Publications
For a fully updated list of publications, check our Google Scholar profile. For a list of our top publications sorted by citations, check our top publications.
Publications by our lab
2024
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Harnessing artificial intelligence to reduce phototoxicity in live imaging Estibaliz Gómez-de-Mariscal, Mario Del Rosario, Joanna W. Pylvänäinen, Guillaume Jacquemet, Ricardo Henriques Perspective published in Journal of Cell Science, January 2024 Technologies: BioImage Model Zoo, CARE, DeepBacs, NanoJ-eSRRF, NanoJ-SQUIRREL, NanoJ-SRRF and ZeroCostDL4Mic Funded by: CZI, EMBO, ERC, H2021 and H2022 DOI: 10.1242/jcs.261545 |
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CellTracksColab is a platform that enables compilation, analysis, and exploration of cell tracking data Estibaliz Gómez-de-Mariscal, Hanna Grobe, Joanna W Pylvänäinen, Laura Xénard, Ricardo Henriques, Jean-Yves Tinevez, Guillaume Jacquemet Published in PLOS Biology, January 2024 Technologies: CARE, CellTracksColab and ZeroCostDL4Mic DOI: 10.1371/journal.pbio.3002740 |
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DL4MicEverywhere - deep learning for microscopy made flexible, shareable and reproducible Iván Hidalgo-Cenalmor, Joanna W. Pylvänäinen, Mariana G. Ferreira, Craig T. Russell, Alon Saguy, Ignacio Arganda-Carreras, Yoav Shechtman, Guillaume Jacquemet, Ricardo Henriques, Estibaliz Gómez-de-Mariscal Paper published in Nature Methods, January 2024 Technologies: BioImage Model Zoo, DL4MicEverywhere and ZeroCostDL4Mic Funded by: EMBO, ERC, H2021 and H2022 News: Labonline, MSN, AZoRobotics and Aamuset Kaupunkimedia Blogs: news-medical.net DOI: 10.1038/s41592-024-02295-6 |
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Structural Repetition Detector - multi-scale quantitative mapping of molecular complexes through microscopy Afonso Mendes, Bruno M Saraiva, Guillaume Jacquemet, Joao I Mamede, Christophe Leterrier, Ricardo Henriques Preprint published in bioRxiv, January 2024 Technologies: Nuclear-Pores as references and SReD Funded by: CZI, EMBO, ERC, H2021 and H2022 DOI: 10.1101/2024.09.16.613204 |
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The rise of data-driven microscopy powered by machine learning Leonor Morgado, Estibaliz Gómez‐de‐Mariscal, Hannah S. Heil, Ricardo Henriques Review published in Journal of Microscopy, January 2024 Technologies: NanoJ and NanoJ-Fluidics Funded by: CZI, EMBO, ERC, FCT, H2021 and H2022 DOI: 10.1111/jmi.13282 |
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PhotoFiTT - A Quantitative Framework for Assessing Phototoxicity in Live-Cell Microscopy Experiments Mario Del Rosario, Estibaliz Gómez-de-Mariscal, Leonor Morgado, Raquel Portela, Guillaume Jacquemet, Pedro M. Pereira, Ricardo Henriques Preprint published in bioRxiv, January 2024 Technologies: DL4MicEverywhere, PhotoFiTT and ZeroCostDL4Mic Funded by: CZI, EMBO, ERC, FCT, H2021 and H2022 DOI: 10.1101/2024.07.16.603046 |
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Cell constriction requires processive septal peptidoglycan synthase movement independent of FtsZ treadmilling in Staphylococcus aureus Simon Schäper, António D. Brito, Bruno M. Saraiva, Georgia R. Squyres, Matthew J. Holmes, Ethan C. Garner, Zach Hensel, Ricardo Henriques, Mariana G. Pinho Paper published in Nature Microbiology, January 2024 Technologies: NanoJ Funded by: EMBO and ERC DOI: 10.1038/s41564-024-01629-6 |
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Nano-org, a functional resource for single-molecule localisation microscopy data Sandeep Shirgill, Daniel J Nieves, Jeremy A Pike, Mohammad A Ahmed, Mohammed HH Baragilly, Kylie Savoye, Jonathan Worboys, Khodor Hazime, Adrian Garcia, David J Williamson, Ricardo Henriques, Steven F Lee, Dylan M Owen Preprint published in bioRxiv, January 2024 Technologies: nano-org Funded by: EMBO, ERC, H2021 and H2022 DOI: 10.1101/2024.08.06.606779 |
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2023
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Decoding life's inner workings - advances in quantitative bioimaging Ricardo Henriques, Christophe Leterrier, Aubrey Weigel Editorial published in Open Biology, January 2023 DOI: 10.1098/rsob.230329 |
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CLEM-Reg - An automated point cloud based registration algorithm for correlative light and volume electron microscopy Daniel Krentzel, Matouš Elphick, Marie-Charlotte Domart, Christopher J. Peddie, Romain F. Laine, Ricardo Henriques, Lucy M. Collinson, Martin L. Jones Preprint published in BioRxiv, January 2023 Technologies: BioImage Model Zoo, CLEM-Reg and ZeroCostDL4Mic Funded by: CZI and ERC DOI: 10.1101/2023.05.11.540445 |
