• 2025
  Carlos Garcia-Lopez-de-Haro, Caterina Fuster-Barcelo, Curtis T. Rueden, Jonathan Heras, Vladimir Ulman, Daniel Franco-Barranco, Adrian Ines, Kevin W. Eliceiri, Jean-Christophe Olivo-Marin, Jean-Yves Tinevez, Daniel Sage, Arrate Munoz-Barrutia, SAMJ: Fast Image Annotation on ImageJ/Fiji via Segment Anything Model, arXiv:2506.02783.
• 2025
  Ambroset M, Marie A, Clément B, Arthur M, Aurélien M, Christian R, Guillaume M, Marine B, Marvin A, Gaëlle L, Antonio T, Volker B, Jérôme M, Fabrice C, Thierry P, Minh-Son P, Stéphane R, Magali F, Perrine PG, Anne-Sophie M, Jean-Yves T, F-BIAS: Towards a distributed national core facility for bioimage analysis., PLoS Comput Biol 2025 Jun; 21(6): e1013058.
• 2025
  Swistak L, Albert M, Valenzuela C, Gokerkucuk EB, Bontems F, Tachon S, Egger KT, Gazi AD, Sartori-Rupp A, Lesser CF, Paul-Gilloteaux P, Tinevez JY, Vos M, Enninga J, The bacterial type three secretion system induces mechanoporation of vacuolar membranes., PLoS Biol 2025 May; 23(5): e3003135.
• 2024
  Jazmin Meza-Torres, Jean-Yves Tinevez, Aline Crouzols, Héloïse Mary, Minhee Kim, Lise Hunault, Susan Chamorro-Rodriguez, Emilie Lejal, Pamela Altamirano-Silva, Déborah Groussard, Samy Gobaa, Johann Peltier, Benoit Chassaing, Bruno Dupuy, Clostridioides difficile binary toxin CDT induces biofilm-like persisting microcolonies, Gut microbes, 2024, 17 (1), pp.2444411. ⟨10.1080/19490976.2024.2444411⟩.
• 2024
  Gómez-de-Mariscal E, Grobe H, Pylvänäinen JW, Xénard L, Henriques R, Tinevez JY, Jacquemet G, CellTracksColab is a platform that enables compilation, analysis, and exploration of cell tracking data., PLoS Biol 2024 Aug; 22(8): e3002740.
• 2024
  Lydie Couturier, Juan Luna-Escalante, Khallil Mazouni, Claire Mestdagh, Minh-Son Phan, Jean-Yves Tinevez, François Schweisguth, Francis Corson, Pulsatile dynamics propagate crystalline order in the developing Drosophila eye, Published in BioRxiv a preprint server for Biology https://www.biorxiv.org/content/10.1101/2024.07.11.603179v1 - July 16 2024.
• 2024
  Oliver Renaud, Nathalie Aulner, Audrey Salles, Nadia Halidi, Maia Brunstein, Adeline Mallet, Karin Aumayr, Stefan Terjung, Daniel Levy, Saskia Lippens, Jean‐marc Verbavatz, Thomas Heuser, Rachel Santarella-Mellwig, Jean-Yves Tinevez, Tatiana Woller, Alexander Botzki, Christopher Cawthorne, Sebastian Munck, Staying on track – Keeping things running in a high‐end scientific imaging core facility, Journal of Microscopy, 2024, 294 (3), pp.276-294. ⟨10.1111/jmi.13304⟩.
• 2024
  Mistretta M, Cimino M, Campagne P, Volant S, Kornobis E, Hebert O, Rochais C, Dallemagne P, Lecoutey C, Tisnerat C, Lepailleur A, Ayotte Y, LaPlante SR, Gangneux N, Záhorszká M, Korduláková J, Vichier-Guerre S, Bonhomme F, Pokorny L, Albert M, Tinevez JY, Manina G, Dynamic microfluidic single-cell screening identifies pheno-tuning compounds to potentiate tuberculosis therapy., Nat Commun 2024 May; 15(1): 4175.
• 2024
  , Dynamic microfluidic single-cell screening identifies pheno-tuning compounds to potentiate tuberculosis therapy, Nature Communications.
