Matthieu Jules

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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

First step towards whole genome cloning of Bacillus subtilis in yeast by CReasPy-Fusion

Julien Barret , Gabrielle Guesdon , Géraldine Gourgues , Anne-Gaëlle Planson , Pascal Sirand-Pugnet et al.

SynCell, Apr 2024, Toulouse, France

Poster de conférence hal-04693592v1

OSIRIS: Orthogonal Sigma for Internal Resources Implementation towards Synthesis

Simon Morin , Maya Long , Matthieu Jules , Etienne Dervyn

Bacell 2023, Nov 2023, Kobe, Japan

Poster de conférence hal-04269820v1
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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

First step towards whole genome cloning of Bacillus subtilis in yeast by CReasPy-Fusion

Barret Julien , Gabrielle Guesdon , Geraldine Gourgues , Anne-Gaëlle Planson , Pascal Sirand-Pugnet et al.

CRISPR conference 2023, Jun 2023, Würzburg, Germany

Poster de conférence hal-04693946v1
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Construction and directed evolution of Bacillus subtilis synthetic consortia

Nathalie Laforge , Léa Wagner , Matthieu Jules , Anne Gaëlle Planson

BACELL2023, Nov 2023, KOBE, Japan

Poster de conférence hal-04291770v1
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Greedy reduction of Bacillus subtilis genome yields emergent phenotypes

Etienne Dervyn , Anne-Gaëlle Planson , Kosei Tanaka , Victor Chubukov , Cyprien Guérin et al.

BACELL2023, Nov 2023, Kobe, Japan.

Poster de conférence hal-04316425v1
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Mismatch repair in Bacillus subtilis compensates for the correction bias of PolC exonuclease

Ira Tanneur , Etienne Dervyn , Matthieu Jules , Pierre Nicolas

Society for Molecular Biology and Evolution ( SMBE ) 2023, Jul 2023, Ferrara, Italy. 2023

Poster de conférence hal-04163622v1

Engineering of synthetic microbial consortia of Bacillus subtilis for lignocellulose degradation

Léa Wagner , Nathalie Laforge , Matthieu Jules , Anne-Gaëlle Planson

Congrès Junior Pluridisciplinaire, Sep 2022, Gif-sur-Yvette (École Normale Supérieure de Paris Saclay), France

Poster de conférence hal-04316369v1
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Ingénierie de consortia microbiens synthétiques de Bacillus subtilis à visée biotechnologique

Léa Wagner , Nathalie Laforge , Matthieu Jules , Anne-Gaëlle Planson

Congrès junior pluridisciplinaire, Jun 2022, Gif-sur Yvette, France

Poster de conférence hal-04298531v1
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Construction of synthetic bacterial consortia based on metabolic mutualism

Nathalie Laforge , Léa Wagner , Matthieu Jules , Anne-Gaëlle Planson

BioSynSys, Sep 2022, Paris, France

Poster de conférence hal-04316339v1

Development of key synthetic biology technologies for the high-throughput construction of semi-synthetic Bacillus subtilis -derived chassis strains

Gabrielle Guesdon , Flavie Metais , Thomas Ipoutcha , Etienne Dervyn , Pascal Sirand-Pugnet et al.

BioSynSys/MaxSynBio/SynBio Symposium, Nov 2019, Bordeaux, France. 2019

Poster de conférence hal-02738277v1

Mechanism of action of flavonoids as antibacterial compounds in the Gram-positive bacterium Bacillus subtilis.

