her persistence in chasing a moonlight project into its beautiful completion. Credit also goes Ethan Chang, the rotation student contributing to this work 9/9
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Amir Mitchell @amitchell.bsky.social · 22/12/2025
Btw, note that “inactivation” can mean more than enzymatic degradation and includes any process that reduces effective drug activity over time (chemical modification, sequestration, etc) 8/9
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Amir Mitchell @amitchell.bsky.social · 22/12/2025
We then tested if this assosiation holds through our entire dataset. We used a functional assay for drug inactivation on all drugs and found the association holds up. A long-lag inhibition phenotype is a strong indicator of drug inactivation 7/9
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Amir Mitchell @amitchell.bsky.social · 22/12/2025
That pushed us to ask whether cellular defenses might impact curve profiles. We cloned different resistance cassettes and measured how they altered the potency-matched growth curves. This strongly hinted that active drug inactivation underlies a long-lag inhibition profile 6/9
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Amir Mitchell @amitchell.bsky.social · 22/12/2025
Overlaying the known mechanisms of action over the barycentric landscape ruled out this effect stem exclusively from how drug target bacteria (since drugs with the same mechanism can land in very different regions of the landscape) 5/9
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Amir Mitchell @amitchell.bsky.social · 22/12/2025
Clustering drug by their impact on lag/rate/yield clearly revealed that they vary hugely in how they inhibited growth. In extreme cases, a drug solely affected only a single parameter 4/9
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Amir Mitchell @amitchell.bsky.social · 22/12/2025
To compare drugs fairly, we didn’t use an arbitrary concentration. Instead, we interpolated each drug to a potency-matched condition (the concentration expected to produce the same overall level of inhibition) 3/9
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Amir Mitchell @amitchell.bsky.social · 22/12/2025
So we assembled a new carefully curated dataset with growth curves across almost forty drugs, measured across multiple sub-inhibitory concentrations. For each curve, we quantified intuitive its key features: lag, growth rate, and yield 2/9
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Amir Mitchell @amitchell.bsky.social · 22/12/2025
Our recent paper in npj Antimicrobials and Resistance is a great example of scientific serendipity: after staring at thousands of bacterial growth curves over many studies, we started wondering whether the curve shapes themselves carry mechanistic information 1/9 🦠🧪 www.nature.com/articles/s44...
nature.com
Predicting drug inactivation by changes in bacterial growth dynamics - npj Antimicrobials and Resistance
npj Antimicrobials and Resistance - Predicting drug inactivation by changes in bacterial growth dynamics
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Amir Mitchell @amitchell.bsky.social · 17/12/2025
This was a true collaboration between physicists (Andrew Mugler and @motasemelgamel.bsky.social), an immunologist (Michael Brehm from @umasschan.bsky.social ), and systems biologists (with @serkansayin.bsky.social and Brittany Rosener from my lab also at @umasschan.bsky.social ) (7/7)
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Amir Mitchell @amitchell.bsky.social · 17/12/2025
Beyond providing (to our knowledge) the first dynamical model for tumor colonization, our study matters given the fierce debate on the tumor microbiome. These statistical “fingerprints” may help distinguish genuine colonizers from technical artifacts/contamination (possibly even by microscopy) (6/7)
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Amir Mitchell @amitchell.bsky.social · 17/12/2025
The surprise: lineage sizes formed a scale-free power law that matches Zipf’s law (rank–frequency slope ~−1). This signature was robust across dozens of tumors and multiple collection days post bacteria intratumor injection (5/7)
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Amir Mitchell @amitchell.bsky.social · 17/12/2025
When we injected bacteria directly into the tumor (circumventing the bottleneck), we detected thousands of colonizing lineages, yet their sizes were still highly uneven (ruling out early tumor arrivers dominate) (4/7)
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Amir Mitchell @amitchell.bsky.social · 17/12/2025
Since we used genetically barcoded bacteria, we could also monitor growth of individual colonizers. We found that growth was extremely uneven with a handful of lineages becoming dominant (“winner-takes-most”) (3/7)
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Amir Mitchell @amitchell.bsky.social · 17/12/2025
Main takeaways: Post systemic infection, there's a tight colonization bottleneck (per-cell colonization probability ~0.005%). Yet, once colonization happens, growth is remarkably fast (~50 min generation time) and bacterial load in tumors approaches saturation within a day (2/7)
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Amir Mitchell @amitchell.bsky.social · 17/12/2025
We just published in @molsystbiol.org with the Mugler lab (UPitt) on bacterial population dynamics during tumor colonization (mouse model). Our study was guided by a Luria–Delbrück-style idea: infer mechanism from statistics (1/7) 🧪🦠 doi.org/10.1038/s443...