• 2024
  Girolamo DD, Benavente-Diaz M, Murolo M, Grimaldi A, Lopes PT, Evano B, Kuriki M, Gioftsidi S, Laville V, Tinevez JY, Letort G, Mella S, Tajbakhsh S, Comai G, Extraocular muscle stem cells exhibit distinct cellular properties associated with non-muscle molecular signatures., Development 2024 Feb; 151(4): .
• 2024
  García López de Haro C, Dallongeville S, Musset T, Gómez-de-Mariscal E, Sage D, Ouyang W, Muñoz-Barrutia A, Tinevez JY, Olivo-Marin JC, JDLL: a library to run deep learning models on Java bioimage informatics platforms., Nat Methods 2024 Jan; 21(1): 7-8.
• 2023
  Serres MP, Shaughnessy R, Escot S, Hammich H, Cuvelier F, Salles A, Rocancourt M, Verdon Q, Gaffuri AL, Sourigues Y, Malherbe G, Velikovsky L, Chardon F, Sassoon N, Tinevez JY, Callebaut I, Formstecher E, Houdusse A, David NB, Pylypenko O, Echard A, MiniBAR/GARRE1 is a dual Rac and Rab effector required for ciliogenesis., Dev Cell 2023 Nov; 58(22): 2477-2494.e8.
• 2023
  Laure Mancini, Boris Guirao, Sara Ortica, Miriam Labusch, Felix Cheysson, Valentin Bonnet, Minh Son Phan, Sébastien Herbert, Pierre Mahou, Emilie Menant, Sébastien Bedu, Jean-Yves Tinevez, Charles Baroud, Emmanuel Beaurepaire, Yohanns Bellaiche, Laure Bally-Cuif, Nicolas Dray, Apical size and deltaA expression predict adult neural stem cell decisions along lineage progression, Science Advances , 2023, 9 (35), pp.eadg7519. ⟨10.1126/sciadv.adg7519⟩.
• 2023
  Carlos Garcia Lopez de Haro, Stephane Dallongeville, Thomas Musset, Estibaliz Gomez de Mariscal, Daniel Sage, Wei Ouyang, Arrate Munoz-Barrutia, Jean-Yves Tinevez, Jean-Christophe Olivo-Marin, JDLL: A library to run Deep Learning models on Java bioimage informatics platforms, Electrical Engineering and Systems Science > Image and Video Processing.
• 2023
  Xingi E, Koutsoudaki PN, Thanou I, Phan MS, Margariti M, Scheller A, Tinevez JY, Kirchhoff F, Thomaidou D, LPS-Induced Systemic Inflammation Affects the Dynamic Interactions of Astrocytes and Microglia with the Vasculature of the Mouse Brain Cortex., Cells 2023 May; 12(10): .
• 2023
  Simon F, Tinevez JY, van Teeffelen S, ExTrack characterizes transition kinetics and diffusion in noisy single-particle tracks., J Cell Biol 2023 May; 222(5): .
• 2023
  Scoca V, Morin R, Collard M, Tinevez JY, Di Nunzio F, HIV-induced membraneless organelles orchestrate post-nuclear entry steps., J Mol Cell Biol 2023 Apr; 14(11): .
• 2022
  Laure Mancini, Boris Guirao, Sara Ortica, Miriam Labusch, Felix Cheysson, Valentin Bonnet, Minh Son Phan, Sébastien Herbert, Pierre Mahou, Emilie Menant, Sébastien Bedu, Jean-Yves Tinevez, Charles Baroud, Emmanuel Beaurepaire, Yohanns Bellaiche, Laure Bally-Cuif, Nicolas Dray, Apical size and deltaA expression predict adult neural stem cell decisions along lineage progression, 2023.
• 2022
  Trébeau C, de Monvel JB, Altay G, Tinevez JY, Etournay R, , Extracting multiple surfaces from 3D microscopy images in complex biological tissues with the Zellige software tool., BMC Biol 2022 08; 20(1): 183.
• 2022
  Ershov D, Phan MS, Pylvänäinen JW, Rigaud SU, Le Blanc L, Charles-Orszag A, Conway JRW, Laine RF, Roy NH, Bonazzi D, Duménil G, Jacquemet G, Tinevez JY, , TrackMate 7: integrating state-of-the-art segmentation algorithms into tracking pipelines., Nat Methods 2022 Jun; (): .
• 2022
  Torres R, Tinevez JY, Daoudi H, Lahlou G, Grislain N, Breil E, Sterkers O, Mosnier I, Nguyen Y, Ferrary E, , Best Fit 3D Basilar Membrane Reconstruction to Routinely Assess the Scalar Position of the Electrode Array after Cochlear Implantation., J Clin Med 2022 Apr; 11(8): .
• 2022
  Nunes Vicente F, Lelek M, Tinevez JY, Tran QD, Pehau-Arnaudet G, Zimmer C, Etienne-Manneville S, Giannone G, Leduc C, , Molecular organization and mechanics of single vimentin filaments revealed by super-resolution imaging., Sci Adv 2022 Feb; 8(8): eabm2696.
• 2021
  Meza-Torres J, Lelek M, Quereda JJ, Sachse M, Manina G, Ershov D, Tinevez JY, Radoshevich L, Maudet C, Chaze T, Giai Gianetto Q, Matondo M, Lecuit M, Martin-Verstraete I, Zimmer C, Bierne H, Dussurget O, Cossart P, Pizarro-Cerdá J, , Listeriolysin S: A bacteriocin from Listeria monocytogenes that induces membrane permeabilization in a contact-dependent manner., Proc Natl Acad Sci U S A 2021 Oct; 118(40): .
• 2021
  Dray N, Mancini L, Binshtok U, Cheysson F, Supatto W, Mahou P, Bedu S, Ortica S, Than-Trong E, Krecsmarik M, Herbert S, Masson JB, Tinevez JY, Lang G, Beaurepaire E, Sprinzak D, Bally-Cuif L, Dynamic spatiotemporal coordination of neural stem cell fate decisions occurs through local feedback in the adult vertebrate brain., Cell Stem Cell 2021 Aug; 28(8): 1457-1472.e12.
• 2021
  Herbert S, Valon L, Mancini L, Dray N, Caldarelli P, Gros J, Esposito E, Shorte SL, Bally-Cuif L, Aulner N, Levayer R, Tinevez JY, LocalZProjector and DeProj: a toolbox for local 2D projection and accurate morphometrics of large 3D microscopy images., BMC Biol 2021 Jul; 19(1): 136.
• 2021
  Martins GG, Cordelières FP, Colombelli J, D'Antuono R, Golani O, Guiet R, Haase R, Klemm AH, Louveaux M, Paul-Gilloteaux P, Tinevez JY, Miura K, , Highlights from the 2016-2020 NEUBIAS training schools for Bioimage Analysts: a success story and key asset for analysts and life scientists., F1000Res 2021 ; 10(): 334.
• 2020
  Samassa F, Ferrari ML, Husson J, Mikhailova A, Porat Z, Sidaner F, Brunner K, Teo TH, Frigimelica E, Tinevez JY, Sansonetti PJ, Thoulouze MI, Phalipon A, , Shigella impairs human T lymphocyte responsiveness by hijacking actin cytoskeleton dynamics and T cell receptor vesicular trafficking., Cell Microbiol 2020 05; 22(5): e13166.
• 2020
  Fazeli E, Roy NH, Follain G, Laine RF, von Chamier L, Hänninen PE, Eriksson JE, Tinevez JY, Jacquemet G, , Automated cell tracking using StarDist and TrackMate., F1000Res 2020 ; 9(): 1279.
• 2019
  Tinevez JY, Arena ET, Anderson M, Nigro G, Injarabian L, André A, Ferrari M, Campbell-Valois FX, Devin A, Shorte SL, Sansonetti PJ, Marteyn BS, , Shigella-mediated oxygen depletion is essential for intestinal mucosa colonization., Nat Microbiol 2019 11; 4(11): 2001-2009.
