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Olivier Borkowski

@oborkowski.bsky.social
1.4K followers 638 following 525 posts

Tenured Scientist in Synthetic Biology (INRAE, Paris Area, France) #CellFree ⦁ #SynBio ⦁ #Bioengineering ⦁ #Microbiology sites.google.com/view/olivierborkow…

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Reposted by Olivier Borkowski
Filippo Caschera @stjle.bsky.social · 29/09/2026
Lights, machines, action! Watching gene expression unfold at the single-molecule level www.sciencedirect.com/science/arti...
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Reposted by Olivier Borkowski
Suckjoon Jun’s lab at UCSD @junlab.bsky.social · 28/09/2026
1/5 Do you use GFP to measure protein abundance? Be very careful. Our new bioRxiv preprint shows that, under translation inhibition, fluorescence can stop tracking how much reporter protein is actually there. Please share widely.
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Olivier Borkowski @oborkowski.bsky.social · 26/09/2026
Programmable Genome Sensing with Visual, Fluorescence, and Glucometer Readings: Cell-Free In Vitro Translation Approach Using RNA Switch-CRISPR doi.org/10.1021/acs....
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Reposted by Olivier Borkowski
Vivek Mutalik @vivekmutalik.bsky.social · 25/09/2026
Mapping structural constraints and adaptive potential in a capsule-degrading phage tailspike protein | Science Advances www.science.org/doi/10.1126/... #phagesky
science.org
Mapping structural constraints and adaptive potential in a capsule-degrading phage tailspike protein
Bacteriophage tailspike proteins (TSPs) degrade bacterial capsules to enable infection, yet the molecular determinants of their function and host range remain unclear. We applied deep mutational scann...
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Olivier Borkowski @oborkowski.bsky.social · 25/09/2026
Cell-free Engineering of LPST153 Bacteriophage Receptor-Binding Proteins Enables Tunable Host-Range Modulation doi.org/10.1021/acss...
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Olivier Borkowski @oborkowski.bsky.social · 25/09/2026
Artificial Biosynthetic Pathways for Cell-Free Production of Raspberry Ketone and the Cardiotonic Drug Dobutamine doi.org/10.1021/acss...
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Reposted by Olivier Borkowski
Ira Zibbu @coolscootre.bsky.social · 24/09/2026
www.asimov.press/p/theory-bio...
asimov.press
On the Role of Theory in Biology
Biology is often seen as an experimental science, with theory serving to generalize patterns from empirical data. But history reveals that theory plays a more generative role in discovery itself.
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Reposted by Olivier Borkowski
Kevin K. Yang 楊凱筌 @kevinkaichuang.bsky.social · 23/09/2026
A genome language model reveals the interactions hidden in non-coding DNA, pointing to new putative RNAs and repetitive elements in bacterial genomes. @garykbrixi.bsky.social @maxewilkinson.bsky.social @mfgrp.bsky.social @brianhie.bsky.social www.biorxiv.org/content/10.6...
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Olivier Borkowski @oborkowski.bsky.social · 23/09/2026
ML4SD: Leveraging Machine Learning and High-Throughput Search Algorithms for an Iterative Growth-Coupled Design Innovation doi.org/10.64898/202...
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Olivier Borkowski @oborkowski.bsky.social · 23/09/2026
Uncovering minimal control of cell fate by natural dynamics doi.org/10.1073/pnas...
doi.org
PNAS
Proceedings of the National Academy of Sciences (PNAS), a peer reviewed journal of the National Academy of Sciences (NAS) - an authoritative source of high-impact, original research that broadly spans...
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Olivier Borkowski @oborkowski.bsky.social · 23/09/2026
Engineering Persistent and Rewritable Genetic Memory in Bacteria through Multiscale Plasmid Competition doi.org/10.64898/202...
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Reposted by Olivier Borkowski
Trends in Biotechnology @cp-trendsbiotech.bsky.social · 23/09/2026
Online now: Plasmid copy number control offers a versatile tool in synthetic biology applications
dlvr.it
Plasmid copy number control offers a versatile tool in synthetic biology applications
Plasmids are central tools in biotechnology, yet their copy number is often treated as fixed. This study shows that plasmid copy number can be dynamically controlled to tune gene expression, growth, stability, and DNA transfer across bacterial hosts, expanding the flexibility and predictability of engineered biological systems.
