🔥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? 🧵
Phage receptor prediction from genome sequencing alone. Bacterial receptor (blue) interacting with phage proteins (purple) is shown here
📣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.
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.
How does the strength of genetic drift evolve over long times?
New preprint out 👇
www.biorxiv.org/content/10.6...
New paper out in PNAS!!! 🎉
Do more plasmid copies mean faster evolution?
🧵 Dive into the story
www.pnas.org/doi/10.1073/...
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)
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...
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...
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...
Love it, devastating that they wouldn't allow it (in a commentary!)
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...
Here's the full image on various genotype-phenotype mapping problems (a first draft to be updated!)
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?
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.
This is so good Pleuni! I’m going to save it as a science communication example where communication aimed at the public is also better for scientists (I just learned a lot), and share with this year’s ramp cohort!
I made a video about my new paper. I hope you enjoy it!
vimeo.com/1113132836?s...
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!
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...
Great big review, and I particularly love the consistent and simple visual language in the figures!
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...
Oh amazing, thanks for making this! Could you add me too? See you tomorrow!
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...
Physalia megalista, a cnidiran with a gas filled float, raised sail, and long blue tentacles hanging below. Image credit: Dalila Destanović
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... 🦑🧪📌
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)
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...
Also shout out to @bkoskella.bsky.social for making RaMP happen and advising on this project!
Screenshot of the following text from the website: Eligibility In order for an applicant to be considered, they must verify they meet the following eligibility requirements: Recent graduate (May 2021-July 2025) of a 4-year degree program (BA or BS) at an accredited institution Must be a U.S. Citizen, U.S. National or Permanent Resident of the United States Must not be currently enrolled in a graduate program Preference will be given to applicants who: Attended community college and/or can demonstrate encountering significant barriers to getting the independent research experience needed to progress on their desired career path Express a strong interest in pursuing a career in STEM research Indicate enthusiasm and/or curiosity toward microbiome sciences
Eligibility info:
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
🚀 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