• 2019
  Jean-Yves Tinevez, Sébastien Herbert, The NEMO Dots Assembly: Single-Particle Tracking and Analysis, Tinevez JY., Herbert S. (2020) The NEMO Dots Assembly: Single-Particle Tracking and Analysis. In: Miura K., Sladoje N. (eds) Bioimage Data Analysis Workflows. Learning Materials in Biosciences. Springer, Cham. https://doi.org/10.1007/978-3-030-22386-1_4.
• 2019
  Gouder L, Vitrac A, Goubran-Botros H, Danckaert A, Tinevez JY, André-Leroux G, Atanasova E, Lemière N, Biton A, Leblond CS, Poulet A, Boland A, Deleuze JF, Benchoua A, Delorme R, Bourgeron T, Cloëz-Tayarani I, , Altered spinogenesis in iPSC-derived cortical neurons from patients with autism carrying de novo SHANK3 mutations., Sci Rep 2019 01; 9(1): 94.
• 2019
  Sônego F, Bouccara S, Pons T, Lequeux N, Danckaert A, Tinevez JY, Alam IS, Shorte SL, Tournebize R, , Imaging of Red-Shifted Light From Bioluminescent Tumors Using Fluorescence by Unbound Excitation From Luminescence., Front Bioeng Biotechnol 2019 ; 7(): 73.
• 2018
  Bertiaux E, Mallet A, Fort C, Blisnick T, Bonnefoy S, Jung J, Lemos M, Marco S, Vaughan S, Trépout S, Tinevez JY, Bastin P, , Bidirectional intraflagellar transport is restricted to two sets of microtubule doublets in the trypanosome flagellum., J Cell Biol 2018 12; 217(12): 4284-4297.
• 2018
  Lancino M, Majello S, Herbert S, De Chaumont F, Tinevez JY, Olivo-Marin JC, Herbomel P, Schmidt A, , Anisotropic organization of circumferential actomyosin characterizes hematopoietic stem cells emergence in the zebrafish., Elife 2018 08; 7(): .
• 2018
  Nathalie Aulner, Anne Danckaert, Julien Fernandes, Marie-Anne Nicola, Pascal Roux, Audrey Salles, Jean-Yves Tinevez, Spencer Shorte, Fluorescence imaging host pathogen interactions: fifteen years benefit of hindsight…, Current Opinion in Microbiology, 2018, 43, pp.193-198. ⟨10.1016/j.mib.2018.03.001⟩.
• 2018
  Dejarnac O, Hafirassou ML, Chazal M, Versapuech M, Gaillard J, Perera-Lecoin M, Umana-Diaz C, Bonnet-Madin L, Carnec X, Tinevez JY, Delaugerre C, Schwartz O, Roingeard P, Jouvenet N, Berlioz-Torrent C, Meertens L, Amara A, , TIM-1 Ubiquitination Mediates Dengue Virus Entry., Cell Rep 2018 05; 23(6): 1779-1793.
• 2018
  Anderson MC, Chaze T, Coïc YM, Injarabian L, Jonsson F, Lombion N, Selimoglu-Buet D, Souphron J, Ridley C, Vonaesch P, Baron B, Arena ET, Tinevez JY, Nigro G, Nothelfer K, Solary E, Lapierre V, Lazure T, Matondo M, Thornton D, Sansonetti PJ, Baleux F, Marteyn BS, , MUB40 Binds to Lactoferrin and Stands as a Specific Neutrophil Marker., Cell Chem Biol 2018 04; 25(4): 483-493.e9.
• 2018
  Wolff C, Tinevez JY, Pietzsch T, Stamataki E, Harich B, Guignard L, Preibisch S, Shorte S, Keller PJ, Tomancak P, Pavlopoulos A, , Multi-view light-sheet imaging and tracking with the MaMuT software reveals the cell lineage of a direct developing arthropod limb., Elife 2018 03; 7(): .
• 2017
  Arena ET, Tinevez JY, Nigro G, Sansonetti PJ, Marteyn BS, , The infectious hypoxia: occurrence and causes during Shigella infection., Microbes Infect 2017 Mar; 19(3): 157-165.