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Reposted by Olivier Borkowski
Richard Lenski @relenski.bsky.social · 22/09/2026
"Philosophy of Biology: The power of theory in the life sciences" elifesciences.org/articles/112... @zdblount.bsky.social shared this thought-provoking paper with the lab group.
elifesciences.org
Philosophy of Biology: The power of theory in the life sciences
Theory can help address cell and molecular biology’s major challenges, particularly those arising from large omics datasets.
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Reposted by Olivier Borkowski
Thomas Gorochowski @chofski.bsky.social · 22/09/2026
Using recombinases to build robust cross-kingdom genetic circuits? 🧬 Need to know what they are *actually* doing? We got you covered! In the latest from the lab, we show the power of nanopore sequencing for unraveling the inner workings of these circuits. doi.org/10.1038/s414...
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Olivier Borkowski @oborkowski.bsky.social · 21/09/2026
Modular synthetic cross-kingdom promoters enable coordinated expression in Escherichia coli and Saccharomyces cerevisiae doi.org/10.1093/nar/...
doi.org
Modular synthetic cross-kingdom promoters enable coordinated expression in Escherichia coli and Saccharomyces cerevisiae
Abstract. Synthetic biology and metabolic engineering increasingly demand predictable and interoperable gene expression across phylogenetically distant org
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Olivier Borkowski @oborkowski.bsky.social · 21/09/2026
Characterization of recombinase-based genetic parts and circuits using nanopore sequencing doi.org/10.1038/s414...
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Reposted by Olivier Borkowski
Prof Jenny Rohn @jennyrohn.bsky.social · 18/09/2026
“Bacterial growth is straightforward to measure, complex in origin and exquisitely sensitive to environmental and genetic perturbations.” Fantastic opening sentence to a deeply interesting topic. Never thought about bacterial growth like this before. #MicroSky #Bacteria
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Olivier Borkowski @oborkowski.bsky.social · 15/09/2026
Thank you to all the organisers of the #Biocontrol26 conference! It was amazing, with a full program of highly interesting talks!
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Reposted by Olivier Borkowski
Jose Jimenez @jjimenez.bsky.social · 15/09/2026
We are recruiting!! We are looking for an expert in the metabolic engineering of non model microorganisms to join our team working on plastic waste upcycling. For details please check the link below. www.imperial.ac.uk/jobs/search-...
imperial.ac.uk
Description
Please note that job descriptions are not exhaustive, and you may be asked to take on additional duties that align with the key responsibilities ment...
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Olivier Borkowski @oborkowski.bsky.social · 15/09/2026
Engineered Orthogonal Translation Systems from Metagenomic Libraries Expand the Genetic Code doi.org/10.1021/acss...
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Olivier Borkowski @oborkowski.bsky.social · 15/09/2026
Second day at #biocontrol26 is starting great with the inspiring presentation of @doyarzun.bsky.social combining ML and metabolic enginneering.
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Olivier Borkowski @oborkowski.bsky.social · 14/09/2026
Very impressive work by Lucia Marucci on an ambitious approach coupling ML and cell engineering #biocontrol26
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Reposted by Olivier Borkowski
Biocontrol Seminars @bioctrl.bsky.social · 09/09/2026
⏰ Last day to register for Biological Control Systems 2026! Join us in Oxford next week for two days of talks, posters and discussion at the intersection of synthetic biology, control, AI and automation. Programme & registration: biocontrolseminars.org/biocontrol26
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Olivier Borkowski @oborkowski.bsky.social · 14/09/2026
Fantastic presentation continues #biocontrol26 with @noaholsman.bsky.social work using mother machine for synthetic circuits charaterization at a scale I have never seen before!
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Olivier Borkowski @oborkowski.bsky.social · 14/09/2026
Very impressive presentation about spatial control in bacteria by @yschaerli.bsky.social at the #biocontrol26 conference at Mathematical institute @ox.ac.uk
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Reposted by Olivier Borkowski
Olivier Borkowski @oborkowski.bsky.social · 10/09/2026
Our paper "Autonomous Control of Gene Expression Using Endogenous Transcription Signals" is finally out in Biotechnology and Bioengineering! #synbio #bioengineering Great publication with @drewendy.bsky.social and Ton Pakpoomton !! doi.org/10.1002/bit....
