• 2024
  H. Nguyen, A. Desgrange, A. Ochandorena-Saa, V. Benhamo, S. Meilhac and C. Zimmer, Deep learning-based detection of murine congenital heart defects from µCT scans, bioRxiv.
• 2023
  Krentzel D, Shorte SL, Zimmer C, Deep learning in image-based phenotypic drug discovery., Trends Cell Biol 2023 Jul; 33(7): 538-554.
• 2023
  Sabaté T, Lelandais B, Bertrand E, Zimmer C, Polymer simulations guide the detection and quantification of chromatin loop extrusion by imaging., Nucleic Acids Res 2023 Apr; 51(6): 2614-2632.
• 2023
  Isnard P, Vergnaud P, Garbay S, Jamme M, Eloudzeri M, Karras A, Anglicheau D, Galantine V, Jalal Eddine A, Gosset C, Pourcine F, Zarhrate M, Gibier JB, Rensen E, Pietropaoli S, Barba-Spaeth G, Duong-Van-Huyen JP, Molina TJ, Mueller F, Zimmer C, Pontoglio M, Terzi F, Rabant M, A specific molecular signature in SARS-CoV-2-infected kidney biopsies., JCI Insight 2023 Mar; 8(5): .
• 2022
  Ouyang W, Bai J, Singh MK, Leterrier C, Barthelemy P, Barnett SFH, Klein T, Sauer M, Kanchanawong P, Bourg N, Cohen MM, Lelandais B, Zimmer C, , ShareLoc – an open platform for sharing localization microscopy data., Nat Methods 2022 Oct; (): .
• 2022
  Imbert A, Ouyang W, Safieddine A, Coleno E, Zimmer C, Bertrand E, Walter T, Mueller F, , FISH-quant v2: a scalable and modular tool for smFISH image analysis., RNA 2022 06; 28(6): 786-795.
• 2022
  Rensen E, Pietropaoli S, Mueller F, Weber C, Souquere S, Sommer S, Isnard P, Rabant M, Gibier JB, Terzi F, Simon-Loriere E, Rameix-Welti MA, Pierron G, Barba-Spaeth G, Zimmer C, Sensitive visualization of SARS-CoV-2 RNA with CoronaFISH., Life Sci Alliance 2022 Apr; 5(4): .
• 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.
• 2022
  Sabate T, Zimmer C, Bertrand E, , Versatile CRISPR-Based Method for Site-Specific Insertion of Repeat Arrays to Visualize Chromatin Loci in Living Cells., Methods Mol Biol 2022 ; 2532(): 275-290.
• 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
  Mickaël Lelek, Melina T Gyparaki, Gerti Beliu, Florian Schueder, Juliette Griffié, Suliana Manley, Ralf Jungmann, Markus Sauer, Melike Lakadamyali, Christophe Zimmer, Single-molecule localization microscopy, 1 (1), 1-27.
• 2021
  Hao X, Parmar JJ, Lelandais B, Aristov A, Ouyang W, Weber C, Zimmer C, , Super-resolution visualization and modeling of human chromosomal regions reveals cohesin-dependent loop structures., Genome Biol 2021 May; 22(1): 150.
• 2021
  Rensen E, Mueller F, Scoca V, Parmar JJ, Souque P, Zimmer C, Di Nunzio F, , Clustering and reverse transcription of HIV-1 genomes in nuclear niches of macrophages., EMBO J 2021 Jan; 40(1): e105247.
• 2020
  Chouaib R, Safieddine A, Pichon X, Imbert A, Kwon OS, Samacoits A, Traboulsi AM, Robert MC, Tsanov N, Coleno E, Poser I, Zimmer C, Hyman A, Le Hir H, Zibara K, Peter M, Mueller F, Walter T, Bertrand E, , A Dual Protein-mRNA Localization Screen Reveals Compartmentalized Translation and Widespread Co-translational RNA Targeting., Dev Cell 2020 Sep; 54(6): 773-791.e5.