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High-fidelity 3D live-cell nanoscopy through data-driven enhanced super-resolution radial fluctuation Romain F. Laine, Hannah S. Heil, Simao Coelho, Jonathon Nixon-Abell, Angélique Jimenez, Theresa Wiesner, Damián Martínez, Tommaso Galgani, Louise Régnier, Aki Stubb, Gautier Follain, Samantha Webster, Jesse Goyette, Aurelien Dauphin, Audrey Salles, Siân Culley, Guillaume Jacquemet, Bassam Hajj, Christophe Leterrier, Ricardo Henriques Paper published in Nature Methods, January 2023 Technologies: NanoJ, NanoJ-eSRRF, NanoJ-SQUIRREL, NanoJ-SRRF, NanoPyx and Nuclear-Pores as references Funded by: CZI, EMBO, ERC, FCT, H2021, H2022, InnOValley and Wellcome Trust News: Photonics.com, The Science Times, Optics.org and Phys.org Blogs: Springer Nature Protocols and Methods Community DOI: 10.1038/s41592-023-02057-w |
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Live-cell imaging in the deep learning era Joanna W Pylvänäinen, Estibaliz Gómez-de-Mariscal, Ricardo Henriques, Guillaume Jacquemet Review published in Current Opinion in Cell Biology, January 2023 Technologies: BioImage Model Zoo, DeepBacs, Fast4DReg, NanoJ, NanoJ-eSRRF, NanoJ-Fluidics and ZeroCostDL4Mic Funded by: CZI, EMBO, ERC and H2021 DOI: 10.1016/j.ceb.2023.102271 |
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Fast4DReg–fast registration of 4D microscopy datasets Joanna W Pylvänäinen, Romain F Laine, Bruno MS Saraiva, Sujan Ghimire, Gautier Follain, Ricardo Henriques, Guillaume Jacquemet Paper published in Journal of Cell Science, January 2023 Technologies: CARE, Fast4DReg, NanoJ and ZeroCostDL4Mic Funded by: CZI and ERC DOI: 10.1242/jcs.260728 |
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This Microtubule Does Not Exist - Super‐Resolution Microscopy Image Generation by a Diffusion Model Alon Saguy, Tav Nahimov, Maia Lehrman, Estibaliz Gómez-de-Mariscal, Iván Hidalgo-Cenalmor, Onit Alalouf, Ashwin Balakrishnan, Mike Heilemann, Ricardo Henriques, Yoav Shechtman Published in Small Methods, January 2023 Technologies: ZeroCostDL4Mic Funded by: CZI, EMBO, ERC, H2021 and H2022 DOI: 10.1002/smtd.202400672 |
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NanoPyx - super-fast bioimage analysis powered by adaptive machine learning Bruno M. Saraiva, Inês M. Cunha, António D. Brito, Gautier Follain, Raquel Portela, Robert Haase, Pedro M. Pereira, Guillaume Jacquemet, Ricardo Henriques Preprint published in bioRxiv, January 2023 Technologies: NanoJ, NanoJ-eSRRF, NanoJ-SQUIRREL, NanoJ-SRRF, NanoJ-VirusMapper and NanoPyx Funded by: CZI, EMBO, ERC, FCT, H2021 and H2022 DOI: 10.1101/2023.08.13.553080 |
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Processive movement of Staphylococcus aureus essential septal peptidoglycan synthases is independent of FtsZ treadmilling and drives cell constriction Simon Schaeper, Antonio D Brito, Bruno M Saraiva, Georgia R Squyres, Matthew J Holmes, Ethan C Garner, Zach Hensel, Ricardo Henriques, Mariana G Pinho Preprint published in bioRxiv, January 2023 Technologies: NanoJ Funded by: EMBO and ERC DOI: 10.1101/2023.06.29.547026 |
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Transertion and cell geometry organize the Escherichia coli nucleoid during rapid growth Christoph Spahn, Stuart Middlemiss, Estibaliz Gómez-de-Mariscal, Ricardo Henriques, Helge B. Bode, Séamus Holden, Mike Heilemann Preprint published in bioRxiv, January 2023 Technologies: CARE, DeepAutoFocus, DeepBacs and ZeroCostDL4Mic Funded by: EMBO, ERC, H2021 and H2022 DOI: 10.1101/2023.10.16.562172 |
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Roadmap on deep learning for microscopy Giovanni Volpe, Carolina Wählby, Lei Tian, Michael Hecht, Artur Yakimovich, Kristina Monakhova, Laura Waller, Ivo F Sbalzarini, Christopher A Metzler, Mingyang Xie, Kevin Zhang, Isaac CD Lenton, Halina Rubinsztein-Dunlop, Daniel Brunner, Bijie Bai, Aydogan Ozcan, Daniel Midtvedt, Hao Wang, Nataša Sladoje, Joakim Lindblad, Jason T Smith, Marien Ochoa, Margarida Barroso, Xavier Intes, Tong Qiu, Li-Yu Yu, Sixian You, Yongtao Liu, Maxim A Ziatdinov, Sergei V Kalinin, Arlo Sheridan, Uri Manor, Elias Nehme, Ofri Goldenberg, Yoav Shechtman, Henrik K Moberg, Christoph Langhammer, Barbora Špačková, Saga Helgadottir, Benjamin Midtvedt, Aykut Argun, Tobias Thalheim, Frank Cichos, Stefano Bo, Lars Hubatsch, Jesus Pineda, Carlo Manzo, Harshith Bachimanchi, Erik Selander, Antoni Homs-Corbera, Martin Fränzl, Kevin de Haan, Yair Rivenson, Zofia Korczak, Caroline Beck Adiels, Mite Mijalkov, Dániel Veréb, Yu-Wei Chang, Joana B Pereira, Damian Matuszewski, Gustaf Kylberg, Ida-Maria Sintorn, Juan C Caicedo, Beth A Cimini, Muyinatu A Lediju Bell, Bruno M Saraiva, Guillaume Jacquemet, Ricardo Henriques, Wei Ouyang, Trang Le, Estibaliz Gómez-de-Mariscal, Daniel Sage, Arrate Muñoz-Barrutia, Ebba Josefson Lindqvist, Johanna Bergman Preprint published in arXiv, January 2023 Technologies: BioImage Model Zoo, CARE and ZeroCostDL4Mic Funded by: CZI, EMBO, ERC and H2021 DOI: 10.48550/arXiv.2303.03793 |
