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Amir Mitchell

@amitchell.bsky.social
696 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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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 · 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
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 · 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
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 · 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 · 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
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 · 02/12/2024
Our second paper on the bacterial toxin colibactin is now out on mBio, this time we critically evaluated the claim that colibactin toxicity necessitates cell-cell contact 🧪🦠🧵(1/9) journals.asm.org/doi/10.1128/...
Cartoon of two bacteria on a petri dish
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Amir Mitchell @amitchell.bsky.social · 28/11/2024
Fantastic resource. Thanks for putting this together Georgia!
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Amir Mitchell @amitchell.bsky.social · 26/11/2024
Very sobering (yet great) thread on the changing landscape of sci publishing. IMO, not all is lost, the arc of justice bends long, but eventually in the right direction - some publishers/journals will tarnish their reputation beyond repair (just like mdpi did)
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Amir Mitchell @amitchell.bsky.social · 25/11/2024
Sorry for flooding your feed! I (automatically) migrated my X posts this weekend and those were showed as new posts here, including some very out-of-date irrelevant posts 🤦
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Amir Mitchell @amitchell.bsky.social · 22/10/2024
Can’t believe we unlocked this level of the #AI hype - huge adds for @AnthropicAI in airports (Boston & Atlanta). Wonder what % of ppl even know what’s the product (<0.1% probably)
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Amir Mitchell @amitchell.bsky.social · 23/09/2024
We found that the bacterial #toxin colibactin acts as a double-edged sword and inflicts self-damage (evident in hundreds of genomes). Our recent collaboration with @DaganLab is now out on @genomeresearch genome.cshlp.org/content/34/8/1154.…
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Amir Mitchell @amitchell.bsky.social · 03/09/2024
Immensely proud of the latest graduate from our lab @emily_lowry23⁩ 🎊🎉🥳⁦. Dr Lowry’s second paper will be published *very* soon … (and hopefully her third paper shortly after that 🤞)
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Amir Mitchell @amitchell.bsky.social · 30/08/2024
Very interesting @biorxiv_micrbio paper: @AnaRitaBrochad1 systematically mapped the interplay between extracellular chemical cues (~100), master regulators and downstream transport system in E. coli. Elegant and...
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Amir Mitchell @amitchell.bsky.social · 29/08/2024
What makes #phd s so hard & depressing (yet also so rewarding), a thread started by @ThePhDPlace made me reflect about my own experience and my students’ journeys. Hoping this self-reflection thread will be useful for students (and PIs too!) 1/9
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Amir Mitchell @amitchell.bsky.social · 07/08/2024
Results are in, mostly saying free (academic) labor is reasonable (seriously?🤦‍♂️). Going forward, I'll review 2 of every 3 such grants I'm asked about 🫡
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Amir Mitchell @amitchell.bsky.social · 31/07/2024
Need your take! Should scientists serve as *unpaid* reviewers on granting mechanisms that they are not eligible for (e.g, US scientists reviewing for a closed dutch grant system)?
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Amir Mitchell @amitchell.bsky.social · 28/06/2024
Signing off a very exciting week at the co-chair of the @GordonConf on Drug Resistance. Hard, yet totally worth it! Lots to share with chairs-to-be (thread on Monday)
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Amir Mitchell @amitchell.bsky.social · 26/06/2024
First time I'm attending a conf with 2/3 of my lab (@GordonConf / drug resistance). Strongly recommend PIs to do that, costly, *but* a really great bonding experience.
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Amir Mitchell @amitchell.bsky.social · 23/05/2024
A @bioRxiv 💎 (by Waldor lab): Inducible transposon mutagenesis circumvents the infection bottle-neck that *severely* limit functional genomic screens of bacteria within hosts (possibly a game changer for many labs): www.biorxiv.org/content/10.1101/202…
biorxiv.org
Inducible transposon mutagenesis for genome-scale forward...
Transposon insertion sequencing (Tn-seq) is a powerful me...
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Amir Mitchell @amitchell.bsky.social · 16/05/2024
Deadline for @GordonConf on Drug Resistance is fast approaching (5/26). Apply by 5/21 for posters and talks. We’ll greatly appreciate help spreading the word 🙏🏼 www.grc.org/drug-resistance-confere…
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Amir Mitchell @amitchell.bsky.social · 12/05/2024
Congrats @asanchez_lab for really elegant work! Assembling *all* possible permutations of N microbes (with a multi-pipette) and evaluate their performance (they explore N=8, P. aeruginosa). www.biorxiv.org/content/10.1101/202…
biorxiv.org
Full factorial construction of synthetic microbial commun...
