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Chromatin mobility upon DNA damage: state of the art and remaining questions

Christophe Zimmer , Emmanuelle Fabre
Current Genetics, 2019, 65 (1), pp.1-9. ⟨10.1007/s00294-018-0852-6⟩
Article dans une revue pasteur-02074352v1
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FISH-quant: automatic counting of transcripts in 3D FISH images

Florian Mueller , Adrien Senecal , Katjana Tantale , Hervé Marie-Nelly , Nathalie Ly , et al.
Nature Methods, 2013, 10 (4), pp.277 - 278. ⟨10.1038/nmeth.2406⟩
Article dans une revue pasteur-01622707v1
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Chromosome-level quality scaffolding of brown algal genomes using InstaGRAAL, a proximity ligation-based scaffolder

Lyam Baudry , Martial Marbouty , Hervé Marie-Nelly , Alexandre Cormier , Nadège Guiglielmoni , et al.
2021
Pré-publication, Document de travail hal-02947625v1
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ImJoy: an open-source computational platform for the deep learning era

Wei Ouyang , Florian Mueller , Martin Hjelmare , Emma Lundberg , Christophe Zimmer
Nature Methods, 2019, 16 (12), pp.1199-1200. ⟨10.1038/s41592-019-0627-0⟩
Article dans une revue pasteur-02401584v1

Chromosome arm length and nuclear constraints determine the dynamic relationship of yeast subtelomeres

Pierre Therizols , Tarn Duong , Bernard Dujon , Christophe Zimmer , Emmanuelle Fabre
Proceedings of the National Academy of Sciences of the United States of America, 2010, 107 (5), pp.2025-2030. ⟨10.1073/pnas.0914187107⟩
Article dans une revue pasteur-02082757v1

Entrapment of Intracytosolic Bacteria by Septin Cage-like Structures

Serge Mostowy , Matteo Bonazzi , Mélanie Anne Hamon , To Nam Tham , Adeline Mallet , et al.
Cell Host and Microbe, 2010, 8 (5), pp.433 - 444. ⟨10.1016/j.chom.2010.10.009⟩
Article dans une revue pasteur-01376115v1
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The imaging tsunami: Computational opportunities and challenges

Wei Ouyang , Christophe Zimmer
Current Opinion in Systems Biology, 2017, Big data acquisition and analysis • Pharmacology and drug discovery, 4, pp.105-113. ⟨10.1016/j.coisb.2017.07.011⟩
Article dans une revue pasteur-02492825v1
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Functional organization of cytoplasmic inclusion bodies in cells infected by respiratory syncytial virus.

Vincent Rincheval , Mickael Lelek , Elyanne Gault , Camille Bouillier , Delphine Sitterlin , et al.
Nature Communications, 2017, 8 (1), pp.563. ⟨10.1038/s41467-017-00655-9⟩
Article dans une revue pasteur-01589539v1

Super-resolution imaging of mitochondrial morphology reveals a close link between mitochondrial dynamics and oxidative phosphorylation in yeast

Manish Kumar Singh , Mickaël Lelek , Laetitia Cavellini , Christophe Zimmer , Mickael M. Cohen
Ecole thématique Mifobio, Nov 2021, Giens (Var), France
Poster de conférence hal-03965416v1
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smiFISH and FISH-quant - a flexible single RNA detection approach with super-resolution capability.

Nikolay Tsanov , Aubin Samacoits , Racha Chouaib , Abdel-Meneem Traboulsi , Thierry Gostan , et al.
Nucleic Acids Research, 2016, ⟨10.1093/nar/gkw784⟩
Article dans une revue pasteur-01375913v1
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How the Genome Folds: The Biophysics of Four-Dimensional Chromatin Organization

Jyotsana J Parmar , Maxime Woringer , Christophe Zimmer
Annual Review of Biophysics and Biomolecular Structure, 2019, Annual Review of Biophysics, 48 (1), ⟨10.1146/annurev-biophys-052118-115638⟩
Article dans une revue pasteur-02082840v1
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Super-resolution visualization and modeling of human chromosomal regions reveals cohesin-dependent loop structures

Xian Hao , Jyotsana J. Parmar , Benoît Lelandais , Andrey Aristov , Wei Ouyang , et al.
Genome Biology, 2021, 22 (1), pp.150. ⟨10.1186/S13059-021-02343-W⟩
Article dans une revue pasteur-03326366v1
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Modulation of the intrinsic chromatin binding property of HIV-1 integrase by LEDGF/p75

Delphine Lapaillerie , Benoît Lelandais , Eric Mauro , Floriane Lagadec , Camille Tumiotto , et al.
Nucleic Acids Research, 2021, 49 (19), pp.11241-11256. ⟨10.1093/nar/gkab886⟩
Article dans une revue hal-03795503v1

Myosin II and the Gal-GalNAc lectin play a crucial role in tissue invasion by Entamoeba histolytica.

