Florian Mueller

Publications

Article dans une revue (32)

Chapter Three - Image processing approaches for microtubule remodeling quantification at the immunological synapse Daniel Krentzel,Maria Isabella Gariboldi,Marie Juzans,Marta Mastrogiovanni,Florian Mülleret al. Methods in Cell Biology, 2025, Methods in Cell Biology, 193, pp.39-67. ⟨10.1016/bs.mcb.2024.02.036⟩ Article dans une revue hal-05091484v1
A deep learning approach for time-consistent cell cycle phase prediction from microscopy data Thomas Bonte,Oriane Pourcelot,Adham Safieddine,Floric Slimani,Florian Muelleret al. PLoS Computational Biology, 2025, 21 (12), pp.e1013800. ⟨10.1371/journal.pcbi.1013800⟩ Article dans une revue hal-05458920v2
A point cloud segmentation framework for image-based spatial transcriptomics Thomas Defard,Hugo Laporte,Mallick Ayan,Juliette Soulier,Sandra Curras-Alonsoet al. Communications Biology, 2024, 7 (1), pp.823. ⟨10.1038/s42003-024-06480-3⟩ Article dans une revue hal-04874000v1
Mitotic bookmarking redundancy by nuclear receptors in pluripotent cells Almira Chervova,Amandine Molliex,H. Irem Baymaz,Rémi-Xavier Coux,Thaleia Papadopoulouet al. Nature Structural and Molecular Biology, 2024, ⟨10.1038/s41594-023-01195-1⟩ Article dans une revue hal-04434602v1
pyHiM: a new open-source, multi-platform software package for spatial genomics based on multiplexed DNA-FISH imaging Xavier Devos,Jean-Bernard Fiche,Marion Bardou,Olivier Messina,Christophe Houbronet al. Genome Biology, 2024, 25 (1), pp.47. ⟨10.1186/s13059-024-03178-x⟩ Article dans une revue hal-04762623v1
An interactive murine single-cell atlas of the lung responses to radiation injury Sandra Curras-Alonso,Juliette Soulier,Thomas Defard,Christian Weber,Sophie Heinrichet al. Nature Communications, 2023, 14 (1), pp.2445. ⟨10.1038/s41467-023-38134-z⟩ Article dans une revue hal-04092147v1
Excessive self-grooming, gene dysregulation and imbalance between the striosome and matrix compartments in the striatum of Shank3 mutant mice Allain-Thibeault Ferhat,Elisabeth Verpy,Anne Biton,Benoît Forget,Fabrice de Chaumontet al. Frontiers in Molecular Neuroscience, 2023, 16, pp.1139118. ⟨10.3389/fnmol.2023.1139118⟩ Article dans une revue hal-04241910v2
A specific molecular signature in SARS-CoV-2 infected kidney biopsies Pierre Isnard,Paul Vergnaud,Serge Garbay,Matthieu Jamme,Maeva Eloudzeriet al. JCI Insight, 2023, 8 (5), pp.e165192. ⟨10.1172/jci.insight.165192⟩ Article dans une revue pasteur-04004769v1
HT-smFISH: a cost effective and flexible workflow for high-throughput single molecule RNA imaging Adham Safieddine,Emeline Coleno,Frederic Lionneton,Abdel-Meneem Traboulsi,Soha Salloumet al. Nature Protocols, 2023, 18, pp.157-187. ⟨10.1038/s41596-022-00750-2⟩ Article dans une revue hal-03834928v1
piRNAs initiate transcriptional silencing of spermatogenic genes during C. elegans germline development Eric Cornes,Loan Bourdon,Meetali Singh,Florian Mueller,Piergiuseppe Quaratoet al. Developmental Cell, 2022, 57 (2), pp.180-196.e7. ⟨10.1016/j.devcel.2021.11.025⟩ Article dans une revue pasteur-03514345v1
FISH-quant v2: a scalable and modular tool for smFISH image analysis Arthur Imbert,Wei Ouyang,Adham Safieddine,Emeline Coleno,Christophe Zimmeret al. RNA, 2022, 28 (6), pp.786-795. ⟨10.1261/rna.079073.121⟩ Article dans une revue hal-03942851v2
Sensitive visualization of SARS-CoV-2 RNA with CoronaFISH Elena Rensen,Stefano Pietropaoli,Florian Mueller,Christian Weber,Sylvie Souquereet al. Life Science Alliance, 2022, 5 (4), pp.e202101124. ⟨10.26508/lsa.202101124⟩ Article dans une revue pasteur-03518024v2
Germline inherited small RNAs facilitate the clearance of untranslated maternal mRNAs in C. elegans embryos Piergiuseppe Quarato,Meetali Singh,Eric Cornes,Blaise Maxime Li,Loan Bourdonet al. Nature Communications, 2021, 12 (1), pp.1441. ⟨10.1038/s41467-021-21691-6⟩ Article dans une revue hal-03163367v1
Live single-cell transcriptional dynamics via RNA labelling during the phosphate response in plants Sahar Hani,Laura Cuyas,Pascale David,David Secco,James Whelanet al. Nature Plants, 2021, 7 (8), pp.1050-1064. ⟨10.1038/s41477-021-00981-3⟩ Article dans une revue hal-03320179v1
A choreography of centrosomal mRNAs reveals a conserved localization mechanism involving active polysome transport Adham Safieddine,Emeline Coleno,Soha Salloum,Arthur Imbert,Abdel-Meneem Traboulsiet al. Nature Communications, 2021, 12 (1), pp.1352. ⟨10.1038/s41467-021-21585-7⟩ Article dans une revue hal-03014936v2
