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- J.P. Gomes obtained the PhD degree in 2006 under the supervision of Deborah Dean (Children¿s Hospital Oakland Research Institute, California/USA), being awarded with the European PathoGenoMics PhD Award 2007. - He is a Coordinating Research (since 2024) and the Head of the Genomics/Bioinformatics Unit (since 2013) of the Department of Infectios Diseases at the Portuguese National Institute of Health (INSA). - He is the national coordinator of the SARS-CoV-2 genomic surveillance and was member of the national Experts group to provide the Government scientific advice towards the pandemics control. - He supervised 14 PhD students (9 as main supervisor) in microbial genomics and has been an invited speaker in more than 30 Meetings. - He has published about 160 peer reviewed papers, including in the New England Journal of Medicine, Nature Medicine and Nature Microbiology. - J.P.Gomes participated in the last 5 years as member of the evaluation panel of Grants funded by International organisms such as the European Food Safety Authority, the European Research Era, the Wellcome Trust and the German Fed Min of Education and Research. - He participated (as collaborator or PI) in more than 30 Grants, including 4 (as collaborator) on behalf of the OneHealth approach (OneHealth EJP-JIP06-COVRIN; OneHealth EJP-JRP13-R2-AMR2.22-FED AMR; OneHealth EJP-JRP24-FBZSH9-BEONE; OneHealth EJP¿JRP21-R2-ET2-TELE-Vir). - He was the PI of a 2.3 M€ Grant funded by the EU (ECDC/HERA/2021/021 ECD.12236) aiming at strengthening the sequencing capacity of Portugal towards better surveillance of infectious diseases. - He is currently the PI of another European Grant of 1.5 M€ funded by the European Comission (EU4H-2022-DGA-MS-IBA-1 - Proposal ID-101113460), aiming at improving the WGS-based surveillance of infectious diseases and the information exchange with national and international health authorities. - His team currently enrolls 14 people (8 PhD, 2 technicians and 4 PhD students) working in microbial genomics.
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Identification

Personal identification

Full name
JOÃO PAULO DOS SANTOS GOMES

Citation names

  • Gomes, João Paulo

Author identifiers

Ciência ID
6212-831B-E115
ORCID iD
0000-0002-2697-2399

Email addresses

  • j.paulo.gomes@insa.min-saude.pt (Professional)

Knowledge fields

  • Medical and Health Sciences - Health Sciences - Infectious Diseases

Languages

Language Speaking Reading Writing Listening Peer-review
English Advanced (C1) Advanced (C1) Advanced (C1) Advanced (C1)
French Beginner (A1) Intermediate (B1) Beginner (A1) Beginner (A1)
Spanish; Castilian Beginner (A1) Beginner (A1) Beginner (A1)
Education
Degree Classification
2016
Concluded
 Habilitation Degree for Coordination of Scientific Activities (Título de Agregado)
Instituto Nacional de Saúde Doutor Ricardo Jorge, Portugal
"Habilitation Degree for Coordination of Scientific Activities" (THESIS/DISSERTATION)
 Habilitation Degree
2006
Concluded
 - (Doutoramento)
Universidade de Lisboa Faculdade de Ciências, Portugal
"Contribution for the understanding of the biological differences among Chlamydia trachomatis serovars using genomics and transcriptomics" (THESIS/DISSERTATION)
 Excellent
1994
Concluded
 Química Aplicada (ramo de Biotecnologia) (Licenciatura)
Universidade Nova de Lisboa Faculdade de Ciências e Tecnologia, Portugal
"_" (THESIS/DISSERTATION)
 16
Affiliation

Science

Category
Host institution 		Employer
2024/06 - Current Coordinating Researcher (Research) Instituto Nacional de Saúde Doutor Ricardo Jorge, Portugal
2006/07/01 - 2008/08/01 Researcher (Research) Instituto Nacional de Saúde Doutor Ricardo Jorge, Portugal
2000/05/01 - 2006/07/01 Research Assistant (Research) Children's Hospital Oakland Research Institute, United States

Teaching in Higher Education

Category
Host institution 		Employer
2020 - Current Invited Associate Professor (University Teacher) Universidade Lusófona de Humanidades e Tecnologias Faculdade de Medicina Veterinária, Portugal

Positions / Appointments

Category
Host institution 		Employer
2024/04 - Current Coordenador do Departamento de Doenças Infeciosas Instituto Nacional de Saúde Doutor Ricardo Jorge, Portugal
2024/01 - Current United Nations Secretary-General's Mechanism for Investigation of Alleged Use of Chemical and Biological Weapons (UNSGM)” for the area of rapid detection of emerging microrganisms European Union Delegation to the United Nations, United States
Instituto Nacional de Saúde Doutor Ricardo Jorge, Portugal
2023 - Current Operational Contact Point for Bioinformatics European Centre for Disease Prevention and Control, Sweden
Instituto Nacional de Saúde Doutor Ricardo Jorge, Portugal

Others

Category
Host institution 		Employer
2020/03 - Current National coordinator of the Task force in charge of monitoring the emergence and dissemination of SARS-CoV-2 genetic variants Ministério da Saúde, Portugal
Instituto Nacional de Saúde Doutor Ricardo Jorge, Portugal
2013/06/01 - Current - Head of the Genomics / Bioinformatics Unit at the Portuguese NIH ; Instituto Nacional de Saúde Doutor Ricardo Jorge, Portugal
2008/09/01 - Current Head of the Research Unit of the Department of Infectious Diseases Instituto Nacional de Saúde Doutor Ricardo Jorge, Portugal
2009/03/01 - 2013/06/30 - Professor of Microbiology in Superior School of Health,Lisbon; Escola Superior de Saúde da Cruz Vermelha Portuguesa, Portugal
Projects

Grant

Designation Funders
2022/11 - 2025/10 Sustainable use and integration of enhanced infrastructure into routine genome-based surveillance and outbreak investigation activities in Portugal
Proposal ID-101113460 (GENEO)
 European Commission
2023/11/01 - 2025/06/30 CENTAUR: Creating and refining whole-genome and core-genome typing schemas for pathogen surveillance
ISID_JRA_gun1
Universidade de Lisboa Instituto de Medicina Molecular João Lobo Antunes, Portugal

Instituto Nacional de Saúde Doutor Ricardo Jorge, Portugal

Institut Pasteur, France
European Union
Ongoing
2018/10 - 2022/09 Significado clínico da diversidade estrutural da parede celular de Mycobacterium tuberculosis: contribuição para novos mecanismos de resistência aos antibióticos e relevância para a progressão e tratamento da tuberculose.
152457PRJ
 Fundação para a Ciência e a Tecnologia

Contract

Designation Funders
2023 - 2027 DURABLE - Delivering a Unified Research Alliance of Biomedical and public health Laboratories against Epidemics
101102733
Researcher
Instituto Nacional de Saúde Doutor Ricardo Jorge, Portugal
 European Union
Ongoing
2022/01/01 - 2024/12/31 Características genotípicas e fenotípicas que contribuem para a persistência de Listeria monocytogenes em ambiente de processamento alimentar
10.54499/PTDC/BAA-AGR/4194/2021
Universidade Católica Portuguesa Portuguesa Centro de Biotecnologia e Química Fina, Portugal

Instituto Nacional de Investigação Agrária e Veterinária, Portugal

Universidade do Porto Instituto de Investigação e Inovação em Saúde, Portugal

Universidade Católica Portuguesa, Portugal
Fundação para a Ciência e a Tecnologia
Ongoing
2022/01 - 2024/12 Genomic and phenotypic traits contributing to persistence of Listeria monocytogenes in food processing environment
PTDC/BAA-AGR/4194/2021
Researcher
Fundação para a Ciência e a Tecnologia
Ongoing
2023/01/02 - 2024/07/01 A tríade da nutrição, microbiota intestinal e Artrite Reumatóide - Um estudo piloto exploratório
2022.07462.PTDC
10.54499/2022.07462.PTDC
Associação para a Investigação e Desenvolvimento da Faculdade de Medicina, Portugal

Universidade de Lisboa Instituto de Medicina Molecular João Lobo Antunes, Portugal
Fundação para a Ciência e a Tecnologia
Ongoing
2020/01 - 2022/12 Tele-Vir-Point-of-incidence toolbox for emerging virus threats
One Health EJP - JRP21-R2-ET2-TELE-Vir
Researcher
European Union
Ongoing
2020/01 - 2022/12 BeONE - Building integrative tools for OneHealth Surveillance
One Health EJP - JRP24-FBZSH9-BEONE
Researcher
European Union
Ongoing
2020/01 - 2022/12 FED-AMR: The role of free extracellular DNA in dissemination of antimicrobial resistance over ecosystem boundaries along the food/feed chain
One Health EJP -JRP13-R2-AMR2.22-FED AMR
Researcher
European Union
Ongoing
2020/01 - 2022/12 COVRIN: One Health research integration on SARS-CoV-2 emergence, risk assessment and preparedness
One Health EJP - JIP06-COVRIN
Researcher
European Union
Ongoing
2021/09 - 2022/09 Enhancing Whole Genome Sequencing (WGS) national infrastructures and capacities to respond to the Covid-19 pandemic in Portugal
ECDC/HERA/2021/021 ECD.12236
Principal investigator
European Union
Ongoing
2018/10/01 - 2021/09/30 Desenvolvimento e avaliação de um surfactante sob a forma de Hidrogel na prevenção de infecções transmitidas por contacto direto
PTDC/BIA-MIC/31561/2017
Associação para a Investigação e Desenvolvimento da Faculdade de Medicina, Portugal

Universidade Nova de Lisboa, Portugal
Fundação para a Ciência e a Tecnologia
Ongoing
2020/04 - 2021 Genetic diversity of the novel coronavirus SARS-CoV-2 (COVID-19) in Portugal
234_596874175
Principal investigator
Instituto Nacional de Saúde Doutor Ricardo Jorge, Portugal
 Fundação para a Ciência e a Tecnologia, I.P.
Ongoing
2015/01/01 - 2020/12/31 Anthrax analysis and screening in soils
ANTARES
Researcher
Laboratory of Bromatology and Biological Defense of the Ministry of National Defense
Ongoing
2020/07 - 2020/12 Monitoring the integrity and genetic evolution of SARS-CoV-2 during infection, to support clinical and public health decision
Research4COVID19_657
Research4COVID19_657
Principal investigator
N/A
Concluded
2018/01 - 2020/12 Clinical significance of Mycobacterium tuberculosis cell wall structural diversity: contribution to novel mechanisms of antibiotic resistance and relevance towards tuberculosis progression and treatment
PTDC/BIA-MIC/31233/2017
Researcher
Fundação para a Ciência e a Tecnologia
Ongoing
2018/01 - 2020/12 TINTAGEL - Development and evaluation of a surfactant-hydrogel for preventing direct contact transmitted infections
PTDC/BIA/MIC/31561/2017
Researcher
Fundação para a Ciência e a Tecnologia
Ongoing
2018/06 - 2020/05 Tracing the Treponema pallidum genetic footprints associated with syphilis outcomes and stages
TraSyph
Researcher
European Society of Clinical Microbiology and Infectious Diseases
Ongoing
2017/06 - 2020/05 GenomePT – National Laboratory for Genome Sequencing and Analysis
POCI-01-0145-FEDER-022184
Researcher
European Union
Ongoing
2017 - 2020 A new antibacterial scaffold and biological applications
NIPHARMIN
Researcher
Jane and Aatos Erkko Foundation
Ongoing
2016 - 2019 A novel cross-sectorial platform for the integration of genomics in surveillance of foodborne pathogens
GP/EFSA/AFSCO/2015/01/CT2
Researcher
European Food Safety Authority
Concluded
2017/06 - 2018/05 Genome-scale scrutiny of chlamydial antigens
Chlantigens
Principal investigator
Genocea Biosciences Inc
Concluded
2015/01 - 2017/12 Efficient response to highly dangerous and emerging pathogens at EU level
HP-JA-2014/JA-04-2014/677066
Researcher
European Union
Concluded
2014/03 - 2015/06 Novel approach to "understand" syphilis
Provided by PTCRIS: 133331
Principal investigator
Fundação para a Ciência e a Tecnologia, I.P.
2011/03/01 - 2014/08/31 Caracterização das vias celulares alteradas pelos efectores de Brucella, Chlamydia e Coxiella: identificação de novos alvos terapêuticos
ERA-PTG/0004/2010
 Fundação para a Ciência e a Tecnologia
Concluded
2011/03 - 2014/08 Characterisation of host cell pathways altered by effectors of Brucella, Chlamydia, and Coxiella: identification of novel therapeutic targets
Provided by PTCRIS: 116473
Principal investigator
Fundação para a Ciência e a Tecnologia, I.P.
2010/02/01 - 2013/07/31 Análises funcionais de proteínas da membrana de inclusão de Chlamydia trachomatis
PTDC/SAU-MII/099623/2008
Universidade Nova de Lisboa Instituto de Tecnologia Química e Biológica António Xavier, Portugal
 Fundação para a Ciência e a Tecnologia
Concluded
2010/02 - 2013/07 Functional analyses of inclusion membrane proteins of Chlamydia trachomatis
Provided by PTCRIS: 99623
Researcher
Fundação para a Ciência e a Tecnologia, I.P.
2010/01 - 2013/07 A novel bacterial system involved in copper tolerance
Provided by PTCRIS: 98882
Researcher
Fundação para a Ciência e a Tecnologia, I.P.
2010/01/01 - 2013/06/30 Estudo de mecanismos de evasão à imunidade inata na infecção por Estreptococcos do grupo B: identificação de novos alvos terapêuticos.
PTDC/SAU-MII/105114/2008
Unidade de Ciências Biomoleculares Aplicadas, Portugal
 Fundação para a Ciência e a Tecnologia
Concluded
2010/01 - 2013/06 Study of evasion mechanisms to innate immunity in group B streptococcal infections: identification of novel therapeutic targets.
Provided by PTCRIS: 105114
Researcher
Fundação para a Ciência e a Tecnologia, I.P.
2010/01/01 - 2013/03/31 Análise da síntese da parede celular em Chlamydia - um paradoxo biológico numa bactéria intracelular e evasiva
PTDC/BIA-MIC/100747/2008
Universidade Nova de Lisboa Instituto de Tecnologia Química e Biológica António Xavier, Portugal
 Fundação para a Ciência e a Tecnologia
Concluded
2010/01 - 2013/03 Tracking the synthesis of the Chlamydia cell wall - a biological paradox in intracellular and evasive bacteria
Provided by PTCRIS: 100747
Researcher
Fundação para a Ciência e a Tecnologia, I.P.
2008/01/01 - 2011/04/30 Análise da estrutura mosaico do cromossoma de Chlamydia trachomatis por microarrays
PTDC/BIA-BCM/71117/2006
Instituto Nacional de Saúde Doutor Ricardo Jorge, Portugal
 Fundação para a Ciência e a Tecnologia
Concluded
2008/01 - 2011/04 Microarray-based surveying of Chlamydia trachomatis chromosomal mosaics
Provided by PTCRIS: 71117
Principal investigator
Fundação para a Ciência e a Tecnologia, I.P.
2004 - 2006 Chlamydia trachomatis genomics, strain typing and evolution
NIAID, NIH, R01 AI59647
Researcher
National Institutes of Health
2002 - 2004 Variation of polymorphic membrane protein genes (pmp) among genotypes of Chlamydia trachomatis
POCTI/39822/ MGI/2001
Researcher
Fundação para a Ciência e a Tecnologia
Concluded
Outputs

Publications

Book chapter
  1. Borges, Vítor; Hyden, Patrick; Gomes, João Paulo; Rattei, Thomas. "Chlamydia Genomics". In Chlamydia Biology: From Genome to Disease. Caister Academic Press, 2020.
    10.21775/9781912530281.12
Conference abstract
  1. Carolina Balbino; Matilde Cordas; Rute Rosa; Silva Camoesas, Mariana; Santos, Maria Isabel; Pedroso, Laurentina Maria Rilhas; Belas, Adriana; et al. "Investigation of multidrug-resistant enteric bacteria in pigs produced for human consumption – Is there a risk for Public Health?". Paper presented in FMVet Research Meetings, Lisboa, 2024.
    Accepted
Conference paper
  1. Silva, Adriana; Silva, Vanessa; Borges, Vítor; Coelho, Anabela; Batista, Rita; Esteves, Alexandra; Igrejas, Gilberto; et al. "Comprehensive typing and genetic analysis of L. monocytogenes isolates: implication for food safety and antibiotic resistance surveillance". Paper presented in The 3rd International Electronic Conference on Antibiotics. Rise of Antibiotic Resistance: Mechanisms Involved and Solutions to Tackle it, 2023.
    Published
  2. Joana Andrade; Catarina Silva; Luis Vieira; Miguel Pinto; João Paulo Gomes; Elisabete Valério. "Assessing the Reason Why Heterotrophic Bacteria Present in Aquatic Environments Are Not Affected by Microcystins and Unraveling Alternative Genes for Microcystin Degradation". 2022.
    10.3390/blsf2022014033
  3. Štefánek, Matúš; Borges, Vítor; Wenner, Sigurd; Nogueira, Isabel D.; Pinto, Miguel; Faria, Isabel; Pessanha, Maria Ana; et al. "Catheter related bloodstream infection caused by E. cloacae and Candida parapsilosis: Are biofilms guilty?". 2022.
  4. Silveira, Leonor; Pista, Ângela; Borges, Vítor; Silva, Catarina; Vieira, Luís; Gomes, João Paulo; Machado, Jorge. "The use of molecular typing for characterization of a Salmonella Enteritidis cluster". 2018.
  5. Gonzalez Diaz, Aida; Pinto, Miguel; Bettencourt, Célia; Duarte, Silvia; Marti, Sara; Gomes, João Paulo; Bajanca-Lavado, Paula. "Whole-genome-based characterization of invasive Haemophilus influenzae isolates from a pre- and post-vaccine era in Portugal". 2017.
  6. Pechirra, Pedro; Borges, Vítor; Mendonça, Joana; Conde, Patrícia; Gomez, Verónica; Rodrigues, Ana Paula; Machado, Ausenda; et al. "Whole-genome deep sequencing of A(H3) influenza virus detected among vaccinated and unvaccinated individuals during 2016/2017 season, Portugal". 2017.
  7. Guiomar, Raquel; Pechirra, Pedro; Costa, Inês; Conde, Patrícia; Cristóvão, Paula; Mendonça, Joana; Vieira, Luís; Borges, Vítor; Gomes, João Paulo. "Phenotypic and genotypic profile of susceptibility to neuraminidase inhibitors of influenza A(H3) circulating in Portugal during 2016/2017 season". 2017.
  8. Isidro, Joana; Santos, Andrea; Nunes, Alexandra; Borges, Vítor; Silva, Catarina; Chaves, Catarina; Sancho, Luísa; et al. "Resistência ao imipenemo em clone endémico de Clostridium difficile do ribotipo 017". 2016.
  9. Jordão, Luísa; Borges, Victor; Vieira, Luís; Gomes, João Paulo; Duarte, Aida. "Next generation sequencing: The key to understand Klebsiella pneumoniae biofilms?". 2016.
  10. Pechirra, Pedro; Maia, Ana Carina; Sampaio, Daniel Ataíde; Borges, Vítor; Gomes, João Paulo; Guiomar, Raquel. "Influenza A(H3) whole genome analysis: searching causes for vaccine failure in 2011/2012". 2016.
  11. Borges, Vítor; Maia, Carla; Barreira, Maria João; Silveira, Leonor; Silva, Catarina; Duarte, Sílvia; Vieira, Luís; et al. "Microevolution and persistence of Listeria monocytogenes in the environment and links to a foodborne outbreak". 2016.
  12. Nunes, A.; Ferreira, R.; Borges, V.; Borrego, M.J.; Gomes, João Paulo. "Molecular features underlying the higher ecological success of C. trachomatis E and F genotypes". 2011.
  13. Santo, I.; Azevedo, J.; Borrego, M.J.; Gomes, João Paulo; Verdasca, N.; Pista, A.. "Chlamydia trachomatis infection in patients selected for HPV detection". 2011.
  14. Borges, V.; Nunes, A.; Ferreira, R.; Borrego, M.J.; Gomes, João Paulo. "A Bioinformática na Identificação dos Processos Moleculares de Interacção entre o Agente Patogénico e o Homem". 2011.
  15. Ferreira, R.; Borges, V.; Nunes, A.; Borrego, M.J.; Gomes, João Paulo. "Transcriptomic analysis of plasmid and plasmid-related chromosomal ORFs in C. trachomatis strains with different cell-appetence". 2011.
Conference poster
  1. Silva, Vanessa; Saraiva, Sónia; Silva, Adriana; Borges, Vítor; Batista, Rita; Gomes, João Paulo; Borrero, Juan; et al. "Foodborne Listeria monocytogenes in chicken viscera products: implications for food safety and public health". Paper presented in ESCMID Global 2025, 2025.
  2. Silva, Vanessa; Caniça, Manuela; Nunes, Alexandra; Gomes, João Paulo; Poeta, Patrícia ; Igrejas, Gilberto. "Wildlife and aquatic reservoirs of mecC-MRSA: a study on prevalence, genetic diversity, and resistance". Paper presented in ESCMID Global 2025, 2025.
  3. Ana Balau; Sobral, Daniel; Márcia M. Medeiros; Antunes, Sandra; Carvalho, Maria; Inês Navalho Morais; Filomena Aréde de Carvalho; et al. "Turning a vulnerability into a strength - deciphering the protective mechanisms of pyruvate kinase deficiency against malaria". Paper presented in EMBL Conference: BioMalPar XX: biology and pathology of the malaria parasite, Heidelberg, Germany, 2024.
  4. Silva, Adriana; Silva, Vanessa; Gomes, João Paulo; Coelho, Anabela; Batista, Rita; Saraiva, Cristina; Esteves, Alexandra; et al. "Whole- genome sequencing reveals antibiotic resistance and genetic diversity of Listeria monocytogenes in food and related environments: Implications for Public Health and Food Safety". Paper presented in 34th European Congress of Clinical Microbiology & Infectious Diseases (ECCMID 2024), 2024.
  5. Ramos, Sónia; Lemos, Maria-Leonor; Ludovica Di Bella; Selma Marques; Margarida Penteado; Margarida Alves; Belas, Adriana; et al. Corresponding author: Alexandra Nunes. "Characterization of Campylobacter spp. isolates from poultry slaughtered for human consumption in Portugal". 2023.
  6. Angela Pista; Silveira, Leonor; Sara Costa; Rute Rosa; Carlota Gonçalves; Margarida Alves; Belas, Adriana; et al. Corresponding author: Alexandra Nunes. "Multidrug-resistant Escherichia coli and Salmonella spp. in pigs slaughtered for human consumption, a potential source for Humans?". Paper presented in The 2nd International Electronic Conference on Microbiology, 2023.
  7. Balau, Ana; Sobral, Daniel; Abrantes, Patrícia; Carvalho, Maria; Morais, Inês; Mixão, Verónica; Medeiros, Márcia Melo; et al. "Unveiling the Protective Mechanisms of Pyruvate Kinase Deficiency against Malaria: Transforming Vulnerability into Resilience". Paper presented in MicroBiotec 2023, 2023.
  8. Penteado, M; Rosa, R; Ramos, S; Alves, Margarida; Belas, A; Santos, I; Lima, A; et al. "Caracterização de Estirpes de Campylobacter spp. Isolados de Animais Abatidos para Consumo Humano, Um Problema de Saúde Pública em Portugal?". Paper presented in Congresso de Saúde Pública 23, 2023.
  9. Rute Rosa; Alexandra Nunes; Margarida Alves; Belas, Adriana; Maria Isabel Santos; Ana Lima; Joana Mota; et al. "Frequência e caracterização fenotípica de estirpes de Campylobacter coli em suínos abatidos para consumo Humano em Portugal". 2023.
  10. Margarida Penteado; Ramos, Sónia; Margarida Alves; Belas, Adriana; Maria Isabel Santos; Ana Lima; Joana Mota; et al. "Avaliação de multirresistências em estirpes de Campylobacter spp. isoladas de diferentes espécies de aves abatidas para consumo humano em Portugal.". 2023.
  11. Margarida Penteado; Ramos, Sónia; Alves, Margarida; Belas, Adriana; Santos, M.I.S.; Marques, Cátia; Lourenço, Armindo; et al. "Assessment of multidrug resistance in Campylobacter spp. isolated from different species of birds slaughtered for human consumption in Portugal". Paper presented in FMVet Research Meetings - II Encontro de Investigação da FMV da Universidade Lusófona, 2023.
  12. Ferreira, Rita; Coelho, Luis; Sobral, Daniel; Dourado, João; Isidro, Joana; Mixão, Verónica; Pinto, Miguel; et al. "Performance of metagenomics NGS probe-based pathogen detection in clinical samples". Paper presented in 3rd Symposium of the National Research Infrastructure for Genome Sequencing and Analysis (GenomePT Symposium 2023), Portuguese National Institute of Health, Lisbon, Portugal, 17th November, 2023.
    DOI: 10.13140/RG.2.2.23888.72963
  13. Batista, Rita; Joana Praça; Coelho, Anabela; Correia, Cristina Belo; Borges, Vítor; Gomes, João Paulo; Angela Pista. "Listeria monocytogenes, Escherichia coli and Coagulase positive Staphylococci in cured milk cheese from Alentejo region, Portugal". Paper presented in 1st International Congress on Food, Nutrition & Public Health- Towards a sustainable future, 2022.
  14. Serrano Pereira, Inês; Pais, Sara Vilela; Borges, Vítor; Borrego, Maria José; Gomes, João Paulo; Mota, Luís Jaime. Corresponding author: Mota, Luís Jaime. "The type III secretion effector CteG mediates host cell lytic exit of Chlamydia trachomatis (2nd prize)". Paper presented in International intracellular bacteria meeting 2022, 2022.
  15. Olivença, Francisco; Ferreira, Cláudia; Silveiro, Cátia; Nunes, Alexandra; Gomes, João Paulo; Catalão, Maria João. "Anticipating Mycobacterial Beta-lactam Resistance: Do we know the whole story?". Paper presented in 32nd European Congress of Clinical Microbiology and Infectious Diseases, 2022.
  16. Melo, Aryse; ana margarida henriques; FAGULHA, TERESA; Margarida Duarte; Catarina Fortunato Martins; Renata Carvalho; Joana Mendonça; et al. "Highly pathogenic Influenza A(H5N1) in Portugal: epidemiological and genetic investigation of multiple outbreaks". Paper presented in OPTIONS for the Control of Influenza XI, 2022.
  17. Calado, Rita; Bárbara B. Mendes; Conniot, João; Gomes, João Paulo; Conde, João; Alexandra Isabel Cardoso Nunes; Otília Vieira. "QAS-hydrogels as a promising microbicide against sexually and perinatal transmitted infections". Paper presented in Microbiotec 2021, 2021.
  18. Bárbara Alves; Calado, Rita; Guerreiro, Íris; Raquel Pereira Portela; Rita G. Sobral; Rijo, Patrícia; Gomes, João Paulo; Candeias, Nuno R.; Alexandra Isabel Cardoso Nunes. "Evaluation of the genetics underlying a putative acquisition of antimicrobial resistance to novel alkylaminophenols". Paper presented in Microbiotec 2021, 2021.
  19. Carolina Ferreira; Calado, Rita; Vieira, Otília V; Gomes, João Paulo; Alexandra Isabel Cardoso Nunes. "Are quaternary ammonium surfactants a good prophylatic option against Streptococcus agalactiae vertical transmission?". Paper presented in Microbiotec 2021, 2021.
  20. Olivença, Francisco; Pires, David; Nunes, Alexandra; Macedo, Rita; ANES, ELSA; Gomes, João Paulo. "Finding Key Genomic Markers of Beta-lactam Susceptibility in Clinical Isolates of Mycobacterium tuberculosis". Paper presented in MICROBIOTEC'21 - Congress of Microbiology and Biotechnology 2021, 2021.
  21. Ferreira, Cláudia; Olivença, Francisco; Nunes, Alexandra; Gomes, João Paulo; Catalão, Maria João. "Ascertaining mycobacterial inducible resistance to peptidoglycan synthesis inhibitors". Paper presented in MICROBIOTEC'21 - Congress of Microbiology and Biotechnology 2021, 2021.
  22. Calado, Rita; Otília Vieira; Gomes, João Paulo; Alexandra Isabel Cardoso Nunes. "Are quaternary ammonium surfactants good prophylatic options for Neisseria gonorrhoeae "superbug"". Paper presented in 31st ECCMID, European Congress of Clinical Microbology and Infectious diseases, 2021.
  23. Francisco Olivença; David Pires; Alexandra Nunes; Elsa Anes; Macedo, Rita; João Paulo Gomes; Maria João Catalão; et al. "Inhibition of Peptidoglican Biosynthesis as a strategy against drug-resistant Mycobacterium tuberculosis". Paper presented in Symposium of Research on Tuberculosis and Nontuberculous Mycobacteria in Portugal, 2021.
  24. Olivença, Francisco; Pires, David; Carmo, Nuno; Macedo, Rita; Nunes, Alexandra; Gomes, João Paulo; Anes, Elsa; Catalão, Maria João. "Inhibition of Peptidoglycan Biosynthesis as a Strategy Against Drug-resistant Mycobacterium tuberculosis". Paper presented in MICROBIOTEC 19 - Congress of Microbiology and Biotechnology’ 19, 2019.
  25. Olivença, Francisco; Pires, David; Carmo, Nuno; Macedo, Rita; Nunes, Alexandra; Gomes, João Paulo; Anes, Elsa; Catalão, Maria João. "Shifting the Paradigm: Repurposing Beta-lactam Antibiotics Against Drug-Resistant Clinical Isolates of Mycobacterium tuberculosis". Paper presented in The Great Wall Symposium 2019, 2019.
  26. Serrano Pereira, Inês; Pais, Sara V.; Key, Charlotte E.; Borges, Vítor; Gomes, João Paulo; Fisher, Derek J.; Mota, Luís Jaime. "Identification and characterization of CteG, a new Chlamydia trachomatis effector protein". Paper presented in FEMS 2019, 2019.
  27. Francisco Olivença; David Pires; Alexandra Nunes; Macedo, Rita; Elsa Anes; João Paulo Gomes; Maria João Catalão; et al. "Shifting the Paradigm: Repurposing beta-lactams antibiotics against drug-resistant clinical isolates of Mycobacterium tuberculosis.". Paper presented in The great Wall Symposium 2019, 2019.
  28. Pinto, Luís; Poeta, Patrícia; Gil, Concha; Reales-Calderón, Jose Antonio; Torres, Carmen; Santos, Hugo M.; Capelo, Jose Luis; et al. "iTRAQ labeling and RNA-Seq used to study the antibiotic stress response of vancomycin-resistant enterococci". Paper presented in NEOH Final Conference Creating impact for One Health and Ecohealth: advancements in implementation, evaluation and governance, 2018.
Journal article
  1. Mixão, Verónica; Pinto, Miguel; Brendebach, Holger; Sobral, Daniel; Dourado Santos, João; Radomski, Nicolas; Majgaard Uldall, Anne Sophie; et al. "Multi-country and intersectoral assessment of cluster congruence between pipelines for genomics surveillance of foodborne pathogens". Nature Communications (2025):
    Accepted • 10.1101/2024.07.24.24310933
  2. Lodhia, Zohra; Costa Da Silva, Jorge; Correia, Cristina; Cordeiro, Dora; João, Inês; Carreira, Teresa; Schäfer, Sandra; et al. "Surveying genetic markers of antibiotic resistance and genomic background in Chlamydia trachomatis: insights from a multiplex NGS-based approach in clinical strains from Portugal". Journal of Antimicrobial Chemotherapy (2025): https://doi.org/10.1093/jac/dkaf036.
    10.1093/jac/dkaf036
  3. Lodhia, Zohra; Cordeiro, Dora; Correia, Cristina; João, Inês; Carreira, Teresa; Vieira, Luís; Nunes, Alexandra; et al. "Distribution of Chlamydia trachomatis ompA-genotypes over three decades in Portugal". Sexually Transmitted Infections (2024): https://sti.bmj.com/content/early/2024/09/11/sextrans-2024-056166.
    Published
  4. Rita Mendonça; Rosália Furtado; Anabela Coelho; Cristina Belo Correia; Elena Suyarko; Vítor Borges; João Paulo Gomes; Angela Pista; Rita Batista. "Raw milk cheeses from Beira Baixa, Portugal—A contributive study for the microbiological hygiene and safety assessment". Brazilian Journal of Microbiology (2024): https://doi.org/10.1007/s42770-024-01332-y.
    10.1007/s42770-024-01332-y
  5. Calado, Rita D.A.; Mendes, Bárbara B.; Conniot, João; Ravasco, João M.J.M.; Sobral, Daniel; Ferreira, Carolina; Ferreira, Rita; et al. Corresponding author: Nunes, Alexandra. "Preclinical assessment of an antibiotic-free cationic surfactant-based cellulose hydrogel for sexually and perinatally transmitted infections". Matter 7 6 (2024): 2205-2235. http://dx.doi.org/10.1016/j.matt.2024.04.002.
    Published • 10.1016/j.matt.2024.04.002
  6. Adriana Silva; Vanessa Silva; João Paulo Gomes; Anabela Coelho; Rita Batista; Cristina Saraiva; Alexandra Esteves; et al. "Listeria monocytogenes from Food Products and Food Associated Environments: Antimicrobial Resistance, Genetic Clustering and Biofilm Insights". Antibiotics (2024): https://doi.org/10.3390/antibiotics13050447.
    10.3390/antibiotics13050447
  7. Inês C. Rodrigues; Marisa Ribeiro-Almeida; Leonor Silveira; Joana C. Prata; André Pinto de Carvalho; Carla Roque; João Paulo Gomes; et al. "Unveiling a Listeria monocytogenes Outbreak in a Rabbit Farm: Clinical Manifestation, Antimicrobial Resistance, Genomic Insights and Environmental Investigation". Microorganisms (2024): https://doi.org/10.3390/microorganisms12040785.
    10.3390/microorganisms12040785
  8. Isidro, Joana; Escudero, Raquel; Luque-Larena, Juan José; Pinto, Miguel; Borges, Vítor; González-Martín-Niño, Rosa; Duarte, Sílvia; et al. "Strengthening the genomic surveillance of Francisella tularensis by using culture-free whole-genome sequencing from biological samples". Frontiers in Microbiology 14 (2024): https://doi.org/10.3389/fmicb.2023.1277468.
    10.3389/fmicb.2023.1277468
  9. Alexandra Nunes; Mónica Oleastro; Frederico Alves; Nadia Liassine; David M. Lowe; Lucie Benejat; Astrid Ducounau; et al. "Erratum for Nunes et al., “Recurrent Campylobacter jejuni Infections with In Vivo Selection of Resistance to Macrolides and Carbapenems: Molecular Characterization of Resistance Determinants”". Microbiology Spectrum (2023): https://doi.org/10.1128/spectrum.03121-23.
    10.1128/spectrum.03121-23
  10. Célia Bettencourt; Alexandra Nunes; Paulo Nogueira; Sílvia Duarte; Catarina Silva; João Paulo Gomes; Maria João Simões. "Epidemiology and genetic diversity of invasive Neisseria meningitidis strains circulating in Portugal from 2003 to 2020". International Microbiology (2023): https://doi.org/10.1007/s10123-023-00463-w.
    10.1007/s10123-023-00463-w
  11. Ana Balau; Daniel Sobral; Patrícia Abrantes; Inês Santos; Verónica Mixão; João Paulo Gomes; Sandra Antunes; Ana Paula Arez. "Differential Gene Expression of Malaria Parasite in Response to Red Blood Cell-Specific Glycolytic Intermediate 2,3-Diphosphoglycerate (2,3-DPG)". International Journal of Molecular Sciences (2023): https://doi.org/10.3390/ijms242316869.
    10.3390/ijms242316869
  12. Áine O’Toole; Richard A. Neher; Nnaemeka Ndodo; Vitor Borges; Ben Gannon; João Paulo Gomes; Natalie Groves; et al. "APOBEC3 deaminase editing in mpox virus as evidence for sustained human transmission since at least 2016". Science (2023): https://doi.org/10.1126/science.adg8116.
    10.1126/science.adg8116
  13. Sofia Carneiro; Miguel Pinto; Sónia Silva; Andrea Santos; Irene Rodrigues; Daniela Santos; Sílvia Duarte; et al. "Genome-Scale Characterization of Mycobacterium abscessus Complex Isolates from Portugal". International Journal of Molecular Sciences (2023): https://doi.org/10.3390/ijms242015402.
    10.3390/ijms242015402
  14. Borges, Vítor; Duque, Mariana Perez; Martins, João Vieira; Vasconcelos, Paula; Ferreira, Rita; Sobral, Daniel; Pelerito, Ana; et al. "Viral genetic clustering and transmission dynamics of the 2022 mpox outbreak in Portugal". Nature Medicine 29 10 (2023): 2509-2517. http://dx.doi.org/10.1038/s41591-023-02542-x.
    Published • 10.1038/s41591-023-02542-x
  15. João Henriques; Verónica Mixão; Joana Cabrita; Tiago Isidoro Duarte; Tânia Sequeira; Sofia Cardoso; Nuno Germano; et al. "Candida auris in Intensive Care Setting: The First Case Reported in Portugal". Journal of Fungi (2023): https://www.mdpi.com/2309-608X/9/8/837.
    10.3390/jof9080837
  16. Alexandra Nunes; Mónica Oleastro; Frederico Alves; Nadia Liassine; David M. Lowe; Lucie Benejat; Astrid Ducounau; et al. "Recurrent Campylobacter jejuni Infections with In Vivo Selection of Resistance to Macrolides and Carbapenems: Molecular Characterization of Resistance Determinants". Microbiology Spectrum (2023): https://doi.org/10.1128/spectrum.01070-23.
    10.1128/spectrum.01070-23
  17. Carneiro, Sofia; Macedo, Rita; Gomes, João Paulo. Corresponding author: Carneiro, Sofia. "Nontuberculous Mycobacteria: A Review". Clinical Infectious Diseases: Open Access 7 3 (2023): https://www.hilarispublisher.com/open-access/nontuberculous-mycobacteria-a-review.pdf.
    Published
  18. Diogo Ramos; Miguel Pinto; Rodrigo Sousa Coutinho; Carolina Silva; Miriam Quina; João Paulo Gomes; Elizabeth Pádua. "Looking at the Molecular Target of NS5A Inhibitors throughout a Population Highly Affected with Hepatitis C Virus". Pathogens (2023): https://doi.org/10.3390/pathogens12060754.
    10.3390/pathogens12060754
  19. Rita Macedo; Joana Isidro; Rita Ferreira; Miguel Pinto; Vítor Borges; Sílvia Duarte; Luís Vieira; João Paulo Gomes. "Molecular Capture of Mycobacterium tuberculosis Genomes Directly from Clinical Samples: A Potential Backup Approach for Epidemiological and Drug Susceptibility Inferences". International Journal of Molecular Sciences (2023): https://doi.org/10.3390/ijms24032912.
    10.3390/ijms24032912
  20. Joana Praça; Rosália Furtado; Anabela Coelho; Cristina Belo Correia; Vítor Borges; João Paulo Gomes; Angela Pista; Rita Batista. "Listeria monocytogenes, Escherichia coli and Coagulase Positive Staphylococci in Cured Raw Milk Cheese from Alentejo Region, Portugal". Microorganisms (2023): https://doi.org/10.3390/microorganisms11020322.
    10.3390/microorganisms11020322
  21. Santos, A.; Pinto, M.; Carneiro, S.; Silva, S.; Rodrigues, I.; Munhá, J.; Gomes, J.P.; Macedo, R.. "Microevolution of a Mycobacteroides abscessus subsp. bolletii strain in a clinical persistent infection". Infection, Genetics and Evolution 112 (2023): http://www.scopus.com/inward/record.url?eid=2-s2.0-85156180801&partnerID=MN8TOARS.
    10.1016/j.meegid.2023.105437
  22. Chen, N.F.G.; Chaguza, C.; Gagne, L.; Doucette, M.; Smole, S.; Buzby, E.; Hall, J.; et al. "Development of an amplicon-based sequencing approach in response to the global emergence of mpox". PLoS Biology 21 6 (2023): http://www.scopus.com/inward/record.url?eid=2-s2.0-85161937127&partnerID=MN8TOARS.
    10.1371/journal.pbio.3002151
  23. Mixão, V.; Pinto, M.; Sobral, D.; Di Pasquale, A.; Gomes, J.P.; Borges, V.. "ReporTree: a surveillance-oriented tool to strengthen the linkage between pathogen genetic clusters and epidemiological data". Genome Medicine 15 1 (2023): http://www.scopus.com/inward/record.url?eid=2-s2.0-85162023893&partnerID=MN8TOARS.
    10.1186/s13073-023-01196-1
  24. Alves, F.; Castro, R.; Pinto, M.; Nunes, A.; Pomba, C.; Oliveira, M.; Silveira, L.; Gomes, J.P.; Oleastro, M.. "Molecular epidemiology of Clostridioides difficile in companion animals: Genetic overlap with human strains and public health concerns". Frontiers in Public Health 10 (2023): http://www.scopus.com/inward/record.url?eid=2-s2.0-85146531632&partnerID=MN8TOARS.
    10.3389/fpubh.2022.1070258
  25. Kislaya, I.; Peralta-Santos, A.; Borges, V.; Vieira, L.; Sousa, C.; Ferreira, B.; Pelerito, A.; et al. "Comparative complete scheme and booster effectiveness of COVID-19 vaccines in preventing SARS-CoV-2 infections with SARS-CoV-2 Omicron (BA.1) and Delta (B.1.617.2) variants: A case–case study based on electronic health records". Influenza and other Respiratory Viruses 17 3 (2023): http://www.scopus.com/inward/record.url?eid=2-s2.0-85150531666&partnerID=MN8TOARS.
    10.1111/irv.13121
  26. Oliveira, M.; Pinto, M.; Simões, H.; Gomes, J.P.; Veríssimo, C.; Sabino, R.. "Molecular detection of Aspergillus in respiratory samples collected from patients at higher risk of chronic pulmonary aspergillosis". Infectious Diseases Now 53 2 (2023): http://www.scopus.com/inward/record.url?eid=2-s2.0-85143286976&partnerID=MN8TOARS.
    10.1016/j.idnow.2022.11.002
  27. Kislaya, I.; Casaca, P.; Borges, V.; Sousa, C.; Ferreira, B.I.; Fonte, A.; Fernandes, E.; et al. "Comparative Effectiveness of COVID-19 Vaccines in Preventing Infections and Disease Progression from SARS-CoV-2 Omicron BA.5 and BA.2, Portugal". Emerging Infectious Diseases 29 3 (2023): 569-575. http://www.scopus.com/inward/record.url?eid=2-s2.0-85148678879&partnerID=MN8TOARS.
    10.3201/eid2903.221367
  28. Cochicho, Daniela; Nunes, Alexandra; Sobral, Daniel; Gomes, João P.; Esteves, Susana; Mendonça, Joana; Vieira, Luis; et al. "Distribution and Clinical Significance of HPV16 Variants in Head and Neck Squamous Cell Carcinomas: Data from a Portuguese Cohort and Systematic Review". Pathobiology 90 5 (2023): 333-343. http://dx.doi.org/10.1159/000529723.
    Published • 10.1159/000529723
  29. Pista, Ângela; Silveira, Leonor; Ribeiro, Sofia; Fontes, Mariana; Castro, Rita; Coelho, Anabela; Furtado, Rosália; et al. "Escherichia coli patogénica, Salmonella spp. e Campylobacter spp. em dois Centros de Conservação da Vida Selvagem em Portugal: caracterização genotípica e fenotípica". (2023): http://hdl.handle.net/10400.18/8885.
  30. Daniela Cochicho; Alexandra Nunes; João Paulo Gomes; Luís Martins; Mário Cunha; Beatriz Medeiros-Fonseca; Paula Oliveira; et al. "Characterization of the Human Papillomavirus 16 Oncogenes in K14HPV16 Mice: Sublineage A1 Drives Multi-Organ Carcinogenesis". International Journal of Molecular Sciences (2022): https://doi.org/10.3390/ijms232012371.
    10.3390/ijms232012371
  31. Angela Pista; Pista Angela; A Pista; Pista A; Â Pista; Pista Â; Ângela Pista; Leonor Silveira; Sofia Ribeiro; Mariana Fontes; Rita Castro; Anabela Coelho; Rosália Furtado; et al. "Pathogenic Escherichia coli, Salmonella spp. and Campylobacter spp. in Two Natural Conservation Centers of Wildlife in Portugal: Genotypic and Phenotypic Characterization". Microorganisms (2022): https://www.mdpi.com/2076-2607/10/11/2132.
    10.3390/microorganisms10112132
  32. Matúš Štefánek; Sigurd Wenner; Vítor Borges; Miguel Pinto; João Paulo Gomes; João Rodrigues; Isabel Faria; et al. "Antimicrobial Resistance and Biofilms Underlying Catheter-Related Bloodstream Coinfection by Enterobacter cloacae Complex and Candida parapsilosis". Antibiotics (2022): https://doi.org/10.3390/antibiotics11091245.
    10.3390/antibiotics11091245
  33. Maria João Gargaté; Anabela Vilares; Idalina Ferreira; Tânia Reis; Susana Martins; Joana Mendonça; Vítor Borges; João Paulo Gomes. "Parallel Propagation of Toxoplasma gondii In Vivo, In Vitro and in Alternate Model: Towards Less Dependence on the Mice Model". Pathogens (2022): https://doi.org/10.3390/pathogens11091038.
    10.3390/pathogens11091038
  34. Francisco Olivença; Alexandra Nunes; Rita Macedo; David Pires; Cátia Silveiro; Elsa Anes; Maria Miragaia; et al. "Uncovering Beta-Lactam Susceptibility Patterns in Clinical Isolates of Mycobacterium tuberculosis through Whole-Genome Sequencing". Microbiology Spectrum (2022): https://doi.org/10.1128/spectrum.00674-22.
    10.1128/spectrum.00674-22
  35. Regina Sá; Joana Isidro; Vítor Borges; Sílvia Duarte; Luís Vieira; João P Gomes; Sofia Tedim; Judite Matias; Andreia Leite. "Unraveling the hurdles of a large COVID-19 epidemiological investigation by viral genomics". Journal of Infection (2022): https://doi.org/10.1016/j.jinf.2022.05.013.
    10.1016/j.jinf.2022.05.013
  36. Massimo Amicone; Vítor Borges; Maria João Alves; Joana Isidro; Líbia Zé-Zé; Sílvia Duarte; Luís Vieira; et al. "Mutation rate of SARS-CoV-2 and emergence of mutators during experimental evolution". Evolution, Medicine, and Public Health (2022): https://doi.org/10.1101/2021.05.19.444774.
    Accepted • 10.1101/2021.05.19.444774
  37. Borges, Vítor; Isidro, Joana; Trovão, Nídia Sequeira; Duarte, Sílvia; Cortes-Martins, Helena; Martiniano, Hugo; Gordo, Isabel; et al. "SARS-CoV-2 introductions and early dynamics of the epidemic in Portugal". Communications Medicine 2 1 (2022): http://dx.doi.org/10.1038/s43856-022-00072-0.
    Published • 10.1038/s43856-022-00072-0
  38. Luís Tanoeiro; Mónica Oleastro; Alexandra Nunes; Andreia T. Marques; Sílvia Vaz Duarte; João Paulo Gomes; António Pedro Alves Matos; Jorge M. B. Vítor; Filipa F. Vale. "Cryptic Prophages Contribution for Campylobacter jejuni and Campylobacter coli Introgression". Microorganisms 10 3 (2022): 516-516. https://doi.org/10.3390/microorganisms10030516.
    10.3390/microorganisms10030516
  39. Célia Bettencourt; Alexandra Nunes; João Paulo Gomes; Maria João Simões. "Genomic surveillance of Neisseria meningitidis serogroup W in Portugal from 2003 to 2019". European Journal of Clinical Microbiology & Infectious Diseases (2022): https://doi.org/10.1007/s10096-021-04371-7.
    10.1007/s10096-021-04371-7
  40. A. Santos; S. Carneiro; A. Silva; J.P. Gomes; R. Macedo. "Nontuberculous Mycobacteria in Portugal: Trends from the last decade". Pulmonology (2022): https://doi.org/10.1016/j.pulmoe.2022.01.011.
    10.1016/j.pulmoe.2022.01.011
  41. Kislaya, Irina; Rodrigues, Eduardo Freire; Borges, Vítor; Gomes, João P.; Sousa, Carlos; Almeida, José P.; Peralta-Santos, André; Nunes, Baltazar. "Comparative Effectiveness of Coronavirus Vaccine in Preventing Breakthrough Infections among Vaccinated Persons Infected with Delta and Alpha Variants". Emerging Infectious Diseases 28 2 (2022): 331-337. http://dx.doi.org/10.3201/eid2802.211789.
    Published • 10.3201/eid2802.211789
  42. Borges, Vítor; Isidro, Joana; Trovão, Nídia Sequeira; Duarte, Sílvia; Cortes-Martins, Helena; Martiniano, Hugo; Gordo, Isabel; et al. "SARS-CoV-2 introductions and early dynamics of the epidemic in Portugal". Communications Medicine 2 1 (2022): http://dx.doi.org/10.1038/s43856-022-00072-0.
    Published
  43. Ribeiro, M.; Sousa, M.; Borges, V.; Gomes, J.P.; Duarte, S.; Isidro, J.; Vieira, L.; et al. "Bioinformatics study of expression from genomes of epidemiologically related MRSA CC398 isolates from human and wild animal samples". Journal of Proteomics 268 (2022): http://www.scopus.com/inward/record.url?eid=2-s2.0-85138085633&partnerID=MN8TOARS.
    10.1016/j.jprot.2022.104714
  44. Isidro, J.; Borges, V.; Pinto, M.; Sobral, D.; Santos, J.D.; Nunes, A.; Mixão, V.; et al. "Addendum: Phylogenomic characterization and signs of microevolution in the 2022 multi-country outbreak of monkeypox virus". Nature medicine 28 10 (2022): 2220-2221. http://www.scopus.com/inward/record.url?eid=2-s2.0-85139804253&partnerID=MN8TOARS.
    10.1038/s41591-022-02036-2
  45. Silvestre, I.; Borges, V.; Duarte, S.; Nunes, A.; Sobral, R.; Vieira, L.; Gomes, J.P.; Borrego, M.J.. "Global gene expression analysis of Streptococcus agalactiae at the exponential growth phase". Cellular and Molecular Biology 68 7 (2022): 1-8. http://www.scopus.com/inward/record.url?eid=2-s2.0-85143917237&partnerID=MN8TOARS.
    10.14715/cmb/2022.68.7.1
  46. Olivença, F.; Ferreira, C.; Nunes, A.; Silveiro, C.; Pimentel, M.; Gomes, J.P.; Catalão, M.J.. "Identification of drivers of mycobacterial resistance to peptidoglycan synthesis inhibitors". Frontiers in Microbiology 13 (2022): http://www.scopus.com/inward/record.url?eid=2-s2.0-85138253784&partnerID=MN8TOARS.
    10.3389/fmicb.2022.985871
  47. Isidro, J.; Borges, V.; Pinto, M.; Sobral, D.; Santos, J.D.; Nunes, A.; Mixão, V.; et al. "Phylogenomic characterization and signs of microevolution in the 2022 multi-country outbreak of monkeypox virus". Nature Medicine 28 8 (2022): 1569-1572. http://www.scopus.com/inward/record.url?eid=2-s2.0-85133727701&partnerID=MN8TOARS.
    10.1038/s41591-022-01907-y
  48. Pereira, I.S.; Pais, S.V.; Borges, V.; Borrego, M.J.; Gomes, J.P.; Mota, L.J.. "The Type III Secretion Effector CteG Mediates Host Cell Lytic Exit of Chlamydia trachomatis". Frontiers in Cellular and Infection Microbiology 12 (2022): http://www.scopus.com/inward/record.url?eid=2-s2.0-85134904576&partnerID=MN8TOARS.
    10.3389/fcimb.2022.902210
  49. Alves, F.; Nunes, A.; Castro, R.; Sequeira, A.; Moreira, O.; Matias, R.; Rodrigues, J.C.; et al. "Assessment of the Transmission Dynamics of Clostridioides difficile in a Farm Environment Reveals the Presence of a New Toxigenic Strain Connected to Swine Production". Frontiers in Microbiology 13 (2022): http://www.scopus.com/inward/record.url?eid=2-s2.0-85128930048&partnerID=MN8TOARS.
    10.3389/fmicb.2022.858310
  50. Monteiro, I.P.; Sousa, S.; Borges, V.; Gonçalves, P.; Gomes, J.P.; Mota, L.J.; Franco, I.S.. "A Search for Novel Legionella pneumophila Effector Proteins Reveals a Strain Specific Nucleotropic Effector". Frontiers in Cellular and Infection Microbiology 12 (2022): http://www.scopus.com/inward/record.url?eid=2-s2.0-85132081313&partnerID=MN8TOARS.
    10.3389/fcimb.2022.864626
  51. Pinto, M.; Borges, V.; Nascimento, M.; Martins, F.; Pessanha, M.A.; Faria, I.; Rodrigues, J.; et al. "Insights on catheter-related bloodstream infections: a prospective observational study on the catheter colonization and multidrug resistance". Journal of Hospital Infection 123 (2022): 43-51. http://www.scopus.com/inward/record.url?eid=2-s2.0-85126328004&partnerID=MN8TOARS.
    10.1016/j.jhin.2022.01.025
  52. Happi, C.; Adetifa, I.; Mbala, P.; Njouom, R.; Nakoune, E.; Happi, A.; Ndodo, N.; et al. "Urgent need for a non-discriminatory and non-stigmatizing nomenclature for monkeypox virus". PLoS Biology 20 8 (2022): http://www.scopus.com/inward/record.url?eid=2-s2.0-85138125659&partnerID=MN8TOARS.
    10.1371/journal.pbio.3001769
  53. Pelerito, Ana; Nunes, Alexandra; Grilo, Teresa; Isidro, Joana; Silva, Catarina; Ferreira, Ana Cristina; Valdezate, Sylvia; et al. "Genetic Characterization of Brucella spp.: Whole Genome Sequencing-Based Approach for the Determination of Multiple Locus Variable Number Tandem Repeat Profiles". Frontiers in Microbiology 12 (2021): http://dx.doi.org/10.3389/fmicb.2021.740068.
    Published • 10.3389/fmicb.2021.740068
  54. Ana M Correia; Vítor Borges; Joana Isidro; Ana R Lima; Alberto Fernandes; Maria Leonor Godinho; Sílvia Duarte; et al. "Potential recurrence of COVID-19 in a healthcare professional: SARS-CoV-2 genome sequencing confirms contagiousness after re-positivity". International Journal of Infectious Diseases (2021): https://doi.org/10.1016/j.ijid.2021.09.035.
    10.1016/j.ijid.2021.09.035
  55. O'Toole, Áine; Hill, Verity; Pybus, Oliver G.; Watts, Alexander; Bogoch, Issac I.; Khan, Kamran; Messina, Jane P.; et al. "Tracking the international spread of SARS-CoV-2 lineages B.1.1.7 and B.1.351/501Y-V2 with grinch". Wellcome Open Research 6 (2021): 121. http://dx.doi.org/10.12688/wellcomeopenres.16661.2.
    Published • 10.12688/wellcomeopenres.16661.2
  56. Borges, Vítor; Isidro, Joana; Cunha, Mário; Cochicho, Daniela; Martins, Luís; Banha, Luís; Figueiredo, Margarida; et al. "Long-Term Evolution of SARS-CoV-2 in an Immunocompromised Patient with Non-Hodgkin Lymphoma". mSphere 6 4 (2021): http://dx.doi.org/10.1128/msphere.00244-21.
    Published • 10.1128/msphere.00244-21
  57. Gomes, João Paulo. "The Contribution of SARS-CoV-2 Genomics to the Handling of the COVID-19 Pandemic in Portugal". Acta Médica Portuguesa 34 13 (2021): http://dx.doi.org/10.20344/amp.16505.
    Published • 10.20344/amp.16505
  58. Funk, Tjede; Pharris, Anastasia; Spiteri, Gianfranco; Bundle, Nick; Melidou, Angeliki; Carr, Michael; Gonzalez, Gabriel; et al. "Characteristics of SARS-CoV-2 variants of concern B.1.1.7, B.1.351 or P.1: data from seven EU/EEA countries, weeks 38/2020 to 10/2021". Eurosurveillance 26 16 (2021): http://dx.doi.org/10.2807/1560-7917.es.2021.26.16.2100348.
    Published • 10.2807/1560-7917.es.2021.26.16.2100348
  59. Borges, Vítor; Isidro, Joana; Macedo, Filipe; Neves, José; Silva, Luís; Paiva, Mário; Barata, José; et al. "Nosocomial Outbreak of SARS-CoV-2 in a “Non-COVID-19” Hospital Ward: Virus Genome Sequencing as a Key Tool to Understand Cryptic Transmission". Viruses 13 4 (2021): 604. http://dx.doi.org/10.3390/v13040604.
    Published • 10.3390/v13040604
  60. Borges, Vítor; Sousa, Carlos; Menezes, Luís; Gonçalves, António Maia; Picão, Miguel; Almeida, José Pedro; Vieita, Margarida; et al. "Tracking SARS-CoV-2 lineage B.1.1.7 dissemination: insights from nationwide spike gene target failure (SGTF) and spike gene late detection (SGTL) data, Portugal, week 49 2020 to week 3 2021". Eurosurveillance 26 10 (2021): http://dx.doi.org/10.2807/1560-7917.es.2021.26.10.2100130.
    Published • 10.2807/1560-7917.es.2021.26.10.2100130
  61. Miguel Pinto; Vítor Borges; Joana Isidro; João Carlos Rodrigues; Luís Vieira; Maria José Borrego; João Paulo Gomes. "Neisseria gonorrhoeae clustering to reveal major European whole-genome-sequencing-based genogroups in association with antimicrobial resistance". Microbial Genomics 7 2 (2021): https://doi.org/10.1099/mgen.0.000481.
    10.1099/mgen.0.000481
  62. Borges, Vítor; Isidro, Joana; Correia, Cristina; Cordeiro, Dora; Vieira, Luís; Lodhia, Zohra; Fernandes, Cândida; et al. "Transcontinental dissemination of the L2b/D-Da recombinant Chlamydia trachomatis Lymphogranuloma venereum (LGV) strain: need of broad multi-country molecular surveillance". Clinical Infectious Diseases (2021): http://dx.doi.org/10.1093/cid/ciab067.
    Open access • Published • 10.1093/cid/ciab067
  63. Silveira, L.; Nunes, A.; Pista, A.; Isidro, J.; Belo Correia, C.; Saraiva, M.; Batista, R.; et al. "Characterization of Multidrug-Resistant Isolates of Salmonella enterica Serovars Heidelberg and Minnesota from Fresh Poultry Meat Imported to Portugal". Microbial Drug Resistance 27 1 (2021): 87-98. http://www.scopus.com/inward/record.url?eid=2-s2.0-85099691602&partnerID=MN8TOARS.
    10.1089/mdr.2019.0384
  64. Borges, V.; Sousa, C.; Menezes, L.; Gonçalves, A.M.; Picão, M.; Almeida, J.P.; Vieita, M.; et al. "Tracking SARS-CoV-2 lineage B.1.1.7 dissemination: insights from nationwide spike gene target failure (SGTF) and spike gene late detection (SGTL) data, Portugal, week 49 2020 to week 3 2021". Eurosurveillance 26 10 (2021): 1-6. http://www.scopus.com/inward/record.url?eid=2-s2.0-85102848051&partnerID=MN8TOARS.
    10.2807/1560-7917.ES.2021.26.10.2100130
  65. O'Toole, A.; Kraemer, M.U.G.; Hill, V.; Pybus, O.G.; Watts, A.; Bogoch, I.I.; Khan, K.; et al. "Tracking the international spread of SARS-CoV-2 lineages B.1.1.7 and B.1.351/501Y-V2". Wellcome Open Research 6 (2021): http://www.scopus.com/inward/record.url?eid=2-s2.0-85107141280&partnerID=MN8TOARS.
    10.12688/wellcomeopenres.16661.1
  66. de Freitas, F.G.R.; Hammond, N.; Li, Y.; de Azevedo, L.C.P.; Cavalcanti, A.B.; Taniguchi, L.; Gobatto, A.; et al. "Resuscitation fluid practices in Brazilian intensive care units: A secondary analysis of Fluid-TRIPS,Práticas de ressuscitação volêmica em unidades de terapia intensiva brasileiras: Uma análise secundária do estudo Fluid-TRIPS". Revista Brasileira de Terapia Intensiva 33 2 (2021): 206-218. http://www.scopus.com/inward/record.url?eid=2-s2.0-85110980671&partnerID=MN8TOARS.
    10.5935/0103-507X.20210028
  67. Funk, T.; Pharris, A.; Spiteri, G.; Bundle, N.; Melidou, A.; Carr, M.; Gonzalez, G.; et al. "Characteristics of SARS-CoV-2 variants of concern B.1.1.7, B.1.351 or P.1: data from seven EU/EEA countries, weeks 38/2020 to 10/2021". Eurosurveillance 26 16 (2021): http://www.scopus.com/inward/record.url?eid=2-s2.0-85105089603&partnerID=MN8TOARS.
    10.2807/1560-7917.ES.2021.26.16.2100348
  68. Silvestre, I.; Nunes, A.; Borges, V.; Isidro, J.; Silva, C.; Vieira, L.; Gomes, J.P.; Borrego, M.J.. "Genomic insights on DNase production in Streptococcus agalactiae ST17 and ST19 strains". Infection, Genetics and Evolution 93 (2021): http://www.scopus.com/inward/record.url?eid=2-s2.0-85108876433&partnerID=MN8TOARS.
    10.1016/j.meegid.2021.104969
  69. Célia Bettencourt; Alexandra Nunes; Ana Maria Correia; João Paulo Gomes; Maria João Simões. "Lung abscess due to Neisseria meningitidis serogroup X—unexpected virulence of a commensal resulting from putative serogroup B capsular switching". European Journal of Clinical Microbiology & Infectious Diseases (2020): https://doi.org/10.1007/s10096-020-03977-7.
    10.1007/s10096-020-03977-7
  70. Borges, Vítor; Isidro, Joana; Cortes-Martins, Helena; Duarte, Sílvia; Vieira, Luís; Leite, Ricardo; Gordo, Isabel; et al. "Massive dissemination of a SARS-CoV-2 Spike Y839 variant in Portugal". Emerging Microbes & Infections 9 1 (2020): 2488-2496. http://dx.doi.org/10.1080/22221751.2020.1844552.
    Published • 10.1080/22221751.2020.1844552
  71. Correia, Cátia R.; Marçal, Mónica; Vieira, Filipa; Santos, Edmundo; Novais, Cristina; Maria, Ana Teresa; Malveiro, Duarte; et al. "Congenital SARS-CoV-2 Infection in a Neonate With Severe Acute Respiratory Syndrome". Pediatric Infectious Disease Journal 39 12 (2020): e439-e443. http://dx.doi.org/10.1097/inf.0000000000002941.
    Published • 10.1097/inf.0000000000002941
  72. Schäfer, Walter; Schmidt, Teresa; Cordsmeier, Arne; Borges, Vítor; Beare, Paul A.; Pechstein, Julian; Schulze-Luehrmann, Jan; et al. "The anti-apoptotic Coxiella burnetii effector protein AnkG is a strain specific virulence factor". Scientific Reports 10 1 (2020): http://dx.doi.org/10.1038/s41598-020-72340-9.
    Published • 10.1038/s41598-020-72340-9
  73. Alm, Erik; Broberg, Eeva K; Connor, Thomas; Hodcroft, Emma B; Komissarov, Andrey B; Maurer-Stroh, Sebastian; Melidou, Angeliki; et al. "Geographical and temporal distribution of SARS-CoV-2 clades in the WHO European Region, January to June 2020". Eurosurveillance 25 32 (2020): http://dx.doi.org/10.2807/1560-7917.es.2020.25.32.2001410.
    Published • 10.2807/1560-7917.es.2020.25.32.2001410
  74. Macedo, Rita; Isidro, Joana; Gomes, Maria Conceição; Botelho, Ana; Albuquerque, Teresa; Sogorb, Arlete; Bernardino, Rui; et al. "Animal-to-human transmission of Mycobacterium pinnipedii". European Respiratory Journal (2020): 2000371. http://dx.doi.org/10.1183/13993003.00371-2020.
    Published • 10.1183/13993003.00371-2020
  75. Pinto, Miguel; Matias, Rui; Rodrigues, João Carlos; Duarte, Sílvia; Vieira, Luís; Gonçalves, Inês; Gonçalves, Maria João; et al. "Cephalosporin-Resistant Neisseria gonorrhoeae Isolated in Portugal, 2019". Sexually Transmitted Diseases 47 11 (2020): e54-e56. http://dx.doi.org/10.1097/olq.0000000000001218.
    Published • 10.1097/olq.0000000000001218
  76. Pinto, Miguel; Rodrigues, João Carlos; Matias, Rui; Água-Doce, Ivone; Cordeiro, Dora; Correia, Cristina; Gomes, João Paulo; Borrego, Maria José. "Fifteen years of a nationwide culture collection of Neisseria gonorrhoeae antimicrobial resistance in Portugal". European Journal of Clinical Microbiology & Infectious Diseases 39 9 (2020): 1761-1770. http://dx.doi.org/10.1007/s10096-020-03907-7.
    Published • 10.1007/s10096-020-03907-7
  77. Joana Isidro; Susana Ferreira; Miguel Pinto; Fernanda Domingues; Mónica Oleastro; João Paulo Gomes; Vítor Borges. "Virulence and antibiotic resistance plasticity of Arcobacter butzleri: Insights on the genomic diversity of an emerging human pathogen". Infection, Genetics and Evolution 80 (2020): 104213-104213. https://doi.org/10.1016/j.meegid.2020.104213.
    10.1016/j.meegid.2020.104213
  78. Pelerito, Ana; Nunes, Alexandra; Núncio, Maria Sofia; Gomes, João Paulo. "Genome-scale approach to study the genetic relatedness among Brucella melitensis strains". PLOS ONE 15 3 (2020): e0229863. http://dx.doi.org/10.1371/journal.pone.0229863.
    10.1371/journal.pone.0229863
  79. Gomes, João; Líbia Zé-Zé; Vítor Borges; Hugo Costa Osório; Jorge Machado; João Paulo Gomes; Maria João Alves. "Mitogenome diversity of Aedes (Stegomyia) albopictus: Detection of multiple introduction events in Portugal and potential within-country dispersal". (2020): https://doi.org/10.1101/2020.02.12.945741.
    10.1101/2020.02.12.945741
  80. Pinto, Luís; Torres, Carmen; Gil, Concha; Santos, Hugo M.; Capelo, José Luís; Borges, Vítor; Gomes, João Paulo; et al. "Multiomics Substrates of Resistance to Emerging Pathogens? Transcriptome and Proteome Profile of a Vancomycin-Resistant Enterococcus faecalis Clinical Strain". OMICS: A Journal of Integrative Biology 24 2 (2020): 81-95. http://dx.doi.org/10.1089/omi.2019.0164.
    10.1089/omi.2019.0164
  81. Vilares, Anabela; Borges, Vítor; Sampaio, Daniel; Ferreira, Idalina; Martins, Susana; Vieira, Luis; Gargaté, Maria João; Gomes, João Paulo. "Towards a rapid sequencing-based molecular surveillance and mosaicism investigation of Toxoplasma gondii". Parasitology Research 119 2 (2020): 587-599. http://dx.doi.org/10.1007/s00436-019-06523-3.
    10.1007/s00436-019-06523-3
  82. Silveira, Leonor; Nunes, Alexandra; Pista, Ângela; Isidro, Joana; Belo Correia, Cristina; Saraiva, Margarida; Batista, Rita; et al. "Characterization of multidrug-resistant isolates of Salmonella enterica serovars Heidelberg and Minnesota from fresh poultry meat imported to Portugal". Microbial Drug Resistance (2020):
    Accepted
  83. Zé-Zé, L.; Borges, V.; Osório, H.C.; Machado, J.; Gomes, J.P.; Alves, M.J.. "Mitogenome diversity of aedes (Stegomyia) albopictus: Detection of multiple introduction events in portugal". PLoS Neglected Tropical Diseases 14 9 (2020): 1-15. http://www.scopus.com/inward/record.url?eid=2-s2.0-85092258271&partnerID=MN8TOARS.
    10.1371/journal.pntd.0008657
  84. Borges, Vítor; Isidro, Joana; Cortes-Martins, Helena; Duarte, Sílvia; Vieira, Luís; Guiomar, Raquel; Gomes, João Paulo. "Estudo da diversidade genética do SARS-CoV-2 (COVID-19) em Portugal". (2020): http://hdl.handle.net/10400.18/7248.
  85. Leonor Silveira; Miguel Pinto; Joana Isidro; Ângela Pista; Patrícia Themudo; Luís Vieira; Jorge Machado; João Paulo Gomes. "Multidrug-Resistant Salmonella enterica Serovar Rissen Clusters Detected in Azores Archipelago, Portugal". International Journal of Genomics (2019): https://doi.org/10.1155/2019/1860275.
    10.1155/2019/1860275
  86. Sara V. Pais; Charlotte E. Key; Vítor Borges; Inês S. Pereira; João Paulo Gomes; Derek J. Fisher; Luís Jaime Mota. "CteG is a Chlamydia trachomatis effector protein that associates with the Golgi complex of infected host cells". Scientific Reports 9 1 (2019): https://doi.org/10.1038/s41598-019-42647-3.
    10.1038/s41598-019-42647-3
  87. Borges, Vítor; Cordeiro, Dora; Salas, Ana Isabel; Lodhia, Zohra; Correia, Cristina; Isidro, Joana; Fernandes, Cândida; et al. "Chlamydia trachomatis: when the virulence-associated genome backbone imports a prevalence-associated major antigen signature". Microbial Genomics 5 11 (2019): http://dx.doi.org/10.1099/mgen.0.000313.
    10.1099/mgen.0.000313
  88. Pinto, Luís; Torres, Carmen; Gil, Concha; Nunes-Miranda, Júlio D.; Santos, Hugo M.; Borges, Vítor; Gomes, João P.; et al. "Multiomics Assessment of Gene Expression in a Clinical Strain of CTX-M-15-Producing ST131 Escherichia coli". Frontiers in Microbiology 10 (2019): http://dx.doi.org/10.3389/fmicb.2019.00831.
    10.3389/fmicb.2019.00831
  89. Sousa, Sara; Borges, Vítor; Joao, Ines; Gomes, João Paulo; Jordao, Luisa. "Nontuberculous Mycobacteria Persistence in a Cell Model Mimicking Alveolar Macrophages". Microorganisms 7 5 (2019): 113. http://dx.doi.org/10.3390/microorganisms7050113.
    10.3390/microorganisms7050113
  90. Macedo, Rita; Pinto, Miguel; Borges, Vítor; Nunes, Alexandra; Oliveira, Olena; Portugal, Isabel; Duarte, Raquel; Gomes, João Paulo. "Evaluation of a gene-by-gene approach for prospective whole-genome sequencing-based surveillance of multidrug resistant Mycobacterium tuberculosis". Tuberculosis 115 (2019): 81-88. http://dx.doi.org/10.1016/j.tube.2019.02.006.
    10.1016/j.tube.2019.02.006
  91. Pinto, M.; González-Díaz, A.; Machado, M.P.; Duarte, S.; Vieira, L.; Carriço, J.A.; Marti, S.; Bajanca-Lavado, M.P.; Gomes, J.P.. "Insights into the population structure and pan-genome of Haemophilus influenzae". Infection, Genetics and Evolution 67 (2019): 126-135. http://dx.doi.org/10.1016/j.meegid.2018.10.025.
    10.1016/j.meegid.2018.10.025
  92. Florindo, Carlos; Barroco, Cinthia Alves; Silvestre, Inês; Damião, Vera; Gomes, João Paulo; Spellerberg, Barbara; Santos-Sanches, Ilda; Borrego, Maria José. "Capsular Type, Sequence Type and Microbial Resistance Factors Impact on DNase Activity of Streptococcus agalactiae Strains from Human and Bovine Origin". European Journal of Microbiology and Immunology 8 4 (2018): 149-154. http://dx.doi.org/10.1556/1886.2018.00026.
    10.1556/1886.2018.00026
  93. Rimpiläinen, Tatu; Andrade, Joana; Nunes, Alexandra; Ntungwe, Epole; Fernandes, Ana S.; Vale, João R.; Rodrigues, João; et al. "Aminobenzylated 4-Nitrophenols as Antibacterial Agents Obtained from 5-Nitrosalicylaldehyde through a Petasis Borono–Mannich Reaction". ACS Omega 3 11 (2018): 16191-16202. http://dx.doi.org/10.1021/acsomega.8b02381.
    10.1021/acsomega.8b02381
  94. Chung, Marilyn; Borges, Vitor; Gomes, João Paulo; de Lencastre, Herminia; Tomasz, Alexander. "Phenotypic signatures and genetic determinants of oxacillin tolerance in a laboratory mutant of Staphylococcus aureus". PLOS ONE 13 7 (2018): e0199707. http://dx.doi.org/10.1371/journal.pone.0199707.
    10.1371/journal.pone.0199707
  95. Borges, Vítor; Pinheiro, Miguel; Pechirra, Pedro; Guiomar, Raquel; Gomes, João Paulo. "INSaFLU: an automated open web-based bioinformatics suite “from-reads” for influenza whole-genome-sequencing-based surveillance". Genome Medicine 10 1 (2018): http://dx.doi.org/10.1186/s13073-018-0555-0.
    10.1186/s13073-018-0555-0
  96. Rita Macedo; Alexandra Nunes; Isabel Portugal; Sílvia Duarte; