Publications

Multiscale physics of living systems

1 Synthetic Ecosystems: From the Test Tube to the Biosphere
Ricard Solé, Victor Maull, Daniel R Amor, Jordi Pla Mauri, Conde-Pueyo Núria
2024 - ACS Synthetic Biology

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2 Stepwise molecular specification of excitatory synapse diversity onto cerebellar Purkinje cells
Maëla Paul, Séverine Sigoillot, Léa Marti, Francisco Urra Quiroz, Marine Delagrange, Hiu Cheung, David Martinelli, Elie Oriol, Vincent Hakim, Philippe Mailly, Fekrije Selimi
2024 - Nature Neuroscience

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3 Cooperative growth in microbial communities is a driver of multistability
William Lopes, Daniel Amor, Jeff Gore
2024 - Nature Communications

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4 Observing G4 formation and its resolution by Pif1 in real time by manipulation under magnetic tweezers
Jessica Valle-Orero, Martin Rieu, Jean-François Allemand, Dulamkhuu Bujaa, Alexandra Joubert, Phong Lan Thao Tran, Vincent Croquette, Jean-Baptiste Boulé
2024 -

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5 Caged Dexamethasone to Photo‐control the Development of Embryos through Activation of the Glucocorticoid Receptor
Mrinal Mandal, Pierluigi Scerbo, Ian Coghill, Jean‐françois Riou, Christian Bochet, Bertrand Ducos, David Bensimon, Thomas Le Saux, Isabelle Aujard, Ludovic Jullien
2024 - Chemistry - A European Journal

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6 Coencapsulation of Immunosuppressive Drug with Anti-Inflammatory Molecule in Pickering Emulsions as an Innovative Therapeutic Approach for Inflammatory Dermatoses
Maxime Sintès, Petra Kovjenic, Liasmine Haine, Kevin Serror, Mohamed Beladjine, Véronique Parietti, Marine Delagrange, Bertrand Ducos, Jean-David Bouaziz, David Boccara, Maurice Mimoun, Armand Bensussan, Martine Bagot, Nicolas Huang, Laurence Michel
2024 - JID Innovations

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7 Fluorescence to measure light intensity
Aliénor Lahlou, Hessam Sepasi Tehrani, Ian Coghill, Yuriy Shpinov, Mrinal Mandal, Marie-Aude Plamont, Isabelle Aujard, Yuxi Niu, Ladislav Nedbal, Dusan Lazár, Pierre Mahou, Willy Supatto, Emmanuel Beaurepaire, Isabelle Eisenmann, Nicolas Desprat, Vincent Croquette, Raphaël Jeanneret, Thomas Le Saux, Ludovic Jullien
2023 - Nature Methods

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8 Smooth functional landscapes in microcosms
Daniel Amor
2023 - Nature Ecology & Evolution

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9 A genome-wide screen reveals new regulators of the 2-cell-like cell state
Nikhil Gupta, Lounis Yakhou, Julien Richard Albert, Anaelle Azogui, Laure Ferry, Olivier Kirsh, Fumihito Miura, Sarah Battault, Kosuke Yamaguchi, Marthe Laisné, Cécilia Domrane, Frédéric Bonhomme, Arpita Sarkar, Marine Delagrange, Bertrand Ducos, Gael Cristofari, Takashi Ito, Maxim Greenberg, Pierre-Antoine Defossez
2023 - Nature Structural and Molecular Biology

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10 Natural antisense transcription of presenilin in sea urchin reveals a possible role for natural antisense transcription in the general control of gene expression during development
Odile Bronchain, Bertrand Ducos, Harald Putzer, Marine Delagrange, Soumaya Laalami, Laetitia Philippe-Caraty, Krystel Saroul, Brigitte Ciapa
2023 - Journal of Cell Science

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11 Resonances at Fundamental and Harmonic Frequencies for Selective Imaging of Sine‐Wave Illuminated Reversibly Photoactivatable Labels
Agnès Pellissier-Tanon, Raja Chouket, Ruikang Zhang, Aliénor Lahlou, Agathe Espagne, Annie Lemarchand, Vincent Croquette, Ludovic Jullien, Thomas Le Saux
2022 - ChemPhysChem

