Olivier Borkowski

Publications

Poster de conférence (16)

Cell-free genome-wide transcriptomics through machine learning optimization Léa Wagner,An Hoang,Olivier Rue,Olivier Delumeau,Valentin Louxet al. SEED 2025, Jun 2025, Houston, United States Poster de conférence hal-05155548v1
Responsible Research and Innovation Exploration of the transcriptional landscapes of culturable and nonculturable bacteria using in vitro transcription emulators Olivier Borkowski,Léa Wagner,Matthieu Jules BioSynSys 2023: Symposium on Synthetic and Systems Biology, Jul 2023, Toulouse, France Poster de conférence hal-04279297v1
A large-scale exploration of cell-free compositions to maximize protein production using active learning Olivier Borkowski,Mathilde Koch,Agnès Zettor,Amir Pandi,Angelo Cardoso Batistaet al. Structural Biology and Chemistry Department days, Dec 2019, paris, France Poster de conférence hal-04292156v1
Large scale active-learning-guided exploration for in vitro protein production optimization Olivier Borkowski,Mathilde Koch,Agnès Zettor,Jean-Loup Faulon Structural Biology and Chemistry Department days, Jun 2019, Paris, France Poster de conférence hal-03852944v1
Cell-free prediction of protein expression costs for growing cells Olivier Borkowski,Carlos Bricio,Maria Murgiano,Guy-Bart Stan,Tom Ellis Synthetic Biology: Engineering, Evolution & Design conference, Jun 2018, Phoenix, United States Poster de conférence hal-03852928v1
Cell-free prediction of protein expression costs Olivier Borkowski,Guy-Bart Stan,Tom Ellis Control Engineering Synthetic Biology Workshop, Jul 2017, London, United Kingdom Poster de conférence hal-03852866v1
Cell-free prediction of protein expression costs for growing cells Olivier Borkowski,Carlos Bricio,Maria Murgiano,Guy-Bart Stan,Tom Ellis SB7.0: The Seventh International Meeting on Synthetic Biology, Jun 2017, Singapore, Singapore Poster de conférence hal-03852886v1
Overloaded and stressed: whole-cell considerations for bacterial synthetic biology Olivier Borkowski,Francesca Ceroni,Guy-Bart Stan,Tom Ellis SBUK 2017, Nov 2017, Manchester, United Kingdom Poster de conférence hal-03852899v1
Cell-free prediction of protein expression costs for growing cells Olivier Borkowski,Carlos Bricio,Maria Murgiano,Guy-Bart Stan,Tom Ellis 1st European Congress on Cell-Free Synthetic Biology, Apr 2017, Ascona, Switzerland Poster de conférence hal-03852856v1
Overloaded and stressed: whole-cell considerations for bacterial synthetic biology Olivier Borkowski,Francesca Ceroni,Guy-Bart Stan,Tom Ellis Synthetic Biology: Engineering, Evolution & Design conference, Jul 2016, Chicago, United States Poster de conférence hal-03852785v1
Cell-free prediction of protein expression costs in bacteria Olivier Borkowski,Guy-Bart Stan,Tom Ellis SBUK 2016, Nov 2016, Edinburgh, United Kingdom Poster de conférence hal-03852836v1
Cell-free prediction of protein expression costs for growing cells Olivier Borkowski,Tom Ellis Synthetic Biology: Engineering, Evolution & Design conference, Jun 2015, Boston, United States Poster de conférence hal-03852769v1
Autonomous control of heterologous gene expression in bacteria Olivier Borkowski,Pakpoom Subsoontorn,Drew Endy SYNBERC symposium, Jul 2014, Berkeley, United States Poster de conférence hal-03852736v1
Hands-free control of heterologous gene expression in batch cultures Olivier Borkowski,Pakpoom Subsoontorn,Drew Endy e Synthetic Biology: Engineering, Evolution & Design conference, Jul 2014, Los angeles, United States Poster de conférence hal-03852754v1
Hands-free control of heterologous gene expression in batch cultures Olivier Borkowski,Pakpoom Subsoontorn,Drew Endy Stanford BioX, Jul 2013, Stanford, United States Poster de conférence hal-03852719v1
Growth-rate-dependent protein production in bacteria Olivier Borkowski,Anne Goelzer,Marc Schaffer,Magali Calabre,Ulrike Mäderet al. 13th international conference on Systems Biology, 2012, 13th international conference on Systems Biology, Canada Poster de conférence hal-03852702v1