• 2020
  Baudry L, Guiglielmoni N, Marie-Nelly H, Cormier A, Marbouty M, Avia K, Mie YL, Godfroy O, Sterck L, Cock JM, Zimmer C, Coelho SM, Koszul R, , instaGRAAL: chromosome-level quality scaffolding of genomes using a proximity ligation-based scaffolder., Genome Biol 2020 06; 21(1): 148.
• 2019
  Ouyang W, Mueller F, Hjelmare M, Lundberg E, Zimmer C, ImJoy: an open-source computational platform for the deep learning era, Nat. Methods 2019 Dec;16(12):1199-1200.
• 2019
  Parmar JJ, Woringer M, Zimmer C, How the Genome Folds: The Biophysics of Four-Dimensional Chromatin Organization, Annu Rev Biophys 2019 May;48:231-253.
• 2018
  Aubin Samacoits, Racha Chouaib, Adham Safieddine, Abdel-Meneem Traboulsi, Christophe Zimmer, Wei Ouyang, Marion Peter, Edouard Bertrand, Thomas Walter, Florian Mueller, A computational framework to study sub-cellular RNA localization, Nature Communications, 2018, 9 (1), pp.4584. ⟨10.1038/s41467-018-06868-w⟩.
• 2018
  Aristov A, Lelandais B, Rensen E, Zimmer C, ZOLA-3D allows flexible 3D localization microscopy over an adjustable axial range, Nat Commun 2018 Jun;9(1):2409.
• 2018
  Zimmer C, Fabre E, Chromatin mobility upon DNA damage: state of the art and remaining questions, Curr. Genet. 2018 Jun;.
• 2018
  King BR, Samacoits A, Eisenhauer PL, Ziegler CM, Bruce EA, Zenklusen D, Zimmer C, Mueller F, Botten J, Visualization of Arenavirus RNA Species in Individual Cells by Single-Molecule Fluorescence Hybridization Suggests a Model of Cyclical Infection and Clearance during Persistence, J. Virol. 2018 06;92(12).
• 2018
  Ouyang W, Aristov A, Lelek M, Hao X, Zimmer C, Deep learning massively accelerates super-resolution localization microscopy, Nat. Biotechnol. 2018 Jun;36(5):460-468.
• 2018
  Fabre E, Zimmer C, From dynamic chromatin architecture to DNA damage repair and back, Nucleus 2018 Jan;9(1):161-170.
• 2017
  Paladino S, Lebreton S, Lelek M, Riccio P, De Nicola S, Zimmer C, Zurzolo C, GPI-anchored proteins are confined in subdiffraction clusters at the apical surface of polarized epithelial cells, Biochem. J. 2017 12;474(24):4075-4090.
• 2017
  Rincheval V, Lelek M, Gault E, Bouillier C, Sitterlin D, Blouquit-Laye S, Galloux M, Zimmer C, Eleouet JF, Rameix-Welti MA, , Functional organization of cytoplasmic inclusion bodies in cells infected by respiratory syncytial virus., Nat Commun 2017 Sep; 8(1): 563.
• 2017
  Herbert S, Brion A, Arbona JM, Lelek M, Veillet A, Lelandais B, Parmar J, Fernández FG, Almayrac E, Khalil Y, Birgy E, Fabre E, Zimmer C, Chromatin stiffening underlies enhanced locus mobility after DNA damage in budding yeast, EMBO J. 2017 09;36(17):2595-2608.
• 2017
  Palaniappan SK, Bertaux F, Pichené M, Fabre E, Batt G, Genest B, Abstracting the dynamics of biological pathways using information theory: a case study of apoptosis pathway, Bioinformatics 2017 Jul; 33(13): 1980-1986.
• 2017
  Woringer M, Darzacq X, Zimmer C, Mir M, Faster and less phototoxic 3D fluorescence microscopy using a versatile compressed sensing scheme, Opt Express 2017 Jun;25(12):13668-13683.
• 2017
  Arbona JM, Herbert S, Fabre E, Zimmer C, Inferring the physical properties of yeast chromatin through Bayesian analysis of whole nucleus simulations, Genome Biol. 2017 05;18(1):81.
