@miloj.bsky.social
Reposted
🧵 New preprint out! We asked: what happens to gut bacteria when the intestine is under chronic inflammation (IBD)? Turns out, the host's inflammatory state reshapes how they evolve, and the results are pretty striking. A thread 👇
www.biorxiv.org
May 28, 2026 at 1:53 PM
🧵 New preprint out! We asked: what happens to gut bacteria when the intestine is under chronic inflammation (IBD)? Turns out, the host's inflammatory state reshapes how they evolve, and the results are pretty striking. A thread 👇
Reposted
This spring I took over and redesigned the only Gen Ed on plants here #IB103. We walked through every core aspect of plant bio in lectures & labs, but also through art & design. I had a blast, the evaluations are rewarding (4.9/5), the redesign got an award from the college, and a little press too!
June 2, 2026 at 2:56 PM
This spring I took over and redesigned the only Gen Ed on plants here #IB103. We walked through every core aspect of plant bio in lectures & labs, but also through art & design. I had a blast, the evaluations are rewarding (4.9/5), the redesign got an award from the college, and a little press too!
Reposted
Saying it because @kenjmloi.bsky.social didn't:
This is really close to a RNA system that targets protein sequences because of wobble bases in codons.
Truly amazing discovery!!
This is really close to a RNA system that targets protein sequences because of wobble bases in codons.
Truly amazing discovery!!
Excited to share our discovery of a new programmable RNA-guided DNA-targeting system hiding inside bacteriophages that predates CRISPR.
We call it VIPR (Viral Interference Programmable Repeat), and it uses an entirely new logic to find its targets.
Thread + link below.
We call it VIPR (Viral Interference Programmable Repeat), and it uses an entirely new logic to find its targets.
Thread + link below.
April 27, 2026 at 10:38 PM
Saying it because @kenjmloi.bsky.social didn't:
This is really close to a RNA system that targets protein sequences because of wobble bases in codons.
Truly amazing discovery!!
This is really close to a RNA system that targets protein sequences because of wobble bases in codons.
Truly amazing discovery!!
Reposted
Thrilled to have my first PhD paper with @mmdesai.bsky.social out! @science.org
Link: www.science.org/doi/10.1126/...
Thread below:
#mevosky #evosky #evobio #popgen #evolsky #ecoevo #molevol
Link: www.science.org/doi/10.1126/...
Thread below:
#mevosky #evosky #evobio #popgen #evolsky #ecoevo #molevol
April 24, 2026 at 5:52 PM
Thrilled to have my first PhD paper with @mmdesai.bsky.social out! @science.org
Link: www.science.org/doi/10.1126/...
Thread below:
#mevosky #evosky #evobio #popgen #evolsky #ecoevo #molevol
Link: www.science.org/doi/10.1126/...
Thread below:
#mevosky #evosky #evobio #popgen #evolsky #ecoevo #molevol
Reposted
🔥Preprint fresh off the press🔥
Hello Bluesky!
I'm delighted to share the story I have been working on for the past 3y in @vivekmutalik.bsky.social's lab at LBNL and Adam Arkin's lab @ucberkeleyofficial.bsky.social.
It's a wild story about 255 phages & 1,000+ HT genetic screens, are you ready? 🧵
Hello Bluesky!
I'm delighted to share the story I have been working on for the past 3y in @vivekmutalik.bsky.social's lab at LBNL and Adam Arkin's lab @ucberkeleyofficial.bsky.social.
It's a wild story about 255 phages & 1,000+ HT genetic screens, are you ready? 🧵
www.biorxiv.org
April 4, 2026 at 1:23 AM
🔥Preprint fresh off the press🔥
Hello Bluesky!
I'm delighted to share the story I have been working on for the past 3y in @vivekmutalik.bsky.social's lab at LBNL and Adam Arkin's lab @ucberkeleyofficial.bsky.social.
It's a wild story about 255 phages & 1,000+ HT genetic screens, are you ready? 🧵
Hello Bluesky!
I'm delighted to share the story I have been working on for the past 3y in @vivekmutalik.bsky.social's lab at LBNL and Adam Arkin's lab @ucberkeleyofficial.bsky.social.
