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...

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...

nature.com

Our latest paper was just published. Will prepare a full thread very soon 🦠🧪🤖

Bioinformatics Advances@bioinfoadv.bsky.social · 5mo ago

🧫 Just out in Bioinformatics Advances: "AssiST: Convolutional neural network for analysis of antibiotic susceptibility testing"  Read the full paper here:  https://doi.org/10.1093/bioadv/vbag063 Authors include: @carmenli.bsky.social, @amitchell.bsky.social

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) 😂

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...

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

nature.com

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...

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...

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...

nature.com

Great opportunity to participate in scientific outreach!

Mark O. Martin@markowenmartin.bsky.social · last yr.

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.

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?...

Matters Microbial #89: Can AI Point Us to New Antibiotics

YouTube video by MicrobeTV

youtu.be

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!

Sebastian S. Cocioba@atinygreencell.bsky.social · 2y ago

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?

Fascinating shift in the geography of drug development (excellent writing too!)

Niko McCarty@nikomccarty.bsky.social · 2y ago

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.

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 🧪

Mike Lee@theleelab.bsky.social · 2y ago

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... 🧪

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...

12 Days of OpenAI - YouTube

12 days. 12 livestreams. A bunch of new things, big and small.

youtube.com

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/...

Fantastic resource. Thanks for putting this together Georgia!

georgia 🏴󠁧󠁢󠁷󠁬󠁳󠁿@blahttodea.bsky.social · 2y ago

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...

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)

Paolo Crosetto@paolocrosetto.bsky.social · 2y ago

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-...

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)

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

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...

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 🫡

Amir Mitchell@amitchell.bsky.social · 2y ago

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)?

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)

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

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/

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