• 2017
  Versari C, Stoma S, Batmanov K, Llamosi A, Mroz F, Kaczmarek A, Deyell M, Lhoussaine C, Hersen P, Batt G, Long-term tracking of budding yeast cells in brightfield microscopy: CellStar and the Evaluation Platform., J R Soc Interface 2017 Feb; 14(127): .
• 2016
  Tsanov N, Samacoits A, Chouaib R, Traboulsi AM, Gostan T, Weber C, Zimmer C, Zibara K, Walter T, Peter M, Bertrand E, Mueller F, smiFISH and FISH-quant – a flexible single RNA detection approach with super-resolution capability, Nucleic Acids Res. 2016 12;44(22):e165.
• 2016
  Tantale K, Mueller F, Kozulic-Pirher A, Lesne A, Victor JM, Robert MC, Capozi S, Chouaib R, Bäcker V, Mateos-Langerak J, Darzacq X, Zimmer C, Basyuk E, Bertrand E, A single-molecule view of transcription reveals convoys of RNA polymerases and multi-scale bursting, Nat Commun 2016 07;7:12248.
• 2016
  Llamosi A, Gonzalez-Vargas AM, Versari C, Cinquemani E, Ferrari-Trecate G, Hersen P, Batt G, What Population Reveals about Individual Cell Identity: Single-Cell Parameter Estimation of Models of Gene Expression in Yeast., PLoS Comput Biol 2016 Feb; 12(2): e1004706.
• 2016
  Spichal M, Brion A, Herbert S, Cournac A, Marbouty M, Zimmer C, Koszul R, Fabre E, Evidence for a dual role of actin in regulating chromosome organization and dynamics in yeast, J. Cell. Sci. 2016 Feb;129(4):681-92.
• 2016
  Maya Spichal, Alice Brion, Sébastien Herbert, Axel Cournac, Martial Marbouty, Christophe Zimmer, Romain Koszul, Emmanuelle Fabre, Evidence for actin dual role in regulating chromosome organization and dynamics in yeast, J Cell Sci 2016 : doi: 10.1242/jcs.175745.
• 2015
  Lelek M, Casartelli N, Pellin D, Rizzi E, Souque P, Severgnini M, Di Serio C, Fricke T, Diaz-Griffero F, Zimmer C, Charneau P, Di Nunzio F, , Chromatin organization at the nuclear pore favours HIV replication., Nat Commun 2015 Mar; 6(): 6483.
• 2015
  Uhlendorf J, Miermont A, Delaveau T, Charvin G, Fages F, Bottani S, Hersen P, Batt G, In silico control of biomolecular processes., Methods Mol Biol 2015 ; 1244(): 277-85.
• 2014
  Marie-Nelly H, Marbouty M, Cournac A, Flot JF, Liti G, Parodi DP, Syan S, Guillén N, Margeot A, Zimmer C, Koszul R, , High-quality genome (re)assembly using chromosomal contact data., Nat Commun 2014 Dec; 5(): 5695.
• 2014
  Duportet X, Wroblewska L, Guye P, Li Y, Eyquem J, Rieders J, Rimchala T, Batt G, Weiss R, A platform for rapid prototyping of synthetic gene networks in mammalian cells., Nucleic Acids Res 2014 Dec; 42(21): 13440-51.
• 2014
  Senecal A, Munsky B, Proux F, Ly N, Braye FE, Zimmer C, Mueller F, Darzacq X, Transcription factors modulate c-Fos transcriptional bursts, Cell Rep 2014 Jul;8(1):75-83.
• 2014
  Marie-Nelly H, Marbouty M, Cournac A, Liti G, Fischer G, Zimmer C, Koszul R, , Filling annotation gaps in yeast genomes using genome-wide contact maps., Bioinformatics 2014 Aug; 30(15): 2105-13.
• 2014
  Lelek M, Di Nunzio F, Zimmer C, , FlAsH-PALM: super-resolution pointillist imaging with FlAsH-tetracysteine labeling., Methods Mol Biol 2014 ; 1174(): 183-93.