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Olivier Borkowski @oborkowski.bsky.social · 13/09/2026
Towards density-optimal DNA storage with practical bijective coding doi.org/10.1038/s414...
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Reposted by Olivier Borkowski
Molecular Microbiology @molmicrounihoh.bsky.social · 12/09/2026
hui: alarmone pGpp inhibits translation through GTP depletion! 👇 academic.oup.com/nar/article/... #subtiwiki #subtilis #alarmone @narjournal.bsky.social
academic.oup.com
Validate User
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Olivier Borkowski @oborkowski.bsky.social · 11/09/2026
Full-length transcriptomics and proteomics reveal how genome minimization reshapes gene expression in synthetic bacteria doi.org/10.64898/202...
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Olivier Borkowski @oborkowski.bsky.social · 10/09/2026
Our paper "Autonomous Control of Gene Expression Using Endogenous Transcription Signals" is finally out in Biotechnology and Bioengineering! #synbio #bioengineering Great publication with @drewendy.bsky.social and Ton Pakpoomton !! doi.org/10.1002/bit....
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Reposted by Olivier Borkowski
Lorraine Reese @lorraine-reese.bsky.social · 08/09/2026
Extended deadline ends tomorrow! Don't miss your opportunity to submit an abstract for the 11th Synthetic Biology UK meeting #synbio 🧪 bit.ly/Synthetic_Biology_2026
bit.ly
Synthetic Biology UK 2026
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Reposted by Olivier Borkowski
European Research Council (ERC) @erc.europa.eu · 07/09/2026
On a light note! Devising a more precise definition of kissing? Proving that babies smell wonderful to their parents, but teenagers don’t? This unexpected and fun science, carried out by ERC grantees Stuart West and Ilona Croy, was awarded 2026 Ig Nobel Prizes. Congratulations to the winners! ✨
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Olivier Borkowski @oborkowski.bsky.social · 05/09/2026
Bacterial growth under confinement requires transcriptional adaptation to resist turgor pressure build-up doi.org/10.1038/s414...
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Olivier Borkowski @oborkowski.bsky.social · 04/09/2026
Autonomous Homeostatic Synthetic Cells via Self-Gating DNA Nanopores doi.org/10.64898/202...
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Olivier Borkowski @oborkowski.bsky.social · 03/09/2026
Rewiring the ribosome to translate proteins encoded in its own RNA doi.org/10.1038/s415...
doi.org
Rewiring the ribosome to translate proteins encoded in its own RNA - Nature
Bacterial ribosomes can synthesize proteins encoded within their own RNA.
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Olivier Borkowski @oborkowski.bsky.social · 02/09/2026
Engineered Vibrio natriegens lysate can replace multiple components of cell culture media doi.org/10.1039/d6fb...
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Olivier Borkowski @oborkowski.bsky.social · 02/09/2026
Limits of deep-learning-based RNA prediction methods doi.org/10.1093/nar/...
doi.org
Limits of deep-learning-based RNA prediction methods
Abstract. In recent years, tremendous advances have been made in predicting protein structures and protein–protein interactions, but progress on RNA struct
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Olivier Borkowski @oborkowski.bsky.social · 29/08/2026
Navigating regulatory fragmentation in the convergence of synthetic biology, artificial intelligence, and automation doi.org/10.1038/s414...
doi.org
Navigating regulatory fragmentation in the convergence of synthetic biology, artificial intelligence, and automation - Nature Communications
The convergence of synthetic biology, AI, and automation creates new challenges for regulatory frameworks. In this Perspective, the authors analyse national regulations and propose the SynBioxAI regul...
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Olivier Borkowski @oborkowski.bsky.social · 29/08/2026
Research progress on Bacillus subtilis expression systems and effects of different promoters on expression efficiency doi.org/10.1016/j.mi...