The kinesin KIF1C transports APC-dependent mRNAs to cell protrusions Xavier Pichon,Konstadinos Moissoglu,Emeline Coleno,Tianhong Wang,Arthur Imbertet al. RNA, 2021, pp.rna.078576.120. ⟨10.1261/rna.078576.120⟩ Article dans une revue hal-03371977v1
Spatial transcriptomics for respiratory research and medicine Sandra Curras-Alonso,Juliette Soulier,Thomas Walter,Florian Mueller,Arturo Londoño-Vallejoet al. European Respiratory Journal, 2021, 58 (1), pp.2004314. ⟨10.1183/13993003.04314-2020⟩ Article dans une revue hal-03376218v1
Stochastic pausing at latent HIV-1 promoters generates transcriptional bursting Katjana Tantale,Encar Garcia-Oliver,Marie-Cécile Robert,Adèle L’hostis,Yueyuxiao Yanget al. Nature Communications, 2021, 12 (1), pp.4503. ⟨10.1038/s41467-021-24462-5⟩ Article dans une revue hal-03382893v1
Clustering and reverse transcription of HIV‐1 genomes in nuclear niches of macrophages Elena Rensen,Florian Mueller,Viviana Scoca,Jyotsana Parmar,Philippe Souqueet al. EMBO Journal, 2021, 40 (1), pp.e105247. ⟨10.15252/embj.2020105247⟩ Article dans une revue pasteur-03088393v1
Remodeling of the core leads HIV-1 pre-integration complex in the nucleus of human lymphocytes. Guillermo Blanco-Rodriguez,Anastasia Gazi,Blandine Monel,Stella Frabetti,Viviana Scocaet al. Journal of Virology, 2020, [Epub ahead of print], pp.JVI.00135-20. ⟨10.1128/JVI.00135-20⟩ Article dans une revue pasteur-02548457v1
mRNA localization is linked to translation regulation in the Caenorhabditis elegans germ lineage Dylan M Parker,Lindsay P Winkenbach,Samuel P Boyson,Matthew N Saxton,Camryn Daidoneet al. Development (Cambridge, England), 2020, 147 (13), pp.dev186817. ⟨10.1242/dev.186817⟩ Article dans une revue pasteur-02559475v2
Functional compensation precedes recovery of tissue mass following acute liver injury Chad Walesky,Kellie Kolb,Carolyn Winston,Jake Henderson,Benjamin Kruftet al. Nature Communications, 2020, 11 (1), pp.5785. ⟨10.1038/s41467-020-19558-3⟩ Article dans une revue pasteur-03648876v1
Co-translational assembly of mammalian nuclear multisubunit complexes Ivanka Kamenova,Pooja Mukherjee,Sascha Conic,Florian Mueller,Farrah El-Saafinet al. Nature Communications, 2019, 10 (1), ⟨10.1038/s41467-019-09749-y⟩ Article dans une revue hal-02130219v1
The molecular logic of Nanog-induced self-renewal in mouse embryonic stem cells Victor Heurtier,Nick Owens,Inma González,Florian Mueller,Caroline Prouxet al. Nature Communications, 2019, 10 (1), pp.1109. ⟨10.1038/s41467-019-09041-z⟩ Article dans une revue pasteur-02083187v1
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 Bruceet al. Journal of Virology, 2018, 92 (12), pp.e2241-17. ⟨10.1128/JVI.02241-17⟩ Article dans une revue pasteur-02075021v1
Single molecule tracking of Ace1p in Saccharomyces cerevisiae defines a characteristic residence time for non-specific interactions of transcription factors with chromatin David A Ball,Gunjan D. Mehta,Ronit Salomon-Kent,Davide Mazza,Tatsuya Morisakiet al. Nucleic Acids Research, 2016, 44 (21), pp.e160. ⟨10.1093/nar/gkw744⟩ Article dans une revue pasteur-01622680v1
Mitotic binding of Esrrb marks key regulatory regions of the pluripotency network Nicola Festuccia,Agnès Dubois,Sandrine Vandormael-Pournin,Elena Gallego Tejeda,Adrien Mourenet al. Nature Cell Biology, 2016, 18 (11), pp.1139-1148. ⟨10.1038/ncb3418⟩ Article dans une revue pasteur-01972743v1
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 Victoret al. Nature Communications, 2016, 7, pp.12248. ⟨10.1038/ncomms12248⟩ Article dans une revue pasteur-01622688v1
smiFISH and FISH-quant - a flexible single RNA detection approach with super-resolution capability. Nikolay Tsanov,Aubin Samacoits,Racha Chouaib,Abdel-Meneem Traboulsi,Thierry Gostanet al. Nucleic Acids Research, 2016, ⟨10.1093/nar/gkw784⟩ Article dans une revue pasteur-01375913v1
Visualization of single endogenous polysomes reveals the dynamics of translation in live human cells Xavier Pichon,Amandine Bastide,Adham Safieddine,Racha Chouaib,Aubin Samacoitset al. Journal of Cell Biology, 2016, 214 (6), pp.769 - 781. ⟨10.1083/jcb.201605024⟩ Article dans une revue pasteur-01622667v1
Transcription Factors Modulate c-Fos Transcriptional Bursts Adrien Senecal,Brian Munsky,Florence Proux,Nathalie Ly,Floriane E. Brayeet al. Cell Reports, 2014, 8 (1), pp.75-83. ⟨10.1016/j.celrep.2014.05.053⟩ Article dans une revue hal-01312884v1
FISH-quant: automatic counting of transcripts in 3D FISH images Florian Mueller,Adrien Senecal,Katjana Tantale,Hervé Marie-Nelly,Nathalie Lyet al. Nature Methods, 2013, 10 (4), pp.277 - 278. ⟨10.1038/nmeth.2406⟩ Article dans une revue pasteur-01622707v1

