Will Shoemaker
@shoestrapped.bsky.social
Biologist applying principles from physics at ICTP 🇺🇳 in Trieste, Italy 🇮🇹 Postdoc researching microbial ecology and evolution in Jacopo Grilli’s research group. PhD w/ @jaytlennon.bsky.social.
https://wrshoemaker.github.io
https://wrshoemaker.github.io
Pinned
Happy to share my solo-authored Perspective "An Interpretation, Survey, and Outlook of Microbial Macroecology"! Making time these last few months to take stock of the patterns us microbial ecologists examine + models we invoke has been invaluable. Feedback welcome!
ecoevorxiv.org/repository/v...
ecoevorxiv.org/repository/v...
Reposted by Will Shoemaker
How does population density affect evolutionary trajectory?
Microbes construct their own niche which in turn reshapes their evolution.
Preprint drop from grad student @noahhoupt.bsky.social whose evolution experiments featured blue/white colonies, 1000 generations, a lab move, and much more!
Microbes construct their own niche which in turn reshapes their evolution.
Preprint drop from grad student @noahhoupt.bsky.social whose evolution experiments featured blue/white colonies, 1000 generations, a lab move, and much more!
Interested in eco-evolutionary feedbacks? Microbial experimental evolution? Pleiotropy? Filamentous phages??
Check out our latest preprint, now up on BioRxiv!
biorxiv.org/content/10.6...
For a quick summary, peep the thread below...🧵 (1/10)
Check out our latest preprint, now up on BioRxiv!
biorxiv.org/content/10.6...
For a quick summary, peep the thread below...🧵 (1/10)
biorxiv.org
February 5, 2026 at 2:08 AM
How does population density affect evolutionary trajectory?
Microbes construct their own niche which in turn reshapes their evolution.
Preprint drop from grad student @noahhoupt.bsky.social whose evolution experiments featured blue/white colonies, 1000 generations, a lab move, and much more!
Microbes construct their own niche which in turn reshapes their evolution.
Preprint drop from grad student @noahhoupt.bsky.social whose evolution experiments featured blue/white colonies, 1000 generations, a lab move, and much more!
Imagine being the resident insect keeper (entomoculturist?) of Dactylopius coccus for Campari pre 2006
February 3, 2026 at 8:42 PM
Imagine being the resident insect keeper (entomoculturist?) of Dactylopius coccus for Campari pre 2006
Glad to have this out in mSystems! We emphasize how this work is informative of the extent that temporal patterns can be gleaned given ~1d sampling. The Q of how measurement shapes the dynamics we can observe is an area of active interest, so feel free to reach out!
doi.org/10.1128/msys...
doi.org/10.1128/msys...
February 2, 2026 at 2:43 PM
Glad to have this out in mSystems! We emphasize how this work is informative of the extent that temporal patterns can be gleaned given ~1d sampling. The Q of how measurement shapes the dynamics we can observe is an area of active interest, so feel free to reach out!
doi.org/10.1128/msys...
doi.org/10.1128/msys...
Acquiring daily matplotlib inspiration from Adam Tooze's Chartbook
January 31, 2026 at 11:51 PM
Acquiring daily matplotlib inspiration from Adam Tooze's Chartbook
Reposted by Will Shoemaker
I wrote this song on Saturday, recorded it yesterday and released it to you today in response to the state terror being visited on the city of Minneapolis. It’s dedicated to the people of Minneapolis, our innocent immigrant neighbors and in memory of Alex Pretti and Renee Good.
Stay free
Stay free
Bruce Springsteen - Streets Of Minneapolis (Official Audio)
YouTube video by Bruce Springsteen
youtu.be
January 28, 2026 at 5:02 PM
I wrote this song on Saturday, recorded it yesterday and released it to you today in response to the state terror being visited on the city of Minneapolis. It’s dedicated to the people of Minneapolis, our innocent immigrant neighbors and in memory of Alex Pretti and Renee Good.
Stay free
Stay free
Happy to share my solo-authored Perspective "An Interpretation, Survey, and Outlook of Microbial Macroecology"! Making time these last few months to take stock of the patterns us microbial ecologists examine + models we invoke has been invaluable. Feedback welcome!
ecoevorxiv.org/repository/v...
ecoevorxiv.org/repository/v...