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2022
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Trimethine cyanine dyes as NA-sensitive probes for visualization of cell compartments in fluorescence microscopy Daria Aristova, Roman Selin, Hannah Sophie Heil, Viktoriia Kosach, Yuriy Slominsky, Sergiy Yarmoluk, Vasyl Pekhnyo, Vladyslava Kovalska, Ricardo Henriques, Andriy Mokhir Paper published in ACS omega, January 2022 Funded by: EMBO, ERC and H2021 DOI: 10.1021/acsomega.2c05231 |
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The LEGO® brick road to open science and biotechnology Etienne Boulter, Julien Colombelli, Ricardo Henriques, Chloé C. Féral Review published in Trends in Biotechnology, January 2022 Technologies: NanoJ and NanoJ-Fluidics Funded by: EMBO, ERC and Wellcome Trust DOI: 10.1016/j.tibtech.2022.02.003 |
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Physical mechanisms of ESCRT-III–driven cell division Lena Harker-Kirschneck, Anne E. Hafner, Tina Yao, Christian Vanhille-Campos, Xiuyun Jiang, Andre Pulschen, Fredrik Hurtig, Dawid Hryniuk, Siân Culley, Ricardo Henriques, Buzz Baum, Anđela Šarić Paper published in Proceedings of the National Academy of Sciences, January 2022 Funded by: Wellcome Trust DOI: 10.1073/pnas.2107763119 |
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Expansion Microscopy on Saccharomyces cerevisiae AG Korovesi, L Morgado, M Fumasoni, R Henriques, HS Heil, M Del Rosario Paper published in microPublication Biology, January 2022 Funded by: EMBO, ERC and Wellcome Trust DOI: 10.17912/micropub.biology.000566 |
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Mapping molecular complexes with super-resolution microscopy and single-particle analysis Afonso Mendes, Hannah S. Heil, Simao Coelho, Christophe Leterrier, Ricardo Henriques Review published in Open Biology, January 2022 Technologies: NanoJ-VirusMapper, Nuclear-Pores as references and ZeroCostDL4Mic Funded by: EMBO, ERC and Wellcome Trust DOI: 10.1098/rsob.220079 |
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Bioimage model zoo - a community-driven resource for accessible deep learning in bioimage analysis Wei Ouyang, Fynn Beuttenmueller, Estibaliz Gómez-de-Mariscal, Constantin Pape, Tom Burke, Carlos Garcia-López-de-Haro, Craig Russell, Lucía Moya-Sans, Cristina de-la-Torre-Gutiérrez, Deborah Schmidt, Dominik Kutra, Maksim Novikov, Martin Weigert, Uwe Schmidt, Peter Bankhead, Guillaume Jacquemet, Daniel Sage, Ricardo Henriques, Arrate Muñoz-Barrutia, Emma Lundberg, Florian Jug, Anna Kreshuk Preprint published in BioRxiv, January 2022 Technologies: BioImage Model Zoo, CARE and ZeroCostDL4Mic Funded by: CZI, EMBO, ERC and H2021 DOI: 10.1101/2022.06.07.495102 |
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DeepBacs for multi-task bacterial image analysis using open-source deep learning approaches Christoph Spahn, Estibaliz Gómez-de-Mariscal, Romain F. Laine, Pedro M. Pereira, Lucas von Chamier, Mia Conduit, Mariana G. Pinho, Guillaume Jacquemet, Séamus Holden, Mike Heilemann, Ricardo Henriques Paper published in Communications Biology, January 2022 Technologies: BioImage Model Zoo, CARE, DeepBacs, NanoJ, NanoJ-SQUIRREL and ZeroCostDL4Mic Funded by: CZI, ERC, FCT and Wellcome Trust DOI: 10.1038/s42003-022-03634-z |
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Nanoscale colocalization of NK cell activating and inhibitory receptors controls signal integration David Tomaz, Pedro Matos Pereira, Nadia Guerra, Julian Dyson, Keith Gould, Ricardo Henriques Paper published in Frontiers in Immunology, January 2022 Technologies: NanoJ and NanoJ-SQUIRREL Funded by: BBSRC, EMBO and ERC DOI: 10.3389/fimmu.2022.868496 |
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2021
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Democratising deep learning for microscopy with ZeroCostDL4Mic Lucas von Chamier, Romain F. Laine, Johanna Jukkala, Christoph Spahn, Daniel Krentzel, Elias Nehme, Martina Lerche, Sara Hernández-Pérez, Pieta K. Mattila, Eleni Karinou, Séamus Holden, Ahmet Can Solak, Alexander Krull, Tim-Oliver Buchholz, Martin L. Jones, Loïc A. Royer, Christophe Leterrier, Yoav Shechtman, Florian Jug, Mike Heilemann, Guillaume Jacquemet, Ricardo Henriques Paper published in Nature communications, January 2021 Technologies: CARE, NanoJ, NanoJ-SQUIRREL, NanoJ-SRRF and ZeroCostDL4Mic Funded by: EMBO, ERC and Wellcome Trust News: AZO Life Sciences, Drug Target Review, Nanotechnology Now and The Medical News Blogs: Microbiome Digest - Bik's Picks DOI: 10.1038/s41467-021-22518-0 |
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Avoiding a replication crisis in deep-learning-based bioimage analysis Romain F Laine, Ignacio Arganda-Carreras, Ricardo Henriques, Guillaume Jacquemet Perspective published in Nature methods, January 2021 Technologies: BioImage Model Zoo and ZeroCostDL4Mic Funded by: EMBO, ERC and Wellcome Trust DOI: 10.1038/s41592-021-01284-3 |