Vidéo (3)

Maximization of production in cell-free systems using active learning - Dr. Olivier Borkowski Olivier Borkowski 2025 Vidéo hal-05019485v1
Build-aCell seminar Olivier Borkowski: Challenges and advantages of resource limitation in cell-free Olivier Borkowski 2023 Vidéo hal-04279327v1
Active learning cell free protein production optimization Olivier Borkowski 2022 Vidéo hal-04279345v1

Pré-publication, Document de travail (2)

Cell-free genome-wide transcriptomics through machine learning optimization Léa Wagner,An Hoang,Olivier Rue,Olivier Delumeau,Valentin Louxet al. 2025 Pré-publication, Document de travail hal-05170246v1
Hands-free control of heterologous gene expression in batch cultures Olivier Borkowski,Drew Endy,Pakpoom Subsoontorn 2022 Pré-publication, Document de travail hal-03851825v1

Communication dans un congrès (6)

mRNA and genome expression in cell-free systems Olivier Borkowski 2025 Synthetic Biology: Engineering, Evolution, & Design (SEED), Jun 2025, Houston, United States Communication dans un congrès hal-05156300v1
Maximization of production in cell-free systems Olivier Borkowski Biomanufacturing and micorbiology symposium and workshop, Beckman, Mar 2024, Dublin, France Communication dans un congrès hal-04505662v1
Study of the molecular mechanisms involved in the use of raffinose, a legume dietary fibre, by bacteria of the intestinal microbiota. Paul Biscarrat,Olivier Borkowski,Claire Cherbuy Symposium Micalis 2022, Dec 2022, Jouy-en-Josas, France Communication dans un congrès hal-04285907v1
A large-scale exploration of cell-free compositions to maximize protein production using active learning Olivier Borkowski,Mathilde Koch,Agnès Zettor,Amir Pandi,Angelo Cardoso Batistaet al. Cell Free Systems Conference, Dec 2019, Boston (MA), United States Communication dans un congrès hal-04291932v1
A large-scale exploration of cell-free compositions to maximize protein production using reinforcement learning Olivier Borkowski,Mathilde Koch,Jean-Loup Faulon EMBO workshop “Creating is Understand-ing: Synthetic Biology Masters Complexity, EMBO, Sep 2019, Heildelberg, Germany Communication dans un congrès hal-04275652v1
Relationship between protein production and cell physiology Olivier Borkowski EUSYNBIOS symposium, Oct 2018, Toulouse, France Communication dans un congrès hal-04291918v1

Article dans une revue (12)

Reconstituting alternative life using the test-bed of cell-free systems Maud Hofmann,Farouk Abdo,Olivier Borkowski,Manish Kushwaha Philosophical Transactions of the Royal Society B: Biological Sciences, In press, 380 (1936), pp.20240293. ⟨10.1098/rstb.2024.0293⟩ Article dans une revue (article de synthèse) hal-05027262v1
What remains from living cells in bacterial lysate-based cell-free systems Léa Wagner,Matthieu Jules,Olivier Borkowski Computational and Structural Biotechnology Journal, 2023, 21, pp. 3173-3182. ⟨10.1016/j.csbj.2023.05.025⟩ Article dans une revue hal-04118475v1
Large scale active-learning-guided exploration for in vitro protein production optimization Olivier Borkowski,Mathilde Koch,Agnes Zettor,Amir Pandi,Angelo Cardoso Batistaet al. Nature Communications, 2020, 11 (1), pp.1872. ⟨10.1038/s41467-020-15798-5⟩ Article dans une revue pasteur-02552065v1
Custom-made transcriptional biosensors for metabolic engineering Mathilde Koch,Amir Pandi,Olivier Borkowski,A.C. Batista,Jean-Loup Faulon Current Opinion in Biotechnology, 2019, 59, pp. 78-84. ⟨10.1016/j.copbio.2019.02.016⟩ Article dans une revue hal-04275369v1
Custom-made transcriptional biosensors for metabolic engineering. Mathilde Koch,Amir Pandi,Olivier Borkowski,Angelo Cardoso Batista,Jean-Loup Faulon Current Opinion in Biotechnology, 2019, 59, pp.78-84. ⟨10.1016/j.copbio.2019.02.016⟩ Article dans une revue (article de synthèse) hal-02627127v1
Optimizing cell-free biosensors to monitor enzymatic production. Amir Pandi,Ioana Grigoras,Olivier Borkowski,Jean-Loup Faulon ACS Synthetic Biology, 2019, 8 (8), pp.1952-1957. ⟨10.1021/acssynbio.9b00160⟩ Article dans une revue hal-02625334v1
Cell-free prediction of protein expression costs for growing cells Olivier Borkowski,Carlos Bricio,Michela Murgiano,Brooke Rothschild-Mancinelli,Guy-Bart Stanet al. Nature Communications, 2018, 9 (1), pp.1457. ⟨10.1038/s41467-018-03970-x⟩ Article dans une revue hal-03851801v1
Burden-driven feedback control of gene expression Francesca Ceroni,Alice Boo,Simone Furini,Thomas Gorochowski,Olivier Borkowskiet al. Nature Methods, 2018, 15 (5), pp.387-393. ⟨10.1038/nmeth.4635⟩ Article dans une revue hal-03851810v1
Models for cell-free synthetic biology: Make prototyping easier, better, and faster Mathilde Koch,Jean-Loup Faulon,Olivier Borkowski Frontiers in Bioengineering and Biotechnology, 2018, 6, pp.1-6. ⟨10.3389/fbioe.2018.00182⟩ Article dans une revue (article de synthèse) hal-02621501v1
On the record with E. coli DNA Olivier Borkowski,Charlie Gilbert,Tom Ellis Science, 2016, 353 (6298), pp.444-445. ⟨10.1126/science.aah4438⟩ Article dans une revue hal-03851816v1
Translation elicits a growth rate-dependent, genome-wide, differential protein production in &lt;em&gt;Bacillus subtilis&lt;/em&gt; Olivier Borkowski,Anne Goelzer,Marc Schaffer,Magali Calabre,Ulrike Mäderet al. Molecular Systems Biology, 2016, 12 (5), pp.870. ⟨10.15252/msb.20156608⟩ Article dans une revue hal-02640581v1
Overloaded and stressed: whole-cell considerations for bacterial synthetic biology Olivier Borkowski,Francesca Ceroni,Guy-Bart Stan,Tom Ellis Current Opinion in Microbiology, 2016, 33, ⟨10.1016/j.mib.2016.07.009⟩ Article dans une revue hal-03851923v1

Proceedings/Recueil des communications (1)

Journées Scientifiques du Département Sciences de la Vie et Santé - AgroParisTech Carmen Bessa-Gomes,Anaïs Cazals,Blanche Collard,François Chiron,Matthieu Juleset al. Journées Scientifiques du Département Sciences de la Vie et Santé - AgroParisTech, Apr 2024, Palaiseau, France. 2025 Proceedings/Recueil des communications hal-05339375v1

Cours (4)

Celullar Economics in Cell-Free Olivier Borkowski Master. Université paris-saclay, France. 2025 Cours hal-04405950v2
Protein synthesis in cell free systems Olivier Borkowski Doctoral. Biomolecule synthesis: Part I, France. 2024 Cours hal-04741476v1
Cell-free systems: Gene expression outside of the cell Olivier Borkowski Doctoral. France. 2024 Cours hal-04837424v1
Cell-free systems Gene expression outside of the cell Olivier Borkowski Engineering school. AgroParisTech - INRAE - Campus Agro Paris-Saclay, France. 2023 Cours hal-04336158v1

Article de blog scientifique (1)

Active learning leads to highly efficient predictions in cell-free systems Olivier Borkowski 2020 Article de blog scientifique hal-04279308v1

Chapitre d'ouvrage (1)

Synthetic Biology at the Hand of Cell-Free Systems Amir Pandi,Olivier Borkowski,Jean-Loup Faulon Advances in Synthetic Biology, Springer Singapore, pp. 275-288, 2020, ⟨10.1007/978-981-15-0081-7_16⟩ Chapitre d'ouvrage hal-03852064v1

Thèse (1)

Growth-rate-dependent protein production in bacteria Olivier Borkowski Molecular biology. Paris 5, 2013. English. ⟨NNT : ⟩ Thèse tel-03853024v1