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miloj.bsky.social

@miloj.bsky.social
143 followers 191 following 15 posts
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Marta Lourenço @martalourenco21.bsky.social · 28/05/2026
🧵 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 👇
biorxiv.org
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闵娅(Min Ya; Minya) PhD @minyaaa.bsky.social · 02/06/2026
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!
screenshots of the press coverage from the siebel center for design. The link to the article will be in the commenta pic of me yapping at the design center
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Enea Maffei @phagemuffin.bsky.social · 18/05/2026
1/6 👻 Something strange in your liquid agar? Who you gonna call? Thermophile hunters. Our new @asm.org #MRA paper reports the complete genome sequence of Geobacillus stearothermophilus strain CS7089 isolated from a commercial agar preparation.
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Ben Adler @benadler.bsky.social · 27/04/2026
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!!
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Shreyas Pai @theshreyaspai.bsky.social · 24/04/2026
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
science.org
Sex decreases the pleiotropic costs of local adaptation by purging hitchhiking load
Understanding the evolutionary mechanisms that maintain sex despite its direct costs is a long-standing challenge. Previous work has shown that sexual recombination can accelerate adaptation, in part ...
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Lucas Moriniere @lucasmoriniere.bsky.social · 04/04/2026
🔥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? 🧵
biorxiv.org
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Vivek Mutalik @vivekmutalik.bsky.social · 03/04/2026
📣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.
Phage receptor prediction from genome sequencing alone. Bacterial receptor (blue) interacting with phage proteins (purple) is shown here
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Arvid Ågren @arvidagren.bsky.social · 29/01/2026
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.
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Joao Ascensao @joaoascensao.bsky.social · 27/01/2026
How does the strength of genetic drift evolve over long times? New preprint out 👇 www.biorxiv.org/content/10.6...
biorxiv.org
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Paula Ramiro-Martínez @paularamiro.bsky.social · 27/01/2026
New paper out in PNAS!!! 🎉 Do more plasmid copies mean faster evolution? 🧵 Dive into the story www.pnas.org/doi/10.1073/...
pnas.org
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...
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Noah Houpt @noahhoupt.bsky.social · 23/01/2026
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)
biorxiv.org
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Manuel Ares-Arroyo @aresarroyom.bsky.social · 14/01/2026
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...
biorxiv.org
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Everyone's least favorite lab mate @kepatitis-c.bsky.social · 20/11/2025
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...
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Avery Noonan @averynoonan.bsky.social · 16/11/2025
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...
biorxiv.org
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Sophie Jean Walton @sophiejwalton.bsky.social · 11/11/2025
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...
biorxiv.org
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miloj.bsky.social @miloj.bsky.social · 12/10/2025
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?
open.substack.com
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...
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Sergey Kryazhimskiy @skryazhi.bsky.social · 08/10/2025
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.
doi.org
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
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Pleuni Pennings @pleunipennings.bsky.social · 29/08/2025
I made a video about my new paper. I hope you enjoy it! vimeo.com/1113132836?s...
vimeo.com
New paper (2025) on better understanding drug-resistance levels in different countries
I made this video about a paper that is coming out in August 2025 in the journal Epidemics. Music is from https://freetouse.com/music/ocean-bloom/summer-bliss https://freetouse.com/music/piki/a-new...
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Samuel Church @shchurch.bsky.social · 28/08/2025
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!
shchurch.github.io
Church Evolution Laboratory
Department of Biology, New York City
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Ben Good @benjaminhgood.bsky.social · 16/08/2025
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.
biorxiv.org
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...
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miloj.bsky.social @miloj.bsky.social · 27/07/2025
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...
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miloj.bsky.social @miloj.bsky.social · 24/07/2025
Great big review, and I particularly love the consistent and simple visual language in the figures!
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Kiseok (Keith) Lee @kiseokmicro.bsky.social · 16/07/2025
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...
nature.com
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...
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Seth Shipman @seth-shipman.bsky.social · 18/06/2025
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...
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Samuel Church @shchurch.bsky.social · 19/06/2025
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... 🦑🧪📌
Physalia megalista, a cnidiran with a gas filled float, raised sail, and long blue tentacles hanging below. Image credit: Dalila Destanović
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Shreyas Pai @theshreyaspai.bsky.social · 02/04/2025
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)
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SeppeKuehnLab @seppekuehnlab.bsky.social · 31/03/2025
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...
biorxiv.org
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...
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miloj.bsky.social @miloj.bsky.social · 28/03/2025
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
sites.google.com
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...
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The Align Foundation @alignbio.bsky.social · 13/03/2025
🚀 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
zenodo.org
Genotype to Phenotype: Design of an Extensible Experimental Platform for Characterizing Microbes
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Will Ratcliff @wcratcliff.bsky.social · 29/01/2025
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!
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Nora Pyenson @norapyenson.bsky.social · 12/12/2024
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/...
science.org
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...
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Grant Kinsler @grantkinsler.bsky.social · 05/12/2024
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...
doi.org
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...
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