Olivier Borkowski

47
Documents

Domaines de recherche

Sciences du Vivant [q-bio]

Compétences

Cell-free Molecular Biology Machine Learning Mathematical modelling Synthetic Biology System Biology Transcriptomics Microbiology

Publications

Publications

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Cell-free genome-wide transcriptomics through machine learning optimization

Léa Wagner , An Hoang , Olivier Rue , Olivier Delumeau , Valentin Loux et al.

SEED 2025, Jun 2025, Houston, United States

Poster de conférence hal-05155548v1
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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

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
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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 Batista et al.

Structural Biology and Chemistry Department days, Dec 2019, paris, France

Poster de conférence hal-04292156v1

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 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

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

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 Mäder et al.

13th international conference on Systems Biology, 2012, 13th international conference on Systems Biology, Canada

Poster de conférence hal-03852702v1
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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 Batista et 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
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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
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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
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Large scale active-learning-guided exploration for in vitro protein production optimization

Olivier Borkowski , Mathilde Koch , Agnes Zettor , Amir Pandi , Angelo Cardoso Batista et 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 Stan et 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 Borkowski et al.

Nature Methods, 2018, 15 (5), pp.387-393. ⟨10.1038/nmeth.4635⟩

Article dans une revue hal-03851810v1
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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
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Translation elicits a growth rate-dependent, genome-wide, differential protein production in <em>Bacillus subtilis</em>

Olivier Borkowski , Anne Goelzer , Marc Schaffer , Magali Calabre , Ulrike Mäder et al.

Molecular Systems Biology, 2016, 12 (5), pp.870. ⟨10.15252/msb.20156608⟩

Article dans une revue hal-02640581v1

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

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
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Journées Scientifiques du Département Sciences de la Vie et Santé - AgroParisTech

Carmen Bessa-Gomes , Anaïs Cazals , Blanche Collard , François Chiron , Matthieu Jules et al.

Journées Scientifiques du Département Sciences de la Vie et Santé - AgroParisTech, Apr 2024, Palaiseau, France. 2025

Proceedings/Recueil des communications hal-05339375v1
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Celullar Economics in Cell-Free

Olivier Borkowski

Master. Université paris-saclay, France. 2025

Cours hal-04405950v2

Cell-free systems: Gene expression outside of the cell

Olivier Borkowski

Doctoral. France. 2024

Cours hal-04837424v1
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Protein synthesis in cell free systems

Olivier Borkowski

Doctoral. Biomolecule synthesis: Part I, France. 2024

Cours hal-04741476v1
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Cell-free systems Gene expression outside of the cell

Olivier Borkowski

Engineering school. AgroParisTech - INRAE - Campus Agro Paris-Saclay, France. 2023

Cours hal-04336158v1