• 2014
  Rosa A, Zimmer C, Computational models of large-scale genome architecture, Int Rev Cell Mol Biol 2014;307:275-349.
• 2013
  Soares H, Henriques R, Sachse M, Ventimiglia L, Alonso MA, Zimmer C, Thoulouze MI, Alcover A, Regulated vesicle fusion generates signaling nanoterritories that control T cell activation at the immunological synapse, J. Exp. Med. 2013 Oct;210(11):2415-33.
• 2013
  Wong H, Arbona JM, Zimmer C, How to build a yeast nucleus, Nucleus 2013 Sep-Oct;4(5):361-6.
• 2013
  Albert B, Mathon J, Shukla A, Saad H, Normand C, Léger-Silvestre I, Villa D, Kamgoue A, Mozziconacci J, Wong H, Zimmer C, Bhargava P, Bancaud A, Gadal O, Systematic characterization of the conformation and dynamics of budding yeast chromosome XII, J. Cell Biol. 2013 Jul;202(2):201-10.
• 2013
  Judith D, Mostowy S, Bourai M, Gangneux N, Lelek M, Lucas-Hourani M, Cayet N, Jacob Y, Prévost MC, Pierre P, Tangy F, Zimmer C, Vidalain PO, Couderc T, Lecuit M, , Species-specific impact of the autophagy machinery on Chikungunya virus infection., EMBO Rep 2013 Jun; 14(6): 534-44.
• 2013
  Agmon N, Liefshitz B, Zimmer C, Fabre E, Kupiec M, Effect of nuclear architecture on the efficiency of double-strand break repair, Nat. Cell Biol. 2013 Jun;15(6):694-9.
• 2013
  Mueller F, Senecal A, Tantale K, Marie-Nelly H, Ly N, Collin O, Basyuk E, Bertrand E, Darzacq X, Zimmer C, FISH-quant: automatic counting of transcripts in 3D FISH images, Nat. Methods 2013 Apr;10(4):277-8.
• 2013
  Mendes ND, Lang F, Le Cornec YS, Mateescu R, Batt G, Chaouiya C, Composition and abstraction of logical regulatory modules: application to multicellular systems., Bioinformatics 2013 Mar; 29(6): 749-57.
• 2013
  Stoma S, Donzé A, Bertaux F, Maler O, Batt G, STL-based analysis of TRAIL-induced apoptosis challenges the notion of type I/type II cell line classification., PLoS Comput Biol 2013 ; 9(5): e1003056.
• 2012
  Zimmer C, From microbes to numbers: extracting meaningful quantities from images, Cell. Microbiol. 2012 Dec;14(12):1828-35.
• 2012
  Herbert S, Soares H, Zimmer C, Henriques R, Single-molecule localization super-resolution microscopy: deeper and faster, Microsc. Microanal. 2012 Dec;18(6):1419-29.
• 2012
  Wong H, Marie-Nelly H, Herbert S, Carrivain P, Blanc H, Koszul R, Fabre E, Zimmer C, A predictive computational model of the dynamic 3D interphase yeast nucleus, Curr. Biol. 2012 Oct;22(20):1881-90.
• 2012
  Ehsani S, Santos JC, Rodrigues CD, Henriques R, Audry L, Zimmer C, Sansonetti P, Tran Van Nhieu G, Enninga J, Hierarchies of host factor dynamics at the entry site of Shigella flexneri during host cell invasion, Infect. Immun. 2012 Jul;80(7):2548-57.
• 2011
  Zimmer C, Fabre E, Principles of chromosomal organization: lessons from yeast, J. Cell Biol. 2011 Mar;192(5):723-33.
• 2011
  Izeddin I, Specht CG, Lelek M, Darzacq X, Triller A, Zimmer C, Dahan M, Super-resolution dynamic imaging of dendritic spines using a low-affinity photoconvertible actin probe, PLoS ONE 2011;6(1):e15611.
