@miloj.bsky.social
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... 🦑🧪📌
Reposted
Why is sex so common if it's so costly?
Super excited to share our new preprint “Sex decreases the pleiotropic costs of local adaptation”, where we bring a new angle to this age-old evolutionary question. Co-led by Parris Humphrey, in Michael Desai's lab. Short thread here: (1/n)
Super excited to share our new preprint “Sex decreases the pleiotropic costs of local adaptation”, where we bring a new angle to this age-old evolutionary question. Co-led by Parris Humphrey, in Michael Desai's lab. Short thread here: (1/n)
Sex decreases the pleiotropic costs of local adaptation https://www.biorxiv.org/content/10.1101/2025.03.28.646016v1
April 2, 2025 at 6:59 PM
Why is sex so common if it's so costly?
Super excited to share our new preprint “Sex decreases the pleiotropic costs of local adaptation”, where we bring a new angle to this age-old evolutionary question. Co-led by Parris Humphrey, in Michael Desai's lab. Short thread here: (1/n)
Super excited to share our new preprint “Sex decreases the pleiotropic costs of local adaptation”, where we bring a new angle to this age-old evolutionary question. Co-led by Parris Humphrey, in Michael Desai's lab. Short thread here: (1/n)
Reposted
Third preprint! – We use community-function landscapes to rationally design communities for bioremediation in soils! Spoiler - it works! Led by Mahmoud Yousef, with @kiseokmicro.bsky.social, J. Tang, V. Charisopoulos, B Willett. @nitmb.bsky.social, NSF, MSTP UChicago. www.biorxiv.org/content/10.1...
Collective Microbial Effects Drive Toxin Bioremediation and Enable Rational Design
The metabolic activity of microbial communities is essential for host and environmental health, influencing processes from immune regulation to bioremediation. Given this importance, the rational desi...
www.biorxiv.org
March 31, 2025 at 1:25 PM
Third preprint! – We use community-function landscapes to rationally design communities for bioremediation in soils! Spoiler - it works! Led by Mahmoud Yousef, with @kiseokmicro.bsky.social, J. Tang, V. Charisopoulos, B Willett. @nitmb.bsky.social, NSF, MSTP UChicago. www.biorxiv.org/content/10.1...
Hi y'all! Know any recent or upcoming college graduates who are interested in microbiology and looking for (full-time! paid!) research experience? Please point them towards RaMP! Darian Doakes and I will be co-mentors for an MGE project that I think is going to be really cool. Apps+recs due 5/25
Bay Area RaMP
Mission
The Bay Area RaMP Program in Microbiome Sciences exists to increase potential for scientific advances by expanding the microbiome research workforce with well-trained, ethical scientists.
Our...
sites.google.com
March 28, 2025 at 9:19 PM
Hi y'all! Know any recent or upcoming college graduates who are interested in microbiology and looking for (full-time! paid!) research experience? Please point them towards RaMP! Darian Doakes and I will be co-mentors for an MGE project that I think is going to be really cool. Apps+recs due 5/25
Reposted
🚀 New proposal from Align! The experimental platform aims to standardize #microbial #phenotyping & support predictive modeling. 🦠 Capturing data across 1k strains & 1k conditions; using BacterAI; generating high-quality datasets for ML @jensen_lab
Genotype to Phenotype: Design of an Extensible Experimental Platform for Characterizing Microbes
zenodo.org
March 13, 2025 at 8:58 PM
🚀 New proposal from Align! The experimental platform aims to standardize #microbial #phenotyping & support predictive modeling. 🦠 Capturing data across 1k strains & 1k conditions; using BacterAI; generating high-quality datasets for ML @jensen_lab
Reposted
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!
Reposted
Is it “winner-takes all” when the simplest living things compete? Check out my fresh publication on phage coexistence in Science and a thread below🧵 www.science.org/doi/10.1126/...
Diverse phage communities are maintained stably on a clonal bacterial host
Bacteriophages are the most abundant and phylogenetically diverse biological entities on Earth, yet the ecological mechanisms that sustain this extraordinary diversity remain unclear. In this study, w...
www.science.org
December 12, 2024 at 7:22 PM
Is it “winner-takes all” when the simplest living things compete? Check out my fresh publication on phage coexistence in Science and a thread below🧵 www.science.org/doi/10.1126/...
Reposted
Do mutations that drive evolution improve many traits or few?
Does this change over the course of evolution?
Excited to share our work in PLOS Biology exploring these questions in the first 2 adaptive steps w/ Yuping Li, @gsherloc.bsky.social, @petrovadmitri.bsky.social 🧵
doi.org/10.1371/jour...
Does this change over the course of evolution?
Excited to share our work in PLOS Biology exploring these questions in the first 2 adaptive steps w/ Yuping Li, @gsherloc.bsky.social, @petrovadmitri.bsky.social 🧵
doi.org/10.1371/jour...
A high-resolution two-step evolution experiment in yeast reveals a shift from pleiotropic to modular adaptation
Evolution is expected to involve mutations that are small and modular in effect, but recent findings suggest that mutations early in an adaptive process can have strong and pleiotropic effects. This s...
doi.org
December 5, 2024 at 9:46 PM
Do mutations that drive evolution improve many traits or few?
Does this change over the course of evolution?
Excited to share our work in PLOS Biology exploring these questions in the first 2 adaptive steps w/ Yuping Li, @gsherloc.bsky.social, @petrovadmitri.bsky.social 🧵
doi.org/10.1371/jour...
Does this change over the course of evolution?
Excited to share our work in PLOS Biology exploring these questions in the first 2 adaptive steps w/ Yuping Li, @gsherloc.bsky.social, @petrovadmitri.bsky.social 🧵
doi.org/10.1371/jour...