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The field guide to 3D printing in microscopy Mario Del Rosario, Hannah S Heil, Afonso Mendes, Vittorio Saggiomo, Ricardo Henriques Review published in Adv. Biol., January 2021 Technologies: CARE, NanoJ, NanoJ-Fluidics and NanoJ-SRRF Funded by: EMBO, ERC and Wellcome Trust DOI: 10.1002/adbi.202100994 |
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eHooke - a tool for automated image analysis of spherical bacteria based on cell cycle progression Bruno M. Saraiva, Ludwig Krippahl, Sérgio R. Filipe, Ricardo Henriques, Mariana G. Pinho Paper published in Biological Imaging, January 2021 Funded by: ERC and Wellcome Trust DOI: 10.1017/s2633903x21000027 |
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Application of super-resolution and advanced quantitative microscopy to the spatio-temporal analysis of influenza virus replication Emma Touizer, Christian Sieben, Ricardo Henriques, Mark Marsh, Romain F. Laine Review published in Viruses, January 2021 Technologies: NanoJ-VirusMapper, Super-Beacons and ZeroCostDL4Mic Funded by: Wellcome Trust DOI: 10.3390/v13020233 |
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FtsZ treadmilling is essential for Z-ring condensation and septal constriction initiation in Bacillus subtilis cell division Kevin D. Whitley, Calum Jukes, Nicholas Tregidgo, Eleni Karinou, Pedro Almada, Yann Cesbron, Ricardo Henriques, Cees Dekker, Séamus Holden Paper published in Nature communications, January 2021 Technologies: DeepAutoFocus Funded by: BBSRC and Wellcome Trust News: Nanowerk DOI: 10.1038/s41467-021-22526-0 |
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Single-Molecule Super-Resolution Imaging of T-Cell Plasma Membrane CD4 Redistribution upon HIV-1 Binding Yue Yuan, Caron A. Jacobs, Isabel Llorente Garcia, Pedro M. Pereira, Scott P. Lawrence, Romain F. Laine, Mark Marsh, Ricardo Henriques Paper published in Viruses, January 2021 Funded by: ERC DOI: 10.3390/v13010142 |
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2020
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An Introduction to Live-Cell Super-Resolution Imaging Siân Culley, Pedro Matos Pereira, Romain F Laine, Ricardo Henriques Book chapter published in Imaging from Cells to Animals In Vivo, January 2020 Technologies: CARE, NanoJ, NanoJ-Fluidics, NanoJ-SQUIRREL and QuickPALM DOI: 10.1201/9781315174662-4 |
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Closed mitosis requires local disassembly of the nuclear envelope Gautam Dey, Siân Culley, Scott Curran, Uwe Schmidt, Ricardo Henriques, Wanda Kukulski, Buzz Baum Paper published in Nature, January 2020 Technologies: CARE, NanoJ, NanoJ-SRRF and Nuclear-Pores as references Funded by: BBSRC and Wellcome Trust News: Nature Asia DOI: 10.1038/s41586-020-2648-3 |
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The cell biologist's guide to super-resolution microscopy Guillaume Jacquemet, Alexandre F. Carisey, Hellyeh Hamidi, Ricardo Henriques, Christophe Leterrier Review published in Journal of Cell Science, January 2020 Technologies: NanoJ, NanoJ-Fluidics and NanoJ-SRRF Funded by: BBSRC and Wellcome Trust News: ScienMag and EurekAlert! DOI: 10.1242/jcs.240713 |
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Super‐beacons - Open‐source probes with spontaneous tuneable blinking compatible with live‐cell super‐resolution microscopy Pedro M Pereira, Nils Gustafsson, Mark Marsh, Musa M Mhlanga, Ricardo Henriques Paper published in Traffic, January 2020 Technologies: NanoJ, NanoJ-Fluidics, NanoJ-SQUIRREL, NanoJ-SRRF and Super-Beacons Funded by: BBSRC and Wellcome Trust DOI: 10.1111/tra.12728 |
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Live imaging of a hyperthermophilic archaeon reveals distinct roles for two ESCRT-III homologs in ensuring a robust and symmetric division Andre Arashiro Pulschen, Delyan R Mutavchiev, Siân Culley, Kim Nadine Sebastian, Jacques Roubinet, Marc Roubinet, Gabriel Tarrason Risa, Marleen van Wolferen, Chantal Roubinet, Uwe Schmidt, Gautam Dey, Sonja-Verena Albers, Ricardo Henriques, Buzz Baum Paper published in Current Biology, January 2020 Technologies: Sulfoscope Funded by: Wellcome Trust DOI: 10.1016/j.cub.2020.05.021 |
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The proteasome controls ESCRT-III–mediated cell division in an archaeon Gabriel Tarrason Risa, Fredrik Hurtig, Sian Bray, Anne E. Hafner, Lena Harker-Kirschneck, Peter Faull, Colin Davis, Dimitra Papatziamou, Delyan R. Mutavchiev, Catherine Fan, Leticia Meneguello, Andre Arashiro Pulschen, Gautam Dey, Siân Culley, Mairi Kilkenny, Diorge P. Souza, Luca Pellegrini, Robertus A. M. de Bruin, Ricardo Henriques, Ambrosius P. Snijders, Anđela Šarić, Ann-Christin Lindås, Nicholas P. Robinson, Buzz Baum Paper published in Science, January 2020 Technologies: NanoJ News: NRK, Scitech Daily, NCYT - Noticias de la Ciencia y la Technologia and UPI.com DOI: 10.1126/science.aaz2532 |
