Olivier Borkowski

A new preprint with Matthew Schmitt, @kiseokmicro.bsky.social and Vincenzo Vitelli makes a huge step forward in learning functional groups of components in complex biological systems. It's dimension reduction that speaks to biological function. www.biorxiv.org/content/10.6...

Epistasis and co-adaptation in bacterial genome evolution - Nature Reviews Genetics Bacterial genome evolution is shaped by epistasis, which can constrain or promote specific evolutionary paths. The authors review how integrating the effects of epistatic interactions into population-...

Epistasis and co-adaptation in bacterial genome evolution
doi.org/10.1038/s415...

Unveiling hidden variables in stressed bacteria Noise in bacterial stress responses is often dismissed as mere randomness. While true stochasticity exists, much variation reflects hidden variables—cell state, history, and microenvironment—that are ...

Unveiling hidden variables in stressed bacteria: Cell Reports www.cell.com/cell-reports...

A symbiotic origin of the ribosome? Abstract. The origin of life is one of the great mysteries of science. Of the multiple unsolved problems, the origin of the translation system (the means b

"we propose that the protoribosome was a parasite (...). If this view is correct, then like the spliceosome in the stem eukaryote, a repurposed host-parasite interaction led to a dramatic change in cell biology at the base of the tree of life, in this case leading to the exit from an RNA world"

An Engineered Variant of E. coli Nissle 1917 with Enhanced Transformation Efficiency and Robustness The gut microbiome and its effects on human health have generated considerable scientific, veterinary, and medical interest in recent years. Several gut bacterial species have emerged as potential cha...

An Engineered Variant of E. coli Nissle 1917 with Enhanced Transformation Efficiency and Robustness
pubs.acs.org/doi/10.1021/...

Preparing my talk in Heidelberg on Cognition Spaces for the @embo.org @embl.org conference, “Collectivity in Living Systems: Emergence, Function, and Evolution.”
An exciting program with outstanding speakers and a great chance to catch up with old colleagues. www.embl.org/about/info/c...

YouTube video by DCB Turing Interest Group The Automation of Science: Past, Present, and Future - Prof. Ross King

The Automation of Science: Past, Present, and Future. Prof. Ross King
youtu.be/WANcDX8g2ow?...

What problem do you hope bioengineering or synthetic biology approaches will enable us to tackle in the next decade?
doi.org/10.1016/j.ce...

A portable orthogonal replication system enables continuous gene evolution near the biological speed limit
doi.org/10.64898/202...

Boosted cell-free gene expression for robust signal readout from a single-copy DNA template in microdroplets
doi.org/10.64898/202...

The Origins of Agar First introduced into laboratories in 1881, agar remains indispensable as a culture medium.

The Origins of Agar
open.substack.com/pub/cell/p/a...

#microsky

Generative AI for synthetic biology: Designing biological parts, circuits, and genomes
doi.org/10.1016/j.ce...

On the nature of the earliest known lifeforms Microfossils reported from Archaean BIFs most likely were liposome-like protocells, which had evolved intracellular mechanisms for energy conservation but not for regulating cell morphology and replic...

On the nature of the earliest known lifeforms elifesciences.org/articles/98637 #biology #life #evolution

Engineering non-exponential proliferation in Escherichia coli using functionalized protein aggregates
doi.org/10.1038/s414...

Dissecting reversible and irreversible single cell state transitions from gene regulatory networks - Molecular Systems Biology Understanding cell state transitions and their governing regulatory mechanisms remains one of the fundamental questions in biology. We develop a computational method, state transition inference using ...

Dissecting reversible and irreversible single cell state transitions from gene regulatory networks
doi.org/10.1038/s443...

Higher-order interactions in auxotroph communities enhance their resilience to resource fluctuations
doi.org/10.1016/j.ce...

Development of a toehold switch detection platform based on a modified cell-free translation system for specific differentiation of coronavirus infectious bronchitis virus genotypes and sensitive detection of phloem-limited bacterium Candidatus Liberibacter asiaticus
doi.org/10.1016/j.bi...

High-Throughput FRET Affinity Screening Technique (HTFAST) For Cell-Free Expressed Binding Protein Characterization
doi.org/10.64898/202...

