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Carina Almeida finished her PhD degree in Biomedical Engineering in 2010, at the University of Minho (UM), in collaboration with the University of Southampton, United Kingdom. From 2010 to 2014 C. Almeida worked as a Post-doctoral researcher at the Center of Biological Engineering (CEB-UM) and the Faculty of Engineering of the University of Porto (FEUP). From 2014 to 2016 she was the CSO at Biomode, a startup company that exploits the commercial potential of technological solutions to the diagnostic market. In 2017, C. Almeida has moved to the National Institute for Agrarian and Veterinary Sciences (INIAV, the national reference laboratory for food safety and animal health) as a Senior Scientist; and since 2020 she also serves as the Head of the Food Safety Unit of INIAV. She is an integrated member of LEPABE (FEUP) since 2021. C. Almeida main research interests are to explore the potential of nucleic acid mimics, in particular for food safety, agrarian and clinical applications. She is also interested on the epidemiological aspects of pathogenic bacteria with human and veterinary impact. During her career C. Almeida has authored or co-authored 60 papers in peer-reviewed international journals, 13 book chapters and 5 patents. She has more than 1600 citations (Google Scholar, December 2022) and an H-index of 18. She is currently supervising or co-supervising 5 PhD students. She participates (or participated) as a PI and as researcher in several FCT-funded projects (POCI-01-0145-FEDER-028659; PTDC/DTP-PIC/4562/2014; POCI-01-0145-FEDER-029628; POCI-01-0145-FEDER-029961; PTDC/BIA-MIC/108811/2008; PIC/IC/82815/2007) and in four European projects (Vibrant, Trice-Rice, NanoDiaBac, and SAFER). She is also engaged on review activities for scientific journal and research funding agencies.
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Identification

Personal identification

Full name
Carina Manuela Fernandes Almeida

Citation names

  • Almeida, Carina
  • C. Almeida

Author identifiers

Ciência ID
0711-B3DC-73A7
ORCID iD
0000-0002-0175-1119
Scopus Author Id
35887166600

Email addresses

  • carina.almeida@iniav.pt (Professional)

Addresses

  • Instituto Nacional de Investigação Agrária e Veterianária (INIAV - Pólo de Vairão). Rua dos Lagidos, Lugar da Madalena, Vairão, 4485-655, Vila do Conde , Vila do Conde, Portugal (Professional)

Websites

Knowledge fields

  • Agrarian Sciences - Agrarian and Food Biotechnology
  • Natural sciences - Biological Sciences - Molecular Biology
  • Natural sciences - Biological Sciences - Microbiology
  • Agrarian Sciences - Veterinary Sciences

Languages

Language Speaking Reading Writing Listening Peer-review
English Advanced (C1) Advanced (C1) Advanced (C1) Advanced (C1)
Education
Degree Classification
2010
Concluded
 Programa doutoral em Engenharia Biomédica (Doutoramento)
Universidade do Minho Escola de Engenharia, Portugal
"Development and application of PNA probes for the detection of specific bacteria by FISH " (THESIS/DISSERTATION)
 n/a
2005
Concluded
 Biologia Aplicada (Licenciatura)
Universidade do Minho Escola de Ciências, Portugal
"Genotyping of Candica albicans isolates by Multilocus Sequence Typing and Microsatellites analyses." (THESIS/DISSERTATION)
Affiliation

Science

Category
Host institution 		Employer
2024/02/01 - Current Principal Investigator (Research) Instituto Nacional de Investigação Agrária e Veterinária (Polo Vairão), Portugal
2017/01/17 - 2024/01/31 Auxiliary Researcher (Research) Instituto Nacional de Investigação Agrária e Veterinária (Polo Vairão), Portugal

Teaching in Higher Education

Category
Host institution 		Employer
2014/09/01 - 2015/03/31 Invited Assistant Professor (University Teacher) Universidade do Minho, Portugal

Positions / Appointments

Category
Host institution 		Employer
2020/07/01 - Current Organic Unit Director Instituto Nacional de Investigação Agrária e Veterinária, Portugal
Unidade de Segurança Alimentar, Portugal

Others

Category
Host institution 		Employer
2017/01/16 - Current External collaborator Universidade do Minho Centro de Engenharia Biológica, Portugal
2017/01/01 - Current External collaborator Universidade do Porto Laboratorio de Engenharia de Processos Ambiente Biotecnologia e Energia, Portugal
2010/12/21 - 2021/01 Promoter/co-founder of Biomode S.A. Biomode SA, Portugal
2016/11/01 - 2017/01/15 Faculty Research Fellow (Investigador FCT) Universidade do Minho Centro de Engenharia Biológica, Portugal
2014/11/01 - 2016/10/31 Chief Science Officer at Biomode S.A. Biomode SA, Portugal
2011/04/01 - 2014/10/31 Postdoctoral researcher Universidade do Minho Centro de Engenharia Biológica, Portugal
2006/11/01 - 2010/11/30 PhD student Universidade do Minho Centro de Engenharia Biológica, Portugal
2006/03/01 - 2006/10/31 Research Fellowship Universidade do Minho Centro de Engenharia Biológica, Portugal
2005/03/01 - 2005/11/30 Research intern Universidade do Minho Escola de Ciências, Portugal
Projects

Contract

Designation Funders
2022/05 - 2025/12 Renovação/Requalificação do Polo de Inovação de Vairão I
PRR-C05-i03-I-000045
Principal investigator
Instituto Nacional de Investigação Agrária e Veterinária (Polo Vairão), Portugal
Ongoing
2022/01/01 - 2024/12/31 APTAcoli - NAM-aptamers for blocking enterotoxins in pig colibacillosis
PTDC/CVT-CVT/4620/2021
Principal investigator
Instituto Nacional de Investigação Agrária e Veterinária, Portugal

Universidade de Trás-os-Montes e Alto Douro, Portugal

International Iberian Nanotechnology Laboratory, Portugal
Fundação para a Ciência e a Tecnologia
Ongoing
2021/09 - 2024/08 Valicet: Valorise foods and Improve Competitiveness through Emerging Technologies applied to food by-products within the circular economy framework
PRIMA/0001/2020
Researcher
2020/09 - 2024/08 Trace-Rice: Tracing rice and valorizing side streams along mediterranean blockchain
PRIMA, Section I, 1934
Researcher
Ongoing
2020/01/01 - 2023/12/31 Laboratório de Engenharia de Processos, Ambiente, Biotecnologia e Energia
UIDP/00511/2020
10.54499/UIDP/00511/2020
Researcher
Universidade do Porto Laboratorio de Engenharia de Processos Ambiente Biotecnologia e Energia, Portugal

Universidade do Porto Faculdade de Engenharia, Portugal
Fundação para a Ciência e a Tecnologia
Concluded
2020/01/01 - 2023/12/31 Laboratório de Engenharia de Processos, Ambiente, Biotecnologia e Energia
UIDB/00511/2020
10.54499/UIDB/00511/2020
Researcher
Universidade do Porto Laboratorio de Engenharia de Processos Ambiente Biotecnologia e Energia, Portugal

Universidade do Porto Faculdade de Engenharia, Portugal
Fundação para a Ciência e a Tecnologia
Concluded
2022/01 - 2023/06 NAMShield: Controlo de Salmonella spp, na indústria pecuária, através de aptâmeros nanoensapsulados
POCI-01-0247-FEDER-069756
Researcher
Ongoing
2020/01/01 - 2022/12/31 Microbial Interactions between Gardnerella, Prevotella, and Atopobium Prior to Incident Bacterial Vaginosis
R01AI146065
Researcher
Universidade do Minho Centro de Engenharia Biológica, Portugal

The University of Alabama at Birmingham, United States
Ongoing
2018/01/01 - 2022/12/31 VIBRANT: VIral and BacteRial Adhesin Network Training
info:eu-repo/grantAgreement/EC/H2020/765042/EU
Supervisor
Universidade do Minho Centro de Engenharia Biológica, Portugal

Biomode SA, Portugal
European Commission
Ongoing
2018/07/26 - 2021/12/31 Encapsulated bacteriophages for pre-slaughter interventions to reduce to Shiga toxin-producing E. coli STEC in ruminants
PTDC/CVT-CVT/29628/2017
Universidade do Minho, Portugal

Universidade de Trás-os-Montes e Alto Douro, Portugal

Instituto Nacional de Investigação Agrária e Veterinária, Portugal

International Iberian Nanotechnology Laboratory, Portugal
Fundação para a Ciência e a Tecnologia
Concluded
2018/07/26 - 2021/07/25 NAM4toxins – De novo selection of toxin-specific aptamers using nucleic acid mimics
POCI-01-0145-FEDER-028659
Principal investigator
Instituto Nacional de Investigação Agrária e Veterinária (Polo Vairão), Portugal

Universidade do Porto Laboratorio de Engenharia de Processos Ambiente Biotecnologia e Energia, Portugal
Fundação para a Ciência e a Tecnologia
Ongoing
2018/07/16 - 2021/07/15 ColorISH - Desenvolvimento de um novo método colorimetrico para a deteção rápida de Legionella spp. em amostras de água
POCI-01-0145-FEDER-029961
Researcher
Universidade do Porto Laboratorio de Engenharia de Processos Ambiente Biotecnologia e Energia, Portugal

Instituto Nacional de Investigação Agrária e Veterinária (Polo Vairão), Portugal
Ongoing
2018/07/16 - 2021/07/15 Desenvolvimento de um novo método colorimetrico para a deteção rápida de Legionella spp. em amostras de água.
PTDC/BTA-GES/29961/2017
Instituto Nacional de Investigação Agrária e Veterinária, Portugal

Universidade do Porto, Portugal
Fundação para a Ciência e a Tecnologia
Ongoing
2018/07/26 - 2020/12/25 PhageSTEC: Development of a formulation of encapsulated bacteriophages to reduce enterotoxigenic E. coli in ruminants
POCI-01-0145-FEDER-029628
Researcher
Universidade do Minho Centro de Engenharia Biológica, Portugal

Instituto Nacional de Investigação Agrária e Veterinária (Polo Vairão), Portugal

Universidade de Trás-os-Montes e Alto Douro, Portugal

International Iberian Nanotechnology Laboratory, Portugal
Fundação para a Ciência e a Tecnologia
Ongoing
2016/07/01 - 2020/03/31 Coded-FISH: Development of a novel colour-coded RING FISH method: an innovative tool for the detection of antibiotic resistant clinical pathogens
PTDC/DTP-PIC/4562/2014
Principal investigator
Universidade do Minho Centro de Engenharia Biológica, Portugal

Universidade do Porto Laboratorio de Engenharia de Processos Ambiente Biotecnologia e Energia, Portugal
Fundação para a Ciência e a Tecnologia
Ongoing
2018/07/26 - 2019/07/25 Antisens4CandiB – Application of antisense oligomers for controlling Candida species biofilm formation on medical surfaces
POCI-01-0145-FEDER-028893
Researcher
Universidade do Minho Centro de Engenharia Biológica, Portugal
Ongoing
2014/01/01 - 2016/12/31 NanoDiaBac - Nanofluidics for ultrafast diagnosis of bacterial infections (EuroNanoMed-II)
ENMed/0003/2014
Researcher
Chalmers tekniska högskola, Sweden

Biomode SA, Portugal

Universidade Católica Portuguesa Escola Superior de Biotecnologia, Portugal
Concluded
2012/02/01 - 2015/07/30 “DNA mimics” - Development and application of DNA mimics for the rapid identification of pathogens
info:eu-repo/grantAgreement/FCT/5646-ICCMS/82815/PT
Universidade do Porto Laboratorio de Engenharia de Processos Ambiente Biotecnologia e Energia, Portugal

Universidade do Minho Centro de Engenharia Biológica, Portugal
Fundação para a Ciência e a Tecnologia
Concluded
2012/02/01 - 2015/07/30 ¿DNA mimics¿ - Desenvolvimento e aplicação de mímicos de DNA para a rápida identificação de microrganismos patogénicos
PIC/IC/82815/2007
Universidade do Minho, Portugal