• 2017
  Tinevez JY, Perry N, Schindelin J, Hoopes GM, Reynolds GD, Laplantine E, Bednarek SY, Shorte SL, Eliceiri KW, , TrackMate: An open and extensible platform for single-particle tracking., Methods 2017 02; 115(): 80-90.
• 2016
  Rajasekaran B, Uriu K, Valentin G, Tinevez JY, Oates AC, , Object Segmentation and Ground Truth in 3D Embryonic Imaging., PLoS One 2016 ; 11(6): e0150853.
• 2015
  Gouder L, Tinevez JY, Goubran-Botros H, Benchoua A, Bourgeron T, Cloëz-Tayarani I, , Three-dimensional Quantification of Dendritic Spines from Pyramidal Neurons Derived from Human Induced Pluripotent Stem Cells., J Vis Exp 2015 Oct; (104): .
• 2015
  Arena ET, Campbell-Valois FX, Tinevez JY, Nigro G, Sachse M, Moya-Nilges M, Nothelfer K, Marteyn B, Shorte SL, Sansonetti PJ, , Bioimage analysis of Shigella infection reveals targeting of colonic crypts., Proc Natl Acad Sci U S A 2015 Jun; 112(25): E3282-90.
• 2015
  Cornelius Sicker, Jörg Heber, Dirk Berndt, Florian Rückerl, Jean-Yves Tinevez, Spencer Shorte, Michael Wagner, Harald Schenk, Spatially resolved contrast measurement of diffractive micromirror arrays, Cornelius Sicker ; Jörg Heber ; Dirk Berndt ; Florian Rückerl ; Jean-Yves Tinevez, et al. " Spatially resolved contrast measurement of diffractive micromirror arrays ", Proc. SPIE 9375, MOEMS and Miniaturized Systems XIV, 93750D (February 27, 2015); doi:10.1117/12.2076921; http://dx.doi.org/10.1117/12.2076921.
• 2015
  F Rückerl, S Bellow, D Berndt, JY Tinevez, J Heber, M Wagner, S Shorte, Spatio-angular light control in microscopes using micro mirror arrays, SPIE BiOS.
• 2015
  Clément Fallet, Maxime Dubois, Jean-Yves Tinevez, Stephane Oddos, Julien Caron, Roger Persson, Spencer L Shorte, Gabriel Y Sirat, A new method to achieve tens of nm axial super-localisation based on conical diffraction PSF shaping, SPIE BiOS, 2015.
• 2014
  Clément Fallet, Julien Caron, Stephane Oddos, Jean-Yves Tinevez, Lionel Moisan, Gabriel Y Sirat, Philippe O Braitbart, Spencer L Shorte, Conical diffraction as a versatile building block to implement new imaging modalities for superresolution in fluorescence microscopy, SPIE NanoScience+ Engineering.
• 2014
  Duval N, Daubas P, Bourcier de Carbon C, St Cloment C, Tinevez JY, Lopes M, Ribes V, Robert B, , Msx1 and Msx2 act as essential activators of Atoh1 expression in the murine spinal cord., Development 2014 Apr; 141(8): 1726-36.
• 2014
  Holland AD, Rückerl F, Dragavon JM, Rekiki A, Tinevez JY, Tournebize R, Shorte SL, , In vitro characterization of Fluorescence by Unbound Excitation from Luminescence: broadening the scope of energy transfer., Methods 2014 Mar; 66(2): 353-61.
• 2014
  Chenouard N, Smal I, de Chaumont F, Maška M, Sbalzarini IF, Gong Y, Cardinale J, Carthel C, Coraluppi S, Winter M, Cohen AR, Godinez WJ, Rohr K, Kalaidzidis Y, Liang L, Duncan J, Shen H, Xu Y, Magnusson KE, Jaldén J, Blau HM, Paul-Gilloteaux P, Roudot P, Kervrann C, Waharte F, Tinevez JY, Shorte SL, Willemse J, Celler K, van Wezel GP, Dan HW, Tsai YS, Ortiz de Solórzano C, Olivo-Marin JC, Meijering E, , Objective comparison of particle tracking methods., Nat Methods 2014 Mar; 11(3): 281-9.
