Research Team
Pedro was a 5-year Postdoc (now PI) in our research group. Worked on 20 publications. Contributed to 10 technologies. Raised 3 grants. Collaborated with 13 labs.
Current path: Pedro Pereira now runs is how laboratory at ITQB NOVA. We continue to collaborate on several projects and he continues to be one of the greatest scientists and contributors to the research in our lab.
Past Overview (as written by Pedro when at his time in our lab): I am a cell biologist with extensive scientific knowledge in microbiology, host-pathogen interaction and advanced microscopy approaches. I have over 10 years experience in scientific project design/management, undergraduate and postgraduate student supervision and writing/communication of scientific information to both expert and non-expert audiences. To attest to this I am lead author in several high profile publications with over 1300 citations (Google Scholar: dQvQ0AAAAJ), have supervised multiple Master and PhD students, and have been actively involved in several outreach initiatives (In2Science, ITQB-NOVA open day). I have served in several decision boards in Universidade Nova de Lisboa, University College London and the Francis Crick Institute where I have worked with academic, industrial and political partners to define scientific and institutional vision and impact strategies. Experience that has provided me with a comprehensive view about the scientific landscape. From a research point of view I have made significant contributions in the fields of S. aureus microbiology (e.g. discovering a link between peptidoglycan and wall teichoic acids biosynthesis), host-pathogen interaction (e.g. importance of autolysins for immune evasion, or the role of septins in the recognition of intracellular pathogens) and hardware and software technological innovations for microscopy (e.g. NanoJ-Fluidics and NanoJ-SRRF).
In the news
- 2022-11-15: News outlet Technology Times highlights Almada et al. Nature Communications 2019
- 2022-06-18: News outlet MSN highlights Almada et al. Nature Communications 2019
- 2022-06-18: News outlet DNYUZ highlights Almada et al. Nature Communications 2019
- 2022-06-18: News outlet Express Informer highlights Almada et al. Nature Communications 2019
- 2020-10-27: News outlet Mirage News highlights Thevathasan et al. Nature Methods 2019
- 2020-08-31: News outlet Azom.com highlights Gustafsson et al. Nature Communications 2016
- 2018-05-14: News outlet physicsworld.com highlights Culley et al. Nature Methods 2018
- 2017-01-11: News outlet Phys.org highlights Clough et al. PLOS Pathogens 2016
- 2016-11-24: Blog The Toxoplasma Blog highlights Clough et al. PLOS Pathogens 2016
- 2016-11-22: News outlet Bionity highlights Clough et al. PLOS Pathogens 2016
Collaborations
Christophe Leterrier
Aix Marseille Université, CNRS, INP
Marseille, France
Joint:
10
Jonas Ries
University of Vienna
Vienna, Austria
Joint:
2
Serge Mostowy
School of Hygiene & Tropical Medicine
London, UK
Joint:
2
Séamus Holden
Warwick University
Warwick, UK
Joint:
5
Technologies
Publications with our group (see more on Google Scholar)
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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, July 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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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, August 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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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, July 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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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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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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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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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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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, September 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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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, March 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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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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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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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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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, February 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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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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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, November 2016 Funded by: BBSRC News: Phys.org and Bionity Blogs: The Toxoplasma Blog DOI: 10.1371/journal.ppat.1006027 |
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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, August 2016 Technologies: NanoJ-SRRF and QuickPALM Funded by: BBSRC News: Azom.com DOI: 10.1038/ncomms12471 |
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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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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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Funding with our group
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Quinoline-Derived Foldamers - A novel approach to combat antibiotic multiresistant and persistent Pedro M. Mateus, Pedro Matos Pereira, Ricardo Henriques Funded by: FCT - LS4Future Seed Funding Duration: March 2024 - September 2024 |
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High-resolution single-molecule imaging via 3D printing Simao Coelho, Ricardo Henriques, Pedro Matos Pereira Funded by: InnOValley - Proof of Concept Duration: July 2022 - December 2023 Publications: 1 |
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Investigating the mechanisms underpinning the interaction between autonomous immunity and intracellular S. aureus cell division and persistence Pedro Matos Pereira, João Paulo Santos Fadista, Mário José Ferreira, Moritz Sorg, Patricia Reed, Pedro Fernandes, Ricardo Henriques Funded by: FCT - R&D Projects Duration: March 2021 - February 2024 Publications: 3 |