Universidade do Porto Faculdade de Engenharia, Portugal

Universidade do Minho Centro de Engenharia Biológica, Portugal
Fundação para a Ciência e a Tecnologia
Concluded
2010/04/01 - 2013/09/30 HELIWATER - Water and associated biofilms as a possible vector for Helicobacter pylori transmission among the human population
info:eu-repo/grantAgreement/FCT/5876-PPCDTI/108811/PT
Universidade do Minho Centro de Engenharia Biológica, Portugal
 Fundação para a Ciência e a Tecnologia
Concluded
2006/01/02 - 2006/09/09 SAFER: Surveillance and control of microbiological stability in drinking water distribution networks
EVK1-CT-2002-00108
Research Fellow
Universidade do Minho Centro de Engenharia Biológica, Portugal

University of Southampton, United Kingdom

Suez Centre International de Recherche sur l'Eau et l'Environnement, France
European Commission Sixth Framework Programme
Concluded

Other

Designation Funders
2011 - 2013 “SI Qualificação de PME”
NORTE-07-0201-FEDER-025012
Researcher
Biomode SA, Portugal
Concluded
Outputs

Publications

Book
  1. Gomes, A.; Bourbon, A.I.; Peixoto, A.R.; Silva, A.S.; Tasso, A.; Almeida, C.; Nobre, C.; et al. Strategies for the reduction of sugar in food products. 2022.
  2. Almeida, C.; Azevedo, N.F.. Preface. 2021.
    10.7717/peerj.780
  3. Almeida, Carina. Livro de Resumos: 1º Simpósio INIAV para a Segurança Alimentar - Ruma à Alimentação do Futuro. Vila do Conde, Portugal: INIAV. 2019.
    Published • 10.7717/peerj.780 • Editor
Book chapter
  1. João David Teixeira; Sanches Silva, Ana; Almeida, Carina; Claudia Sánchez. Corresponding author: Sanches Silva, Ana. "Regulatory framework of clean label food products at European Union". In Clean Label Ingredients and Processes for The Food And Beverage Industry. 2023.
    Accepted
  2. Gomes, Ana; Bourbon, Ana I.; Peixoto, Ana Rita; Silva, Ana Sanches; Tasso, Ana; Almeida, Carina; Nobre, Clarisse; et al. "Chapter 9 - Strategies for the reduction of sugar in food products". Academic Press, 2022.
    10.1016/B978-0-323-85513-6.00008-6
  3. Almeida, C.; Azevedo, N.F.. "An Introduction to Fluorescence in situ Hybridization in Microorganisms". 1-15. 2021.
    10.1007/978-1-0716-1115-9_1
  4. Guimarães, N.M.; Azevedo, N.F.; Almeida, C.. "FISH Variants". 17-33. 2021.
    10.1007/978-1-0716-1115-9_2
  5. Rocha, R.; Almeida, C.; Azevedo, N.F.. "FISH in Food Samples". 279-290. 2021.
    10.1007/978-1-0716-1115-9_18
  6. Oliveira, Ricardo; Almeida, Carina; Azevedo, Nuno F.. "Detection of Microorganisms by Fluorescence In Situ Hybridization Using Peptide Nucleic Acid". In Methods in Molecular Biology, 217-230. Springer US, 2020.
    10.1007/978-1-0716-0243-0_13
  7. Rocha, Rui; Almeida, Carina. "Detection of bacteria by PNA-FISH". In RNA-FISH - METHODS AND PROTOCOLS - Methods in Molecular Biology, edited by Giselbert Hauptmann. Springer, Springer Nature 2020,, 2020.
    Accepted • 10.7717/peerj.780
  8. Boas, Diana Vilas; Almeida, Carina; Azevedo, Nuno; Sillankorva, Sanna; Azeredo, Joana. "Techniques to Assess Phage–Biofilm Interaction". In Methods in Molecular Biology, 137-146. Springer New York, 2018.
    10.1007/978-1-4939-8940-9_11
  9. Azevedo, Andreia S.; Almeida, Carina; Melo, L. F.; Azevedo, N. F.. "Role of E. coli on catheter-associated urinary tract infections". Universidade do Minho. Centro de Engenharia Biológica (CEB), 2015.
  10. Almeida, Carina; Azevedo, N.. "Multi-species biofilms". In Clinical Biofilms – current concepts and advanced techniques, 63-75. Braga, Portugal: Universidade do Minho. Departamento de Engenharia Biológica (DEB), 2014.
    Published
  11. Boas, Diana Patrícia Andrade Vilas; Alves, Diana; Almeida, Carina; Sillankorva, Sanna; Nicolau, Ana. "Microscopy techniques for the study of biofilm". In Clinical Biofilms: Current Concepts and Advanced Techniques. Braga: Universidade do Minho. Departamento de Engenharia Biológica (DEB), 2014.
    Published
  12. Almeida, Carina; Rodrigues, Célia F.; Jorge, Paula; Costa, Ana Rita. "Analysis of biofilm metabolites". In Clinical Biofilms: Current Concepts and Advanced Techniques. Universidade do Minho. Departamento de Engenharia Biológica (DEB), 2014.
  13. Almeida, Carina; Vieira, Maria João; Nicolau, Ana. "31. Técnicas de microscopia para o estudo de biofilmes". In Biofilmes - Na Saúde, No Ambiente, Na Indústria. Publindústria, 2012.
  14. Almeida, Carina; Azevedo, N. F.; Cerqueira, L.; Keevil, C. W.; Vieira, M. J.. "RT-PCR and PNA-FISH as novel methods for the detection of specific microorganisms in heterotrophic biofilm communities". In Bolfilms : coming of age. 2007.
Conference abstract
  1. DIAS, CARLA ; Ballem, Andressa; Pinto, Ana; Almeida, Gonçalo; Fuciños, Pablo; Almeida, Carina; Saavedra, Maria José ; et al. Corresponding author: Oliveira, Hugo. "Prevalence and control of Shiga toxin-producing E. coli: from diversity in dairy cattle to phage therapy. Microbiotec". Paper presented in Microbiotec 21 - Congress of Microbiology and Biotechnology, LISBOA, 2022.
    Published
  2. Dias, Carla; Ballem, Andressa; Ana Pinto; Almeida, Gonçalo; Fuciños, Pablo; Almeida, Carina; M. J. Saavedra; et al. Corresponding author: Dias, Carla. "Prevalence and control of Shiga toxin-producing E. coli: from diversity in dairy cattle to phage therapy". Paper presented in Congress of microbiology and Biotechnology 2021 (MicroBiotec21), Lisboa, 2021.
    Published
Conference paper
  1. Teixeira, João David; Sánchez, Cláudia; Almeida, Carina; Sanches-Silva, Ana; Parpot, Pier. "Classification of apple and pear species from Alcobaça region (Portugal) and their cultivars with machine learning algorithms". 2023.
  2. Teixeira, João David; Mateus, Ana Rita Soares; Parpot, Pier; Sousa, Miguel Leão de; Sánchez, Cláudia; Almeida, Carina; Sanches-Silva, Ana. "Comparison of the phenolics profile of regional and commercial cultivars of apples (Malus domestica) from Alcobaça region (Portugal)". 2023.
  3. Teixeira, João David; Mateus, Ana Rita Soares; Sánchez, Claudia; Parpot, Pier; Almeida, Carina; Sanches-Silva, Ana. "Evaluation of the individual phenolic compounds of regional cultivars of pears (Pyrus communis L.) by Liquid Chromatography combined with High Resolution Mass Spectrometry". 2023.
  4. Teixeira, João David; Sánchez, Claudia; Parpot, Pier; Almeida, Carina; Sanches-Silva, Ana. "Regional apple and pear cultivars from Alcobaça region (Portugal): comparison of the antioxidant properties of the edible part and by-products". 2023.
  5. Rodriguez-Mateos, P.; Rodrigues, C.F.; Azevedo, N.F.; Almeida, C.; Dyer, C.E.; Iles, A.; Pamme, N.. "Fish and chips - ifast microfluidic device for E. Coli O157:H7 capture and detection via on-chip fish assay". 2019.
    10.7717/peerj.780
  6. Azevedo, Andreia; Almeida, Carina; Melo, Luís F.; Azevedo, N. F.. "Biofilm formation on a microtiter-plate using artificial urine to mimic catheter-associated urinary tract infections". 2012.
  7. Azevedo, N. F.; Almeida, Carina; Guimarães, N.; Keevil, C. W.; Vieira, M. J.. "Maintenance of spiral morphology and formation of biofilms on copper surfaces by water-exposed Helicobacter pylori". Paper presented in INTERNATIONAL CONFERENCE BIOFILM SYSTEMS, Amsterdam, 2006.
Conference poster
  1. Campos, Ana Maria; de Sousa, Inês Gonçalves; Almeida, Carina; Brites, Carla. "Molecular profiling of hidden insect infestation in stored rice grains: A Comprehensive RT-PCR Approach for Species Discrimination and Limit of Detection Assessment". Paper presented in Microbiotec - Congress of Microbiology and Biotechnology 2023, 2023.
  2. Campos, Ana Maria; de Sousa, Inês Gonçalves; Almeida, Carina; Brites, Carla. "Enhancing molecular screening of hidden insect infestation in rice grains by coi barcoding: primer performance and limit of detection". Paper presented in IV International Meeting of the Portuguese Society of Genetics, 2023.
  3. Fokt, Hanna; Cleto, Sara; Oliveira, Hugo; Araújo, Daniela; Castro, Joana; Cerca, Nuno; Vieira, Maria João; Almeida, Carina. Corresponding author: Castro, Joana. "The Evolution of Bacteriocin Production in Escherichia coliassociated biofilms". Paper presented in SurfSAFE Conference - Biofilm detection and control in the food industry, 2023.
  4. Vilas Boas, Diana; Araújo, Daniela; Castro, Joana; Azevedo, Nuno Filipe; Vieira, Maria João; Almeida, Carina. "Flagellum and flagellum-based motility role on Salmonella Enteritidis and Escherichia coli biofilm formation". Paper presented in SurfSAFE Conference - Biofilm detection and control in the food industry, 2023.
  5. de Sousa, Inês Gonçalves; Campos, Ana Maria; Almeida, Carina; Brites, Carla. "How to detect hidden insect infestation in rice grains?". Paper presented in Encontro Ciência 2023, 2023.
  6. Campos, Ana Maria; de Sousa, Inês Gonçalves; Almeida, Carina; Brites, Carla. "Development of a rapid molecular methodology for the detection of hidden insect infestation in rice". Paper presented in New advances from PRIMA projects for improving Mediterranean Agro-Food value chains, 2023.
  7. de Sousa, Inês Gonçalves; Campos, Ana Maria; Almeida, Carina; Brites, Carla. Corresponding author: Brites, Carla. "Identification of molecular rapid methods for hidden insect infestation determination in rice". Paper presented in Dare2Change, 2023.
  8. João David Teixeira; Parpot, Pier; Leão de Sousa, Miguel; Almeida, Carina; Sanches Silva, Ana. Corresponding author: Sanches Silva, Ana. "Antioxidant properties of thirty commercial cultivars of apples from Alcobaça region (Portugal): edible portion versus by-products". Paper presented in Dare2Change, 2023.
  9. Almeida, Carina; Castro, Joana; Araújo, Daniela. "Production of a safe and a natural red extract by Monascus Purpureus fungus for applications". Paper presented in Dare2Change, 2023.
  10. Mário Sousa; Rui Rocha; Araújo, Daniela; Castro, Joana; Ana Barbosa; Azevedo, Nuno Filipe; Cerqueira, Laura; Almeida, Carina. "Validation of a Peptide Nucleic Acid Fluorescence in situ Hybridization for the specific detection of Salmonella species in food matrices". Paper presented in Dare2Change, 2023.
