Gilberto Alvarez

Fine-tuning mechanical constraints reveals uncoupled patterning and gene expression programs in murine gastruloids Highlighted Article: A bioinert confinement system enables dissection of how stiffness and timing shape gastruloid development, revealing uncoupling between polarization and transcriptional programs.

Mechanical constraints disrupt gastruloid polarisation without changing gene expression - uncouples morphogenesis & patterning

Gregor & co use tunable hydrogels to show cell motility, not gene expression, drives axis formation in gastruloids

journals.biologists.com/dev/article/...

Love #protists? Then you'd love this! Beautiful collection of hand-drawn critters represented here at the Oxford-Japan symposium on ethological dynamics in diorama environments sites.google.com/view/oxford-... #ciliates #testateamoeba #diatoms

@niklaskemp.bsky.social will present our new CREsted framework at the next scverse community meeting!

CREsted allows you to train sequence-to-function models tailored to cell type-specific enhancers (including synthetic enhancer design) www.biorxiv.org/content/10.1... github.com/aertslab/cre...

Essay: Emergent Holographic Spacetime from Quantum Information In a new forward-looking PRL Essay, Tadashi Takayanagi explores the intersection of quantum information theory with quantum gravity within the framework of holographic duality, and its potential to he...

For anyone wanting to follow up on my brief mention at the Helgoland meeting of how spacetime might be an emergent property of quantum entanglement, here's a nice but pretty high-level essay on it.
journals.aps.org/prl/abstract...

Excited to share our new paper in @cellreports.bsky.social that reshapes our understanding of chromosome organization's deep evolutionary roots! Our work dives into the origins of the machinery that structures our very genomes.

🔗: doi.org/10.1016/j.ce...

#Genomics #Evolution #CellBiology #LECA

How did evolution drive massive genome contraction during oceanic island colonization? A new paper from our lab.
www.biorxiv.org/content/10.1...

Wow - one of the largest coronal holes of solar cycle 25! This coronal hole has survived for over NINE MONTHS, one of the most persistent coronal holes I have ever seen. We are seeing the high speed solar wind at Earth now which may intensify in the coming days.

#heliophysics

Of course there's also the answer that Twitter/X got shit and is run by a neo-Nazi ket-head but this is still genuinely interesting.

In 1984, Francis Crick described a biological conundrum: Memories last years, while most molecules degrade in days or weeks. “How then is memory stored in the brain so that its trace is relatively immune to molecular turnover?” he wrote in Nature. www.quantamagazine.org/the-molecula...

The diffused evolutionary dynamics of morphological novelty | PNAS Rates of evolution are fundamental to understand the processes that shaped the history of life. The predominant view holds that high rates of pheno...

Happy to share my new article on how morphological diversification proceeds during evolutionary radiations: "The diffused evolutionary dynamics of morphological novelty" www.pnas.org/doi/10.1073/... 🧵 1/12

Our BAT paper is accepted in Nature Ecology & Evolution! Single cell, gene regulation, TADs and key TFs that shape the bat wing. Genomics goes Evodevo 😍

Modelling and design of transcriptional enhancers Nature Reviews Bioengineering, Published online: 28 February 2025; doi:10.1038/s44222-025-00280-yEnhancers are genomic elements critical for regulating gene expression. In this Review, the authors discuss how sequence-to-function models can be used to…

ICYMI: Modelling and design of transcriptional enhancers

Solanum pan-genetics reveals paralogues as contingencies in crop engineering - Nature Gene duplication and subsequent paralogue diversification are major obstacles to genotype-to-phenotype predictability.

🚨New paper published in @nature.com! Using pan-genetics across the Solanum genus🍅🥔🍆we reveal why gene duplications🧬are major contingencies in crop engineering. My postdoc work in the Lippman lab @CSHL, collab. with @katiejenike.bsky.social @mikeschatz.bsky.social chatz.bsky.social and many others!

New #preprint: "A model for boundary-driven tissue morphogenesis" arxiv.org/abs/2503.03688.

A great collaboration with @danielalber.bsky.social @zhaoshh.bsky.social, Alexandre Jacinto, Eric Wieschaus, Stas Shvartsman.

@flatironinstitute.org @mpipks.bsky.social @mpi-cbg.de @csbdresden.bsky.social

A must read :D

The living world offers discoveries from bacteria to ecosystems, but how do we turn vast data into meaningful concepts? 🧬🌍
Join the 2nd edition of #EESTCBio to explore the interplay between theory and biology!

📥 Abstract deadline: 11 Feb
💻 s.embl.org/ees25-03-bl

Very much looking forward to this conference @embl.org in May! Abstract deadline coming up soon!

