Research Team


Pedro Matos Pereira

Pedro Matos Pereira

Postdoc (now PI)


Started in: January 2014

Ended in: December 2018

Funding: BBSRC Grant


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


Collaborations

Buzz Baum

Buzz Baum

MRC-LMB
Cambridge, UK

Joint: 6 3 1

Caron Jacobs

Caron Jacobs

University of Cape Town
Cape Town, South Africa

Joint: 3 2

Christophe Leterrier

Christophe Leterrier

Aix Marseille Université, CNRS, INP
Marseille, France

Joint: 10

Dylan Owen

Dylan Owen

University of Birmingham
Birmingham, UK

Joint: 1 1

Guillaume Jacquemet

Guillaume Jacquemet

Abo Akademi University
Turku, Finland

Joint: 16 1

Jason Mercer

Jason Mercer

University of Birmingham
Birmingham, UK

Joint: 6 4

Jonas Ries

Jonas Ries

University of Vienna
Vienna, Austria

Joint: 2

Mariana Pinho

Mariana Pinho

ITQB NOVA
Oeiras, Portugal

Joint: 4 1 2

Mark Marsh

Mark Marsh

UCL
London, UK

Joint: 4 2

Mike Heilemann

Mike Heilemann

Goethe University
Frankfurt, Germany

Joint: 3 1

Pedro Matos Pereira

Pedro Matos Pereira

ITQB NOVA
Oeiras, Portugal

Joint: 20 3

Serge Mostowy

Serge Mostowy

School of Hygiene & Tropical Medicine
London, UK

Joint: 2

Séamus Holden

Séamus Holden

Warwick University
Warwick, UK

Joint: 5


Technologies

DeepBacs DeepBacs
NanoJ-Fluidics NanoJ-Fluidics
NanoJ-SQUIRREL NanoJ-SQUIRREL
NanoJ-SRRF NanoJ-SRRF
NanoJ-VirusMapper NanoJ-VirusMapper
NanoPyx NanoPyx
Nuclear-Pores as references Nuclear-Pores as references
PhotoFiTT PhotoFiTT
Super-Beacons Super-Beacons

Publications with our group (see more on Google Scholar)

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: CARE, DL4MicEverywhere, NanoJ-SRRF, PhotoFiTT and ZeroCostDL4Mic
Funded by: CZI, EMBO, ERC, FCT, H2021 and H2022
DOI: 10.1101/2024.07.16.603046
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: CARE, 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
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, NanoJ-SRRF and ZeroCostDL4Mic
Funded by: CZI, ERC, FCT and Wellcome Trust
DOI: 10.1038/s42003-022-03634-z
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
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
Technologies: CARE
Funded by: ERC
DOI: 10.3390/v13010142
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, NanoJ-Fluidics and NanoJ-SRRF
Funded by: BBSRC and Wellcome Trust
DOI: 10.1088/1361-6463/ab6b95
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, NanoJ-SRRF and QuickPALM
DOI: 10.1201/9781315174662-4
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
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: CARE, 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
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
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: NanoJ, NanoJ-Fluidics, NanoJ-SQUIRREL, NanoJ-SRRF, NanoJ-VirusMapper and QuickPALM
Funded by: BBSRC and Wellcome Trust
DOI: 10.1088/1361-6463/ab0261
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
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: CARE, NanoJ, NanoJ-Fluidics and NanoJ-SQUIRREL
Funded by: BBSRC and Wellcome Trust
DOI: 10.3389/fimmu.2019.00675
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, NanoJ-SRRF and QuickPALM
Funded by: BBSRC and Wellcome Trust
News: physicsworld.com
DOI: 10.1038/nmeth.4605
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
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
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
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: QuickPALM
Funded by: BBSRC
News: Azom.com
DOI: 10.1038/ncomms12471
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
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

Funding with our group

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
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
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