Joshua Ricouvier

New on @biorxiv!!!!!!
We’re excited to share our latest paper on combining cell-free systems and machine learning to express full genome in vitro.

Check it out now! 👉 www.biorxiv.org/content/10.1...

Catch us at SEED in Houston this June to discuss this work.
#CellFree

Yes, especially when you study ribosome assembly!!!

@pianocktailiste.bsky.social did you check who is Ada Yonath?

Congratulations to Noa Avidan who defended her PhD supervised by Pr Roy Bar-Ziv in front of Pr Ada Yonath
at the Weizmann Institute of Science

Autonomous synthesis of ribosomal large subunit intermediates in a minimal system

Confronting risks of mirror life Broad discussion is needed to chart a path forward

www.science.org/doi/10.1126/...

Disentangling microbial interaction networks
www.cell.com/trends/micro...

New study in @cellpress.bsky.social by Allen Distinguished Investigator @elowitzlab.bsky.social and collaborators explores the versatility of protein dimers. #FrontierScience

🔗 www.cell.com/cell/fulltex...

YouTube video by Build-a-Cell Build-a-Cell seminar Roy Bar-Ziv: Toward autonomous DNA compartments in 2D

Build-a-cell seminar with Roy Bar-Ziv
youtu.be/yvbPmAS_cPM?...

Our review, What remains from living cells in bacterial lysate-based cell-free systems, is available on HAL (the french open archive):
hal.science/hal-04118475...

Finally published: A fluorescence microscope that performs microscale MRI using NV centers in diamond. www.nature.com/articles/s41... 🔬💎 #QuantumTech #MRI #NMR #Microscopy

De novo designed proteins neutralize lethal snake venom toxins - Nature Deep learning methods have been used to design proteins that can neutralize the effects of three-finger toxins found in snake venom, which could lead to the development of safer and more accessible antivenom treatments.

Nature research paper: De novo designed proteins neutralize lethal snake venom toxins

https://go.nature.com/4fZU9EI

A cell-free biosensor signal amplification circuit with polymerase strand recycling - Nature Chemical Biology A signal amplification circuit based on recycling nucleic acid inputs with RNA polymerase off-target transcription improves the sensitivity of transcription factor-based cell-free biosensors, achievin...

A cell-free biosensor signal amplification circuit with polymerase strand recycling
www.nature.com/articles/s41...

Five years of hard work has paid off! 🎉 What a nice new year surprise—we made it to the cover of Nature Microbiology! 🌟
Acknowledgment to all co-authors and specially Elisa Atza for producing this cover image!

Applications of bacteriophages in precision engineering of the human gut microbiome
doi.org/10.1016/j.en...

Tandem kinase proteins across the plant kingdom Nature Genetics - This genomic analysis of tandem kinase proteins across 104 plant species highlights their mechanisms of convergent molecular evolution and potential roles in plant immunity.

First paper of the year is out! A collaboration with Tzion Fahima @University of Haifa with heavy lifting by Tamara Reveguk, who was a pleasure to co-supervise. We generated an atlas of tandem kinase proteins (TKPs). TKPs are known to confer disease resistance in monocots. 🧵(1/4)
rdcu.be/d5ADS

Integrating bioelectronics with cell-based synthetic biology - Nature Reviews Bioengineering Biohybrid devices based on engineered cells interfaced with bioelectronics combine the strengths of each field, resulting in constructs with properties that are not otherwise achievable. In this Revie...

Integrating bioelectronics with cell-based synthetic biology
www.nature.com/articles/s44...

Exciting new #synbio engineered living materials work from Chao Zhong, Peng Huang and Bolin An's team in Shenzhen has just come out on bioRxiv. Lovely demonstration of how engineered E.coli can sense and treat in vivo.
www.biorxiv.org/content/10.1...

Happy to kick off 2025 with this new review on gut microbiota-neuroepithelial signaling by the very talented Taka Ohara!

1/n Some time ago my colleague, excellent cook, and friend Ivan told me: "Cacio e pepe is the recipe that I screw up more often. Let's make a project studying systematically the physics of that sauce".

Prepare to get cheesy, I'm glad to share the Cacio e paper preprint:

arxiv.org/abs/2501.00536

I remember doing this maze with our lab after lunch one day! Great work on collective cognition comparing humans vs. ants in trying to solve a maze by Dreyer et al. www.pnas.org/doi/10.1073/...

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...

There are always many ways to look at your data.

Good job Matt! The PURE expression system made a leap ahead thanks to you

This is our latest preprint about the biogenesis of the translation proteins in a minimal translation system (PURE). www.biorxiv.org/content/10.1...

Tracking transcription–translation coupling in real time - Nature Single-molecule fluorescence microscopy experiments with a recombinant Escherichia coli transcription–translation system provides insights into the coordination of the transcription and translation ma...

Tracking transcription–translation coupling in real time
doi.org/10.1038/s415...

The cellular dogma In this essay, I will put forth what I see as a major conceptual challenge for biology in the next decade, one that is inspired by Crick’s Central Dogma: understanding information flow in the cell in ...

The cellular dogma
www.cell.com/cell/fulltex...

Large-scale-integration and collective oscillations of 2D artificial cells - Nature Communications Large-scale-integration of artificial cells on a chip can reveal emergent multicellular phenomena. Here, authors report 2D coupled lattices of artificial cells programmed by genetic oscillators, exhib...

My latest article is out! 1000 artificial cells synchronize in 2D and collective behavior emerges!
#microfluidics #artificialcells #syntheticcells #cellfreeexpression
doi.org/10.1038/s414...