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Amir Mitchell @amitchell.bsky.social · 31/05/2025
The (very real) cost of changing your research field. Absolutely true! But the freedom to pivot is one of the greatest things in this profession. www.nature.com/articles/s41...
nature.com
The pivot penalty in research - Nature
An analysis of millions of scientific papers and patents reveals a ‘pivot penalty’ when researchers shift direction, with the impact of studies decreasing rapidly the further they move from their prev...
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Amir Mitchell @amitchell.bsky.social · 22/05/2025
Great opportunity to participate in scientific outreach!
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Amir Mitchell @amitchell.bsky.social · 05/05/2025
Had a fantastic time with @markowenmartin.bsky.social’s on his #MattersMicrobial podcast (@microbetv.bsky.social). We discussed how to uncover the killing mechanisms of hundreds of antibacterials simultaneously and how #AI can transform the search for new antibiotics 🧪🦠💊 youtu.be/Wa0zd-TRCO8?...
youtu.be
Matters Microbial #89: Can AI Point Us to New Antibiotics
YouTube video by MicrobeTV
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Reposted by Amir Mitchell
Will Ratcliff @wcratcliff.bsky.social · 29/01/2025
Yo, micro/evo/qbio/physics of living systems/astrobiology/renegade cell bio folks- if you are interested in starting a feed, reply/repost this. Let's get the crew back together!
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Amir Mitchell @amitchell.bsky.social · 26/01/2025
Fascinating shift in the geography of drug development (excellent writing too!)
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Amir Mitchell @amitchell.bsky.social · 18/01/2025
The inherent stochasticity of biological systems 😉
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Amir Mitchell @amitchell.bsky.social · 17/01/2025
Interested in Antimicrobial Resistance & Quantitative Bio? Join a 3-day meeting+workshop with some of my favorite #AMR #QBio scientists this April (University of Exeter, UK). Register here: tinyurl.com/QAMR2025reg 🧪🦠
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Amir Mitchell @amitchell.bsky.social · 28/12/2024
Amazing book, shaped my worldview on Science. Kuhn’s genius was also in claiming that “paradigm shifts” are not purely logical, but are tainted by social & psychological factors. He claimed that established scientists are often conservatives resisting such shifts.
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Amir Mitchell @amitchell.bsky.social · 14/12/2024
It was all code written in Matlab
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Amir Mitchell @amitchell.bsky.social · 14/12/2024
Sure, email me I can attach a copy
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Amir Mitchell @amitchell.bsky.social · 14/12/2024
The drug-drug similarity networks are based on how these drugs impact a library of E. coli mutants (profiles of resistance or sensitivity). We in fact show the chemical similarity fails to capture many of these similarities.
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Amir Mitchell @amitchell.bsky.social · 14/12/2024
Beautiful detective work disentangling what is the actual trigger for cell death upon transcriptional arrest 🧪
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Amir Mitchell @amitchell.bsky.social · 09/12/2024
Never-have-I-ever seen technology racing forward as fast as #LMMs in the past two years. Watching the #openAI releases coming out in real-time in their twelves-days series is jaw dropping! 🤖🌊 www.youtube.com/playlist?lis...
youtube.com
12 Days of OpenAI - YouTube
12 days. 12 livestreams. A bunch of new things, big and small.
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Amir Mitchell @amitchell.bsky.social · 07/12/2024
My only complain is that I feel a bit like Cassandra, from the greek mythology, barely anyone listens 😞
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Amir Mitchell @amitchell.bsky.social · 07/12/2024
The ability of LMMs (chatGPT here) to *assist* in generating useful code for biologists a mind-blowing power multiplier 🤯! My advice to biologists at all career stages: Learn to code, its a superpower 🦸‍♀️🦹‍♂️ (simple example, counting fluorescent colonies isolated from mouse gut microbiome) 🧪🦠
Microscopy image of fluorescent colonies of E. coli after automatic image segmentation
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Amir Mitchell @amitchell.bsky.social · 04/12/2024
There is also a lot to be said about doing a "proper" postdoc in a good lab. It opens your eyes to different research directions, lab techniques, mentoring style, institutions, and so much more!
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