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vLUME - 3D virtual reality for single-molecule localization microscopy Alexander Spark, Alexandre Kitching, Daniel Esteban-Ferrer, Anoushka Handa, Alexander R. Carr, Lisa-Maria Needham, Aleks Ponjavic, Ana Mafalda Santos, James McColl, Christophe Leterrier, Simon J. Davis, Ricardo Henriques, Steven F. Lee Paper published in Nature Methods, January 2020 Technologies: Nuclear-Pores as references, QuickPALM and vLume Funded by: BBSRC and Wellcome Trust News: Technology Networks, La Razon (ESP), ZAP and Medium US Blogs: Qubit, , Tech Explorist and Whats New DOI: 10.1038/s41592-020-0962-1 |
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Fluctuation-based super-resolution traction force microscopy Aki Stubb, Romain F Laine, Mitro Miihkinen, Hellyeh Hamidi, Camilo Guzmán, Ricardo Henriques, Guillaume Jacquemet, Johanna Ivaska Paper published in Nano letters, January 2020 Technologies: FBSR-TFM, NanoJ, NanoJ-SQUIRREL and NanoJ-SRRF Funded by: BBSRC DOI: 10.1021/acs.nanolett.9b04083 |
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Between life and death - strategies to reduce phototoxicity in super-resolution microscopy Kalina L Tosheva, Yue Yuan, Pedro Matos Pereira, Siân Culley, Ricardo Henriques Review published in Journal of Physics D - Applied Physics, January 2020 Technologies: CARE, NanoJ and NanoJ-Fluidics Funded by: BBSRC and Wellcome Trust DOI: 10.1088/1361-6463/ab6b95 |
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2019
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Automating multimodal microscopy with NanoJ-Fluidics Pedro Almada, Pedro M. Pereira, Siân Culley, Ghislaine Caillol, Fanny Boroni-Rueda, Christina L. Dix, Guillaume Charras, Buzz Baum, Romain F. Laine, Christophe Leterrier, Ricardo Henriques Paper published in Nature communications, January 2019 Technologies: NanoJ, NanoJ-Fluidics, NanoJ-SQUIRREL, NanoJ-SRRF and NanoJ-VirusMapper Funded by: BBSRC and Wellcome Trust News: Technology Times, MSN, DNYUZ and Express Informer DOI: 10.1038/s41467-019-09231-9 |
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TMEM16F activation by Ca2+ triggers plasma membrane expansion and directs PD-1 trafficking Christopher Bricogne, Michael Fine, Pedro M. Pereira, Julia Sung, Maha Tijani, Youxue Wang, Ricardo Henriques, Mary K. Collins, Donald W. Hilgemann Paper published in Scientific reports, January 2019 Funded by: BBSRC DOI: 10.1038/s41598-018-37056-x |
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Artificial intelligence for microscopy - what you should know Lucas von Chamier, Romain F. Laine, Ricardo Henriques Review published in Biochemical Society Transactions, January 2019 Technologies: CARE, NanoJ, NanoJ-Fluidics, NanoJ-SQUIRREL and NanoJ-SRRF Funded by: BBSRC and Wellcome Trust News: Azooptics.com DOI: 10.1042/bst20180391 |
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Real time multi-modal super-resolution microscopy through Super-Resolution Radial Fluctuations (SRRF-Stream) Justin Cooper, Mark Browne, Hugh Gribben, Martin Catney, Colin Coates, Alan Mullan, Geraint Wilde, Ricardo Henriques Paper published in Single molecule spectroscopy and superresolution imaging XII, January 2019 Technologies: NanoJ and NanoJ-SRRF DOI: 10.1117/12.2510761 |
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Nanoscale polarization of the entry fusion complex of vaccinia virus drives efficient fusion Robert D. M. Gray, David Albrecht, Corina Beerli, Moona Huttunen, Gary H. Cohen, Ian J. White, Jemima J. Burden, Ricardo Henriques, Jason Mercer Paper published in Nature microbiology, January 2019 Technologies: NanoJ and NanoJ-VirusMapper Funded by: BBSRC and Wellcome Trust Blogs: Nature Microbiology Community DOI: 10.1038/s41564-019-0488-4 |
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NanoJ - a high-performance open-source super-resolution microscopy toolbox Romain F Laine, Kalina L Tosheva, Nils Gustafsson, Robert D M Gray, Pedro Almada, David Albrecht, Gabriel T Risa, Fredrik Hurtig, Ann-Christin Lindås, Buzz Baum, Jason Mercer, Christophe Leterrier, Pedro M Pereira, Siân Culley, Ricardo Henriques Paper published in Journal of physics D - Applied physics, January 2019 Technologies: CARE, NanoJ, NanoJ-Fluidics, NanoJ-SQUIRREL, NanoJ-SRRF, NanoJ-VirusMapper and QuickPALM Funded by: BBSRC and Wellcome Trust DOI: 10.1088/1361-6463/ab0261 |
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A hidden Markov model approach to characterizing the photo-switching behavior of fluorophores Lekha Patel, Nils Gustafsson, Yu Lin, Raimund Ober, Ricardo Henriques, Edward Cohen Published in The annals of applied statistics, January 2019 Funded by: BBSRC DOI: 10.1214/19-AOAS1240 |
