• 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
  Dubois R, Imbert A, Samacoïts A, Peter M, Bertrand E, Mueller F, Walter T, A Deep Learning Approach To Identify MRNA Localization Patterns, IEEE 16th International Symposium on Biomedical Imaging, 2019; 1386 - 1390.
• 2019
  Ouyang W, Mueller F, Hjelmare M, Lundberg E, Zimmer C, Private: ImJoy: an open-source computational platform for the deep learning era, 1905.13105.
• 2019
  Kamenova I, Mukherjee P, Conic S, Mueller F, El-Saafin F, Bardot P, Garnier JM, Dembele D, Capponi S, Timmers HTM, Vincent SD, Tora L, Co-translational assembly of mammalian nuclear multisubunit complexes, Nat Commun 2019 04;10(1):1740.
• 2019
  Heurtier V, Owens N, Gonzalez I, Mueller F, Proux C, Mornico D, Clerc P, Dubois A, Navarro P, The molecular logic of Nanog-induced self-renewal in mouse embryonic stem cells, Nat Commun 2019 03;10(1):1109.
• 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
  Samacoits A, Chouaib R, Safieddine A, Traboulsi AM, Ouyang W, Zimmer C, Peter M, Bertrand E, Walter T, Mueller F, A computational framework to study sub-cellular RNA localization, Nat Commun 2018 Nov;9(1):4584.
• 2018
  Pichon X, Lagha M, Mueller F, Bertrand E, A Growing Toolbox to Image Gene Expression in Single Cells: Sensitive Approaches for Demanding Challenges, Mol. Cell 2018 Aug;71(3):468-480.
• 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 09;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
  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.
• 2016
  Christian Weber, Mikael Koutero, Marie-Agnes Dillies, Hugo Varet, Cesar Lopez-Camarillo, Jean Yves Coppée, Chung-Chau Hon, Nancy Guillén, Extensive transcriptome analysis correlates the plasticity of Entamoeba histolytica pathogenesis to rapid phenotype changes depending on the environment, Sci Rep. 2016 Oct 21;6:35852. doi: 10.1038/srep35852..
• 2016
  Festuccia N, Dubois A, Vandormael-Pournin S, Gallego Tejeda E, Mouren A, Bessonnard S, Mueller F, Proux C, Cohen-Tannoudji M, Navarro P, Mitotic binding of Esrrb marks key regulatory regions of the pluripotency network, Nat. Cell Biol. 2016 Oct;.
• 2016
  Pichon X, Bastide A, Safieddine A, Chouaib R, Samacoits A, Basyuk E, Peter M, Mueller F, Bertrand E, Visualization of single endogenous polysomes reveals the dynamics of translation in live human cells, J. Cell Biol. 2016 Sep;.
• 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
  Ball DA, Mehta GD, Salomon-Kent R, Mazza D, Morisaki T, Mueller F, McNally JG, Karpova TS, Single molecule tracking of Ace1p in Saccharomyces cerevisiae defines a characteristic residence time for non-specific interactions of transcription factors with chromatin, Nucleic Acids Res. 2016 Aug;.
• 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
  Tesikova M, Dezitter X, Nenseth HZ, Klokk TI, Mueller F, Hager GL, Saatcioglu F, Divergent Binding and Transactivation by Two Related Steroid Receptors at the Same Response Element, J. Biol. Chem. 2016 Apr;.
• 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.
• 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
  Nenseth HZ, Dezitter X, Tesikova M, Mueller F, Klokk TI, Hager GL, Saatcioglu F, Distinctly different dynamics and kinetics of two steroid receptors at the same response elements in living cells, PLoS ONE 2014;9(8):e105204.
• 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
  Vandenbunder B, Fourré N, Leray A, Mueller F, Völkel P, Angrand PO, Héliot L, PRC1 components exhibit different binding kinetics in Polycomb bodies, Biol. Cell 2014 Apr;106(4):111-25.
• 2014
  Mfotie Njoya E, Weber C, Hernandez-Cuevas NA, Hon CC, Janin Y, Kamini MF, Moundipa PF, Guillén N, Bioassay-guided fractionation of extracts from Codiaeum variegatum against Entamoeba histolytica discovers compounds that modify expression of ceramide biosynthesis related genes, PLoS Negl Trop Dis 2014;8(1):e2607.
• 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
  Nawroth I, Mueller F, Basyuk E, Beerens N, Rahbek UL, Darzacq X, Bertrand E, Kjems J, Schmidt U, Stable assembly of HIV-1 export complexes occurs cotranscriptionally, RNA 2014 Jan;20(1):1-8.
• 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
  Mueller F, Stasevich TJ, Mazza D, McNally JG, Quantifying transcription factor kinetics: at work or at play?, Crit. Rev. Biochem. Mol. Biol. 2013 Sep-Oct;48(5):492-514.