Communication dans un congrès (2)

A Deep Learning Approach To Identify MRNA Localization Patterns Rémy Dubois,Arthur Imbert,Aubin Samacoits,Marion Peter,Edouard Bertrandet al. 2019 IEEE 16th International Symposium on Biomedical Imaging (ISBI), Apr 2019, Venice, France. pp.1386-1390, ⟨10.1109/ISBI.2019.8759235⟩ Communication dans un congrès hal-02343547v1
Comprehensive Improvement of Industrial Energy Efficiency: Pilot Case in a European Rolling Stock Factory Nils Weinert,Rafael Fink,Christian Mose,Friedrich Lupp,Florian Mülleret al. IFIP International Conference on Advances in Production Management Systems (APMS), Sep 2014, Ajaccio, France. pp.334-341, ⟨10.1007/978-3-662-44736-9_41⟩ Communication dans un congrès hal-01387891v1

Poster de conférence (1)

Single molecule imaging reveals a conserved family of centrosomal mRNAs and a novel translation-dependent localization mechanism Adham Safieddine,Emeline Coleno,S. Salloum,A. Imbert,Oh Sung Kwonet al. 2022 ASCB Annual Meeting - Cell Bio Virtual 2022, Dec 2022, Washington (DC), United States. , Molecular Biology of the Cell, 34 (2), pp.B298/P1290, 2023 Poster de conférence hal-05484086v1

Pré-publication, Document de travail (7)

RNA2seg: a generalist model for cell segmentation in image-based spatial transcriptomics Thomas Defard,Alice Blondel,Sebastien Bellow,Anthony Coleon,Guilherme Dias de Meloet al. 2025 Pré-publication, Document de travail hal-05230880v1
The ANKS3/BICC1 protein complex is a master post-transcriptional regulator of NPHP1 ciliopathy-gene transcripts Alexia Mahuzier,Gweltas Odye,Valentina Grampa,Albane Bizet,Amandine Viauet al. 2024 Pré-publication, Document de travail hal-04986015v1
A point cloud segmentation framework for image-based spatial transcriptomics Thomas Defard,Hugo Laporte,Mallick Ayan,Soulier Juliette,Sandra Curras-Alonsoet al. 2024 Pré-publication, Document de travail hal-04396330v1
MYC and MAX drive the reactivation of the genome after mitosis Inma Gonzalez,Almira Chervova,Pedro Escoll,Luis Altamirano-Pacheco,Florian Muelleret al. 2024 Pré-publication, Document de travail (preprint/prepublication) hal-04603198v1
The kinesin KIF1C transports APC-dependent mRNAs to cell protrusions Xavier Pichon,Konstadinos Moissoglu,Emeline Coleno,Tianhong Wang,Arthur Imbertet al. 2021 Pré-publication, Document de travail hal-03116720v1
Clustering and reverse transcription of HIV-1 genomes in nuclear niches of macrophages Elena Rensen,Florian Mueller,Viviana Scoca,Jyotsana Parmar,Philippe Souqueet al. 2020 Pré-publication, Document de travail pasteur-02559460v1
Stochastic pausing at latent HIV-1 promoters generates transcriptional bursting Katiana Tantale,Encarnation Garcia-Oliver,Adèle L'Hostis,Yueyuxio Yang,Marie- Cécile Robertet al. 2020 Pré-publication, Document de travail hal-03019157v1