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12 Extra kinetic dimensions for label discrimination
Raja Chouket, Agnès Pellissier-Tanon, Aliénor Lahlou, Ruikang Zhang, Diana Kim, Marie-Aude Plamont, Mingshu Zhang, Xi Zhang, Pingyong Xu, Nicolas Desprat, Dominique Bourgeois, Agathe Espagne, Annie Lemarchand, Thomas Le Saux, Ludovic Jullien
2022 - Nature Communications

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13 Fate and biological impact of persistent luminescence nanoparticles after injection in mice: a one-year follow-up
Thomas Lécuyer, Johanne Seguin, Alice Balfourier, Marine Delagrange, Pierre Bürckel, René Lai-Kuen, Virginie Mignon, Bertrand Ducos, Michael Tharaud, Bruno Saubaméa, Daniel Scherman, Nathalie Mignet, Florence Gazeau, Cyrille Richard
2022 - Nanoscale

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14 Strand switching mechanism of Pif1 helicase induced by its collision with a G-quadruplex embedded in dsDNA
Jessica Valle-Orero, Martin Rieu, Phong Lan Thao Tran, Alexandra Joubert, Saurabh Raj, Jean-François Allemand, Vincent Croquette, Jean-Baptiste Boulé
2022 - Nucleic Acids Research

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15 The success of the bloom-forming cyanobacteria Planktothrix: Genotypes variability supports variable responses to light and temperature stress
Sandra Kim Tiam, Katia Comte, Caroline Dalle, Marine Delagrange, Chakib Djediat, Bertrand Ducos, Charlotte Duval, Kathleen Feilke, Sahima Hamlaoui, Séverine Le Manach, Pierre Setif, Claude Yéprémian, B Marie, Diana Kirilovsky, Muriel Gugger, Cécile Bernard
2022 - Harmful Algae

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16 Critical slowing down may account for the robustness of development
Weiting Zhang, Pierluigi Scerbo, Bertrand Ducos, David Bensimon
2022 - Proceedings of the National Academy of Sciences of the United States of America

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17 Nucleosome positioning on large tandem DNA repeats of the ’601’ sequence engineered in Saccharomyces cerevisiae
Astrid Lancrey, Alexandra Joubert, Evelyne Duvernois-Berthet, Etienne Routhier, Saurabh Raj, Agnès Thierry, Marta Sigarteu, Loic Ponger, Vincent Croquette, Julien Mozziconacci, Jean-Baptiste Boulé
2022 - Journal of Molecular Biology

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18 Fgf8 dynamics and critical slowing down may account for the temperature independence of somitogenesis
Weiting Zhang, Pierluigi Scerbo, Marine Delagrange, Virginie Candat, Vanessa Mayr, Sophie Vriz, Martin Distel, Bertrand Ducos, David Bensimon
2022 - Communications Biology

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19 Vertebrate Cell Differentiation, Evolution, and Diseases: The Vertebrate-Specific Developmental Potential Guardians VENTX/NANOG and POU5/OCT4 Enter the Stage
Bertrand Ducos, David Bensimon, Pierluigi Scerbo
2022 - Cells

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20 Novel approaches to study helicases using magnetic tweezers
Nadia Ruiz-Gutierrez, Martin Rieu, Jimmy Ouellet, Jean-François Allemand, Vincent Croquette, Hervé Le Hir
2022 -

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21 Hepatitis C virus core protein uses triacylglycerols to fold onto the endoplasmic reticulum membrane
Dalila Ajjaji, Kalthoum Ben M’barek, Bertrand Boson, Mohyeddine Omrane, Ama Gassama‐diagne, Magali Blaud, François Penin, Elise Diaz, Bertrand Ducos, François-Loïc Cosset, Abdou Rachid Thiam
2022 - Traffic

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22 Displacement and dissociation of oligonucleotides during DNA hairpin closure under strain
Fangyuan Ding, Simona Cocco, Saurabh Raj, Maria Manosas, Thao Thi Thu Nguyen, Michelle M Spiering, David Bensimon, Jean-François Allemand, V. Croquette
2022 - Nucleic Acids Research

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23 Confinement-induced accumulation and de-mixing of microscopic active-passive mixtures
Stephen Williams, Raphaël Jeanneret, Idan Tuval, Marco Polin
2022 - Nature Communications

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24 Detection of genetic variation and base modifications at base-pair resolution on both DNA and RNA
Zhen Wang, Jérôme Maluenda, Laurène Giraut, Thibault Vieille, Andréas Lefevre, David Salthouse, Gaël Radou, Rémi Moulinas, Sandra Astete, Pol d'Avezac, Geoff Smith, Charles André, Jean-François Allemand, David Bensimon, Vincent Croquette, Jimmy Ouellet, Gordon Hamilton
2021 - Communications Biology

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25 The Unity of Science
David Bensimon
2021 -

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26 Folding and persistence times of intramolecular G-quadruplexes transiently embedded in a DNA duplex
Phong Lan Thao Tran, Martin Rieu, Samar Hodeib, Alexandra Joubert, Jimmy Ouellet, Patrizia Alberti, Anthony Bugaut, Jean-François Allemand, Jean-Baptiste Boulé, Vincent Croquette
2021 - Nucleic Acids Research

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27 Magnetic Tweezers-Based Single-Molecule Assays to Study Interaction of E. coli SSB with DNA and RecQ Helicase
Debjani Bagchi, Weiting Zhang, Samar Hodeib, Bertrand Ducos, V. Croquette, Maria Manosas
2021 -

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28 Parallel, linear, and subnanometric 3D tracking of microparticles with Stereo Darkfield Interferometry
Martin Rieu, Thibault Vieille, Gaël Radou, Raphael Jeanneret, Nadia Ruiz-Gutierrez, Bertrand Ducos, Jean-François Allemand, Vincent Croquette
2021 - Science Advances

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29 Single-molecule kinetic locking allows fluorescence-free quantification of protein/nucleic-acid binding
Martin Rieu, Jessica Valle-Orero, Bertrand Ducos, Jean-François Allemand, Vincent Croquette
2021 - Communications Biology

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30 Fluorescent secreted bacterial effectors reveal active intravacuolar proliferation of Listeria monocytogenes in epithelial cells
Caroline Peron Cane, José Carlos Fernandez, Julien Leblanc, Laure Wingertsmann, Arnaud Gautier, Nicolas Desprat, Alice Lebreton
2020 - PLoS Pathogens

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31 Visualizing the dynamics of exported bacterial proteins with the chemogenetic fluorescent reporter FAST
Yankel Chekli, Caroline Peron-Cane, Dario Dell’arciprete, Jean-François Allemand, Chenge Li, Jean-Marc Ghigo, Arnaud Gautier, Alice Lebreton, Nicolas Desprat, Christophe Beloin
2020 - Scientific Reports

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32 Correction to “Dynamic Contrast for Plant Phenotyping”
Zsolt Kelemen, Ruikang Zhang, Lionel Gissot, Raja Chouket, Yannick Bellec, Vincent Croquette, Ludovic Jullien, Jean-Denis Faure, Thomas Le Saux
2020 - ACS Omega

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33 On the fate of sinking diatoms: the transport of active buoyancy-regulating cells in the ocean
J. Arrieta, R. Jeanneret, P. Roig, I. Tuval
2020 - Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences

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34 Dynamic Contrast for Plant Phenotyping
Zsolt Kelemen, Ruikang Zhang, Lionel Gissot, Raja Chouket, Yannick Bellec, Vincent Croquette, Ludovic Jullien, Jean-Denis Faure, Thomas Le Saux
2020 - ACS Omega

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35 A transition to stable one-dimensional swimming enhances E. coli motility through narrow channels
Gaszton Vizsnyiczai, Giacomo Frangipane, Silvio Bianchi, Filippo Saglimbeni, Dario Dell’arciprete, Roberto Di Leonardo
2020 - Nature Communications

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36 Method for the determination of preferential orientation of marine particles from laser diffraction measurements
J. S. Font-Munoz, Raphael Jeanneret, Idan Tuval, Gotzon Basterretxea
2020 - Optics Express

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37 Reduced central and peripheral inflammatory responses and increased mitochondrial activity contribute to diet-induced obesity resistance in WSB/EiJ mice
Jérémy Terrien, Isabelle Seugnet, Bolaji Seffou, Maria Herrero, James Bowers, Lamis Chamas, Stéphanie Decherf, Evelyne Duvernois-Berthet, Chakib Djediat, Bertrand Ducos, Barbara Demeneix, Marie-Stéphanie Clerget-Froidevaux
2019 - Scientific Reports

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38 Tunable and switchable soft adsorption of polymer-coated microparticles on a flat substrate
Giuseppe Boniello, Christophe Tribet, Emmanuelle Marie, Vincent Croquette, Dražen Zanchi
2019 - Colloids and Surfaces A: Physicochemical and Engineering Aspects

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39 Parallelized DNA tethered bead measurements to scrutinize DNA mechanical structure
Jean-François Allemand, Catherine Tardin, Laurence Salomé
2019 - Methods

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40 A Model of Somitogenesis
Weiting Zhang, Vanessa Mayr, Bertrand Ducos, Martin Distel, David Bensimon
2019 - Journal of Statistical Physics

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41 Mechanistic characterization of the DEAD-box RNA helicase Ded1 from yeast as revealed by a novel technique using single-molecule magnetic tweezers
Saurabh Raj, Debjani Bagchi, Jessica Valle Orero, Josette Banroques, N kyle Tanner, Vincent Croquette
2019 - Nucleic Acids Research

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42 Anisotropic cellular forces support mechanical integrity of the Stratum Corneum barrier
Shuo Guo, Yegor Domanov, Mark Donovan, Bertrand Ducos, Yves Pomeau, Christine Gourier, Eric Perez, Gustavo S. Luengo
2019 - Journal of the mechanical behavior of biomedical materials

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43 PICH and TOP3A cooperate to induce positive DNA supercoiling
Anna Bizard, Jean-François Allemand, Tue Hassenkam, Manikandan Paramasivam, Kata Sarlós, Manika Indrajit Singh, Ian Hickson
2019 - Nature Structural and Molecular Biology

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44 Optical control of protein activity and gene expression by photoactivation of caged cyclofen
Fatima Hamouri, Weiting Zhang, Isabelle Aujard, Thomas Le Saux, Bertrand Ducos, Sophie Vriz, Ludovic Jullien, David Bensimon
2019 -

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45 Longitudinal Analyses of Blood Transcriptome During Conversion to Psychosis
Boris Chaumette, Oussama Kebir, Juliette Pouch, Bertrand Ducos, Fekrije Selimi, Raphael Gaillard, Marie-Odile Krebs, I. Amado, C. Gaillard, M. Plaze, E. Magaud, M. Kazes, C. Mam-Lam-Fook, C. Daban, O. Gay, J. Bourgin, G. Martinez, M-N Vacheron, A. Viala, X. Laqueille, Alain Dervaux, F. Petitjean, O. Canceil, B. Garnier, M. Fishmann-Mathis, B. Gal, J. P. Benoit, M. R. Moro
2019 - Schizophrenia Bulletin

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46 Simple imaging protocol for autofluorescence elimination and optical sectioning in fluorescence endomicroscopy
Ruikang Zhang, Raja Chouket, Alison G Tebo, Marie-Aude Plamont, Zsolt Kelemen, Lionel Gissot, Jean-Denis Faure, Arnaud Gautier, Vincent Croquette, Ludovic Jullien, Thomas Le Saux
2019 - Optica

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47 Super-resolution Microscopy
Xiyu Yi, Tal-Zvi Markus, Xavier Michalet, Shimon Weiss, David Bensimon
2018 -

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