  11. João David Teixeira; Mateus, Ana Rita Soares; Silva, Sónia; Almeida, Carina; Sanches Silva, Ana. Corresponding author: Almeida, Carina. "Characterization by UHPLC-ToF-MS of phenolic compounds of citron (Citrus medica), an ancient species of the genus Citrus". Paper presented in Dare2Change, 2023.
  12. João David Teixeira; Almeida, Carina; Mateus, Ana Rita Soares; Silva, Sónia; Sanches Silva, Ana. Corresponding author: Almeida, Carina. "Towards Citron (Citrus medica L.) valorization: an ancient citrus with excellent antioxidant properties and appreciated aroma". Paper presented in Dare2Change, 2023.
  13. Sousa, Lúcia G. V.; Almeida, Carina; Muzny, Christina A.; Cerca, Nuno. "The use of a novel PNA-FISH multiplex protocol for bacterial vaginosis diagnosis". Paper presented in Biofilms and Microbiomes: Global Impact on Public and Ecosystem Health, 2022.
  14. Sousa, Lúcia G. V.; Almeida, Carina; Sharma, Jyoti ; Muzny, Christina A.; Cerca, Nuno. "A new PNA-FISH multiplex approach is capable of detecting bacterial vaginosis-associated species on vaginal samples". Paper presented in EuroBiofilms 2022, 2022.
  15. Oliveira, Ricardo; Pinho, Eva; DeStefano, Jeffrey; Azevedo, Nuno Filipe; Almeida, Carina. "Aptamers For Detection of Staphylococcal Enterotoxins in Food Samples". Paper presented in Dare2Change, 2021.
  16. Oliveira, Ricardo; Pinho, Eva; Almeida, Gonçalo; Azevedo, Nuno Filipe; Almeida, Carina. "Prevalence of Staphylococcus aureus and staphylococcal enterotoxins in raw milk from Northern Portugal". Paper presented in Dare2Change, 2021.
  17. Ana Rita Barata; Oliveira, Ricardo; Bárbara Nunes; Guedes, Hugo; Almeida, Carina; Saavedra, Maria José ; Silva, Gabriela; Almeida, Gonçalo. "Raw milk as a source of food zoonotic pathogens". Paper presented in Dare2Change, 2021.
  18. Ballem, Andressa; Almeida, Gonçalo; Almeida, Carina; Fernandes, Conceição; Saavedra, Maria José. "Antibiotic Resistance Profile among Shiga Toxin-Producing Escherichia coli Isolated from dairy cattle". Paper presented in Dare2Change, 2021.
  19. João David Teixeira; Parpot, Pier; Claudia Sánchez; Almeida, Carina; Sanches Silva, Ana. Corresponding author: João David Teixeira. "Evaluation of the antioxidant properties of pears from different Portuguese varieties: edible part versus by-products". Paper presented in Dare2Change, 2021.
  20. João David Teixeira; Parpot, Pier; Claudia Sánchez; Almeida, Carina; Sanches Silva, Ana. Corresponding author: João David Teixeira. "Apples from Alcobaça region (Portugal): comparison of the antioxidant properties of the edible part and by-products". Paper presented in Dare2Change, 2021.
  21. Oliveira, Ricardo; Pinho, Eva; Azevedo, Nuno Filipe; Almeida, Carina. "In silico prediction of the functional 3D conformation of NAM aptamers". Paper presented in 1st Symposium on Oligonucleotide Technologies and Therapeutics, 2021.
  22. Oliveira, Ricardo; Pinho, Eva; Azevedo, Nuno Filipe; Almeida, Carina. "Prediction of single-stranded nucleic acids structure: from the sequence to the three-dimensional docking of aptamers". Paper presented in World Microbe Forum 2021, 2021.
  23. Oliveira, Ricardo; Pinho, Eva; Azevedo, Nuno Filipe; Almeida, Carina. "De novo SELEX of toxin specific aptamers using nucleic acid mimics (NAMs)". Paper presented in Encontro Ciência 2020, 2020.
  24. Oliveira, Hugo; Ballem, Andressa; Gonçalves, Soraia; Garcia-Meniño, I.; Flament-Simon, S.C.; Blanco, J.E.; Pinto, J.; Almeida, Gonçalo; Almeida, Carina. "Prevalence and Genetic Characterization of Shiga Toxin-Producing Escherichia coli (STEC) Isolates from cattle in Portugal.". Paper presented in 30th European Congress of Clinical Microbiology and Infectious Diseases (ECCMID), 2020.
  25. Sousa, Ana Luísa; Oliveira, Ricardo; Pinho, Eva; Azevedo, Nuno Filipe Ribeiro Pinto Oliveira; Almeida, Carina. "Prediction and design of aptamer structures and their interaction with a target molecule". Paper presented in Microbiotec 19, 2019.
    10.7717/peerj.780
  26. Oliveira, Ricardo; Ferreira-Bravo, Irani A; Sousa, Ana Luísa; Pinho, Eva; Azevedo, Nuno Filipe; DeStefano, Jeffrey; Almeida, Carina. "Application of nucleic acid mimics (NAMs) in the selection of aptamers against staphylococcal enterotoxins". Paper presented in 1º Simpósio INIAV para a Segurança Alimentar - Rumo à Alimentação do Futuro, Vila do Conde, Portugal, 2019.
  27. Oliveira, Ricardo; Ferreira- Bravo, Irani; Sousa, Ana Luísa; Pinho, Eva; Azevedo, Nuno Filipe Ribeiro Pinto Oliveira; DeStefano, Jeffrey; Almeida, Carina. "De novo selection of Staphylococcal enterotoxin A-specific aptamers using nucleic acid mimics (NAM)". Paper presented in 1º Simpósio INIAV para a Segurança Alimentar, 2019.
    10.7717/peerj.780
  28. Sousa, Ana Luísa; Oliveira, Ricardo; Pinho, Eva; Azevedo, Nuno Filipe Ribeiro Pinto Oliveira; Almeida, Carina. "Prediction of aptamers´ structures and their interaction with Staphylococcal enterotoxin A". Paper presented in 1º Simpósio INIAV para a Segurança Alimentar, 2019.
    10.7717/peerj.780
  29. Azevedo, Andreia Sofia Mateus; Fernandes, Ricardo Manuel; Faria, Ana Rita; Silvestre, Óscar Ferreira; Nieder, Jana Berit; Wengel, Jesper; Azevedo, Nuno Filipe; Almeida, Carina Manuela Fernandes. "Application of nucleic acid mimics and spectral imaging to fluorescence in situ hybridization for the characterization of microbial communities". Paper presented in BioRemid2019 - 2nd International Meeting on New Strategies in Bioremediation Processes, 2019.
  30. Oliveira, Ricardo; Sousa, Ana Luísa; Pinho, Eva; Azevedo, Nuno Filipe Ribeiro Pinto Oliveira; Almeida, Carina. "De novo selection of toxin-specific aptamers using nucleic acid mimics". Paper presented in 3rd Doctoral Congress in Engineering, 2019.
  31. Ballem, Andressa; Gonçalves, Soraia; Ferreira, A. I.; Fernandes, C.; Saavedra, Maria J.; Pinto, Carlos; Oliveira, Hugo Alexandre Mendes; Almeida, Gonçalo; Almeida, Carina Manuela Fernandes. "Prevalence of shigatoxigenic Escherichia coli in bovine cattle: a survey in the north region of portugal". Paper presented in SAlimentar 2019 - 1º Simpósio INIAV para a Segurança Alimentar, 2019.
    10.7717/peerj.780
  32. Oliveira, Ricardo Bruno Costa; Azevedo, Andreia Sofia Mateus; Azevedo, Nuno; Almeida, Carina Manuela Fernandes. "Identification of genes associated with beta-lactam resistance in clinical isolates of Gram-negative bacteria". Paper presented in FEMS 2019 - 8th Congress of European Microbiologists, 2019.
    10.7717/peerj.780
  33. Azevedo, Andreia S.; Teixeira, H.; Ferreira, R.; Figueiredo, C.; Wengel, J.; Almeida, Carina; Azevedo, N. F.. "Combining nucleic acid mimics and spectral imaging with fluorescence in situ hybridization for the analysis of the gastric micro-biogeography". Paper presented in Helicobacter, 2019.
    10.7717/peerj.780
  34. Gonçalves, Soraia; Ferreira, Isabel; Guedes, Hugo; Oliveira, Hugo Alexandre Mendes; Almeida, Carina Manuela Fernandes; Afonso, Isabel; Almeida, Gonçalo. "Perfil de resistência a antibióticos de Escherichia coli produtoras e não produtoras da toxina Shiga". Paper presented in SAlimentar 2019 - 1º Simpósio INIAV para a Segurança Alimentar, 2019.
    10.7717/peerj.780
  35. Araújo, Daniela; Azevedo, N.; Barbosa, Ana; Almeida, Carina; Rodrigues, M. Elisa; Henriques, Mariana; Silva, Sónia Carina. "2´OMethylRNA EFG1 antisense oligomer to control Candida albicans filamentation". Paper presented in 15th Annual Meeting of the Oligonucleotide Therapeutics Society, 2019.
    10.7717/peerj.780
  36. Azevedo, Andreia Sofia Mateus; Fernandes, R.; Azevedo, Nuno; Almeida, Carina. "Optimizing locked nucleic acid/2'-o-methyl-RNA fluorescence in situ hybridization (LBA/2'OME-FISH) procedures for bacterial detection". Paper presented in FEMS 2019 - 8th Congress of European Microbiologists, 2019.
    10.7717/peerj.780
  37. Azevedo, Andreia S.; Sousa, I. M.; Fernandes, R.; Azevedo, N. F.; Almeida, Carina. "Optimizing locked nucleic acid/2-O-methyl-RNA fluorescence in situ hybridization (LNA/2OMe-FISH) for bacterial detection". Paper presented in CHEMPOR 2018 - 13th International Chemical and Biological Engineering Conference, 2018.
    10.7717/peerj.780
  38. Oliveira, Ricardo; Rocha, Rui; Sousa, Mário; Cerqueira, Laura; Azevedo, Nuno Filipe; Almeida, Carina. "Rapid identification of Campylobacter spp. using peptide nucleic acid fluorescence in situ hybridization (PNA-FISH) in food samples". Paper presented in V AEICBAS Biomedical Congress - Abel Salazar Biomedical Sciences Institute (ICBAS), Porto, Portugal, 2017.
  39. Melo, Luís D. R.; Pinto, Graça; Oliveira, Fernando E.; França, Ângela Maria Oliveira Sousa; Boas, Diana Patrícia Andrade Vilas; Almeida, Carina; Sillankorva, Sanna; Cerca, Nuno; Azeredo, Joana. "Disclosing the complexity involved in phage-biofilm interaction: the case study of a Sep1virus phage infecting S. epidermidis". Paper presented in Book of Abstracts of CEB Annual Meeting 2017, 2017.
    10.7717/peerj.780
  40. Azevedo, Andreia Sofia; Almeida, Carina; Gomes, Luciana Calheiros; Ferreira, Carla; Mergulhão, Filipe J.; Melo, Luís F.; Azevedo, Nuno Filipe Ribeiro Pinto Oliveira. "An in vitro dynamic model of catheter-associated urinary tract infections to investigate the role of uncommon bacteria on the Escherichia coli microbial consortium". Paper presented in Biofilms 7 - Microbial Works of Art, 2016.
  41. Gerola, Gislaine P.; Azevedo, Andreia S.; Almeida, Carina Manuela Fernandes; Peres, Joana; Mergulhão, Filipe J.; Azevedo, Nuno F.. "Cooperation or conflict? Impact of intraspecific diversity on Escherichia coli biofilms". 2016.
  42. Azevedo, A. S.; Pereira, B.; Almeida, Carina; Melo, Luís F.; Wengel, J.; Azevedo, N. F.. "Detection and discrimination of microorganisms using Locked Nucleic Acid - Fluorescence In Situ Hybridization (LNA-FISH)". Paper presented in CHEMPOR 2014 - Book of Extended Abstracts of the 12th International Chemical and Biological Engineering Conference, 2014.