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Fix your membrane receptor imaging - actin cytoskeleton and CD4 membrane organization disruption by chemical fixation Pedro M Pereira, David Albrecht, Siân Culley, Caron Jacobs, Mark Marsh, Jason Mercer, Ricardo Henriques Published in Frontiers in immunology, January 2019 Technologies: NanoJ, NanoJ-Fluidics and NanoJ-SQUIRREL Funded by: BBSRC and Wellcome Trust DOI: 10.3389/fimmu.2019.00675 |
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Super-resolution fight club - assessment of 2D and 3D single-molecule localization microscopy software Daniel Sage, Thanh-An Pham, Hazen Babcock, Tomas Lukes, Thomas Pengo, Jerry Chao, Ramraj Velmurugan, Alex Herbert, Anurag Agrawal, Silvia Colabrese, Ann Wheeler, Anna Archetti, Bernd Rieger, Raimund Ober, Guy M. Hagen, Jean-Baptiste Sibarita, Jonas Ries, Ricardo Henriques, Michael Unser, Seamus Holden Paper published in Nature methods, January 2019 Technologies: QuickPALM Funded by: BBSRC DOI: 10.1038/s41592-019-0364-4 |
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Nuclear pores as versatile reference standards for quantitative superresolution microscopy Jervis Vermal Thevathasan, Maurice Kahnwald, Konstanty Cieśliński, Philipp Hoess, Sudheer Kumar Peneti, Manuel Reitberger, Daniel Heid, Krishna Chaitanya Kasuba, Sarah Janice Hoerner, Yiming Li, Yu-Le Wu, Markus Mund, Ulf Matti, Pedro Matos Pereira, Ricardo Henriques, Bianca Nijmeijer, Moritz Kueblbeck, Vilma Jimenez Sabinina, Jan Ellenberg, Jonas Ries Paper published in Nature methods, January 2019 Technologies: NanoJ, NanoJ-SQUIRREL, NanoJ-SRRF and Nuclear-Pores as references Funded by: BBSRC and Wellcome Trust News: Mirage News DOI: 10.1038/s41592-019-0574-9 |
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2018
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Quantitative mapping and minimization of super-resolution optical imaging artifacts Siân Culley, David Albrecht, Caron Jacobs, Pedro Matos Pereira, Christophe Leterrier, Jason Mercer, Ricardo Henriques Paper published in Nature methods, January 2018 Technologies: NanoJ, NanoJ-SQUIRREL and QuickPALM Funded by: BBSRC and Wellcome Trust News: physicsworld.com DOI: 10.1038/nmeth.4605 |
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SRRF - Universal live-cell super-resolution microscopy Siân Culley, Kalina L Tosheva, Pedro Matos Pereira, Ricardo Henriques Paper published in The international journal of biochemistry & cell biology, January 2018 Technologies: NanoJ, NanoJ-SQUIRREL and NanoJ-SRRF Funded by: BBSRC and Wellcome Trust DOI: 10.1016/j.biocel.2018.05.014 |
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The role of mitotic cell-substrate adhesion re-modeling in animal cell division Christina L Dix, Helen K Matthews, Marina Uroz, Susannah McLaren, Lucie Wolf, Nicholas Heatley, Zaw Win, Pedro Almada, Ricardo Henriques, Michael Boutros, Xavier Trepat, Buzz Baum Published in Developmental cell, January 2018 Funded by: BBSRC DOI: 10.1016/j.devcel.2018.03.009 |
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Septins recognize and entrap dividing bacterial cells for delivery to lysosomes Sina Krokowski, Damian Lobato-Marquez, Arnaud Chastanet, Pedro Matos Pereira, Dimitrios Angelis, Dieter Galea, Gerald Larrouy-Maumus, Ricardo Henriques, Elias T Spiliotis, Rut Carballido-Lopez, Serge Mostowy Published in Cell host & microbe, January 2018 Technologies: NanoJ-VirusMapper Funded by: BBSRC DOI: 10.1016/j.chom.2018.11.005 |
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Content-aware image restoration - pushing the limits of fluorescence microscopy Martin Weigert, Uwe Schmidt, Tobias Boothe, Andreas Müller, Alexandr Dibrov, Akanksha Jain, Benjamin Wilhelm, Deborah Schmidt, Coleman Broaddus, Siân Culley, Mauricio Rocha-Martins, Fabián Segovia-Miranda, Caren Norden, Ricardo Henriques, Marino Zerial, Michele Solimena, Jochen Rink, Pavel Tomancak, Loic Royer, Florian Jug, Eugene W. Myers Paper published in Nature methods, January 2018 Technologies: CARE and NanoJ-SQUIRREL Funded by: BBSRC and Wellcome Trust News: Technology Networks, VBIO, Innovations Report and Informationsdienst Wissenschaft DOI: 10.1038/s41592-018-0216-7 |
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Heterogeneous localisation of membrane proteins in Staphylococcus aureus Felix Weihs, Katarzyna Wacnik, Robert D. Turner, Siân Culley, Ricardo Henriques, Simon J. Foster Paper published in Scientific Reports, January 2018 Technologies: NanoJ and NanoJ-SRRF Funded by: BBSRC and Wellcome Trust DOI: 10.1038/s41598-018-21750-x |
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2017
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Open-source single-particle analysis for super-resolution microscopy with VirusMapper Robert DM Gray, Jason Mercer, Ricardo Henriques Paper published in JoVE, January 2017 Technologies: NanoJ-VirusMapper Funded by: BBSRC DOI: 10.3791/55471 |