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Olivier Borkowski @oborkowski.bsky.social · 28/08/2026
Establishing Cell Free Protein Expression as the Preferred Screening Platform for AI Driven Drug Discovery doi.org/10.1021/bk-2...
doi.org
Establishing Cell Free Protein Expression as the Preferred Screening Platform for AI Driven Drug Discovery
AbstractAdvances in artificial intelligence and machine learning (AI/ML) have transformed protein design by enabling efficient exploration of vast sequence
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Reposted by Olivier Borkowski
bioRxiv SysBio @biorxiv-sysbio.bsky.social · 26/08/2026
A Bayesian Multi-Species Approach Infers Gene Regulatory Networks Across Non-Model Organisms www.biorxiv.org/content/10.64898/20…
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Olivier Borkowski @oborkowski.bsky.social · 26/08/2026
An insoluble de novo protein enables survival of Escherichia coli by sequestering a gene repressor doi.org/10.1073/pnas...
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Olivier Borkowski @oborkowski.bsky.social · 26/08/2026
Advancing Human Artificial Chromosomes at the Dawn of Synthetic Genomics www.annualreviews.org/content/jour...
annualreviews.org
Advancing Human Artificial Chromosomes at the Dawn of Synthetic Genomics
Human artificial chromosomes (HACs) are engineered, chromosome-scale DNA molecules that replicate and segregate autonomously in mammalian cells, offering a unique platform for large, stable, nonintegr...
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Olivier Borkowski @oborkowski.bsky.social · 24/08/2026
Engineering erythrocytes into synthetic cells using cell-free gene expression doi.org/10.64898/202...
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Reposted by Olivier Borkowski
Christian Kost @kostchristian.bsky.social · 24/08/2026
Very happy that our paper Obligate cross-feeding of metabolites is common in soil microbial communities just came out in Nature Microbiology. See here 👇 Paywalled version: www.nature.com/articles/s41... Free read-only version: rdcu.be/fBHAb
nature.com
Obligate cross-feeding of metabolites is common in soil microbial communities - Nature Microbiology
Cultivation-dependent techniques, computational analyses and genome-scale metabolic models show widespread amino acid auxotrophies, suggesting that soil microorganisms exist within integrated ecologic...
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Olivier Borkowski @oborkowski.bsky.social · 22/08/2026
The structural origin of irreversible transitions in biological networks doi.org/10.1073/pnas...
doi.org
The structural origin of irreversible transitions in biological networks | PNAS
Cellular processes often exhibit irreversible state transitions even after external signals responsible for a transition are withdrawn. Long-standi...
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Reposted by Olivier Borkowski
Grainger Lab @graingerlab.bsky.social · 21/08/2026
A new pre-print out - we show that promoters and terminators of transcription are frequently coupled, throughout the bacteria, and this is regulatory. www.biorxiv.org/content/10.6...
biorxiv.org
Widespread coupling of promoters and terminators of transcription in bacteria
Transcription underpins the expression of genetic information and is viewed as a series of independent initiation and termination events. In bacteria, promoters and terminators of transcription are th...
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Reposted by Olivier Borkowski
Nature Chemical Biology @natchembio.nature.com · 17/08/2026
Biological circuit boards are engineered that compute functions based on the spatial arrangement of different bacterial strains printed on a surface www.nature.com/articles/s41...
nature.com
Living circuit boards built by printing bacterial transistors - Nature Chemical Biology
Electronic circuit boards carry out different operations on the basis of the configuration of their components. Now, equivalent biological circuits are engineered that compute functions on the basis o...
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Reposted by Olivier Borkowski
Gabriel Neurohr @gabrielneurohr.bsky.social · 15/07/2026
Also check out the preprint by the Skotheim lab that reaches similar conclusions using and orthogonal system to alter non-coding DNA content. www.biorxiv.org/content/10.6...
biorxiv.org
Synthetic expansion of non-coding DNA reveals physiological constraints on genome size
Genome size varies widely across eukaryotes, largely because of differences in non-coding DNA, but the physiological consequences of this variation remain unclear. To directly test how non-coding DNA ...
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Reposted by Olivier Borkowski
Zeynep Baharoglu @zeynepbaharoglu.bsky.social · 18/08/2026
academic.oup.com/nar/article/... 🦠
academic.oup.com
The leading region of many plasmids is adapted for translational efficiency
Abstract. To successfully transfer, conjugative plasmids must overcome a recipient cell’s defence mechanisms. The leading region of many plasmids—the first
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