  43. Azevedo, Andreia; Almeida, Carina; Melo, L. F.; Azevedo, N. F.. "Interaction between non-disease causing microorganism and E. coli in catheter-associated urinary tract biofilms". Paper presented in Eurobiofilms 2013, 2013.
  44. Carvalho, Joana; Fokt, Hanna; Cleto, S.; Almeida, Carina; Vieira, M. J.. "Enterobactin : like siderophore gene cluster induction in Cronobacter sakazakii strain". Paper presented in FEMS 2013 - 5th Congress of European Microbiologists, 2013.
  45. Almeida, Carina; Cerqueira, L.; Azevedo, N. F.; Vieira, M. J.. "Helicobacter pylori : role of water on survival and transmission". Paper presented in 3rd SCIENTIFIC MEETING OF THE INSTITUTE FOR BIOTECHNOLOGY AND BIOENGINEERING, 2012.
  46. Machado, António; Salgueiro, Débora; Almeida, Carina; Henriques, Ana Filipa Frutuoso Mendes; Haesebrouck, Freddy; Vaneechoutte, Mario; Rodrigues, L. R.; Cerca, Nuno. "Detection of Lactobacillus and Gardnerella species in vaginal samples by PNA-FISH". Paper presented in 6th ASM conference on Biofilms, 2012.
  47. Machado, António; Almeida, Carina; Carvalho, A.; Salgueiro, D.; Vieira, M. J.; Rodrigues, L. R.; Azevedo, N. F.; Cerca, Nuno; Henriques, Ana Filipa Frutuoso Mendes. "Comparison between classical and molecular (FISH and PCR) methods for Lactobacillus spp. detection in Clinical Samples". Paper presented in Gordon Research Conference on Microbial Adhesion & Signal Transduction, 2011.
  48. Almeida, Carina; Azevedo, N. F.; Cerqueira, L.; Bento, Joana C.; Vieira, M. J.; Keevil, C. W.. "Development of a rapid method for Proteus spp. detection in urine by peptide nucleic acid fluorescence in situ hybridisation (PNA)". Paper presented in European Congress of Clinical Microbiology and Infectious Diseases (ECCMID), 2011.
  49. Almeida, Carina; Vieira, M. J.; Keevil, C. W.; Fernandes, R. M.; Azevedo, N. F.. "Characterization of multispecies biofilms by peptide nucleic acid fluorescence in situ hybridization (PNA-FISH)". 2010.
  50. Almeida, Carina; Azevedo, N. F.; Keevil, C. W.; Vieira, M. J.. "Discriminating multi-species populations in biofilms with peptide nucleic acid fluorescence in situ hybridization (PNA FISH)". 2010.
  51. Almeida, Carina; Azevedo, N. F.; Keevil, C. W.; Vieira, M. J.. "Salmonella enterica adhesion to different surfaces in the presence of Echerichia coli – biofilm analyses by fluorescence in situ hybridization using a new peptide nucleic acid probe". Paper presented in Eurobiofilms 2009, 2009.
  52. Almeida, Carina; Azevedo, N. F.; Iversen, C.; Fanning, S.; Keevil, C. W.; Vieira, M. J.. "Development and application of a novel Peptide Nucleic Acid probe for the specific detection of Cronobacter (Enterobacter sakazakii) in powdered infant formula". Paper presented in 1st International Conference on Cronobacter, 2009.
  53. Azevedo, N. F.; Jardim, T.; Almeida, Carina; Melo, A.; Gomes, C.; Keevil, C. W.; Vieira, M. J.. "Detection of staphylococcus epidermidis on biofilms by fluorescence in situ hybridization (FISH) using a novel peptide nucleic acid (PNA) probe". Paper presented in International Symposium on Microbial Ecology (ISME12), 2008.
  54. Almeida, Carina; Azevedo, N. F.; Keevil, C. W.; Vieira, M. J.. "A fluorescence in situ hybridization method using a peptide nucleic acid probe for the detection of Salmonella spp. in biofilms". Paper presented in Eurobiofilms 2008, 2008.
  55. Azevedo, N. F.; Almeida, Carina; Keevil, C. W.; Vieira, M. J.. "Cultivability and viability of enterohepatic and gastric Helicobacter spp. in water: implications for transmission". Paper presented in Zoonoses and Public Health, 2007.
  56. Azevedo, N. F.; Almeida, Carina; Jardim, T.; Keevil, C. W.; Vieira, M. J.. "Development of novel peptide nucleic acid (PNA) probes for the rapid identification of pathogens by fluorescence in situ hybridizationd (FISH)". Paper presented in CONGRESSO NACIONAL MICRO'07 BIOTEC'07, 2007.
Journal article
  1. Diana Vilas Boas; Joana Castro; Daniela Araújo; Franklin L. Nóbrega; Charles W. Keevil; Nuno F. Azevedo; Maria João Vieira; Carina Almeida. "The Role of Flagellum and Flagellum-Based Motility on Salmonella Enteritidis and Escherichia coli Biofilm Formation". Microorganisms (2024): https://doi.org/10.3390/microorganisms12020232.
    10.3390/microorganisms12020232
  2. João David Teixeira; Ana Rita Soares Mateus; Claudia Sanchez; Pier Parpot; Carina Almeida; Ana Sanches Silva. "Antioxidant Capacity and Phenolics Profile of Portuguese Traditional Cultivars of Apples and Pears and Their By-Products: On the Way to Newer Applications". Foods (2023): https://doi.org/10.3390/foods12071537.
    10.3390/foods12071537
  3. Maria Margarida Barros; Joana Castro; Daniela Araújo; Ana Maria Campos; Ricardo Oliveira; Sónia Silva; Divanildo Outor-Monteiro; Carina Almeida. "Swine Colibacillosis: Global Epidemiologic and Antimicrobial Scenario". Antibiotics (2023): https://doi.org/10.3390/antibiotics12040682.
    10.3390/antibiotics12040682
  4. Inês Gonçalves de Sousa; Jorge Oliveira; António Mexia; Graça Barros; Carina Almeida; Carla Brazinha; Anna Vega; Carla Brites. "Advances in Environmentally Friendly Techniques and Circular Economy Approaches for Insect Infestation Management in Stored Rice Grains". Foods (2023): https://doi.org/10.3390/foods12030511.
    10.3390/foods12030511
  5. Ana Oliveira; Carla Dias; Ricardo Oliveira; Carina Almeida; Pablo Fuciños; Sanna Sillankorva; Hugo Oliveira. "Paving the way forward: Escherichia coli bacteriophages in a One Health approach". Critical Reviews in Microbiology (2023): https://doi.org/10.1080/1040841X.2022.2161869.
    10.1080/1040841X.2022.2161869
  6. Soares Mateus, Ana Rita; Pena, Angelina; Sendón, Raquel; Almeida, Carina; Nieto, Gonçalo Almeida; Khwaldia, Khaoula; Sanches Silva, Ana. "By-products of dates, cherries, plums and artichokes: A source of valuable bioactive compounds". Trends in Food Science & Technology 131 (2023): 220-243. http://dx.doi.org/10.1016/j.tifs.2022.12.004.
    10.1016/j.tifs.2022.12.004
  7. Araújo, D.; Castro, J.; Matos, F.; Oliveira, R.; Ramos, C.; Almeida, C.; Silva, S.. "Exploring the prevalence and antibiotic resistance profile of Klebsiella pneumoniae and Klebsiella oxytoca isolated from clinically ill companion animals from North of Portugal". Research in Veterinary Science 159 (2023): 183-188. http://www.scopus.com/inward/record.url?eid=2-s2.0-85154612892&partnerID=MN8TOARS.
    10.1016/j.rvsc.2023.04.009
  8. Sousa, L.G.V.; Almeida, C.; Muzny, C.A.; Cerca, N.. "Development of a Prevotella bivia PNA probe and a multiplex approach to detect three relevant species in bacterial vaginosis-associated biofilms". npj Biofilms and Microbiomes 9 1 (2023): http://www.scopus.com/inward/record.url?eid=2-s2.0-85162755063&partnerID=MN8TOARS.
    10.1038/s41522-023-00411-6
  9. Mário Sousa; Rui Rocha; Daniela Eira Araújo; Castro, Joana; Barbosa, Ana; Azevedo, Nuno Filipe; Cerqueira, Laura; Almeida, Carina. "A new PNA-FISH probe for the specific detection of Salmonella in food matrices". (2023):
    Under revision
  10. Barata, Ana Rita; Nunes, Bárbara; Oliveira, Ricardo; Guedes, Hugo; Almeida, Carina; Saavedra, Maria José; da Silva, Gabriela Jorge; Almeida, Gonçalo. "Occurrence and seasonality of Campylobacter spp. in Portuguese dairy farms". International Journal of Food Microbiology 383 (2022): 109961. http://dx.doi.org/10.1016/j.ijfoodmicro.2022.109961.
    10.1016/j.ijfoodmicro.2022.109961
  11. Sousa, Mário; Barbosa, Ana; Azevedo, N.F.; Cerqueira, Laura; Almeida, Carina. Corresponding author: Cerqueira, Laura. "Evaluation of different enrichment broths for simultaneous growth of Escherichia coli O157:H7, Salmonella spp. and Listeria monocytogenes in food sample analysis (submitted)". (2022):
    Under revision
  12. Ricardo Oliveira; Joana Castro; Sónia Silva; Hugo Oliveira; Maria José Saavedra; Nuno Filipe Azevedo; Carina Almeida. "Exploring the Antibiotic Resistance Profile of Clinical Klebsiella pneumoniae Isolates in Portugal". Antibiotics (2022): https://doi.org/10.3390/antibiotics11111613.
    10.3390/antibiotics11111613
  13. Castro, Joana; Barros, Maria Margarida; Araújo, Daniela; Campos, Ana Maria; Oliveira, Ricardo; Silva, Sónia; Almeida, Carina. "Swine enteric colibacillosis: Current treatment avenues and future directions". Frontiers in Veterinary Science 9 (2022): http://dx.doi.org/10.3389/fvets.2022.981207.
    10.3389/fvets.2022.981207
  14. Almeida, Carina; Bakaletz, Lauren O.. "Editorial: Women in biofilms 2021". Frontiers in Cellular and Infection Microbiology 12 (2022): http://dx.doi.org/10.3389/fcimb.2022.1035280.
    10.3389/fcimb.2022.1035280
  15. Azevedo, Andreia S.; Fernandes, Ricardo M.; Faria, Ana R.; Silvestre, Oscar F.; Nieder, Jana B.; Lou, Chenguang; Wengel, Jesper; Almeida, Carina; Azevedo, Nuno F.. "Spectral imaging and nucleic acid mimics fluorescence in situ hybridization (SI-NAM-FISH) for multiplex detection of clinical pathogens". Frontiers in Microbiology 13 (2022): http://dx.doi.org/10.3389/fmicb.2022.976639.
    10.3389/fmicb.2022.976639
  16. Pinto, Graça; Shetty, Sudarshan A.; Zoetendal, Erwin G.; Gonçalves, Raquel F. S.; Pinheiro, Ana C.; Almeida, Carina; Azeredo, Joana; Smidt, Hauke. "An in vitro fermentation model to study the impact of bacteriophages targeting Shiga toxin-encoding Escherichia coli on the colonic microbiota". npj Biofilms and Microbiomes 8 1 (2022): http://dx.doi.org/10.1038/s41522-022-00334-8.
    10.1038/s41522-022-00334-8
  17. Fokt, Hanna; Cleto, Sara; Oliveira, Hugo; Araújo, Daniela; Castro, Joana; Cerca, Nuno; Vieira, Maria João; Almeida, Carina. "Bacteriocin Production by Escherichia coli during Biofilm Development". Foods 11 17 (2022): 2652. http://dx.doi.org/10.3390/foods11172652.
    10.3390/foods11172652
  18. Nácher-Vázquez, Montserrat; Barbosa, Ana; Armelim, Inês; Azevedo, Andreia Sofia; Almeida, Gonçalo Nieto; Pizarro, Cristina; Azevedo, Nuno Filipe; Almeida, Carina; Cerqueira, Laura. "Development of a Novel Peptide Nucleic Acid Probe for the Detection of Legionella spp. in Water Samples". Microorganisms 10 7 (2022): 1409. http://dx.doi.org/10.3390/microorganisms10071409.
