Amir Mitchell
@amitchell.bsky.social
Systems biologist trying to disentangle host-drug-microbiome interactions | PI at UMass medical school | trying to keep the BS to a minimum (not always successful)
https://mitchell-lab.umassmed.edu
https://mitchell-lab.umassmed.edu
Pinned
Amir Mitchell
@amitchell.bsky.social
· Nov 23
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)
https://www.science.org/doi/10.1126/science.adk7368
https://www.science.org/doi/10.1126/science.adk7368
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...
www.nature.com/articles/s41...
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...
www.nature.com
May 31, 2025 at 1:37 PM
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...
www.nature.com/articles/s41...
Great opportunity to participate in scientific outreach!
Starting to write to folks to consider appear on my #MattersMicrobial podcast. Would love an astrobiologist! Looking for other cool and #OMG #WTM microbial enthusiasts to appear. Happy to hear suggestions. I need to fill July and August.
May 22, 2025 at 6:05 PM
Great opportunity to participate in scientific outreach!
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/Wa0zd-TRCO8?...
Matters Microbial #89: Can AI Point Us to New Antibiotics
YouTube video by MicrobeTV
youtu.be
May 5, 2025 at 4:47 PM
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/Wa0zd-TRCO8?...
Reposted by Amir Mitchell
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!
Would anyone be interested in starting a microbial evolution feed on here? EvoSky is rather organismal, which is great, but would love to see experimental evo folks' feeds too. Thoughts?
January 29, 2025 at 11:40 PM
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!
Fascinating shift in the geography of drug development (excellent writing too!)
If you haven't read this article yet, you should! Link here: atelfo.github.io/2024/12/20/...
I think Alex should write more because he's really, really great at it.
I think Alex should write more because he's really, really great at it.
Will all our drugs come from China?
Personal site for posts about my interests: the biotech industry, medicine, molecular biology, neuroscience, biorisk, science, consciousness, AI, innovation, decision making, philosophy, games, sci-fi, probability, and forecasting (among other things). I write to learn, mostly about biotech.
atelfo.github.io
January 26, 2025 at 3:29 AM
Fascinating shift in the geography of drug development (excellent writing too!)
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 🧪🦠
January 17, 2025 at 3:16 PM
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 🧪🦠
Beautiful detective work disentangling what is the actual trigger for cell death upon transcriptional arrest 🧪
We just posted a preprint about a death mechanism that we find truly surprising.
When you turn off transcription, cells die (duh!)... but did you know this happens due to loss of Pol II itself, not loss of Pol II activity!?!
preprint here and a thread (1/n): www.biorxiv.org/content/10.1...
🧪
When you turn off transcription, cells die (duh!)... but did you know this happens due to loss of Pol II itself, not loss of Pol II activity!?!
preprint here and a thread (1/n): www.biorxiv.org/content/10.1...
🧪
Pol II degradation activates cell death independently from the loss of transcription
Pol II-mediated transcription is essential for eukaryotic life. While loss of transcription is thought to be universally lethal, the associated mechanisms promoting cell death are not yet known. Here,...
www.biorxiv.org
December 14, 2024 at 3:09 PM
Beautiful detective work disentangling what is the actual trigger for cell death upon transcriptional arrest 🧪
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...
www.youtube.com/playlist?lis...
12 Days of OpenAI - YouTube
12 days. 12 livestreams. A bunch of new things, big and small.
www.youtube.com
December 9, 2024 at 10:48 PM
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...
www.youtube.com/playlist?lis...
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) 🧪🦠
December 7, 2024 at 11:04 PM
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) 🧪🦠
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/...
journals.asm.org/doi/10.1128/...
December 2, 2024 at 4:44 PM
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/...
journals.asm.org/doi/10.1128/...
Fantastic resource. Thanks for putting this together Georgia!
hey everyone! i made a list of some useful starter packs (primarily biology/earth sciences with a few bonus things thrown in) to share with friends who have joined bsky in the last week and thought it may be useful for some people here too! 🌍🧪 #SciSky #BioSky docs.google.com/document/d/1...
Starter packs
BIOLOGY Ecology Macroecology https://go.bsky.app/GBn9pNZ Global ecology https://go.bsky.app/V6tN4cv Trait based ecology and evolution https://go.bsky.app/PThMXeX Invasion biology https://go.b...
docs.google.com
November 28, 2024 at 11:05 PM
Fantastic resource. Thanks for putting this together Georgia!
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)
The Economist covered our "Strain on scientific publishing" paper.
What is this all about?
We collectively churn out more & more papers *per scientist*, an increasing pace, in a rapidly changing publication landscape.
Why? How? Want to make sense of this? 🧵
www.economist.com/science-and-...
What is this all about?
We collectively churn out more & more papers *per scientist*, an increasing pace, in a rapidly changing publication landscape.
Why? How? Want to make sense of this? 🧵
www.economist.com/science-and-...
Scientific publishers are producing more papers than ever
Concerns about some of their business models are building
www.economist.com
November 26, 2024 at 1:02 AM
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)
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 🤦
November 25, 2024 at 1:30 PM
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 🤦
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)
November 23, 2024 at 6:14 AM
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)
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
https://genome.cshlp.org/content/34/8/1154.full
https://genome.cshlp.org/content/34/8/1154.full
November 23, 2024 at 6:14 AM
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
https://genome.cshlp.org/content/34/8/1154.full
https://genome.cshlp.org/content/34/8/1154.full
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 🤞)
November 23, 2024 at 6:14 AM
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 🤞)
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...
November 23, 2024 at 6:14 AM
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...
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
November 23, 2024 at 6:14 AM
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
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 🫡
November 23, 2024 at 6:28 AM
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 🫡
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)?
November 23, 2024 at 6:21 AM
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)?
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)
November 23, 2024 at 6:21 AM
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)
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.
November 23, 2024 at 6:28 AM
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.
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):
https://www.biorxiv.org/content/10.1101/2024.05.21.595064v1
https://www.biorxiv.org/content/10.1101/2024.05.21.595064v1
Inducible transposon mutagenesis for genome-scale forward...
Transposon insertion sequencing (Tn-seq) is a powerful me...
www.biorxiv.org
November 23, 2024 at 6:35 AM
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):
https://www.biorxiv.org/content/10.1101/2024.05.21.595064v1
https://www.biorxiv.org/content/10.1101/2024.05.21.595064v1
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 🙏🏼
https://www.grc.org/drug-resistance-conference/2024/
https://www.grc.org/drug-resistance-conference/2024/
November 23, 2024 at 6:35 AM
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 🙏🏼
https://www.grc.org/drug-resistance-conference/2024/
https://www.grc.org/drug-resistance-conference/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).
https://www.biorxiv.org/content/10.1101/2024.05.03.592148v1
https://www.biorxiv.org/content/10.1101/2024.05.03.592148v1
Full factorial construction of synthetic microbial commun...
Constructing combinatorially complete species assemblages...
www.biorxiv.org
November 23, 2024 at 6:42 AM
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).
https://www.biorxiv.org/content/10.1101/2024.05.03.592148v1
https://www.biorxiv.org/content/10.1101/2024.05.03.592148v1