It's a wild story about 255 phages & 1,000+ HT genetic screens, are you ready? 🧵
Reposted
📣Huge preprint 🔔
Today we share something our group has been working toward for a long time, led by @lucasmoriniere.bsky.social We asked can we predict which receptor a phage targets from its genome sequence alone? For most phages, we couldn’t. So Lucas set out to do something I had only dreamed of.
Today we share something our group has been working toward for a long time, led by @lucasmoriniere.bsky.social We asked can we predict which receptor a phage targets from its genome sequence alone? For most phages, we couldn’t. So Lucas set out to do something I had only dreamed of.
April 3, 2026 at 4:33 AM
📣Huge preprint 🔔
Today we share something our group has been working toward for a long time, led by @lucasmoriniere.bsky.social We asked can we predict which receptor a phage targets from its genome sequence alone? For most phages, we couldn’t. So Lucas set out to do something I had only dreamed of.
Today we share something our group has been working toward for a long time, led by @lucasmoriniere.bsky.social We asked can we predict which receptor a phage targets from its genome sequence alone? For most phages, we couldn’t. So Lucas set out to do something I had only dreamed of.
Reposted
If you can only visit one place at Harvard, make it the glass flower exhibit at the Museum of Natural History.
4000 models, 847 species.
Commissioned by the university for teaching botany and created by the Czech father and son Leopold and Rudolf Blaschka 1887 through 1936.
4000 models, 847 species.
Commissioned by the university for teaching botany and created by the Czech father and son Leopold and Rudolf Blaschka 1887 through 1936.
January 29, 2026 at 4:14 PM
If you can only visit one place at Harvard, make it the glass flower exhibit at the Museum of Natural History.
4000 models, 847 species.
Commissioned by the university for teaching botany and created by the Czech father and son Leopold and Rudolf Blaschka 1887 through 1936.
4000 models, 847 species.
Commissioned by the university for teaching botany and created by the Czech father and son Leopold and Rudolf Blaschka 1887 through 1936.
Reposted
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
New paper out in PNAS!!! 🎉
Do more plasmid copies mean faster evolution?
🧵 Dive into the story
www.pnas.org/doi/10.1073/...
Do more plasmid copies mean faster evolution?
🧵 Dive into the story
www.pnas.org/doi/10.1073/...
Plasmid mutation rates scale with copy number | PNAS
Plasmids are extrachromosomal DNA molecules that spread by horizontal transfer and
shape bacterial evolution. Plasmids are typically present at mul...
www.pnas.org
January 27, 2026 at 12:02 PM
New paper out in PNAS!!! 🎉
Do more plasmid copies mean faster evolution?
🧵 Dive into the story
www.pnas.org/doi/10.1073/...
Do more plasmid copies mean faster evolution?
🧵 Dive into the story
www.pnas.org/doi/10.1073/...
Reposted
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
January 23, 2026 at 6:04 PM
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)
Reposted
Bacteria chromosomes contain Genomic Islands that provide virulence, antibiotic resistance, MGE-defence,... They transfer between cells, but the mechanism of most remains elusive.
Here we explore the conjugative capacity of these mysterious Genomic Islands.
www.biorxiv.org/content/10.6...
Here we explore the conjugative capacity of these mysterious Genomic Islands.
www.biorxiv.org/content/10.6...
www.biorxiv.org
January 14, 2026 at 10:14 AM
Bacteria chromosomes contain Genomic Islands that provide virulence, antibiotic resistance, MGE-defence,... They transfer between cells, but the mechanism of most remains elusive.
Here we explore the conjugative capacity of these mysterious Genomic Islands.
www.biorxiv.org/content/10.6...
Here we explore the conjugative capacity of these mysterious Genomic Islands.
www.biorxiv.org/content/10.6...
Reposted
What is the best strategy to win any contest?
Eliminate your opponents of course.
Recently, my friend @fernpizza.bsky.social showed how plasmids compete intracellularly (check out his paper published in Science today!). With @baym.lol, we now know they can fight.
www.biorxiv.org/content/10.1...