• 2010
  Henriques R, Lelek M, Fornasiero EF, Valtorta F, Zimmer C, Mhlanga MM, QuickPALM: 3D real-time photoactivation nanoscopy image processing in ImageJ, Nat. Methods 2010 May;7(5):339-40.
• 2010
  Therizols P, Duong T, Dujon B, Zimmer C, Fabre E, Chromosome arm length and nuclear constraints determine the dynamic relationship of yeast subtelomeres, Proc. Natl. Acad. Sci. U.S.A. 2010 Feb;107(5):2025-30.
• 2008
  Berger AB, Cabal GG, Fabre E, Duong T, Buc H, Nehrbass U, Olivo-Marin JC, Gadal O, Zimmer C, High-resolution statistical mapping reveals gene territories in live yeast, Nat. Methods 2008 Dec;5(12):1031-7.
• 2008
  Marcio Marim, Bo Zhang, Jean-Christophe Olivo-Marin and Christophe Zimmer, Improving single particle localization with an empirically calibrated Gaussian kernel, IEEE International Symposium on Biomedical Imaging ISBI, 2008.
• 2006
  Cabal GG, Genovesio A, Rodriguez-Navarro S, Zimmer C, Gadal O, Lesne A, Buc H, Feuerbach-Fournier F, Olivo-Marin JC, Hurt EC, Nehrbass U, SAGA interacting factors confine sub-diffusion of transcribed genes to the nuclear envelope, Nature 2006 Jun;441(7094):770-3.
• 2006
  Dey N, Blanc-Feraud L, Zimmer C, Roux P, Kam Z, Olivo-Marin JC, Zerubia J, Richardson-Lucy algorithm with total variation regularization for 3D confocal microscope deconvolution, Microsc. Res. Tech. 2006 Apr;69(4):260-6.
• 2006
  Blazquez S, Zimmer C, Guigon G, Olivo-Marin JC, Guillén N, Labruyère E, Human tumor necrosis factor is a chemoattractant for the parasite Entamoeba histolytica, Infect. Immun. 2006 Feb;74(2):1407-11.
• 2005
  Zimmer C, Olivo-Marin JC, Coupled parametric active contours, IEEE Trans Pattern Anal Mach Intell 2005 Nov;27(11):1838-42.
• 2005
  Dufour A, Shinin V, Tajbakhsh S, Guillén-Aghion N, Olivo-Marin JC, Zimmer C, Segmenting and tracking fluorescent cells in dynamic 3-D microscopy with coupled active surfaces, IEEE Trans Image Process 2005 Sep;14(9):1396-410.
• 2005
  Coudrier E, Amblard F, Zimmer C, Roux P, Olivo-Marin JC, Rigothier MC, Guillén N, Myosin II and the Gal-GalNAc lectin play a crucial role in tissue invasion by Entamoeba histolytica, Cell. Microbiol. 2005 Jan;7(1):19-27.
• 2004
  Frischknecht F, Baldacci P, Martin B, Zimmer C, Thiberge S, Olivo-Marin JC, Shorte SL, Ménard R, Imaging movement of malaria parasites during transmission by Anopheles mosquitoes, Cell. Microbiol. 2004 Jul;6(7):687-94.
• 2003
  Labruyère E, Zimmer C, Galy V, Olivo-Marin JC, Guillén N, EhPAK, a member of the p21-activated kinase family, is involved in the control of Entamoeba histolytica migration and phagocytosis, J. Cell. Sci. 2003 Jan;116(Pt 1):61-71.
• 2002
  Das V, Nal B, Roumier A, Meas-Yedid V, Zimmer C, Olivo-Marin JC, Roux P, Ferrier P, Dautry-Varsat A, Alcover A, Membrane-cytoskeleton interactions during the formation of the immunological synapse and subsequent T-cell activation, Immunol. Rev. 2002 Nov;189:123-35.
• 2002
  Zimmer C, Labruyère E, Meas-Yedid V, Guillén N, Olivo-Marin JC, Segmentation and tracking of migrating cells in videomicroscopy with parametric active contours: a tool for cell-based drug testing, IEEE Trans Med Imaging 2002 Oct;21(10):1212-21.