Constructing combinatorially complete species assemblages...
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Amir Mitchell @amitchell.bsky.social · 29/03/2024
Just covered this paper in our journal club. Beautiful work by Erdal Topeka’s lab (@UTSWNews) on bacterial adaptation to antibiotics in mice GI tract (without evolving resistance) www.cell.com/cell-host-microbe/full…
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Amir Mitchell @amitchell.bsky.social · 14/03/2024
Why are some non-antibiotic drugs toxic to bacteria 💊☠️🦠? Do they work like standard #antibiotics (ABX)? Our latest work by @MarianaNoto published @ScienceMagazine addresses this fundamental question (1/n) www.science.org/doi/10.1126/science…
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Amir Mitchell @amitchell.bsky.social · 11/03/2024
(potentially) an unpopular opinion, scientific publishers need to *embrace* #LLMs (e.g., @ChatGPTapp) rather than try to curb their wide adoption. One area already ripe for an LLM revolution is scientific literature reviews.
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Amir Mitchell @amitchell.bsky.social · 28/02/2024
Hard to admit, but being a PI is not everything I hoped it would be … I’m sure this might resonate with other PIs out there
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Amir Mitchell @amitchell.bsky.social · 12/02/2024
I keep on preaching to my lab about the usefulness @ChatGPTapp for coding, but real-life demos might be more effective. A thread on a neural network we quickly developed to classify antibiotics sensitivity 🧵 (1/10)
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Amir Mitchell @amitchell.bsky.social · 20/09/2023
Systems and synthetic biologists, we are recruiting at the department of Systems Biology at the @UMassChan. Position is open to faculty at all levels. academicjobsonline.org/ajo/jobs/254…
academicjobsonline.org
University of Massachusetts Chan Medical School, Departme...
Full service online faculty recruitment and application m...
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Amir Mitchell @amitchell.bsky.social · 09/09/2023
The mundane beauty of the simplest experiments always gets me (bacteria enjoying nutrient-rich medium). Credit to Carmen Li from our lab. #MundaneLabBeauty
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Amir Mitchell @amitchell.bsky.social · 19/05/2023
Even more remarkable than #ChatGPT, is the bustling ecology of *paid* services already thrive on top of it. Did you know there are market places for buying/selling #AI prompts …
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Amir Mitchell @amitchell.bsky.social · 01/05/2023
That was a tough one. There were ~2,500 colonies, most humans and machines considerably underestimated. Follow the thread for details and anecdotes ... 🧵
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Amir Mitchell @amitchell.bsky.social · 29/04/2023
Biologists, #AI is out for your jobs. Fantastic talk by Jim Collins on drug discovery opens @HarvardMSI’s #MSIsymposium. Related anecdote, I realized I used #chatGPT every day this week for work
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Amir Mitchell @amitchell.bsky.social · 28/04/2023
So you (still) consider yourself a (micro)biologist. Another #FridayLabChallenge In 10sec, eyeball the colony number 🧵
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Amir Mitchell @amitchell.bsky.social · 24/04/2023
Following my #FridayLabChallange by analyzing your tweet replies 🙋🏻‍♀️🙋🏽🙋🏿‍♂️. Results first (I’ll tweet later and explain how I scraped the results. Hint, #chatGTP was my co-pilot)
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Amir Mitchell @amitchell.bsky.social · 21/04/2023
So you call yourself a microbiologist … quick Friday challenge (with surprising results). In 10sec, eyeball the colony number 🧵🧵🧵
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Amir Mitchell @amitchell.bsky.social · 16/03/2023
Useful data for those working with the confetti strains that @ATinyGreenCell cloned and shared with us and many other (collected by @MarianaNoto) 🧵.
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Amir Mitchell @amitchell.bsky.social · 08/02/2023
Just attended a session for future @GordonConf chairs and realized the remarkable scale of this enterprise: ~400 meetings/seminars per year. 400!! Will do my best to contribute with co-chair @Alexisns to this endeavor!
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Amir Mitchell @amitchell.bsky.social · 09/12/2022
Enjoying the seminar live-streamed from Qatar
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Amir Mitchell @amitchell.bsky.social · 26/11/2022
Interesting analysis of ⁦@NIH⁩ funding data. Falling just below funding threshold predicts better publishing success than just above the threshold (perseverance pays off) www.nature.com/articles/s41467-019-…
nature.com
Early-career setback and future career impact - Nature Co...
Little is known about the long-term effects of early-care...
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