Eliminate your opponents of course.
Recently, my friend @fernpizza.bsky.social showed how plasmids compete intracellularly (check out his paper published in Science today!). With @baym.lol, we now know they can fight.
www.biorxiv.org/content/10.1...
November 20, 2025 at 10:12 PM
What is the best strategy to win any contest?
Eliminate your opponents of course.
Recently, my friend @fernpizza.bsky.social showed how plasmids compete intracellularly (check out his paper published in Science today!). With @baym.lol, we now know they can fight.
www.biorxiv.org/content/10.1...
Eliminate your opponents of course.
Recently, my friend @fernpizza.bsky.social showed how plasmids compete intracellularly (check out his paper published in Science today!). With @baym.lol, we now know they can fight.
www.biorxiv.org/content/10.1...
Reposted
We built GenoPHI: a machine learning workflow that predicts phage-host interactions at strain level. This could help rapidly select phages to treat drug-resistant bacterial infections or for microbiome engineering without exhaustive lab testing.
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
www.biorxiv.org
November 16, 2025 at 11:16 PM
We built GenoPHI: a machine learning workflow that predicts phage-host interactions at strain level. This could help rapidly select phages to treat drug-resistant bacterial infections or for microbiome engineering without exhaustive lab testing.
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Reposted
Super excited that the bulk of my PhD work is now preprinted! Here we used whole-community competition, or coalescence, experiments to quantify selection acting on genetically diverged strains within larger communities. (1/n)
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
www.biorxiv.org
November 11, 2025 at 5:15 PM
Super excited that the bulk of my PhD work is now preprinted! Here we used whole-community competition, or coalescence, experiments to quantify selection acting on genetically diverged strains within larger communities. (1/n)
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Excited to share pt. 2 of my blog on genotype-phenotype maps. We are now quite good at predicting protein sequence -> structure. How did this happen? Why was it possible? Can we make similar predictions for protein function, whole-cell phenotypes, or community function?
An optimistic introduction to genotype-phenotype mapping: the protein structure problem
For billions of years, life has been on a grand search through a combinatorial expanse of possibility, stretching out rootlike tendrils this way and that, fanning out at the tips into thousands of int...
open.substack.com
October 12, 2025 at 10:37 PM
Excited to share pt. 2 of my blog on genotype-phenotype maps. We are now quite good at predicting protein sequence -> structure. How did this happen? Why was it possible? Can we make similar predictions for protein function, whole-cell phenotypes, or community function?
Reposted
Dear colleagues!
@davidmccandlish.bsky.social and I are serving as guest editors for the new special issue of GENETICS on fitness landscapes:
doi.org/10.1093/gene...
Submissions are due on March 18, 2026. Please spread the word! And reach out if you have questions.
@davidmccandlish.bsky.social and I are serving as guest editors for the new special issue of GENETICS on fitness landscapes:
doi.org/10.1093/gene...
Submissions are due on March 18, 2026. Please spread the word! And reach out if you have questions.
The Fitness Landscape: A Call for Papers
Ruth Isaacson; The Fitness Landscape: A Call for Papers, Genetics, , iyaf206, https://doi.org/10.1093/genetics/iyaf206
doi.org
October 8, 2025 at 5:59 AM
Dear colleagues!
@davidmccandlish.bsky.social and I are serving as guest editors for the new special issue of GENETICS on fitness landscapes:
doi.org/10.1093/gene...
Submissions are due on March 18, 2026. Please spread the word! And reach out if you have questions.
@davidmccandlish.bsky.social and I are serving as guest editors for the new special issue of GENETICS on fitness landscapes:
doi.org/10.1093/gene...
Submissions are due on March 18, 2026. Please spread the word! And reach out if you have questions.
Reposted
August 29, 2025 at 1:43 PM
Reposted
The Church Evolution Laboratory (CEL@NYU) will be official as of Sep 1st: shchurch.github.io. We are recruiting at all levels, including a postdoc to work on evolutionary patterns and processes via comparative genomics in Hawaiian Drosophila. Please share widely!