Cécile Jacry , Matthieu Jules , Anne-Gaëlle Planson

Biosynsys, Nov 2019, Bordeaux, France

Poster de conférence hal-04316382v1

Development of screening methods to detect flavonoids from engineered Escherichia coli strains

Cécile Jacry , Matthieu Jules , Anne-Gaëlle Planson

BioSynSys, Oct 2017, Toulouse, France

Poster de conférence hal-04316454v1

Bacillus subtilis genome engineering and streamlining

Anne-Gaëlle Planson , Etienne Dervyn , Kosei Tanaka , Philippe Noirot , Matthieu Jules

Synthetic Biology Congress, Oct 2016, Londres, United Kingdom

Poster de conférence hal-04316478v1

Genome engineering in Bacillus subtilis

Anne-Gaëlle Planson , Michael Mangan , Philippe Noirot , Etienne Dervyn , Matthieu Jules

BioSynSys, Jun 2016, Bordeaux, France

Poster de conférence hal-04316527v1

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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Comprehensive mapping of transcription terminator Rho utilization (Rut) sites across the Bacillus subtilis genome

Mildred Delaleau , Vladimir Bidnenko , Eric Eveno , Gergana Kostova , Johnathan C Black et al.

Nucleic Acids Research, 2025, 53 (15), ⟨10.1093/nar/gkaf765⟩

Article dans une revue hal-05229886v1
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Multiplex Genome Editing and Regulation in <i>Bacillus subtilis</i> with CRISPR-MAD7

Nathalie Laforge , Magali Calabre , Matthieu Jules , Anne-Gaëlle Planson

ACS Synthetic Biology, 2025, 14, pp.3142 - 3153. ⟨10.1021/acssynbio.5c00274⟩

Article dans une revue hal-05237953v1
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The mutational landscape of Bacillus subtilis conditional hypermutators shows how proofreading skews DNA polymerase error rates

Ira Tanneur , Etienne Dervyn , Cyprien Guérin , Guillaume Kon Kam King , Matthieu Jules et al.

Nucleic Acids Research, 2025, 53 (5), pp.gkaf147. ⟨10.1093/nar/gkaf147⟩

Article dans une revue hal-04986201v1

Deciphering the mechanisms of action underlying probiotic properties of Shouchella clausii by a functional genomics approach

A. Lashermes , E. Mathieu , L. Marinelli , V. Léjard , E. Dervyn et al.

Beneficial Microbes, 2025, 16 (3), pp.347-362. ⟨10.1163/18762891-bja00050⟩

Article dans une revue hal-05322017v1
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Complex sporulation-specific expression of transcription termination factor Rho highlights its involvement in Bacillus subtilis cell differentiation

Vladimir Bidnenko , Arnaud Chastanet , Christine Péchoux , Yulia Redko-Hamel , Olivier Pellegrini et al.

Journal of Biological Chemistry, 2024, 300 (12), pp.107905. ⟨10.1016/j.jbc.2024.107905⟩

Article dans une revue hal-04773401v1
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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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Greedy reduction of Bacillus subtilis genome yields emergent phenotypes of high resistance to a DNA damaging agent and low evolvability

Etienne Dervyn , Anne-Gaëlle Planson , Kosei Tanaka , Victor Chubukov , Cyprien Guérin et al.

Nucleic Acids Research, 2023, 51 (6), pp.2974-2992. ⟨10.1093/nar/gkad145⟩

Article dans une revue hal-04094194v1
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Termination factor Rho mediates transcriptional reprogramming of Bacillus subtilis stationary phase

Vladimir Bidnenko , Pierre Nicolas , Cyprien Guérin , Sandra Dérozier , Arnaud Chastanet et al.

PLoS Genetics, 2023, 19 (2), pp.e1010618. ⟨10.1371/journal.pgen.1010618⟩

Article dans une revue hal-03974108v1
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Combining Fusion of Cells with CRISPR-Cas9 Editing for the Cloning of Large DNA Fragments or Complete Bacterial Genomes in Yeast

Gabrielle Guesdon , Géraldine Gourgues , Fabien Rideau , Thomas Ipoutcha , Lucía Manso-Silván et al.