Maximizing Free Energy Gain Maximizing the amount of work harvested from an environment is important for a wide variety of biological and technological processes, from energy-harvesting processes such as photosynthesis to energy storage systems such as fuels and batteries. Here, we consider the maximization of free energy—and by extension, the maximum extractable work—that can be gained by a classical or quantum system that undergoes driving by its environment. We consider how the free energy gain depends on the initial state of the system while also accounting for the cost of preparing the system. We provide simple necessary and sufficient conditions for increasing the gain of free energy by varying the initial state. We also derive simple formulae that relate the free energy gained using the optimal initial state rather than another suboptimal initial state. Finally, we demonstrate that the problem of finding the optimal initial state may have two distinct regimes, one easy and...

How do systems—biological or technological—maximize energy harvested from their environments? A new study explores how the initial state of a system impacts free energy gain and extractable work and illustrates the findings through a simple information-engine model. https://doi.org/10.3390/e27

When Kurt Gödel was applying for US citizenship, he had to attend a hearing and so he studied the Constitution carefully - and was worried. According to Oskar Morgenstern, "To his distress, he had found some inner contradictions and [thought] he could show how in a perfectly legal manner...

Agrochemicals: Insect declines in a warming world Worldwide declines in the abundance of non-pest insects threaten ecosystems, food production and human wellbeing. A large-scale study has systematically examined field and environmental levels of 1,02...

Nice write-up about our work from Philip Batterham. Agrochemicals: Insect declines in a warming world: Current Biology www.cell.com/current-biol...

🪰 🧬 Do you want to enhance your knowledge of Drosophila as a model organism? Then 'Drosophila genetics and genomics' might be the right course for you!

Apply now and join us in Heidelberg for lectures and practical sessions delivered by renowned experts 👉 s.embl.org/drg25-01-bl

#EMBODrosophila

Back in 1943 Schrödinger argued that "present-day physics and chemistry could not possibly account for what happens in space and time within a living organism." I wrote up why he said that and how thermodynamics + new single-fiber sequencing tech answer him.

open.substack.com/pub/thisgeno...

My thesis work on active machine learning to model regulatory DNA is now out in Cell Systems!

We answer the question: When you can synthesize any DNA sequence you want, how do you decide which ones are worth testing?

www.sciencedirect.com/science/arti...

Insects in the Mail - JSTOR Daily The efficiency of the postal system and generosity of local experts played important roles in the advancement of entomology in eighteenth-century France.

Ferchault de Réaumur had people send him insects through the mail in the 18th century. Fascinating episode from the Republic of Letters, showing early forms of citizen science and the importance of local knowledge.

#histsci 🗃️

daily.jstor.org/insects-in-t...

🎇🎄Some holiday reading: Overdue TWEETORIAL on the latest preprint from our lab 🎇🎄

In this work, superstar postdoc @xinhexue.bsky.social combined 2 kinds of pooled CRISPR screens to pinpoint noncoding regulatory elements and the transcription factors that activate these elements.

“In the end, science doesn’t move one paper at a time; it moves one inspired person at a time. That’s really our currency as scientists—and it’s our duty to pass that inspiration along to the public. We need to make science a much more human endeavor, because one inspired person…

Here is the link to last course @collegedefrance.bsky.social on biological information, devoted to cellular learning & memory. From molecular memory (allostery, protein modification) to signalling networks with memory (bistability etc),structural memory & cell memory. Enjoy!

tinyurl.com/n4hfx4ec

A three-node Turing gene circuit forms periodic spatial patterns in bacteria Engineering Turing patterns has been one of the most challenging problems in synthetic biology because even tiny changes in the reaction parameters destroy patterning. Here, the authors construct a more robust three-node genetic circuit in E. coli to generate different kinds of reproducible spot and stripe patterns.

Building a capacity for making Turing patterns into bacteria. This is very cool.
www.cell.com/cell-systems...

A cartoon illustration of an anthropomorphic titin protein as a massive, muscular figure wearing a lab coat, glasses, and a red tie, flexing its biceps confidently. To the left, there is a text box titled "TITIN" that says: "Look at this absolute unit of a protein (appearance as hallucinated by AI): 3,800 kD, ~0.4 kg of your body, critical for heart function, mutations: most common genetic cause of heart failure." The background includes a colorful DNA helix, and a smaller version of the character appears at the bottom left.

Titin is massive in size – at 3,800kD it’s the largest protein in your body and really important for heart function.

In a new paper, led by Yuri Kim and the Seidman lab, we describe an enhancer critical for normal Titin expression.

Here is the overview (1/n)

Paper: www.jci.org/articles/vie...

How insects deploy their wings. Highlight by IBDM
@centuri-ls.bsky.social on Simon's paper in Nature Com
@natureportfolio.bsky.social :
www.ibdm.univ-amu.fr/how-insects-...