Church Evolution Laboratory
Department of Biology, New York City
shchurch.github.io
August 28, 2025 at 6:16 PM
The Church Evolution Laboratory (CEL@NYU) will be official as of Sep 1st: shchurch.github.io. We are recruiting at all levels, including a postdoc to work on evolutionary patterns and processes via comparative genomics in Hawaiian Drosophila. Please share widely!
Reposted
Excited to share a new preprint w/ the Sonnenberg lab, led by Matt Carter, @zzzhiru.bsky.social & @mattolm.bsky.social. We analyzed the microbiomes of two non-industrialized populations from opposite sides of the globe to try to reconstruct the recent evolutionary history of our gut microbiota.
Prehistoric Global Migration of Vanishing Gut Microbes With Humans
The gut microbiome is crucial for health and greatly affected by lifestyle. Many microbes common in non-industrialized populations are disappearing or extinct in industrialized populations. Understand...
www.biorxiv.org
August 16, 2025 at 6:25 PM
Excited to share a new preprint w/ the Sonnenberg lab, led by Matt Carter, @zzzhiru.bsky.social & @mattolm.bsky.social. We analyzed the microbiomes of two non-industrialized populations from opposite sides of the globe to try to reconstruct the recent evolutionary history of our gut microbiota.
I'm very excited to share something I've been working on off-and-on for a long time now: a new blog about genotype-phenotype landscapes! The first post is a Gödel-Escher-Bach-style dialogue to introduce the topic. If you like it please share/repost! open.substack.com/pub/topossib...
July 27, 2025 at 8:18 PM
I'm very excited to share something I've been working on off-and-on for a long time now: a new blog about genotype-phenotype landscapes! The first post is a Gödel-Escher-Bach-style dialogue to introduce the topic. If you like it please share/repost! open.substack.com/pub/topossib...
Great big review, and I particularly love the consistent and simple visual language in the figures!
Here's our new broad review on the extended mobility of plasmids, about all mechanisms driving and limiting their transfer. From conjugation to conduction, phage-plasmids to hitchers, molecular to evolutionary dynamics, ecology to biotech. The state of affairs. 1/9 academic.oup.com/nar/article/...
July 24, 2025 at 6:03 PM
Great big review, and I particularly love the consistent and simple visual language in the figures!
Reposted
Published in Nature today! Here, we sought to systematically ask how natural community's metabolism changes with the environment. A simple consumer-resource model can predict N-cycle metabolism (nitrate use) and, more importantly, the mechanism behind its change.
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Functional regimes define soil microbiome response to environmental change - Nature
Experimental perturbation of soil pH leads to a generalizable model of the soil microcosm comprising three functional regimes with distinct mechanisms linking environmental change to metabolite dynami...
www.nature.com
July 16, 2025 at 3:19 PM
Published in Nature today! Here, we sought to systematically ask how natural community's metabolism changes with the environment. A simple consumer-resource model can predict N-cycle metabolism (nitrate use) and, more importantly, the mechanism behind its change.
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Reposted
New Preprint!! Alejandro González-Delgado accomplished a major feat on this one: ported retron recombineering, which we love so much in E. coli, into 14 new bacterial species via a massive collaborative effort involving 9 labs!
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
June 18, 2025 at 7:22 PM
New Preprint!! Alejandro González-Delgado accomplished a major feat on this one: ported retron recombineering, which we love so much in E. coli, into 14 new bacterial species via a massive collaborative effort involving 9 labs!
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Reposted
Excited to share our study on sailing siphonophores, AKA bluebottles or man-o'-war! 🌊 we received hundreds of samples from scientists around the world, part of a huge effort to sequence genomes and test for multiple species 🧬 out today in @currentbiology.bsky.social doi.org/10.1016/j.cu... 🦑🧪📌
June 19, 2025 at 7:51 PM
Excited to share our study on sailing siphonophores, AKA bluebottles or man-o'-war! 🌊 we received hundreds of samples from scientists around the world, part of a huge effort to sequence genomes and test for multiple species 🧬 out today in @currentbiology.bsky.social doi.org/10.1016/j.cu... 🦑🧪📌