ACS Synthetic Biology, 2023, 12 (11), pp.3252-3266. ⟨10.1021/acssynbio.3c00248⟩

Article dans une revue hal-04522926v1
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Four species of bacteria deterministically assemble to form a stable biofilm in a millifluidic channel

A. Monmeyran , W. Benyoussef , P. Thomen , N. Dahmane , Aurélie Baliarda et al.

npj Biofilms and Microbiomes, 2021, 7 (1), pp.64. ⟨10.1038/s41522-021-00233-4⟩

Article dans une revue hal-03342840v1

SppI Forms a Membrane Protein Complex with SppA and Inhibits Its Protease Activity in Bacillus subtilis

Gabriela Henriques , Stephen Mcgovern , Jolanda Neef , Minia Antelo-Varela , Friedrich Götz et al.

MSphere, 2020, 5 (5), ⟨10.1128/mSphere.00724-20⟩

Article dans une revue hal-03334428v1

Bacterial growth physiology and RNA metabolism

Anne-Gaëlle Planson , Vincent Sauveplane , Etienne Dervyn , Matthieu Jules

Biochimica et Biophysica Acta - Gene Regulatory Mechanisms , 2020, 1863 (5), pp.194502. ⟨10.1016/j.bbagrm.2020.194502⟩

Article dans une revue hal-02940832v1
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Extrinsic noise prevents the independent tuning of gene expression noise and protein mean abundance in bacteria

A. Deloupy , V. Sauveplane , J. Robert , S. Aymerich , M. Jules et al.

Science Advances , 2020, 6 (41), pp.eabc3478. ⟨10.1126/sciadv.abc3478⟩

Article dans une revue hal-02989817v1
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Differentiation of vegetative cells into spores: a kinetic model applied to <em>bacillus subtilis</em>

Emilie Gauvry , Anne-Gabrielle Mathot , Olivier Couvert , Ivan Leguerinel , Matthieu Jules et al.

Applied and Environmental Microbiology, 2019, 85 (10), pp. 1-13. ⟨10.1128/AEM.00322-19⟩

Article dans une revue hal-02617842v1
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The logics of metabolic regulation in bacteria challenges biosensor-based metabolic engineering

Matthieu Jules

Microbial Cell , 2018, 5 (1), pp.56-59. ⟨10.15698/mic2018.01.610⟩

Article dans une revue hal-02620319v1
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Molecular and Physiological Logics of the Pyruvate-Induced Response of a Novel Transporter in Bacillus subtilis

Teddy Charbonnier , Dominique Le Coq , Stephen T Mcgovern , Magali Calabre , Olivier Delumeau et al.

mBio, 2017, 8 (5), pp.1-16. ⟨10.1128/mBio.00976-17⟩

Article dans une revue hal-01814500v1
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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
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A part toolbox to tune genetic expression in Bacillus subtilis

Sarah Guiziou , Vincent Sauveplane , Hung-Ju Chang , Caroline Clerté , Nathalie Declerck et al.

Nucleic Acids Research, 2016, 44 (15), pp.7495-7508. ⟨10.1093/nar/gkw624⟩

Article dans une revue hal-02639876v1

Quantitative prediction of genome-wide resource allocation in bacteria

Anne Goelzer , Jan Muntel , Victor Chubukov , Matthieu Jules , Eric Prestel et al.

Metabolic Engineering, 2015, 32, pp.232-243. ⟨10.1016/j.ymben.2015.10.003⟩

Article dans une revue hal-01536511v1
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Nicotinic acid modulates Legionella pneumophila gene expression and induces virulence traits.

Rachel L Edwards , Andrew Bryan , Matthieu Jules , Kaoru Harada , Carmen Buchrieser et al.

Infection and Immunity, 2013, 81 (3), pp.945-55. ⟨10.1128/IAI.00999-12⟩

Article dans une revue pasteur-01422856v1
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Transcriptional regulation is insufficient to explain substrate-induced flux changes in [i]Bacillus subtilis[/i]

Victor Chubukov , Markus Uhr , Ludovic Le Chat , Roelco J Kleijn , Matthieu Jules et al.

Molecular Systems Biology, 2013, 9, ⟨10.1038/msb.2013.66⟩

Article dans une revue hal-01204283v1

Condition-dependent transcriptome reveals high-level regulatory architecture in Bacillus subtilis

Pierre P. Nicolas , Ulrike U. Mäder , Etienne Dervyn , Tatiana Rochat , Aurelie A. Leduc et al.

Science, 2012, 335 (6072), pp.1103-1106. ⟨10.1126/science.1206848⟩

Article dans une revue hal-01000245v1
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Reconciling molecular regulatory mechanisms with noise patterns of bacterial metabolic promoters in induced and repressed states

Matthew L. M. L. Ferguson , Dominique D. Le Coq , Matthieu Jules , Stephane S. Aymerich , Ovidiu O. Radulescu et al.

Proceedings of the National Academy of Sciences of the United States of America, 2012, 109 (1), pp.155 - 160. ⟨10.1073/pnas.1110541108⟩

Article dans une revue hal-01004232v1

Condition-Dependent Transcriptome Reveals High-Level Regulatory Architecture in Bacillus subtilis

P. Nicolas , U. Mader , Etienne Dervyn , T. Rochat , A. Leduc et al.

Science, 2012, 335 (6072), pp.1103-1106. ⟨10.1126/science.1206848⟩

Article dans une revue hal-03343060v1

BasyLiCA: a tool for automatic processing of a Bacterial Live Cell Array

Leslie Aïchaoui , Matthieu Jules , Ludovic Le Chat , Stephane Aymerich , Vincent Fromion et al.

Bioinformatics, 2012, 28 (20), pp.2705-2706. ⟨10.1093/bioinformatics/bts422⟩

Article dans une revue hal-01204252v1
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Global Network Reorganization During Dynamic Adaptations of Bacillus subtilis Metabolism

Joerg Martin Buescher , Wolfram Liebermeister , Matthieu Jules , Markus Uhr , Jan Muntel et al.

Science, 2012, 335 (6072), pp. 1099-1103. ⟨10.1126/science.1206871⟩

Article dans une revue hal-03968015v1
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Malate-mediated carbon catabolite repression in bacillus subtilis involves the HPrK/CcpA pathway

Frederik M. Meyer , Matthieu Jules , Felix M. P. Mehne , Dominique Le Coq , Jens J. Landmann et al.

The Journal of applied bacteriology, 2011, 193 (24), pp.6939 - 6949. ⟨10.1128/JB.06197-11⟩

Article dans une revue hal-01019483v1

GamA is a eukaryotic-like glucoamylase responsible for glycogen- and starch-degrading activity of <em>Legionella pneumophila</em>

Vroni Herrmann , Anja Eidner , Kerstin Rydzewski , Inga Blädel , Matthieu Jules et al.

International Journal of Medical Microbiology, 2011, 301 (2), pp.133-139. ⟨10.1016/j.ijmm.2010.08.016⟩

Article dans une revue istex hal-02647334v1

Absolute quantification of gene expression in individual bacterial cells using two-photon fluctuation microscopy

Matthew L. Ferguson , Dominique Le Coq , Matthieu Jules , Stephane Aymerich , Nathalie Declerck et al.

Analytical Biochemistry, 2011, 419 (2), pp.250 - 259. ⟨10.1016/j.ab.2011.08.017⟩

Article dans une revue istex hal-01019478v1

The <em>Legionella pneumophila</em> LetA/LetS two-component system exhibits rheostat-like behavior

Rachel L Edwards , Matthieu Jules , Tobias Sahr , Carmen Buchrieser , Michele S. Swanson

Infection and Immunity, 2010, 78 (6), pp.2571-2583. ⟨10.1128/IAI.01107-09⟩

Article dans une revue hal-02662798v1
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Isotopologue profiling of <em>Legionella pneumophila</em>: role of serine and glucose as carbon substrates.

Eva Eylert , Vroni Herrmann , Matthieu Jules , Nadine Gillmaier , Monika Lautner et al.

Journal of Biological Chemistry, 2010, 285 (29), pp.22232-22243. ⟨10.1074/jbc.M110.128678⟩

Article dans une revue hal-02661810v1
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Metabolic fluxes during strong carbon catabolite repression by malate in <em>Bacillus subtilis</em>

Roelco J. Kleijn , Joerg M. Buescher , Ludovic L. Le Chat , Matthieu Jules , Stephane S. Aymerich et al.

Journal of Biological Chemistry, 2010, 285 (3), pp.1587-1596. ⟨10.1074/jbc.M109.061747⟩

Article dans une revue hal-02663413v1

The <em>Legionella pneumophila</em> F-box protein Lpp2082 (AnkB) modulates ubiquitination of the host protein parvin B and promotes intracellular replication.

Mariella Lomma , Delphine Dervins-Ravault , Monica Rolando , T. Nora , Hayley J. Newton et al.

Cellular Microbiology, 2010, 12 (9), pp.1272-1291. ⟨10.1111/j.1462-5822.2010.01467.x⟩

Article dans une revue hal-02661576v1

pBaSysBioII: an integrative plasmid generating gfp transcriptional fusions for high-throughput analysis of gene expression in <em>Bacillus subtilis</em>

Eric Botella , Mark Fogg , Matthieu Jules , Sjouke Piersma , Geoff Doherty et al.

Microbiology, 2010, 156 (Pt 6), pp.1600-1608. ⟨10.1099/mic.0.035758-0⟩

Article dans une revue hal-02663195v1

Two small ncRNAs jointly govern virulence and transmission in <em>Legionella pneumophila</em>

Tobias Sahr , Holger Brüggemann , Matthieu Jules , Mariella Lomma , Christiane Albert-Weissenberger et al.

Molecular Microbiology, 2009, 72 (3), pp.741-762. ⟨10.1111/j.1365-2958.2009.06677.x⟩

Article dans une revue hal-02657418v1
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The <em>Bacillus subtilis ywjI (glpX)</em> gene encodes a class II fructose-1,6-bisphosphatase, functionally equivalent to the class III Fbp enzyme

Matthieu Jules , Ludovic L. Le Chat , Stephane S. Aymerich , Dominique D. Le Coq

Journal of Bacteriology, 2009, 191 (9), pp.3168-3171. ⟨10.1128/JB.01783-08⟩

Article dans une revue hal-02658797v1
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New Insights into Trehalose Metabolism by Saccharomyces cerevisiae: NTH2 Encodes a Functional Cytosolic Trehalase, and Deletion of TPS1 Reveals Ath1p-Dependent Trehalose Mobilization

Matthieu Jules , Gemma Beltran , Jean Marie François , Jean-Luc Parrou

Applied and Environmental Microbiology, 2008, 74 (3), pp.605-614. ⟨10.1128/AEM.00557-07⟩

Article dans une revue hal-02559752v1

Legionella pneumophila adaptation to intracellular life and the host response: clues from genomics and transcriptomics

Matthieu Jules , Carmen Buchrieser

FEBS Letters, 2007, 581 (15), pp.2829-2838. ⟨10.1016/j.febslet.2007.05.026⟩

Article dans une revue (article de synthèse) istex hal-02661231v1

Virulence strategies for infecting phagocytes deduced from the <em>in vivo</em> transcriptional program of <em>Legionella pneumophila</em>

Holger Brüggemann , Arne Hagman , Matthieu Jules , Odile Sismeiro , Marie-Agnès Dillies et al.

Cellular Microbiology, 2006, 8 (8), pp.1228-1240. ⟨10.1111/j.1462-5822.2006.00703.x⟩

Article dans une revue hal-02661574v1
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Acid trehalase in yeasts and filamentous fungi: Localization, regulation and physiological function

Jean-Luc Parrou , Matthieu Jules , Gemma Beltran , Jean François

FEMS Yeast Research, 2005, 5 (6-7), pp.503-511. ⟨10.1016/j.femsyr.2005.01.002⟩

Article dans une revue hal-02559672v1
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Autonomous oscillations in Saccharomyces cerevisiae during batch cultures on trehalose

Matthieu Jules , Jean Marie François , Jean-Luc Parrou

FEBS Journal, 2005, 272 (6), pp.1490-1500. ⟨10.1111/j.1742-4658.2005.04588.x⟩

Article dans une revue hal-02559635v1
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Two Distinct Pathways for Trehalose Assimilation in the Yeast Saccharomyces cerevisiae

Matthieu Jules , Vincent Guillou , Jean Marie François , Jean-Luc Parrou

Applied and Environmental Microbiology, 2004, 70 (5), pp.2771-2778. ⟨10.1128/AEM.70.5.2771-2778.2004⟩

Article dans une revue hal-02559418v1
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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

Functional characterization of the genome of the Bacillus subtilis phage SPP1 using Synthetic Biology approaches

Arthur Loubat , Paulo Tavares , Matthieu Jules

BioSynSys 2024, Jun 2024, Montpellier, France

Communication dans un congrès hal-05111109v1

Construction and directed evolution of Bacillus subtilis synthetic consortia

Nathalie Laforge , Léa Wagner , Matthieu Jules , Anne-Gaëlle Planson

BioSynSys, Jul 2023, Toulouse, France

Communication dans un congrès hal-04316327v1

Genome-scale engineering of Bacillus subtilis yields emergent phenotypes and allows to revisit concepts of minimal genomes

Matthieu Jules , Etienne Dervyn , Anne-Gaëlle Planson , Kosei Tanaka , Victor Chubukov et al.

Bioengineering and Synthetic Biology, Nov 2022, Gif-sur-Yvette | Île-de-France, France

Communication dans un congrès hal-05123414v1

Exploring mutational landscapes of Bacillus subtilis strains with increased replication error rate and/or impaired mismatch repair

Ira Tanneur , Matthieu Jules , Pierre Nicolas

Subtillery 2021, Jun 2021, Online conference, United States

Communication dans un congrès hal-05111147v1

Mechanism of action of flavonoids in the Gram-positive bacterium Bacillus subtilis

Cécile Jacry , Matthieu Jules , Anne-Gaëlle Planson

MICROBES - 15ème congrès national de la SFM, Sep 2019, Paris, France

Communication dans un congrès hal-04316436v1

Mechanism of action of flavonoids as antibacterial compounds in the Gram-positive bacterium Bacillus subtilis.

Cécile Jacry , Matthieu Jules , Anne-Gaëlle Planson

EMBO workshop - Creating is Understanding: Synthetic Biology Masters Complexity, Sep 2019, Heidelberg, Germany

Communication dans un congrès hal-04316392v1
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Quantitative prediction of genome-wide resource allocation in bacteria

Anne Goelzer , Jan Muntel , Victor Chubukov , Matthieu Jules , Eric Prestel et al.

ISGSB 2016: International Study Group for Systems Biology, Oct 2016, Jena, Germany

Communication dans un congrès hal-02798691v1
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Two types of transcriptional repression in living cells of [i]Bacillus subtilis[/i] characterized by number and brightness analysis

Matthew L. Ferguson , Dominique Le Coq , Matthieu Jules , Bryan Chun , Stephane Aymerich et al.

55. Annual Meeting of the Biophysical-Society, Mar 2011, Baltimore, Maryland, United States. ⟨10.1016/j.bpj.2010.12.1179⟩

Communication dans un congrès hal-01190611v1