    10.3390/microorganisms10071409
  19. Carina Almeida. "SARS-CoV-2 Diagnostics Based on Nucleic Acids Amplification: From Fundamental Concepts to Applications and Beyond". Frontiers in Cellular and Infection Microbiology (2022): http://dx.doi.org/10.3389/fcimb.2022.799678.
    10.3389/fcimb.2022.799678
  20. Oliveira, R.; Pinho, E.; Sousa, A.L.; Dias, Ó.; Azevedo, N.F.; Almeida, C.. "Modelling aptamers with nucleic acid mimics (NAM): From sequence to three-dimensional docking". PLoS ONE 17 3 March (2022): http://www.scopus.com/inward/record.url?eid=2-s2.0-85126869671&partnerID=MN8TOARS.
    10.1371/journal.pone.0264701
  21. Oliveira, R.; Pinho, E.; Almeida, G.; Azevedo, N.F.; Almeida, C.. "Prevalence and Diversity of Staphylococcus aureus and Staphylococcal Enterotoxins in Raw Milk From Northern Portugal". Frontiers in Microbiology 13 (2022): http://www.scopus.com/inward/record.url?eid=2-s2.0-85128192549&partnerID=MN8TOARS.
    10.3389/fmicb.2022.846653
  22. Vindeirinho, Joao; Pinho, Eva; Azevedo, Nuno Filipe; Almeida, Carina. "SARS-CoV-2 diagnostics based on nucleic acids amplification: from fundamental concepts to current applications and beyond". Frontiers in Cellular and Infection Microbiology (2022):
    In press
  23. Sousa, Lúcia G. V.; Castro, Joana; França, Angela; Almeida, Carina; Muzny, Christina A.; Cerca, Nuno. "A New PNA-FISH Probe Targeting Fannyhessea vaginae". Frontiers in Cellular and Infection Microbiology 11 (2021): http://dx.doi.org/10.3389/fcimb.2021.779376.
    Published • 10.3389/fcimb.2021.779376
  24. Oliveira, Ricardo; Pinho, Eva; Sousa, Ana Luísa; DeStefano, Jeffrey J.; Azevedo, Nuno Filipe; Almeida, Carina. "Improving aptamer performance with nucleic acid mimics: de novo and post-SELEX approaches". Trends in Biotechnology (2021): http://dx.doi.org/10.1016/j.tibtech.2021.09.011.
    10.1016/j.tibtech.2021.09.011
  25. Pinto, Graça; Minnich, Scott A; Hovde, Carolyn J; Oliveira, Hugo; Smidt, Hauke; Almeida, Carina; Azeredo, Joana. "The interactions of bacteriophage Ace and Shiga toxin-producing Escherichia coli during biocontrol". FEMS Microbiology Ecology 97 8 (2021): http://dx.doi.org/10.1093/femsec/fiab105.
    10.1093/femsec/fiab105
  26. van Belkum, Alex; Almeida, Carina; Bardiaux, Benjamin; Barrass, Sarah V.; Butcher, Sarah J.; Çaykara, Tugçe; Chowdhury, Sounak; et al. "Host-Pathogen Adhesion as the Basis of Innovative Diagnostics for Emerging Pathogens". Diagnostics 11 7 (2021): 1259. http://dx.doi.org/10.3390/diagnostics11071259.
    10.3390/diagnostics11071259
  27. Pinto, Graça; Sampaio, Marta; Dias, Oscar; Almeida, Carina; Azeredo, Joana; Oliveira, Hugo. "Insights into the genome architecture and evolution of Shiga toxin encoding bacteriophages of Escherichia coli". BMC Genomics 22 1 (2021): http://dx.doi.org/10.1186/s12864-021-07685-0.
    10.1186/s12864-021-07685-0
  28. Ballem, Andressa; Gonçalves, Soraia; Garcia-Meniño, Isidro; Flament-Simon, Saskia C.; Blanco, Jesús E.; Fernandes, Conceição; Saavedra, Maria José; et al. "Prevalence and serotypes of Shiga toxin-producing Escherichia coli (STEC) in dairy cattle from Northern Portugal". PLOS ONE 15 12 (2020): e0244713. http://dx.doi.org/10.1371/journal.pone.0244713.
    10.1371/journal.pone.0244713
  29. Laura Cerqueira; Sara Moura; Carina Almeida; Maria João Vieira; Nuno Filipe Azevedo. "Establishment of a New PNA-FISH Method for Aspergillus fumigatus Identification: First Insights for Future Use in Pulmonary Samples". Microorganisms (2020): https://www.mdpi.com/2076-2607/8/12/1950.
    10.3390/microorganisms8121950
  30. Fiedler, Gregor; Ballem, Andressa; Brinks, Erik; Almeida, Carina; Franz, Charles M. A. P.; Oliveira, Hugo. "Draft Genome Sequences of 12 Shiga Toxin-Producing Escherichia coli Strains Isolated from Dairy Cattle in Portugal". Microbiology Resource Announcements 9 38 (2020): http://dx.doi.org/10.1128/mra.00790-20.
    10.1128/mra.00790-20
  31. Dias, Carla; Almeida, Carina; Lobocka, Malgorzata; Oliveira, Hugo. "Genome Sequences of Four Potentially Therapeutic Bacteriophages Infecting Shiga Toxin-Producing Escherichia coli". Microbiology Resource Announcements 9 36 (2020): http://dx.doi.org/10.1128/mra.00749-20.
    10.1128/mra.00749-20
  32. Pinto, Graça; Almeida, Carina; Azeredo, Joana. "Bacteriophages to control Shiga toxin-producing E. coli – safety and regulatory challenges". Critical Reviews in Biotechnology 40 8 (2020): 1081-1097. http://dx.doi.org/10.1080/07388551.2020.1805719.
    10.1080/07388551.2020.1805719
  33. Rodriguez-Mateos, Pablo; Azevedo, Nuno Filipe; Almeida, Carina; Pamme, Nicole. "FISH and chips: a review of microfluidic platforms for FISH analysis". Medical Microbiology and Immunology 209 3 (2020): 373-391. http://dx.doi.org/10.1007/s00430-019-00654-1.
    10.1007/s00430-019-00654-1
  34. Azevedo, A.S.; Gerola, G.P.; Baptista, J.; Almeida, C.; Peres, J.; Mergulhão, F.J.; Azevedo, N.F.. "Increased intraspecies diversity in Escherichia coli biofilms promotes cellular growth at the expense of matrix production". Antibiotics 9 11 (2020): 1-14. http://www.scopus.com/inward/record.url?eid=2-s2.0-85096522298&partnerID=MN8TOARS.
    10.3390/antibiotics9110818
  35. Melo, L.D.R.; Pinto, G.; Oliveira, F.; Vilas-Boas, D.; Almeida, C.; Sillankorva, S.; Cerca, N.; Azeredo, J.. "The protective effect of Staphylococcus epidermidis biofilm matrix against phage predation". Viruses 12 10 (2020): http://www.scopus.com/inward/record.url?eid=2-s2.0-85091833975&partnerID=MN8TOARS.
    10.3390/v12101076
  36. Cerqueira, Laura; Sara Moura; Almeida, Carina; Maria João Vieira; Nuno Filipe Azevedo. "Establishment of a New PNA-FISH Method for Aspergillus fumigatus Identification: First insights for future use in Pulmonary Samples (IF: 4.152)". Microorganisms (2020): DOI: 10.3390/microorganisms8121950.
    Published
  37. Araújo, Daniela; Azevedo, Nuno Miguel; Barbosa, Ana; Almeida, Carina; Rodrigues, Maria Elisa; Henriques, Mariana; Silva, Sónia. "Application of 2'-OMethylRNA' Antisense Oligomer to Control Candida albicans EFG1 Virulence Determinant". Molecular Therapy - Nucleic Acids 18 (2019): 508-517. http://dx.doi.org/10.1016/j.omtn.2019.09.016.
    10.1016/j.omtn.2019.09.016
  38. Rocha, Rui; Sousa, José M.; Cerqueira, Laura; Vieira, Maria J.; Almeida, Carina; Azevedo, Nuno F.. "Development and application of Peptide Nucleic Acid Fluorescence in situ Hybridization for the specific detection of Listeria monocytogenes". Food Microbiology 80 (2019): 1-8. http://dx.doi.org/10.1016/j.fm.2018.12.009.
    10.1016/j.fm.2018.12.009
  39. Azevedo, Andreia S.; Sousa, Inês M.; Fernandes, Ricardo M.; Azevedo, Nuno F.; Almeida, Carina. "Optimizing locked nucleic acid/2’-O-methyl-RNA fluorescence in situ hybridization (LNA/2’OMe-FISH) procedure for bacterial detection". PLOS ONE 14 5 (2019): e0217689. http://dx.doi.org/10.1371/journal.pone.0217689.
    10.1371/journal.pone.0217689
  40. Almeida, C.; Azevedo, N.F.; Bastin, B.; Bird, P.; Joseph Benzinger, M.; Agin, J.; Goins, D.; et al. "Validation of biomode S.A. Probe4CronobacterTM for the identification of Cronobacter spp.". Journal of AOAC International 102 3 (2019): 855-864. http://www.scopus.com/inward/record.url?eid=2-s2.0-85065327649&partnerID=MN8TOARS.
    10.5740/jaoacint.18-0328
  41. Rocha, Rui; Almeida, Carina; Azevedo, Nuno F.. "Influence of the fixation/permeabilization step on peptide nucleic acid fluorescence in situ hybridization (PNA-FISH) for the detection of bacteria". PLOS ONE 13 5 (2018): e0196522. http://dx.doi.org/10.1371/journal.pone.0196522.
    10.1371/journal.pone.0196522
  42. Lima, J.F.; Carvalho, J.; Pinto-Ribeiro, I.; Almeida, C.; Wengel, J.; Cerqueira, L.; Figueiredo, C.; Oliveira, C.; Azevedo, N.F.. "Targeting miR-9 in gastric cancer cells using locked nucleic acid oligonucleotides". BMC Molecular Biology 19 1 (2018): http://www.scopus.com/inward/record.url?eid=2-s2.0-85048131114&partnerID=MN8TOARS.
    10.1186/s12867-018-0107-6
  43. Rocha, R.; Almeida, C.; Azevedo, N.F.. "Correction: Influence of the fixation/permeabilization step on peptide nucleic acid fluorescence in situ hybridization (PNA-FISH) for the detection of bacteria (PLoS ONE (2018) 13, 5 (e0196522) DOI: 10.1371/journal.pone.0196522)". PLoS ONE 13 12 (2018): http://www.scopus.com/inward/record.url?eid=2-s2.0-85057957341&partnerID=MN8TOARS.
    10.1371/journal.pone.0208867
  44. Fernandes, Ricardo M; Silva, Hélder; Oliveira, Ricardo; Almeida, Carina; Azevedo, Nuno F; Vieira, Maria J. "Morphological transition ofHelicobacter pyloriadapted to water". Future Microbiology 12 13 (2017): 1167-1179. http://dx.doi.org/10.2217/fmb-2016-0174.
    10.2217/fmb-2016-0174
  45. Azevedo, Andreia S.; Almeida, Carina; Gomes, Luciana C.; Ferreira, Carla; Mergulhão, Filipe J.; Melo, Luís F.; Azevedo, Nuno F.. "An in vitro model of catheter-associated urinary tract infections to investigate the role of uncommon bacteria on the Escherichia coli microbial consortium". Biochemical Engineering Journal 118 (2017): 64-69. http://dx.doi.org/10.1016/j.bej.2016.11.013.
    10.1016/j.bej.2016.11.013
  46. Azevedo, A.S.; Almeida, C.; Pereira, B.; Madureira, P.; Wengel, J.; Azevedo, N.F.; Azevedo, Andreia; et al. "Detection and discrimination of biofilm populations using locked nucleic acid/2'-O-methyl-RNA fluorescence in situ hybridization (LNA/2'OMe-FISH)". Biochemical Engineering Journal 104 (2017): http://www.scopus.com/inward/record.url?eid=2-s2.0-84928966884&partnerID=MN8TOARS.
    10.1016/j.bej.2015.04.024
  47. Azevedo, Andreia S.; Almeida, Carina; Melo, Luís F.; Azevedo, Nuno F.. "Impact of polymicrobial biofilms in catheter-associated urinary tract infections". Critical Reviews in Microbiology 43 4 (2016): 423-439. http://dx.doi.org/10.1080/1040841x.2016.1240656.
    10.1080/1040841x.2016.1240656