• 2013
  Wong H, Arbona JM, Zimmer C, How to build a yeast nucleus, Nucleus 2013 Sep-Oct;4(5):361-6.
• 2013
  Mazza D, Mueller F, Stasevich TJ, McNally JG, Convergence of chromatin binding estimates in live cells, Nat. Methods 2013 Aug;10(8):691-2.
• 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
  Hubsch C, Roze E, Popa T, Russo M, Balachandran A, Pradeep S, Mueller F, Brochard V, Quartarone A, Degos B, Vidailhet M, Kishore A, Meunier S, Defective cerebellar control of cortical plasticity in writer’s cramp, Brain 2013 Jul;136(Pt 7):2050-62.
• 2013
  Lickwar CR, Mueller F, Lieb JD, Genome-wide measurement of protein-DNA binding dynamics using competition ChIP, Nat Protoc 2013;8(7):1337-53.
• 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
  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
  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.
• 2012
  Abrahamsson S, Chen J, Hajj B, Stallinga S, Katsov AY, Wisniewski J, Mizuguchi G, Soule P, Mueller F, Dugast Darzacq C, Darzacq X, Wu C, Bargmann CI, Agard DA, Dahan M, Gustafsson MG, Fast multicolor 3D imaging using aberration-corrected multifocus microscopy, Nat. Methods 2013 Jan;10(1):60-3.
• 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
  Lelek M, Di Nunzio F, Henriques R, Charneau P, Arhel N, Zimmer C, Superresolution imaging of HIV in infected cells with FlAsH-PALM, Proc. Natl. Acad. Sci. U.S.A. 2012 May;109(22):8564-9.
• 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.
• 2012
  Lickwar CR, Mueller F, Hanlon SE, McNally JG, Lieb JD, Genome-wide protein-DNA binding dynamics suggest a molecular clutch for transcription factor function, Nature 2012 Apr;484(7393):251-5.
• 2012
  Mueller F, Morisaki T, Mazza D, McNally JG, Minimizing the impact of photoswitching of fluorescent proteins on FRAP analysis, Biophys. J. 2012 Apr;102(7):1656-65.
• 2012
  Mueller F, Karpova TS, Mazza D, McNally JG, Monitoring dynamic binding of chromatin proteins in vivo by fluorescence recovery after photobleaching, Methods Mol. Biol. 2012;833:153-76.
• 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
  Mostowy S, Bonazzi M, Hamon MA, Tham TN, Mallet A, Lelek M, Gouin E, Demangel C, Brosch R, Zimmer C, Sartori A, Kinoshita M, Lecuit M, Cossart P, Entrapment of intracytosolic bacteria by septin cage-like structures, Cell Host Microbe 2010 Nov;8(5):433-44.
• 2010
  Schneider G, Guttmann P, Heim S, Rehbein S, Mueller F, Nagashima K, Heymann JB, Müller WG, McNally JG, Three-dimensional cellular ultrastructure resolved by X-ray microscopy, Nat. Methods 2010 Dec;7(12):985-7.
• 2010
  Stasevich TJ, Mueller F, Michelman-Ribeiro A, Rosales T, Knutson JR, McNally JG, Cross-validating FRAP and FCS to quantify the impact of photobleaching on in vivo binding estimates, Biophys. J. 2010 Nov;99(9):3093-101.
• 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
  Mueller F, Mazza D, Stasevich TJ, McNally JG, FRAP and kinetic modeling in the analysis of nuclear protein dynamics: what do we really know?, Curr. Opin. Cell Biol. 2010 Jun;22(3):403-11.
• 2010
  Stasevich TJ, Mueller F, Brown DT, McNally JG, Dissecting the binding mechanism of the linker histone in live cells: an integrated FRAP analysis, EMBO J. 2010 Apr;29(7):1225-34.
• 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
  Sprouse RO, Karpova TS, Mueller F, Dasgupta A, McNally JG, Auble DT, Regulation of TATA-binding protein dynamics in living yeast cells, Proc. Natl. Acad. Sci. U.S.A. 2008 Sep;105(36):13304-8.
• 2008
  Nishiyama A, Mochizuki K, Mueller F, Karpova T, McNally JG, Ozato K, Intracellular delivery of acetyl-histone peptides inhibits native bromodomain-chromatin interactions and impairs mitotic progression, FEBS Lett. 2008 Apr;582(10):1501-7.
• 2008
  Mueller F, Wach P, McNally JG, Evidence for a common mode of transcription factor interaction with chromatin as revealed by improved quantitative fluorescence recovery after photobleaching, Biophys. J. 2008 Apr;94(8):3323-39.
• 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
  Sprague BL, Müller F, Pego RL, Bungay PM, Stavreva DA, McNally JG, Analysis of binding at a single spatially localized cluster of binding sites by fluorescence recovery after photobleaching, Biophys. J. 2006 Aug;91(4):1169-91.
• 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.