PL-display: A cell-free platform for tunable selection of affinity peptides
doi.org/10.1093/pnas...

Impact of Reducing Agents on Protein Synthesis in a Reconstituted Cell-Free Protein Synthesis System Maintaining proper redox conditions is essential for protein stability and function. In cell-free protein synthesis, reducing agents, such as dithiothreitol and reduced glutathione, are commonly added...

Impact of Reducing Agents on Protein Synthesis in a Reconstituted Cell-Free Protein Synthesis System
pubs.acs.org/doi/10.1021/...

Model-Driven Cell-Free Synthesis of the C4 Amino Acid Aspartate Directly from CO2 The synthesis of amino acids from CO2 as the sole carbon source is a critical goal for sustainable biomanufacturing, offering a green alternative to conventional production methods plagued by greenhou...

Model-Driven Cell-Free Synthesis of the C4 Amino Acid Aspartate Directly from CO2
pubs.acs.org/doi/10.1021/...

Transcriptional competition biases the effects of second messengers in Escherichia coli
doi.org/10.1101/2025...

Engineering Basal Cognition: Minimal Genetic Circuits for Habituation, Sensitization, and Massed–Spaced Learning Cognition is often associated with complex brains, yet many forms of learning─such as habituation, sensitization, and even spacing effects─have been observed in single cells and aneural organisms. These simple cognitive abilities, despite their cost, offer evolutionary advantages by allowing organisms to reduce environmental uncertainty and improve survival. Recent studies have confirmed early claims of learning-like behavior in protists and slime molds, pointing to the presence of basal cognitive functions long before the emergence of nervous systems. In this work, we adopt a synthetic biology approach to explore how minimal genetic circuits can implement nonassociative learning in unicellular systems. Building on theoretical models and using well-characterized regulatory elements, we design and simulate synthetic circuits capable of reproducing habituation, sensitization, and the massed–spaced learning effect. Our designs incorporate activators, repressors, fluorescent reporters, and quorum-sensing molecules, offering a platform for experimental validation. By examining the structural and dynamical constraints of these circuits, we highlight the distinct temporal dynamics of gene-based learning systems compared to neural counterparts and provide insights into the evolutionary and engineering challenges of building synthetic cognitive behavior at the cellular level.

Engineering Basal Cognition: Minimal Genetic Circuits for Habituation, Sensitization, and Massed–Spaced Learning
pubs.acs.org/doi/10.1021/...

Integrated microdroplet workflow for high-throughput cell-free transcription in double emulsion picoreactors
doi.org/10.1101/2025...

"Are you not worried that engineered microbes can be released into the environment and eat all the plastic?" The answer is not really. Pleased to share our latest piece addressing this question by evaluating the current status of whole-cell plastic degradation: www.sciencedirect.com/science/arti...

Resolving emergent transient oscillations in gene circuits with a growth-coupled model Multiscale modeling reveals how growth and proteolysis-linked recycling cause transient oscillations in synthetic gene circuits.

Resolving emergent transient oscillations in gene circuits with a growth-coupled model
doi.org/10.1126/scia...

Integrase-On-Demand: bioprospecting integrases for targeted genomic insertion of genetic cargo Abstract. Integrases serve as powerful biotechnology tools that catalyze recombination at specific DNA sequences (att sites) and facilitate chromosomal int

Integrase-On-Demand: bioprospecting integrases for targeted genomic insertion of genetic cargo Open Access
doi.org/10.1093/nar/...

I have to take some time to read everything in depth. But I already like the scale of the experiment and the use of gpt in real time.

AI in biology has a wet lab bottleneck.

We solved it with our automated lab-in-the-loop system.

📍Demo our RAC automation platform at NVIDIA GTC and see how AI models can:

- Design experiments
- Run them autonomously
- Learn from physical results

🔗 Schedule: automation.ginkgo.bio/nvidia-gtc-2...

AI & cell-free OpenAi & Ginkgo !!!!

Using a GPT-5-driven autonomous lab to optimize the cost and titer of cell-free protein synthesis
doi.org/10.64898/202...