  48. Vilas Boas, D.; Almeida, C.; Sillankorva, S.; Nicolau, A.; Azeredo, J.; Azevedo, N.F.. "Discrimination of bacteriophage infected cells using locked nucleic acid fluorescent in situ hybridization (LNA-FISH)". Biofouling 32 2 (2016): 179-190. http://www.scopus.com/inward/record.url?eid=2-s2.0-84958956424&partnerID=MN8TOARS.
    10.1080/08927014.2015.1131821
  49. Rocha, R.; Santos, R.S.; Madureira, P.; Almeida, C.; Azevedo, N.F.; Rocha, Rui; Santos, Rita S.; et al. "Optimization of peptide nucleic acid fluorescence in situ hybridization (PNA-FISH) for the detection of bacteria: The effect of pH, dextran sulfate and probe concentration". Journal of Biotechnology 226 (2016): 1-7. http://www.scopus.com/inward/record.url?eid=2-s2.0-84962217759&partnerID=MN8TOARS.
    10.1016/j.jbiotec.2016.03.047
  50. Melo, L.D.R.; Veiga, P.; Cerca, N.; Kropinski, A.M.; Almeida, C.; Azeredo, J.; Sillankorva, S.. "Development of a phage cocktail to control Proteus mirabilis catheter-associated urinary tract infections". Frontiers in Microbiology 7 JUN (2016): http://www.scopus.com/inward/record.url?eid=2-s2.0-84980360847&partnerID=MN8TOARS.
    10.3389/fmicb.2016.01024
  51. Azevedo, A.S.; Almeida, C.; Pereira, B.; Melo, L.F.; Azevedo, N.F.. "Impact of Delftia tsuruhatensis and Achromobacter xylosoxidans on Escherichia coli dual-species biofilms treated with antibiotic agents". Biofouling 32 3 (2016): 227-241. http://www.scopus.com/inward/record.url?eid=2-s2.0-84959356076&partnerID=MN8TOARS.
    10.1080/08927014.2015.1124096
  52. Machado, A.; Castro, J.; Cereija, T.; Almeida, C.; Cerca, N.. "Diagnosis of bacterial vaginosis by a new multiplex peptide nucleic acid fluorescence in situ hybridization method". PeerJ 2015 2 (2015): http://www.scopus.com/inward/record.url?eid=2-s2.0-84926453746&partnerID=MN8TOARS.
    10.7717/peerj.780
  53. Rocha, Rui; Almeida, Carina; Azevedo, N. F.. "Metodologias para a identificação de microrganismos patogénicos em amostras alimentares: a técnica de PNA-FISH". (2015): http://hdl.handle.net/1822/35325.
  54. Almeida, C.; Constante, D.; Ferreira, A.; Cerqueira, L.; Vieira, M.J.; Azevedo, N.F.. "A new colorimetric peptide nucleic acid-based assay for the specific detection of bacteria". Future Microbiology 9 10 (2014): 1131-1142. http://www.scopus.com/inward/record.url?eid=2-s2.0-84911493243&partnerID=MN8TOARS.
    10.2217/FMB.14.68
  55. Azevedo, A.S.; Almeida, C.; Melo, L.F.; Azevedo, N.F.. "Interaction between atypical microorganisms and E. coli in catheter-associated urinary tract biofilms". Biofouling 30 8 (2014): 893-902. http://www.scopus.com/inward/record.url?eid=2-s2.0-84908023766&partnerID=MN8TOARS.
    10.1080/08927014.2014.944173
  56. Danko, A.S.; Fontenete, S.J.; De Aquino Leite, D.; Leitão, P.O.; Almeida, C.; Schaefer, C.E.; Vainberg, S.; Steffan, R.J.; Azevedo, N.F.. "Detection of Dehalococcoides spp. by peptide nucleic acid fluorescent in situ hybridization". Journal of Molecular Microbiology and Biotechnology 24 3 (2014): 142-149. http://www.scopus.com/inward/record.url?eid=2-s2.0-84902920096&partnerID=MN8TOARS.
    10.1159/000362790
  57. Cleto, S.; Van der Auwera, G.; Almeida, C.; Vieira, M.J.; Vlamakis, H.; Kolter, R.. "Genome sequence of Serratia plymuthica V4". Genome Announcements 2 3 (2014): http://www.scopus.com/inward/record.url?eid=2-s2.0-84999232962&partnerID=MN8TOARS.
    10.1128/genomeA.00340-14
  58. Machado, A.; Almeida, C.; Carvalho, A.; Boyen, F.; Haesebrouck, F.; Rodrigues, L.; Cerca, N.; Azevedo, N.F.. "Fluorescence in situ hybridization method using a peptide nucleic acid probe for identification of Lactobacillus spp. in milk samples". International Journal of Food Microbiology 162 1 (2013): 64-70. http://www.scopus.com/inward/record.url?eid=2-s2.0-84872955498&partnerID=MN8TOARS.
    10.1016/j.ijfoodmicro.2012.09.024
  59. Almeida, C.; Cerqueira, L.; Azevedo, N.F.; Vieira, M.J.. "Detection of Salmonella enterica serovar Enteritidis using real time PCR, immunocapture assay, PNA FISH and standard culture methods in different types of food samples". International Journal of Food Microbiology 161 1 (2013): 16-22. http://www.scopus.com/inward/record.url?eid=2-s2.0-84871998766&partnerID=MN8TOARS.
    10.1016/j.ijfoodmicro.2012.11.014
  60. Almeida, C.; Azevedo, N.F.; Santos, S.; Keevil, C.W.; Vieira, M.J.. "Correction: Discriminating multi-species populations in biofilms with Peptide Nucleic Acid Fluorescence In Situ Hybridization (PNA FISH) (PLoS ONE)". PLoS ONE 8 6 (2013): http://www.scopus.com/inward/record.url?eid=2-s2.0-84896744586&partnerID=MN8TOARS.
    10.1371/annotation/2b7e391f-b0cb-4d9f-8e90-85d080f8cbd4
  61. Pires, D.P.; Silva, S.; Almeida, C.; Henriques, M.; Anderson, E.M.; Lam, J.S.; Sillankorva, S.; Azeredo, J.. "Evaluation of the ability of C. albicans to form biofilm in the presence of phage-resistant phenotypes of P. aeruginosa". Biofouling 29 10 (2013): 1169-1180. http://www.scopus.com/inward/record.url?eid=2-s2.0-84885895351&partnerID=MN8TOARS.
    10.1080/08927014.2013.831842
  62. Almeida, C.; Sousa, J.M.; Rocha, R.; Cerqueira, L.; Fanning, S.; Azevedo, N.F.; Vieira, M.J.. "Detection of Escherichia coli O157 by peptide nucleic acid fluorescence in situ hybridization (PNA-FISH) and comparison to a standard culture method". Applied and Environmental Microbiology 79 20 (2013): 6293-6300. http://www.scopus.com/inward/record.url?eid=2-s2.0-84885043580&partnerID=MN8TOARS.
    10.1128/AEM.01009-13
  63. Almeida, C.; Azevedo, N.F.; Bento, J.C.; Cerca, N.; Ramos, H.; Vieira, M.J.; Keevil, C.W.. "Rapid detection of urinary tract infections caused by Proteus spp. using PNA-FISH". European Journal of Clinical Microbiology and Infectious Diseases 32 6 (2013): 781-786. http://www.scopus.com/inward/record.url?eid=2-s2.0-84878237552&partnerID=MN8TOARS.
    10.1007/s10096-012-1808-2
  64. Machado, A.; Almeida, C.; Salgueiro, D.; Henriques, A.; Vaneechoutte, M.; Haesebrouck, F.; Vieira, M.J.; et al. "Fluorescence in situ Hybridization method using Peptide Nucleic Acid probes for rapid detection of Lactobacillus and Gardnerella spp.". BMC Microbiology 13 1 (2013): http://www.scopus.com/inward/record.url?eid=2-s2.0-84876910736&partnerID=MN8TOARS.
    10.1186/1471-2180-13-82
  65. Azevedo, N.F.; Bragança, S.M.; Simes, L.C.; Cerqueira, L.; Almeida, C.; Keevil, C.W.; Vieira, M.J.. "Proposal for a method to estimate nutrient shock effects in bacteria". BMC Research Notes 5 (2012): http://www.scopus.com/inward/record.url?eid=2-s2.0-84864569924&partnerID=MN8TOARS.
    10.1186/1756-0500-5-422
  66. Azevedo, N.F.; Jardim, T.; Almeida, C.; Cerqueira, L.; Almeida, A.J.; Rodrigues, F.; Keevil, C.W.; Vieira, M.J.. "Application of flow cytometry for the identification of Staphylococcus epidermidis by peptide nucleic acid fluorescence in situ hybridization (PNA FISH) in blood samples". Antonie van Leeuwenhoek, International Journal of General and Molecular Microbiology 100 3 (2011): 463-470. http://www.scopus.com/inward/record.url?eid=2-s2.0-80054101666&partnerID=MN8TOARS.
    10.1007/s10482-011-9595-9
  67. Almeida, C.; Azevedo, N.F.; Santos, S.; Keevil, C.W.; Vieira, M.J.. "Discriminating multi-species populations in biofilms with peptide nucleic acid fluorescence in situ hybridization (PNA FISH)". PLoS ONE 6 3 (2011): http://www.scopus.com/inward/record.url?eid=2-s2.0-79953228039&partnerID=MN8TOARS.
    10.1371/journal.pone.0014786
  68. Almeida, C.; Azevedo, N.F.; Fernandes, R.M.; Keevil, C.W.; Vieira, M.J.. "Fluorescence in situ hybridization method using a peptide nucleic acid probe for identification of salmonella spp. in a broad spectrum of samples". Applied and Environmental Microbiology 76 13 (2010): 4476-4485. http://www.scopus.com/inward/record.url?eid=2-s2.0-77954245728&partnerID=MN8TOARS.
    10.1128/AEM.01678-09
  69. Almeida, C.; Azevedo, N.F.; Iversen, C.; Fanning, S.; Keevil, C.W.; Vieira, M.J.. "Development and application of a novel peptide nucleic acid probe for the specific detection of Cronobacter genomospecies (enterobacter sakazakii) in powdered infant formula". Applied and Environmental Microbiology 75 9 (2009): 2925-2930. http://www.scopus.com/inward/record.url?eid=2-s2.0-65549111597&partnerID=MN8TOARS.
    10.1128/AEM.02470-08
  70. Cerqueira, L.; Azevedo, N.F.; Almeida, C.; Jardim, T.; Keevil, C.W.; Vieira, M.J.. "DNA mimics for the rapid identification of microorganisms by fluorescence in situ hybridization (FISH)". International Journal of Molecular Sciences 9 10 (2008): 1944-1960. http://www.scopus.com/inward/record.url?eid=2-s2.0-54349113792&partnerID=MN8TOARS.
    10.3390/ijms9101944
  71. Azevedo, N.F.; Almeida, C.; Fernandes, I.; Cerqueira, L.; Dias, S.; Keevil, C.W.; Vieira, M.J.. "Survival of gastric and enterohepatic Helicobacter spp. in water: Implications for transmission". Applied and Environmental Microbiology 74 6 (2008): 1805-1811. http://www.scopus.com/inward/record.url?eid=2-s2.0-40849087921&partnerID=MN8TOARS.
    10.1128/AEM.02241-07
  72. Azevedo, N.F.; Almeida, C.; Cerqueira, L.; Dias, S.; Keevil, C.W.; Vieira, M.J.. "Coccoid form of Helicobacter pylori as a morphological manifestation of cell adaptation to the environment". Applied and Environmental Microbiology 73 10 (2007): 3423-3427. http://www.scopus.com/inward/record.url?eid=2-s2.0-34249660577&partnerID=MN8TOARS.
    10.1128/AEM.00047-07
Magazine article
  1. de Sousa, Inês Gonçalves; Campos, Ana Maria; Almeida, Carina; Brites, Carla. "Métodos de deteção da infestação oculta nos grãos de arroz", Vida Rural, 2023, https://www.vidarural.pt/premium/metodos-detecao-infestacao-oculta-arroz/.
  2. Sousa, Inês; Sanches Silva, Ana; Oliveira, Jorge; Almeida, Carina; Almeida, Gonçalo; Barros, Graça; Mexia, António; Brites, Carla. "Prevenção de infestações e contaminações microbiológicas no armazenamento do arroz", Vida Rural, 2022, https://www.vidarural.pt/premium/prevencao-infestacoes-armazenamento-arroz/.
Thesis / Dissertation
  1. Almeida, Carina. "Development and application of PNA probes for the detection of specific bacteria by FISH". PhD, Universidade do Minho, 2010. http://hdl.handle.net/1822/11782.

