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José Aguilar-Rodríguez

@jaguilarrod.bsky.social
401 followers 713 following 59 posts

Evolutionary systems/cell biologist. EMBO and SNSF Postdoctoral Fellow with Dmitri Petrov and Dan Jarosz at Stanford. PhD with Andreas Wagner at the University of Zurich. Studying how molecular and cellular systems shape, and are shaped by, evolution.

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Reposted by José Aguilar-Rodríguez
Sasha (Alexandra) Khristich @khristich.bsky.social · 22/09/2026
I’m excited to share our preprint with @oliviamghosh.bsky.social, where we explore what it takes to ‘win’ in long-term evolutionary competition: www.biorxiv.org/content/10.1...
biorxiv.org
Adaptive evolution can overwrite initial natural fitness variation only in highest-fitness yeast isolates
The fitness of an organism determines its likelihood of succeeding in short-term competition, but many other factors can influence its long-term success. In this study, we investigate the relative con...
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Dmitri Petrov @petrovadmitri.bsky.social · 15/07/2026
Cannot be more excited about the lineup for the inaugural Function of Evolving Systems GRC conference I am co-organizing with the amazing Joy Bergelson. Less than a month away: August 9 - 14, 2026. Still a few spots left! And do check out the amazing list of speakers: www.grc.org/function-of-...
grc.org
2026 Function of Evolving Systems Conference GRC
The 2026 Gordon Research Conference on Function of Evolving Systems will be held in Waterville Valley, New Hampshire. Apply today to reserve your spot.
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Dmitri Petrov @petrovadmitri.bsky.social · 21/04/2026
We are revising this ms www.biorxiv.org/content/10.1... and responding to reviewers who liked the paper but had issues with how we thought of balancing selection and its relationship to ecological, local adaptation 1/n
biorxiv.org
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Olivia Ghosh @oliviamghosh.bsky.social · 30/03/2026
Really excited that this major work from my PhD is finally published in @plosbiology.org ! In it, we were trying to tackle a fundamental question in evolution - how do genetic mutations map onto evolutionary fitness? (1/n) journals.plos.org/plosbiology/...
journals.plos.org
Genotype-fitness mapping of adaptive mutants reveals shifting low-dimensional structure across divergent environments
Predicting the effect of a genetic mutation on fitness is a major challenge in evolutionary biology. This study uses fitness effects of a large collection of adaptive yeast mutants in multiple lab env...
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Dmitri Petrov @petrovadmitri.bsky.social · 06/03/2026
Very proud of this paper, now officially out at PRX LIFE journals.aps.org/prxlife/abst.... Here @mrazo.bsky.social shows that geometry-aware autoencoder architecture can discover low dimensional phenotypic spaces traversed by evolution. 1/2
scholar.google.com
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Yogi Jaeger @yoginho.spore.social.ap.brid.gy · 18/01/2026
We have a new preprint out! And one that is especially dear to my heart: "Re-Engineering Wimsatt for Limited Beings" zenodo.org/records/18293424 Bill Wimsatt is possibly the most underrated philosopher of science of our times. In this paper, I attempt […] [Original post on spore.social]
A drawing of our multi-leveled world. By Marcus Neustetter.A drawing comparing simple and complex systems and how their decompositions relate to each other. Artwork by Marcus Neusttetter.A drawing of the three causal regimes of the world: levels, perspectives, and thickets. Artwork by Marcus Neustetter.
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James Hemker @jahemker.bsky.social · 11/03/2026
Proud that this work is now published! We hope it helps orient future #Nanopore long-read sequencing studies hunting for structural variants Also really happy to share eight new high-coverage (>100x) long-read read pools and assemblies with the #Drosophila community! doi.org/10.1093/g3jo...
