• 2024
  Defard T, Laporte H, Ayan M, Soulier J, Curras-Alonso S, Weber C, Massip F, Londoño-Vallejo JA, Fouillade C, Mueller F, Walter T, A point cloud segmentation framework for image-based spatial transcriptomics., Commun Biol 2024 Jul; 7(1): 823.
• 2024
  Devos X, Fiche JB, Bardou M, Messina O, Houbron C, Gurgo J, Schaeffer M, Götz M, Walter T, Mueller F, Nollmann M, pyHiM: a new open-source, multi-platform software package for spatial genomics based on multiplexed DNA-FISH imaging., Genome Biol 2024 Feb; 25(1): 47.
• 2023
  Curras-Alonso S, Soulier J, Defard T, Weber C, Heinrich S, Laporte H, Leboucher S, Lameiras S, Dutreix M, Favaudon V, Massip F, Walter T, Mueller F, Londoño-Vallejo JA, Fouillade C, , An interactive murine single-cell atlas of the lung responses to radiation injury., Nat Commun 2023 Apr; 14(1): 2445.
• 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): .
• 2023
  Imbert A, Mueller F, Walter T, PointFISH: Learning Point Cloud Representations for RNA Localization Patterns, Computer Vision – ECCV 2022 Workshops.
• 2023
  Ferhat AT, Verpy E, Biton A, Forget B, De Chaumont F, Mueller F, Le Sourd AM, Coqueran S, Schmitt J, Rochefort C, Rondi-Reig L, Leboucher A, Boland A, Fin B, Deleuze JF, Boeckers TM, Ey E, Bourgeron T, , Excessive self-grooming, gene dysregulation and imbalance between the striosome and matrix compartments in the striatum of Shank3 mutant mice., Front Mol Neurosci 2023 ; 16(): 1139118.
• 2022
  Safieddine A, Coleno E, Lionneton F, Traboulsi AM, Salloum S, Lecellier CH, Gostan T, Georget V, Hassen-Khodja C, Imbert A, Mueller F, Walter T, Peter M, Bertrand E, , HT-smFISH: a cost-effective and flexible workflow for high-throughput single-molecule RNA imaging., Nat Protoc 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
  Cornes E, Bourdon L, Singh M, Mueller F, Quarato P, Wernersson E, Bienko M, Li B, Cecere G, , piRNAs initiate transcriptional silencing of spermatogenic genes during C. elegans germline development., Dev Cell 2022 Jan; 57(2): 180-196.e7.
• 2021
  Pichon X, Moissoglu K, Coleno E, Wang T, Imbert A, Robert MC, Peter M, Chouaib R, Walter T, Mueller F, Zibara K, Bertrand E, Mili S, , The kinesin KIF1C transports APC-dependent mRNAs to cell protrusions., RNA 2021 Dec; 27(12): 1528-1544.
• 2021
  Hani S, Cuyas L, David P, Secco D, Whelan J, Thibaud MC, Merret R, Mueller F, Pochon N, Javot H, Faklaris O, Maréchal E, Bertrand E, Nussaume L, , Live single-cell transcriptional dynamics via RNA labelling during the phosphate response in plants., Nat Plants 2021 08; 7(8): 1050-1064.
• 2021
  Tantale K, Garcia-Oliver E, Robert MC, L'Hostis A, Yang Y, Tsanov N, Topno R, Gostan T, Kozulic-Pirher A, Basu-Shrivastava M, Mukherjee K, Slaninova V, Andrau JC, Mueller F, Basyuk E, Radulescu O, Bertrand E, , Stochastic pausing at latent HIV-1 promoters generates transcriptional bursting., Nat Commun 2021 07; 12(1): 4503.
• 2021
  Curras-Alonso S, Soulier J, Walter T, Mueller F, Londoño-Vallejo A, Fouillade C, , Spatial transcriptomics for respiratory research and medicine., Eur Respir J 2021 Apr; (): .
• 2021
  Quarato P, Singh M, Cornes E, Li B, Bourdon L, Mueller F, Didier C, Cecere G, , Germline inherited small RNAs facilitate the clearance of untranslated maternal mRNAs in C. elegans embryos., Nat Commun 2021 03; 12(1): 1441.
• 2021
  Safieddine A, Coleno E, Salloum S, Imbert A, Traboulsi AM, Kwon OS, Lionneton F, Georget V, Robert MC, Gostan T, Lecellier CH, Chouaib R, Pichon X, Le Hir H, Zibara K, Mueller F, Walter T, Peter M, Bertrand E, , A choreography of centrosomal mRNAs reveals a conserved localization mechanism involving active polysome transport., Nat Commun 2021 Mar; 12(1): 1352.
• 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
  Walesky CM, Kolb KE, Winston CL, Henderson J, Kruft B, Fleming I, Ko S, Monga SP, Mueller F, Apte U, Shalek AK, Goessling W, , Functional compensation precedes recovery of tissue mass following acute liver injury., Nat Commun 2020 11; 11(1): 5785.
• 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
  Parker DM, Winkenbach LP, Boyson S, Saxton MN, Daidone C, Al-Mazaydeh ZA, Nishimura MT, Mueller F, Nishimura EO, , mRNA localization is linked to translation regulation in the Caenorhabditis elegans germ lineage., Development 2020 Jun; (): .
• 2020
  Blanco-Rodriguez G, Gazi A, Monel B, Frabetti S, Scoca V, Mueller F, Schwartz O, Krijnse-Locker J, Charneau P, Di Nunzio F, , Remodeling of the Core Leads HIV-1 Preintegration Complex into the Nucleus of Human Lymphocytes., J Virol 2020 05; 94(11): .
• 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
  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.
• 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
  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
  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).
• 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;.
• 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
  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.
• 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
  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
  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
  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
  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
  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.
• 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
  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.
• 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
  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.