Intellectual property

Patent
  1. Araújo, Daniela; Azevedo, Nuno; Almeida, Carina; Henriques, Mariana; Silva, Sónia. 2019. "Antisense Oligomers for controlling Candida albicans infections". Portugal.
    Pending
  2. Cerqueira, Laura; Almeida, Carina; Azevedo, NF; Vieira, MJ. 2014. "Peptide Nucleic Acid probe (PNA), Kit and method for detection of Aspergillus fumigatus and applications thereof".
  3. Almeida, Carina; Sousa, José Mário; Rocha, Rui; Cerqueira, Laura; Vieira, Maria João; Azevedo, Nuno Filipe Ribeiro Pinto Oliveira. 2014. "Peptide nucleic acid probe, kit and method for detection and/or quantification of Escherichia coli O157:H7 and applications thereof.".
  4. Cerqueira, Laura; Almeida, Carina; Azevedo, Nuno Filipe Ribeiro Pinto Oliveira; Vieira, Maria João. 2014. "Peptide nucleic acid probe, kit and method for detection and/or quantification of Aspergillus fumigatus and applications thereof".
  5. Vieira, Maria João; Almeida, Carina; Azevedo, N. F.; Soares, José António Baptista Machado; Cerca, Nuno. 2012. "Sondas de ácido péptido nucleico, estojo e método para detectar espécies do género Lactobacillus spp. e/ou Gardnerella spp. e respectivas aplicações". Portugal.
    Expired
  6. Almeida, Carina; Azevedo, N. F.; Keevil, C. W.; Vieira, M. J.. 2011. "Peptide nucleicacid probe, kit and method for detection and/or quantification of Salmonella spp. and applications thereof".

Other

Other output
  1. Probe4Salmonella Test Kit Certification by AOAC RI. This method has been evaluated in the AOAC® Performance Tested MethodsSM Program, and found to perform as stated by the manufacturer contingent to the comments contained in the manuscript. This certificate means that an AOAC® Certification Mark License Agreement has been executed which authorizes the manufacturer to display the AOAC Performance Tested SM certification mark.. 2018. De Sousa, José Mário; Rocha, Rui; Cerqueira, Laura; Almeida, Carina; Azevedo, Nuno Filipe.
  2. Probe4Monocytogenes Test Kit Certification by AOAC RI. This method has been evaluated in the AOAC® Performance Tested MethodsSM Program, and found to perform as stated by the manufacturer contingent to the comments contained in the manuscript. This certificate means that an AOAC® Certification Mark License Agreement has been executed which authorizes the manufacturer to display the AOAC Performance Tested SM certification mark. 2017. Rocha, Rui; De Sousa, José Mário; Cerqueira, Laura; Almeida, Carina; Azevedo, Nuno Filipe.
  3. Probe4Cronobacter Test Kit Certification by AOAC RI. first product in the world certified by AOAC for Cronocbacter Evaluation under the AOAC® PTM Program, and found to perform as stated by the manufacturer contingent to the comments contained in the manuscript. This certificate means that an AOAC® Certification Mark License Agreement has been executed which authorizes the manufacturer to display the AOAC Performance Tested SM certification mark;. 2017. Rocha, Rui; De Sousa, José Mário; Cerqueira, Laura; Almeida, Carina; Azevedo, Nuno Filipe.
Activities

Oral presentation

Presentation title Event name
Host (Event location)
2022/03 Opening Section of the Seminar “O Futuro da alimentação” Feira AGRO
AGRO (Portugal)
2021/07 Aptamers for food toxins 1st Symposium on Oligonucleotide Technologies and Therapeutics@Portugal (OTP2021)
University of Porto (Porto, Portugal)
2019/01 The challenges of technology transfer: a personal perspective 2019 NanoGateway Winter School
INL (Braga, Portugal)
2018/11 CodedFISH: an innovative tool for the detection of clinical pathogens BMeeting 2018
IPP (Porto, Portugal)
2014/12 Chromoperformance I Encontro Anual de Spin-offs da Universidade do Minho
(Braga, Portugal)
2014/05 Biomode – Biomolecular Determination, SA. Biotecnologia e Bioengenharia: Tecnologias de largo espectro para a especialização inteligente e transferência de valor para a economia
(Braga, Portugal)
2013/03 Biomolecular Determination SA - Entrepreneurship in bioinformatics. Bioinformatics Open Days
(Braga, Portugal)
2013/02 Biomode – Biomolecular Determination, SA. Enterprise Research in Portugal. 3rd Portuguese Meeting of Bioengineering
(Braga, Portugal)
2013/02 From the lab to the market: the challenges for scientists. Special Session Women in Engineering. 3rd Portuguese Meeting of Bioengineering
(Braga, Portugal)
2012/03 Helicobacter pylori: role of water on survival and transmission 3rd Scientific Meeting of Institute for Biotechnology and Bioengineering
Instituto Superior Técnico (Lisboa, Portugal)
2007/09 RT-PCR and PNA-FISH as novel methods for the detection of specific microorganisms in heterotrophic biofilm communities Biofilm Club
(Gregynog, United Kingdom)

Supervision

Thesis Title
Role 		Degree Subject (Type)
Institution / Organization
2022/07 - Current Aptamers to control colibacillosis in piglets
Supervisor of Maria Margarida Barros
 Programa Doutoral em Ciência Animal (PhD)
Universidade de Trás-os-Montes e Alto Douro Escola de Ciências Agrárias e Veterinárias, Portugal

Instituto Nacional de Investigação Agrária e Veterinária (Polo Vairão), Portugal
2021/02 - Current Microbial Interactions between Gardnerella, Prevotella, and Atopobium Prior to Incident Bacterial Vaginosis
Co-supervisor of Lúcia Filipa Guimarães Vieira de Sousa
 Programa Doutoral em Engenharia Química e Biológica (PhD)
Universidade do Minho, Portugal
2020/10 - Current Nucleic acid mimic-based point-of-care test for Covid19 diagnosis
Co-supervisor
 Doctoral Program in Chemical and Biological Engineering (PhD)
Universidade do Porto, Portugal
2018/05 - Current Shiga toxin-producing E. coli in ruminants: assessing prevalence, animal reservoirs and new bacteriophage-derived control strategies
Co-supervisor of Andressa Ballen
 Doctoral Program in Chemical and Biological Sciences (PhD)
Instituto Nacional de Investigação Agrária e Veterinária (Polo Vairão), Portugal

Universidade de Trás-os-Montes e Alto Douro, Portugal
2017/04 - Current Quantification and categorization of E. coli in food samples by a novel color-coded tag FISH method
Co-supervisor of Ricardo Manuel Fernandes
 Doctoral Program in Chemical and Biological Engineering (PhD)
Universidade do Minho, Portugal

Universidade do Porto Faculdade de Engenharia, Portugal
2023/09 - 2024/07 Aptamers for enterotoxigenic Escherichia coli
Supervisor of Ana Maria da Silva Campos
 Mestrado em Biologia Molecular (Master)
Universidade do Minho, Portugal

Instituto Nacional de Investigação Agrária e Veterinária (Polo Vairão), Portugal
2018/10 - 2023/09 Locked nucleic acid (LNA) aptamers for the detection of Staphylococcal Enterotoxins
Supervisor of Ricardo Bruno da Costa Oliveira
 Doctoral Program in Chemical and Biological Engineering (PhD)
Instituto Nacional de Investigação Agrária e Veterinária (Polo Vairão), Portugal

Universidade do Porto Faculdade de Engenharia, Portugal
2019/03 - 2022/07/25 Selection of toxin-specific aptamers using nucleic acid mimics
Supervisor of Eva Patricia Paiva dos Santos Pinho
Post-doctoral researcher (Other)
Instituto Nacional de Investigação Agrária e Veterinária (Polo Vairão), Portugal
2022/02 - 2022/07 Otimização de uma metodologia molecular para deteção de fatores de virulência de Escherichia coli enterotoxigénica para diagnóstico de colibacilose suína
Supervisor of Ana Maria da Silva Campos
Degree in Biomedical Sciences (Degree)
Instituto Politécnico do Porto, Portugal
2018/07 - 2022 Lab on a Chip for Pathogen Analysis
Co-supervisor of Pablo Rodriguez Mateos
 ViBrANT International Training Network (PhD)
University of Hull, United Kingdom

Biomode SA, Portugal
2017/10 - 2021/12 Safety and efficacy evaluation of a phage cocktail for the biocontrol of STEC E. coli in food products
Co-supervisor of Maria da Graça Cerqueira Pinto
 Doctoral Program in Chemical and Biological Engineering (PhD)
Instituto Nacional de Investigação Agrária e Veterinária (Polo Vairão), Portugal

Universidade do Minho, Portugal
2021/01 - 2021/07 Aptameros para enterotoxina A de Staphylococcus: efeito da incorporação de mímicos de ácidos nucleicos
Co-supervisor
 Degree in Medical Biothecnology (Degree)
Instituto Politécnico do Porto, Portugal
2018 - 2019 Tipagem de genes de isolados de Escherichia coli que codificam a toxina shiga
Supervisor of Ana Isabel Nunes Janeiro Ferreira
 Degree in Medical Biothecnology (Degree)
Instituto Nacional de Investigação Agrária e Veterinária (Polo Vairão), Portugal

Instituto Politécnico do Porto, Portugal
2017 - 2019 NAM-CLASI-FISH: a new accurate tool for the analysis of gastric microbiome
Supervisor of Andreia Sofia Mateus Azevedo
 Post-doctoral researcher (Other)
Universidade do Minho, Portugal
2017 - 2018 Caracterização de uma coleção de culturas de bactérias láticas de diferentes origens com vista à sua utilização industrial
Supervisor of Ana Rita Martins
Degree in Biothecnology (Degree)
Instituto Nacional de Investigação Agrária e Veterinária (Polo Vairão), Portugal

Instituto Politécnico de Viana do Castelo, Portugal
2013/09 - 2017/12 Development of a universal fixation step for FISH procedures
Co-supervisor of Rui Rocha
 Doctoral Program in Chemical and Biological Engineering (PhD)
Universidade do Minho, Portugal

Universidade do Porto Faculdade de Engenharia, Portugal

Biomode SA, Portugal
2016/09 - 2017/11 Design and validation of a peptide nucleic acid fluorescence in situ hybridization (PNA FISH) method for the detection of Campylobacter spp.
Supervisor of Ricardo Bruno da Costa Oliveira
Master n Bioengineering (Master)
Universidade do Minho, Portugal
2015/09 - 2016/12 Validation of a PNA-FISH method for Vibrio detection in food matrices
Supervisor of Francisca Marçal Queiroz Pinheiro Guedes
 Master in Bioengineering (Master)
Universidade do Minho, Portugal
2015/09 - 2016/12 Development and validation of a PNA-FISH method for Aeromonas detection
Supervisor of Cátia Filipa Magalhães Ferreira
 Master in Bioengineering (Master)
Universidade do Minho, Portugal
2013/09 - 2014/11 Characterization of Proteus mirabilis bacteriophages and their action against biofilms
Co-supervisor of Patrícia Isabel Martins Veiga
 Master in Bioengineering (Master)
Universidade do Minho, Portugal
2013 - 2014 Characterization of antimicrobial metabolites produced by Pseudoalteromonas atlantica
Co-supervisor of Francisco Ventura
 Master in Biomedical Engineering (Master)
Universidade do Minho, Portugal
2012 - 2013 Optimizing a multiplex PNA-FISH method for foodborne bacteria
Co-supervisor of José Mario Sousa
 Master in Bioengineering (Master)
Universidade do Minho, Portugal
2012 - 2013 Interference studies for a PNA-FISH based product (Probe4Pylori)
Co-supervisor of Teresa Maria Conde Lopes
 Master in Biological Engineering (Master)
Universidade do Minho, Portugal