January 28, 2026 at 8:22 PM
Happy to share my solo-authored Perspective "An Interpretation, Survey, and Outlook of Microbial Macroecology"! Making time these last few months to take stock of the patterns us microbial ecologists examine + models we invoke has been invaluable. Feedback welcome!
ecoevorxiv.org/repository/v...
ecoevorxiv.org/repository/v...
Reposted by Will Shoemaker
How does the strength of genetic drift evolve over long times?
New preprint out 👇
www.biorxiv.org/content/10.6...
New preprint out 👇
www.biorxiv.org/content/10.6...
www.biorxiv.org
January 27, 2026 at 11:20 PM
How does the strength of genetic drift evolve over long times?
New preprint out 👇
www.biorxiv.org/content/10.6...
New preprint out 👇
www.biorxiv.org/content/10.6...
Reposted by Will Shoemaker
Alex Pretti’s coworkers take a moment of silence this morning
January 26, 2026 at 8:12 PM
Alex Pretti’s coworkers take a moment of silence this morning
RIP Michael Parenti. Your voice will be missed.
January 24, 2026 at 6:05 PM
RIP Michael Parenti. Your voice will be missed.
Reposted by Will Shoemaker
Attention folks in the weather, climate, disaster, wildfire, and Earth science communities: NSF has just published a new "Dear Colleague" letter inviting feedback (by Mar 13) on the proposal to dismantle the National Center for Atmospheric Research (NCAR). www.nsf.gov/funding/...
January 23, 2026 at 9:57 PM
Attention folks in the weather, climate, disaster, wildfire, and Earth science communities: NSF has just published a new "Dear Colleague" letter inviting feedback (by Mar 13) on the proposal to dismantle the National Center for Atmospheric Research (NCAR). www.nsf.gov/funding/...
Reposted by Will Shoemaker
Reposted by Will Shoemaker
Another product from Dr. Ying-Chih 'Ella' Chuang's time in my lab - bacteria that excrete purines are better equipped to tolerate inhibitory effects of purines, suggesting a physiological basis behind some cross-feeding interactions. www.biorxiv.org/content/10.6...
January 23, 2026 at 3:05 PM
Another product from Dr. Ying-Chih 'Ella' Chuang's time in my lab - bacteria that excrete purines are better equipped to tolerate inhibitory effects of purines, suggesting a physiological basis behind some cross-feeding interactions. www.biorxiv.org/content/10.6...
You are not “correcting” your biased estimator by running black box simulations, calculating the difference between the true value and the estimate, then arguing that it’s fine because said difference is less than some arbitrary threshold
January 21, 2026 at 10:00 PM
You are not “correcting” your biased estimator by running black box simulations, calculating the difference between the true value and the estimate, then arguing that it’s fine because said difference is less than some arbitrary threshold
Reposted by Will Shoemaker
🥁 NEW
Our study on infant gut microbiome and #straintransmission is now published in @nature.com:
doi.org/10.1038/s415...
1/10
Our study on infant gut microbiome and #straintransmission is now published in @nature.com:
doi.org/10.1038/s415...
1/10
Baby-to-baby strain transmission shapes the developing gut microbiome - Nature
A metagenomic survey of babies attending the first year of nursery detected extensive baby-to-baby microbial strain transmission, pointing to social interactions in infancy as crucial drivers of infan...
doi.org
January 21, 2026 at 6:24 PM
🥁 NEW
Our study on infant gut microbiome and #straintransmission is now published in @nature.com:
doi.org/10.1038/s415...
1/10
Our study on infant gut microbiome and #straintransmission is now published in @nature.com:
doi.org/10.1038/s415...
1/10
Reposted by Will Shoemaker
Expressions of interest: Director at MPI EvolBio (f/m/d) — We invite expressions of interest from distinguished scientists in evolutionary biology with a bold, long-term research vision that complements our Institute. More information: www.evolbio.mpg.de/3856225/Dire...
Directors
www.evolbio.mpg.de
January 21, 2026 at 11:15 AM
Expressions of interest: Director at MPI EvolBio (f/m/d) — We invite expressions of interest from distinguished scientists in evolutionary biology with a bold, long-term research vision that complements our Institute. More information: www.evolbio.mpg.de/3856225/Dire...
Reposted by Will Shoemaker
ICE’s actions tear families apart, intimidate communities, & undermine the conditions that make education, research, healthcare, & public trust possible.
We’re calling on scientists to join the general anti-ICE strike in Minnesota on January 23rd.
We’re calling on scientists to join the general anti-ICE strike in Minnesota on January 23rd.