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2016
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K63-linked ubiquitination targets Toxoplasma gondii for endo-lysosomal destruction in IFNγ-stimulated human cells Barbara Clough, Joseph D. Wright, Pedro M. Pereira, Elizabeth M. Hirst, Ashleigh C. Johnston, Ricardo Henriques, Eva-Maria Frickel Paper published in PLoS pathogens, January 2016 Funded by: BBSRC News: Phys.org and Bionity Blogs: The Toxoplasma Blog DOI: 10.1371/journal.ppat.1006027 |
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Infection counter - automated quantification of in vitro virus replication by fluorescence microscopy Siân Culley, Greg Towers, David Selwood, Ricardo Henriques, Joe Grove Paper published in Viruses, January 2016 Technologies: Infection-Counter Funded by: BBSRC DOI: 10.3390/v8070201 |
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VirusMapper - open-source nanoscale mapping of viral architecture through super-resolution microscopy Robert DM Gray, Corina Beerli, Pedro Matos Pereira, Kathrin Maria Scherer, Jerzy Samolej, Christopher Karl Ernst Bleck, Jason Mercer, Ricardo Henriques Paper published in Scientific reports, January 2016 Technologies: NanoJ-VirusMapper Funded by: BBSRC DOI: 10.1038/srep29132 |
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Fast live-cell conventional fluorophore nanoscopy with ImageJ through super-resolution radial fluctuations Nils Gustafsson, Siân Culley, George Ashdown, Dylan M. Owen, Pedro Matos Pereira, Ricardo Henriques Paper published in Nature communications, January 2016 Technologies: NanoJ-SRRF and QuickPALM Funded by: BBSRC News: Azom.com DOI: 10.1038/ncomms12471 |
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Super-resolution microscopy reveals a preformed NEMO lattice structure that is collapsed in incontinentia pigmenti Janine Scholefield, Ricardo Henriques, Anca F Savulescu, Elisabeth Fontan, Alix Boucharlat, Emmanuel Laplantine, Asma Smahi, Alain Israël, Fabrice Agou, Musa M Mhlanga Paper published in Nature Communications, January 2016 Technologies: QuickPALM Funded by: BBSRC and FCT DOI: 10.1038/ncomms12629 |
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HIV-1 Nef impairs the formation of calcium membrane territories controlling the signaling nanoarchitecture at the immunological synapse Joana G. Silva, Nuno P. Martins, Ricardo Henriques, Helena Soares Paper published in The Journal of Immunology, January 2016 Funded by: BBSRC DOI: 10.4049/jimmunol.1601132 |
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Mitochondria mediate septin cage assembly to promote autophagy of Shigella Andrea Sirianni, Sina Krokowski, Damián Lobato‐Márquez, Stephen Buranyi, Julia Pfanzelter, Dieter Galea, Alexandra Willis, Siân Culley, Ricardo Henriques, Gerald Larrouy‐Maumus, Michael Hollinshead, Vanessa Sancho‐Shimizu, Michael Way, Serge Mostowy Paper published in EMBO reports, January 2016 Funded by: BBSRC DOI: 10.15252/embr.201541832 |
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2015
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PALM and STORM - Into large fields and high-throughput microscopy with sCMOS detectors Pedro Almada, Siân Culley, Ricardo Henriques Review published in Methods, January 2015 Technologies: QuickPALM DOI: 10.1016/j.ymeth.2015.06.004 |
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High-content 3D multicolor super-resolution localization microscopy Pedro M Pereira, Pedro Almada, Ricardo Henriques Book chapter published in Methods in cell biology, January 2015 Technologies: QuickPALM |
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2014
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TNF and IL-1 exhibit distinct ubiquitin requirements for inducing NEMO–IKK supramolecular structures Nadine Tarantino, Jean-Yves Tinevez, Elizabeth Faris Crowell, Bertrand Boisson, Ricardo Henriques, Musa Mhlanga, Fabrice Agou, Alain Israël, Emmanuel Laplantine Paper published in Journal of Cell Biology, January 2014 DOI: 10.1083/jcb.201307172 |
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2013
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Regulated vesicle fusion generates signaling nanoterritories that control T cell activation at the immunological synapse Helena Soares, Ricardo Henriques, Martin Sachse, Leandro Ventimiglia, Miguel A Alonso, Christophe Zimmer, Maria-Isabel Thoulouze, Andrés Alcover Paper published in Journal of Experimental Medicine, January 2013 Technologies: QuickPALM DOI: 10.1084/jem.20130150 |
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2012
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Hierarchies of host factor dynamics at the entry site of Shigella flexneri during host cell invasion Soudeh Ehsani, José Carlos Santos, Cristina D Rodrigues, Ricardo Henriques, Laurent Audry, Christophe Zimmer, Philippe Sansonetti, Guy Tran Van Nhieu, Jost Enninga Paper published in Infection and immunity, January 2012 Technologies: QuickPALM DOI: 10.1128/IAI.06391-11 |