Biomode SA, Portugal
2012 - 2013 Conjugates of peptide nucleic acid-biotin for the detection of bacteria using in situ hybridization
Co-supervisor of Diogo Henrique Fernandes Constante
Master in Bioengineering (Master)
Universidade do Porto Faculdade de Engenharia, Portugal
2011 - 2012 Certification of biotechnological processes and products
Co-supervisor of Vasco Rafael Fernandes dos Santos
 Master in Biological Engineering (Master)
Universidade do Minho, Portugal
2011 - 2012 Development of PNA-FISH methods for the detection of food pathogens
Co-supervisor of Ana Isabel Oliveira Rocha Fontão
 Master in Biological Engineering (Master)
Universidade do Minho, Portugal

Biomode SA, Portugal
2010 - 2011 Desenvolvimento de sonda de PNA para detecção de Escherichia coli O157:H7 por FISH
Co-supervisor of José Mário Sousa
 Degree in Applied Biochemistry (Degree)
Universidade do Minho, Portugal

Event organisation

Event name
Type of event (Role) 		Institution / Organization
2019 - Current 1º Simpósio INIAV para a Segurança Alimentar - Rumo à Alimentação do Futuro (2019)
Conference (Member of the Organising Committee)
 Instituto Nacional de Investigação Agrária e Veterinária (Polo Vairão), Portugal
2022/03 - 2022/03 O Futuro da Alimentação. Feira AGRO (2022/03 - 2022/03)
Seminar (Member of the Organising Committee)
 Instituto Nacional de Investigação Agrária e Veterinária (Polo Vairão), Portugal
2021/05 - 2021/05 Summer School “FISHing for Bacteria” (2021/05 - 2021/05)
Workshop (Member of the Organising Committee)
 Universidade do Porto, Portugal
2013/07/18 - 2013/07/20 FISH - Fundamentals and Applications Workshop (2013)
Workshop (Member of the Organising Committee)
 Universidade do Porto Faculdade de Engenharia, Portugal

Event participation

Activity description
Type of event 		Event name
Institution / Organization
2014 - 2014 Collaboration in the organization of the “IV International Practical Course - Advanced Practical Course on Biofilms”
Workshop
 IV International Practical Course in Biofilms
Universidade do Minho, Portugal
2011 - 2011 Collaboration in the organization, and attendance, of the “Third International Practical Course on Biofilm Sciences”
Workshop
 Third International Practical Course on Biofilm Sciences
Universidade do Minho, Portugal
2009 - 2009 Collaboration in the organization, and attendance, of the “Second International Practical Course on Biofilm Sciences"
Workshop
 Second International Practical Course on Biofilm Sciences
Universidade do Minho, Portugal
2006 - 2006 Collaboration in the organization, and attendance, of the “First International Practical Course on Biofilm Sciences”
Workshop
 First International Practical Course on Biofilm Sciences
Universidade do Minho, Portugal

Jury of academic degree

Topic
Role 		Candidate name (Type of degree)
Institution / Organization
2024/01/25 Engineering a biosynthetic pathway for high value glycosaminoglycans production in Saccharomyces cerevisiae
(Thesis) Arguer
 Márcia Regina Linhares Couto (PhD)
Universidade do Minho, Portugal
2023/10 Locked nucleic acid (LNA) aptamers for the detection of Staphylococcal Enterotoxins
Supervisor
 Ricardo Bruno da Costa Oliveira (PhD)
Universidade do Porto Faculdade de Engenharia, Portugal

Instituto Nacional de Investigação Agrária e Veterinária (Polo Vairão), Portugal
2023/10 Integrated Risk Assessment Model for Multiple Mycotoxins in the Food Value Chain: a scientific approach for food security and sustainability
(Thesis) Arguer
 Marta Sofia Carvalho Ferreira Malheiro Leite (PhD)
Universidade de Coimbra, Portugal
2022/12 Development of targeted delivery platforms against highly metastatic cancers
(Thesis) Main arguer
 Diana Andrade e Sousa (PhD)
Universidade do Minho, Portugal
2022/07 Evaluation of losses in an Ultra-High-Temperature (UHT) milk processing plant
(Thesis) Arguer
 Inês Martins Oliveira (Master)
Universidade do Porto, Portugal
2021/07 Multi-species biofilms in bacterial vaginosis: ecological interactions and susceptibility to novel antimicrobial agents
(Thesis) Main arguer
 Aliona Rosca (PhD)
Universidade do Minho, Portugal
2021/07 Evaluation of the packaging process and fat content of UHT milk
(Thesis) Arguer
 Carolina Columbano Couto (Master)
Universidade do Porto, Portugal
2021/07 Aptameros para enterotoxina A de Staphylococcus: efeito da incorporação de mímicos de ácidos nucleicos
Supervisor
 Roberto Miguel Pais Pinto (Other)
Instituto Politécnico do Porto, Portugal
2020/09 The adaptation of Staphylococcus epidermidis commensal and clinical isolates to human blood: the search for molecular diagnostics markers
Thesis Member
 Susana Maria Pereira Brás (PhD)
Universidade do Minho, Portugal
2018/12 Development of a fast phage-based tool for the detection of nosocomial bacteria
(Thesis) Arguer
 Mariana Jeremias Macedo (Master)
Universidade do Minho, Portugal
2018/12 Caracterização de uma coleção de culturas de bactérias láticas de diferentes origens com vista à sua utilização industrial
Supervisor
 Ana Rita Martins (Other)
Instituto Politécnico de Viana do Castelo, Portugal
2018/03 The use of antisense nucleic acid mimics for suppressing microRNAs involved in Gastric Cancer
(Thesis) Arguer
 Joana Filipa Torrinha Ferreira Lima (PhD)
Universidade do Porto Faculdade de Engenharia, Portugal
2018 Rapid detection of microorganisms in food containers
(Thesis) Arguer
 Isabel Maria Cruz Pinto Aveleda de Oliveira (Master)
Universidade do Porto, Portugal
2017/12 Metodologia para deteção e diferenciação entre a estirpe vacinal e estirpes selvagens de Salmonella spp. por RT-PCR
(Thesis) Main arguer
 Bárbara da Costa Branco (Master)
Universidade de Aveiro, Portugal
2017/11 Antisense therapy to control adhesion and filamentation of Candida albicans
(Thesis) Main arguer
 Nuno Morais Azevedo (Master)
Universidade do Minho, Portugal
2017/11 P. aeruginosa adaptation in cystic fibrosis environment challenged by the presence of other bacteria
(Thesis) Main arguer
 Rosana Isabel Araújo Monteiro (Master)
Universidade do Minho, Portugal
2017/11 Design and validation of a peptide nucleic acid fluorescence in situ hybridization (PNA FISH) method for the detection of Campylobacter spp
Supervisor
 Ricardo Bruno da Costa Oliveira (Master)
Universidade do Minho, Portugal
2017/07 Unraveling the potential of nucleic acid mimics to target Helicobacter pylori infections - the effect of biological barriers
(Thesis) Arguer
 Rita Sobral Fernandes Machado dos Santos (PhD)
Universidade do Porto Faculdade de Engenharia, Portugal
2016/11 Validation of a PNA-FISH method for Vibrio detection in food matrices
Supervisor
 Francisca Marçal Queiroz Pinheiro Guedes, (Master)
Universidade do Minho, Portugal
2016/11 Development and validation of a PNA-FISH method for Aeromonas detection
Supervisor
 Cátia Filipa Magalhães Ferreira (Master)
Universidade do Minho, Portugal
2016/11 The role of prophages on virulence transduction in Acinetobacter baumanii biofilms
(Thesis) Main arguer
 Rodrigo Pimenta de Oliveira Monteiro (Master)
Universidade do Minho, Portugal
2014/12 Characterization of antimicrobial metabolites produced by Pseudoalteromonas atlantica
Supervisor
 Francisco Duarte da Cunha Ventura (Master)
Universidade do Minho, Portugal
2014/11 Virulence of Salmonella enterica Enteritidis biofilms after exposure to disinfectants
(Thesis) Main arguer
 Maria João Romeu (Master)
Universidade do Minho, Portugal
2013/12 Development of a multiplex assay using peptide nucleic acid fluorescence in situ hybridization (PNA FISH) for identification of foodborne pathogens
Supervisor
 José Mário Sousa (Master)
Universidade do Minho, Portugal
2011/07 Desenvolvimento de sonda de PNA para detecção de Escherichia coli O157:H7 por FISH
Supervisor
 José Mário Sousa (Other)
Universidade do Minho, Portugal

Committee member

Activity description
Role 		Institution / Organization
2019 - Current Part of the scientific committee of the “1º Simpósio INIAV para a Segurança Alimentar”, under the subject "Rumo à Alimentação do Futuro"
Member
 Instituto Nacional de Investigação Agrária e Veterinária (Polo Vairão), Portugal

Conference scientific committee

Conference name Conference host
2023 - 2023 Dare2Change 2023 - Innovation-Driven Agrifood Business Porto
2021 - 2021 Dare2Change 2021 - Innovation-Driven Agrifood Business Porto

Consulting

Activity description Institution / Organization
2018 - 2018 Expert report on "Quick and accurate methods for bacteria detection" PRESANS, France

Course / Discipline taught

Academic session Degree Subject (Type) Institution / Organization
2014 - 2015 Laboratory of Chemical Technology Integrated Master in Biological Engineering (Mestrado integrado) Universidade do Minho, Portugal
2014 - 2015 Engineering Science Topics (Licenciatura) Universidade do Minho, Portugal

Evaluation committee

Activity description
Role 		Institution / Organization Funding entity
2022 - 2022 Membro do painel de avaliadores de pedidos de extensão de bolsas FCT de doutoramento e de pós-doutoramento - “Bolsas Excecionais de Mitigação de Impactos da COVID-19 nas Atividades de Investigação”
Evaluator
2020 - 2020 Reviewer of H2020 European Commission projects European Commission
2018/07/09 - 2018/07/09 Evaluation of entrepreneurship projects under the scope of the iTeams program, MIT-Portuga Doctoral program
2016 - 2016 Reviewer of H2020 European Commission projects
Evaluator
 European Commission

Journal scientific committee

Journal title (ISSN) Publisher
2019 - Current Jornal of Virology
2017 - Current Frontiers in Microbiology (1664-302X) Frontiers Media SA
2016 - Current PLoS ONE (1932-6203) Public Library of Science
2016 - Current Virology Journal (1743-422X) Springer (Biomed Central Ltd.)
2016 - Current Journal of Zhejiang University SCIENCE B (1862-1783) Zhejiang University Press
2016 - Current Food Control (0956-7135) Elsevier
2015 - Current Antibiotics (2079-6382) MDPI AG
2015 - Current International Journal of Food Microbiology (0168-1605) Elsevier
2014 - Current Infection and Drug Resistance (1178-6973) Dove Medical Press
2013 - Current Journal of Clinical Microbiology (1098-660X) American Society for Microbiology
2011 - Current BMC Research Notes (1756-0500) Springer (Biomed Central Ltd.)
Distinctions

Other distinction

2014 Series A funds (1.600.000€): The spin-off Biomode SA was award with an investment to support the certification and the market entry
2012 BES National Innovation Contest (60 000€), in the Natural Resources & Food section
2011 Post-Doc fellowship (SFRH/BPD/74480/2010)
Fundação para a Ciência e a Tecnologia, Portugal
2010 Seed funds (300.000€): The spin-off Biomode was awarded with an investment (InovCapital-ACTec venture fund) intended to support the products development and certification.
2009 Prize for Best Poster - Cronobacter Conference 2009
University College Dublin, Ireland
2006 PhD fellowship (SFRH/BD/29297/2006)
Fundação para a Ciência e a Tecnologia, Portugal
2005 Merit scholarship
Universidade do Minho, Portugal
2004 Merit scholarship
Universidade do Minho, Portugal