January 19, 2026 at 10:22 PM
ICE’s actions tear families apart, intimidate communities, & undermine the conditions that make education, research, healthcare, & public trust possible.
We’re calling on scientists to join the general anti-ICE strike in Minnesota on January 23rd.
We’re calling on scientists to join the general anti-ICE strike in Minnesota on January 23rd.
Reposted by Will Shoemaker
A brilliant analysis of how sanctions have transformed the Iranian government into a Chicago School regime of austerity that benefits those attached to the regime, creates precarious labour, and rolls back all the redistributive and social measures of the past:
www.nplusonemag.com/online-only/...
www.nplusonemag.com/online-only/...
January 19, 2026 at 11:21 AM
A brilliant analysis of how sanctions have transformed the Iranian government into a Chicago School regime of austerity that benefits those attached to the regime, creates precarious labour, and rolls back all the redistributive and social measures of the past:
www.nplusonemag.com/online-only/...
www.nplusonemag.com/online-only/...
Reposted by Will Shoemaker
Deadline approaching!
Submission open for the eighth YB Meeting (deadline - 21st January)! Abstract submission link: forms.gle/SBeQeAp9MR2U...
January 9, 2026 at 3:17 PM
Deadline approaching!
How to tell you're in for a good read
January 17, 2026 at 3:38 PM
How to tell you're in for a good read
Reposted by Will Shoemaker
This was a very interesting read:
An untold story in biology: the historical continuity of evolutionary ideas of Muslim scholars from the 8th century to Darwin's time 🧪
www.tandfonline.com/doi/abs/10.1...
An untold story in biology: the historical continuity of evolutionary ideas of Muslim scholars from the 8th century to Darwin's time 🧪
www.tandfonline.com/doi/abs/10.1...
January 13, 2026 at 3:54 PM
This was a very interesting read:
An untold story in biology: the historical continuity of evolutionary ideas of Muslim scholars from the 8th century to Darwin's time 🧪
www.tandfonline.com/doi/abs/10.1...
An untold story in biology: the historical continuity of evolutionary ideas of Muslim scholars from the 8th century to Darwin's time 🧪
www.tandfonline.com/doi/abs/10.1...
Reposted by Will Shoemaker
One of my concerns with AI-assisted research in biology is that we're already looking only in the lamplight and AI incentivizes us to narrow the beam. Seems like it's happening...
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Artificial intelligence tools expand scientists’ impact but contract science’s focus - Nature
Artificial intelligence boosts individual scientists’ output, citations and career progression, but collectively narrows research diversity and reduces collaboration, concentrating work in data-rich a...
www.nature.com
January 15, 2026 at 4:08 PM
One of my concerns with AI-assisted research in biology is that we're already looking only in the lamplight and AI incentivizes us to narrow the beam. Seems like it's happening...
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Reposted by Will Shoemaker
We just released a @biorxivpreprint.bsky.social describing the *microntology*, a lightweight controlled vocabulary that we have been using for a while to tag metagenomes with contextual data.
Study by @fullam.bsky.social @vishnuprasoodanan.bsky.social et al:
1/
www.biorxiv.org/content/10.6...
Study by @fullam.bsky.social @vishnuprasoodanan.bsky.social et al:
1/
www.biorxiv.org/content/10.6...
microntology: a lightweight, data-driven controlled vocabulary to describe Earth's microbial habitats
Summary. We introduce microntology v1.0, a pragmatic controlled vocabulary of 148 terms to describe microbial habitats and lifestyles, and provide manually curated microntology annotations for >300k m...
www.biorxiv.org
January 13, 2026 at 4:33 PM
We just released a @biorxivpreprint.bsky.social describing the *microntology*, a lightweight controlled vocabulary that we have been using for a while to tag metagenomes with contextual data.
Study by @fullam.bsky.social @vishnuprasoodanan.bsky.social et al:
1/
www.biorxiv.org/content/10.6...
Study by @fullam.bsky.social @vishnuprasoodanan.bsky.social et al:
1/
www.biorxiv.org/content/10.6...
Reposted by Will Shoemaker
We’re very happy to share the results from the last chapter of my PhD, now out as a preprint on bioRxiv
www.biorxiv.org/content/bior...
www.biorxiv.org/content/bior...
www.biorxiv.org
January 14, 2026 at 8:25 PM
We’re very happy to share the results from the last chapter of my PhD, now out as a preprint on bioRxiv
www.biorxiv.org/content/bior...
www.biorxiv.org/content/bior...