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Highly dynamic host actin reorganization around developing Plasmodium inside hepatocytes Carina SS Gomes-Santos, Maurice A Itoe, Cristina Afonso, Ricardo Henriques, Rui Gardner, Nuno Sepulveda, Pedro D Simoes, Helena Raquel, Antonio Paulo Almeida, Luis F Moita, Friedrich Frischknecht, Maria M Mota Paper published in PLoS One, January 2012 DOI: 10.1371/journal.pone.0029408 |
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Enhanced epifluorescence microscopy by uniform and intensity optimized illumination Sébastien Herbert, Ricardo Henriques Perspective published in Cytometry Part A, January 2012 DOI: 10.1002/cyto.a.21177 |
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Single-molecule localization super-resolution microscopy - deeper and faster Sébastien Herbert, Helena Soares, Christophe Zimmer, Ricardo Henriques Review published in Microscopy and microanalysis, January 2012 Technologies: QuickPALM DOI: 10.1017/S1431927612013347 |
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Superresolution imaging of HIV in infected cells with FlAsH-PALM Mickaël Lelek, Francesca Di Nunzio, Ricardo Henriques, Pierre Charneau, Nathalie Arhel, Christophe Zimmer Paper published in Proceedings of the National Academy of Sciences, January 2012 DOI: 10.1073/pnas.1013267109 |
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2011
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PALM and STORM - a super-resolution molecular view into living cells C Griffiths, R Henriques, MM Mhlanga Review published in Biotechnology International, January 2011 |
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PALM and STORM - unlocking live‐cell super‐resolution Ricardo Henriques, Caron Griffiths, E Hesper Rego, Musa M Mhlanga Review published in Biopolymers, January 2011 Technologies: QuickPALM DOI: 10.1002/bip.21586 |
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2010
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QuickPALM - 3D real-time photoactivation nanoscopy image processing in ImageJ Ricardo Henriques, Mickael Lelek, Eugenio F Fornasiero, Flavia Valtorta, Christophe Zimmer, Musa M Mhlanga Paper published in Nature Methods, January 2010 Technologies: QuickPALM DOI: 10.1038/nmeth0510-339 |
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2009
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High-throughput SNP genotyping - combining tag SNPs and molecular beacons Luis B Barreiro, Ricardo Henriques, Musa M Mhlanga Book chapter published in Single Nucleotide Polymorphisms - Methods and Protocols, January 2009 DOI: 10.1007/978-1-60327-411-1_17 |
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Chronic arthritis directly induces quantitative and qualitative bone disturbances leading to compromised biomechanical properties J Caetano-Lopes, AM Nery, R Henriques, H Canhão, J Duarte, PM Amaral, M Vale, R Moura, PA Pereira, P Weinmann, S Abdulghani, M Souto-Carneiro, P Rego, J Monteiro, S Sakagushi, M Viana Queiroz, YT Konttinen, L Graça, MF Vaz, JE Fonseca Paper published in Clinical & Experimental Rheumatology, January 2009 |
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Imaging host-pathogen interactions Friedrich Frischknecht, Spencer Shorte, Ulrike Engel, Keira Melican, Agneta Richter-Dahlfors, Petra Rohrbach, Miguel Prudêncio, Maik J Lehmann, Nicolas Chenouard, Alexandre Dufour, Jean-Christophe Olivo-Marin, Ricardo Henriques, Musa M Mhlanga, Matthias F Langhorst, Joerg Schaffer, Bernhard Goetze, Freddy Frischknecht, Matthias Gunzer, Simone Lepper Editorial published in Biotechnol. J, January 2009 DOI: 10.1002/biot.200900129 |
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PALM and STORM - what hides beyond the Rayleigh limit? Ricardo Henriques, Musa M Mhlanga Review published in Biotechnology Journal - Healthcare Nutrition Technology, January 2009 DOI: 10.1002/biot.200900024 |
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Frontiers in fluorescence microscopy José Rino, José Braga, Ricardo Henriques, Maria Carmo-Fonseca Review published in International Journal of Developmental Biology, January 2009 DOI: 10.1387/ijdb.072351jr |
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2008
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Degradation of bone biomechanical properties secondary to quantitative and qualitative bone disturbances induced by arthritis in SKG mice J Caetano-Lopes, AM Nery, R Henriques, H Canhao, J Duarte, P Amaral, M Vale, R Moura, PA Pereira, P Weinmann, M Souto-Carneiro, P Rego, J Monteiro, S Sakagushi, L Graca, M Viana Queiroz, MF Vaz, JE Fonseca Paper published in Calcified Tissue International, January 2008 |
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