• 2014
  Tarantino N, Tinevez JY, Crowell EF, Boisson B, Henriques R, Mhlanga M, Agou F, Israël A, Laplantine E, , TNF and IL-1 exhibit distinct ubiquitin requirements for inducing NEMO-IKK supramolecular structures., J Cell Biol 2014 Jan; 204(2): 231-45.
• 2014
  Caron J, Fallet C, Tinevez JY, Moisan L, Braitbart LP, Sirat GY, Shorte SL, , Conical diffraction illumination opens the way for low phototoxicity super-resolution imaging., Cell Adh Migr 2014 ; 8(5): 430-9.
• 2013
  Crowell EF, Tinevez JY, Echard A, , A simple model for the fate of the cytokinesis midbody remnant: implications for remnant degradation by autophagy., Bioessays 2013 May; 35(5): 472-81.
• 2013
  Firmino J, Tinevez JY, Knust E, , Crumbs affects protein dynamics in anterior regions of the developing Drosophila embryo., PLoS One 2013 ; 8(3): e58839.
• 2013
  F. Rückerl, Martin Kielhorn, J-Y. Tinevez, J. Heber, R. Heintzmann, S. Shorte, Micro mirror arrays as high-resolution spatial light modulators for photoactivation and optogenetics, Proc. SPIE 8586, Optogenetics: Optical Methods for Cellular Control, 85860U (8 March 2013); doi: 10.1117/12.2010408;.
• 2012
  Schindelin J, Arganda-Carreras I, Frise E, Kaynig V, Longair M, Pietzsch T, Preibisch S, Rueden C, Saalfeld S, Schmid B, Tinevez JY, White DJ, Hartenstein V, Eliceiri K, Tomancak P, Cardona A, , Fiji: an open-source platform for biological-image analysis., Nat Methods 2012 Jun; 9(7): 676-82.
• 2012
  Tinevez JY, Salbreux G, Paluch E, [The mechanics of the cellular division or how to split a sphere into two?], Med Sci (Paris) 2012 Feb;28(2):144-6.
• 2012
  Tinevez JY, Dragavon J, Baba-Aissa L, Roux P, Perret E, Canivet A, Galy V, Shorte S, , A quantitative method for measuring phototoxicity of a live cell imaging microscope., Methods Enzymol 2012 ; 506(): 291-309.
• 2011
  Colucci-Guyon E, Tinevez JY, Renshaw SA, Herbomel P, , Strategies of professional phagocytes in vivo: unlike macrophages, neutrophils engulf only surface-associated microbes., J Cell Sci 2011 Sep; 124(Pt 18): 3053-9.
• 2011
  Sedzinski J, Biro M, Oswald A, Tinevez JY, Salbreux G, Paluch E, , Polar actomyosin contractility destabilizes the position of the cytokinetic furrow., Nature 2011 Aug; 476(7361): 462-6.
• 2009
  Michalski N, Michel V, Caberlotto E, Lefèvre GM, van Aken AF, Tinevez JY, Bizard E, Houbron C, Weil D, Hardelin JP, Richardson GP, Kros CJ, Martin P, Petit C, , Harmonin-b, an actin-binding scaffold protein, is involved in the adaptation of mechanoelectrical transduction by sensory hair cells., Pflugers Arch 2009 Nov; 459(1): 115-30.
• 2009
  Tinevez JY, Schulze U, Salbreux G, Roensch J, Joanny JF, Paluch E, , Role of cortical tension in bleb growth., Proc Natl Acad Sci U S A 2009 Nov; 106(44): 18581-6.
• 2009
  Renaud Boistel, Nicolas Pollet, Jean-Yves Tinevez, Peter Cloetens, Michel Schlenker, Irradiation damage to frog inner ear during synchrotron radiation tomographic investigation, Journal of Electron Spectroscopy and Related Phenomena, Volume 170, Issues 1–3, 2009, Pages 37-41.
• 2007
  Tinevez JY, Jülicher F, Martin P, Unifying the various incarnations of active hair-bundle motility by the vertebrate hair cell, Biophys. J. 2007 Dec;93(11):4053-67.