Evelyne Coudrier , François Amblard , Christophe Zimmer , Pascal Roux , Jean-Christophe Olivo-Marin , et al.
Cellular Microbiology, 2005, 7 (1), pp.19-27. ⟨10.1111/j.1462-5822.2004.00426.x⟩
Article dans une revue hal-00014474v1
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Chromatin stiffening underlies enhanced locus mobility after DNA damage in budding yeast

Sébastien Herbert , Alice Brion , Jean-Michel Arbona , Mickaël Lelek , Adeline Veillet , et al.
EMBO Journal, 2017, 36 (17), pp.2595-2608. ⟨10.15252/embj.201695842⟩
Article dans une revue pasteur-02078756v1

When mitochondrial dynamics and high-resolution imaging get together

Manish Kumar Singh , Laetitia Cavellini , Lea Dietrich , Mickaël Lelek , Perrine Bomme , et al.
The 21rst European Bioenergetics Conference, Aug 2022, Aix en provence, France
Poster de conférence hal-03965466v1
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instaGRAAL: chromosome-level quality scaffolding of genomes using a proximity ligation-based scaffolder

Lyam Baudry , Nadège Guiglielmoni , Hervé Marie-Nelly , Alexandre Cormier , Komlan Avia , et al.
Genome Biology, 2020, 21 (1), ⟨10.1186/s13059-020-02041-z⟩
Article dans une revue pasteur-02873422v1
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Filling annotation gaps in yeast genomes using genome-wide contact maps.

Hervé Marie-Nelly , Martial Marbouty , Axel Cournac , Gianni Liti , Gilles Fischer , et al.
Bioinformatics, 2014, 30 (15), pp.2105-13. ⟨10.1093/bioinformatics/btu162⟩
Article dans une revue pasteur-01488132v1

Human Tumor Necrosis Factor is a Chemoattractant for the Parasite Entamoeba histolytica

Samantha Blazquez , Christophe Zimmer , Ghislaine Guigon , Jean-Christophe Olivo-Marin , Nancy Guillén , et al.
Infection and Immunity, 2006, 74 (2), pp.1407-1411. ⟨10.1128/IAI.74.2.1407-1411.2006⟩
Article dans une revue pasteur-03719948v1

From microbes to numbers: extracting meaningful quantities from images

Christophe Zimmer
Cellular Microbiology, 2012, 14 (12), pp.1828-1835. ⟨10.1111/cmi.12032⟩
Article dans une revue pasteur-02079529v1
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Visualization of Arenavirus RNA Species in Individual Cells by Single-Molecule Fluorescence In Situ Hybridization Suggests a Model of Cyclical Infection and Clearance during Persistence

Benjamin R King , Aubin Samacoits , Philip L Eisenhauer , Christopher M. Ziegler , Emily A Bruce , et al.
Journal of Virology, 2018, 92 (12), pp.e2241-17. ⟨10.1128/JVI.02241-17⟩
Article dans une revue pasteur-02075021v1
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Deep learning massively accelerates super-resolution localization microscopy

Wei Ouyang , Andrey Aristov , Mickaël Lelek , Xian Hao , Christophe Zimmer
Nature Biotechnology, 2018, 36 (5), pp.460-468. ⟨10.1038/nbt.4106⟩
Article dans une revue pasteur-02074397v1
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Inferring the physical properties of yeast chromatin through Bayesian analysis of whole nucleus simulations

Jean-Michel Arbona , Sébastien Herbert , Emmanuelle Fabre , Christophe Zimmer
Genome Biology, 2016, 18 (1), pp.81. ⟨10.1186/s13059-017-1199-x⟩
Article dans une revue inserm-01517883v1

Single-Molecule Localization Super-Resolution Microscopy: Deeper and Faster

Sébastien Herbert , Helena Soares , Christophe Zimmer , Ricardo Henriques
Microscopy and Microanalysis, 2012, 18 (6), pp.1419-1429. ⟨10.1017/S1431927612013347⟩
Article dans une revue pasteur-02446747v1
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A single-molecule view of transcription reveals convoys of RNA polymerases and multi-scale bursting

Katjana Tantale , Florian Müller , Alja Kozulic-Pirher , Annick Lesne , Jean-Marc Victor , et al.
Nature Communications, 2016, 7, pp.12248. ⟨10.1038/ncomms12248⟩
Article dans une revue pasteur-01622688v1

Hierarchies of Host Factor Dynamics at the Entry Site of Shigella flexneri during Host Cell Invasion

Soudeh Ehsani , José Carlos Santos , Cristina Rodrigues , Ricardo Henriques , Laurent Audry , et al.
Infection and Immunity, 2012, 80 (7), pp.2548 - 2557. ⟨10.1128/IAI.06391-11⟩
Article dans une revue pasteur-01899474v1
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A specific molecular signature in SARS-CoV-2 infected kidney biopsies

Pierre Isnard , Paul Vergnaud , Serge Garbay , Matthieu Jamme , Maeva Eloudzeri , et al.
JCI Insight, In press, pp.e165192. ⟨10.1172/jci.insight.165192⟩
Article dans une revue pasteur-04004769v1

Computational Models of Large-Scale Genome Architecture

Angelo Rosa , Christophe Zimmer
Ronald Hancock, Kwang W. Jeon. International Review of Cell and Molecular Biology, 307, Elsevier, pp.275-349, 2014, ⟨10.1016/B978-0-12-800046-5.00009-6⟩
Chapitre d'ouvrage pasteur-02079507v1
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How to build a yeast nucleus

Hua Wong , Jean-Michel Arbona , Christophe Zimmer
Nucleus, 2013, 4 (5), pp.361 - 366. ⟨10.4161/nucl.26226⟩
Article dans une revue pasteur-02079519v1
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Single-molecule localization microscopy

Mickaë Lelek , Melina T Gyparaki , Gerti Beliu , Florian Schueder , Juliette Griffié , et al.
Nature Reviews Methods Primers, 2021, 1 (1), pp.39. ⟨10.1038/s43586-021-00038-x⟩
Article dans une revue pasteur-03695794v1