doi.org
Manual validation finds ultra-long-read sequencing best enables faithful, population-level structural variant calling in Drosophila melanogaster euchromatin with nanopore
Abstract. The increasing accessibility of long-read sequencing and the rapid development of automated variant callers are promoting the generation of popul
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Dmitri Petrov @petrovadmitri.bsky.social · 19/02/2026
The next BAPG has been announced! April 11 at Davis organized by the inimitable @jrossibarra.bsky.social! bapg-conference.github.io
bapg-conference.github.io
BAPG Spring 2026
Bay Area Population Genomics Conference
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Dmitri Petrov @petrovadmitri.bsky.social · 29/01/2026
Registration is open for the inaugural GRC conference in the Function of Evolving Systems. Aug 9-14, 2026, Waterville Valley. Truly stellar speaker lineup. Student/postdoc fellowships are available! Please come join us! www.grc.org/function-of-... @joybergelson.bsky.social
grc.org
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Dmitri Petrov @petrovadmitri.bsky.social · 24/11/2025
Super excited about our schedule for BAPG at stanford on Dec 6. bapg2025.github.io/bapg2025stan... Amazing talks, a fabulous keynote, a lively poster session. A brilliant and interactive community. What’s not to love? 1/2 @sophiejwalton.bsky.social
bapg2025.github.io
BAPG Fall 2025
Bay Area Population Genomics Conference @ Stanford
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Nora Martin @n-martin.bsky.social · 01/12/2025
Submit an abstract to our symposium "S20 Mapping fitness landscapes with mechanistic models, machine learning and experiments" 🧬 - organised with @meikewortel.bsky.social
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Marc Robinson-Rechavi @marcrr.ecoevo.social.ap.brid.gy · 03/12/2025
I'm excited to present this new model to detect positive selection on regulatory sequences, which has been 3 years in the making! Thanks to Alexandre Laverré and @Phylogenetrips for their amazing work on this project. 😃 doi.org/10.1101/2025.11.26.690685 #bioinformatics #molecularEvolution
Graphical summary of the evolutionary model, in 4 rows, A to D.
A: left, bell shaped distribution of phenotypic changes; right, observed substitutions between an ancestral sequence and a modern one, using an outgroup.
B: 4 fitness landscapes: no selection, alpha=beta=1, uniform distribution; stabilizing selection, alpha=beta≠1, bell shape; directional selection, either alpha>beta, curve skewed right, or alpha<beta, curve skewed left.
C: 4 distributions which are the product of the distribution in A and each of the fitness landscapes. Observed subtitutions are mapped onto them, falling outside of the high density area except for the third, i.e. directional selection alpah>beta.
D: cartoon likelihood indicating that only the third fitness landscape is supported.
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José Aguilar-Rodríguez @jaguilarrod.bsky.social · 05/12/2025
Excited to co-organize with @weieli.bsky.social a symposium at SMBE 2026 on how synthetic & systems biology can illuminate the molecular mechanisms of evolution. Honored to have @christianlandry.bsky.social as invited speaker! Join us!
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Jess Smiley-Rhodes @j-smiley-rhodes.bsky.social · 18/11/2025
Thrilled to finally share the magnum opus of my PhD that focuses on the genetic basis of evolutionary change! Specifically, we know we can map the genetic basis of a trait, but can we tell which genes will underlie the trait shift when it evolves? doi.org/10.1101/2025...
doi.org
High-resolution mapping of a rapidly evolving complex trait reveals genotype-phenotype stability and an unpredictable genetic architecture of adaptation
The extent to which adaptation can be predicted, particularly for traits with complex genetic bases, is unknown. Here, we leveraged a model complex trait, model species, and high-powered longitudinal ...
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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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Claudia Bank @cbank.bsky.social · 28/10/2025
We have an open PhD position (application deadline 9 January 2026) in "Theory of fitness landscapes" at @unibe.ch 🤓⛰️📊👩‍💻🎓: banklab.github.io/positions/ Please share widely! #QueerInSTEM #DisabledInSTEM #BlackInSTEM #WomenInSTEM #CarersInSTEM #AcademicSky #HigherED
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Vincent J Lynch 🐘🦣🦥 🦇🐋🐢🐍 @devoevomed.bsky.social · 29/10/2025
50 years ago, King & Wilson published a foundational paper that underlies the cis-regulatory paradigm (CRP) of #DevoEvo #EvoDevo, i.e., that *almost* all morphological evolution is driven by mutations in regulatory elements, rather than proteins, and it all arose from simple misunderstanding 🧪 🧵
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Alvaro San Millan @sanmillan.bsky.social · 22/10/2025
New paper with my (amazing) friend and mentor @jrpenades.bsky.social Really looking forward to see what plasmid aficionados think of this one!! With @asantoslopez.bsky.social @wfigueroac3.bsky.social Akshay Sabins and others www.cell.com/cell-reports...
cell.com
Non-conjugative plasmids limit their mobility to persist in nature
Sabnis et al. explain why non-conjugative plasmids move at a low rate in nature. While increased mobility can easily evolve by incorporating phage DNA into plasmids, this is disadvantageous because it...
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Daniel Tamarit @danieltamarit.bsky.social · 24/10/2025
This is a beautiful study. Congrats Jose and all authors!
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Raquel Fueyo @fueyoraquel.bsky.social · 23/10/2025
Check out @jaguilarrod.bsky.social and @petrovadmitri.bsky.social thought provoking work! If like me, you feel this work may be out of your comfort zone, make sure to read Jose's bluetorial, clearly explained! Congratulations!
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Raquel Fueyo @fueyoraquel.bsky.social · 23/10/2025
My lab is seeking two PhD candidates to investigate the function and regulation of endogenous retroviruses in the early stages of human development 🦠👩‍🔬. Apply through the International Max Planck Research School (IMPRS) program: www.molgen.mpg.de/IMPRS/applic.... www.molgen.mpg.de/5094682/Fuey...
molgen.mpg.de
[2026] – Endogenous retroviruses in human embryogenesis
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Cedric Boeckx @cedricboeckx.bsky.social · 23/10/2025
Terrific work! 👏👏
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Dvir Schirman @dvirschirman.bsky.social · 23/10/2025
Wow! Very impressive work 🤯
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C. Brandon Ogbunu @cbo.bsky.social · 14/10/2025
1/5 🦖 Michael Crichton’s Jurassic Park (1990) turns 35 in November. In a new preprint, I argue that it was a prescient meditation on evolutionary genetics, complexity, & control. I also examine analogous efforts of today (e.g. “de-extinction.") Select points below: ecoevorxiv.org/repository/v...
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Timothy Fuqua 🏳️‍🌈 @timothyfuqua.bsky.social · 21/10/2025
A fun little side project I've been working on with @stepadenisov.bsky.social , Mato Lagator, and Andreas Wagner: "Strong promoters are mutationally robust". Briefly... www.biorxiv.org/content/10.1...
biorxiv.org
Strong promoters are mutationally robust
Mutational robustness is the persistence of a phenotype upon mutation. It facilitates molecular evolution and has been characterized in a variety of biological systems, but studies of prokaryotic prom...
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Reposted by José Aguilar-Rodríguez
Shady Saad @shadys11.bsky.social · 21/04/2025
I am incredibly proud to share that my work has officially been published in Cell! @cp-cell.bsky.social This work was a product of years of dedication and countless hours of research in the labs of Joanna Wysocka and Dan Jarosz labs @stanfordmedicine.bsky.social www.cell.com/cell/fulltex...
cell.com
DNA binding and mitotic phosphorylation protect polyglutamine proteins from assembly formation
DNA binding and phosphorylation protect FOXP2, a transcription factor with the longest polyQ track in the proteome, from aggregation during interphase and mitosis. Harnessing these native solubility-p...
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Reposted by José Aguilar-Rodríguez
Raquel Fueyo @fueyoraquel.bsky.social · 01/10/2025
Today in @nature.com, we present our work leveraging functional genomics and human blastoids to uncover a human-specific mechanism in preimplantation development driven by the endogenous retrovirus HERVK. Special thanks to the reviewers whose comments improved our manuscript a lot! rdcu.be/eI3tD
rdcu.be
A human-specific regulatory mechanism revealed in a pre-implantation model
Nature - Genetic manipulation of blastoids reveals the role of recently emerged transposable elements and genes in human development.
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Kathleen Kay @kathleenmkay.bsky.social · 22/10/2025
This paper is SO COOL! Congrats, and thanks for sharing!
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Cauã Westmann @cauawest.bsky.social · 20/10/2025
I’m excited to announce the launch of my lab at EPFL in Jan 2026 🎉. We’ll combine evolution & synthetic biology to study and (re)engineer bacterial communication. I’m recruiting PhD students to start in the first semester of 2026. Apply via EPFL PhD programs by Nov 1 drive.google.com/file/d/1cm-t...
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Craig Kaplan @triggerloop.bsky.social · 22/10/2025
What a cool paper. Also note that this very careful analysis does not support the majority of synonymous variants being non-neutral in yeast
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José Aguilar-Rodríguez @jaguilarrod.bsky.social · 22/10/2025
One of the most exciting works of my career, years in the making. We used high-throughput precision genome editing to test the fitness effects of thousands of natural variants. Our findings challenge the long-held assumption that common variants are inconsequential. www.biorxiv.org/content/10.1...
biorxiv.org
Massively parallel interrogation of the fitness of natural variants in ancient signaling pathways reveals pervasive local adaptation
The nature of standing genetic variation remains a central debate in population genetics, with differing perspectives on whether common variants are almost always neutral as suggested by neutral and n...
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Dmitri Petrov @petrovadmitri.bsky.social · 20/10/2025
For population genetics and evolutionary biology folks in the Bay Area: the next BAPG will be hosted by Stanford CEHG and the Petrov lab at Stanford on 12/6. Registration is free but required. The deadline for talk submission is Nov. 16. Hope to see you soon! Pls RT! docs.google.com/forms/d/e/1F...
docs.google.com
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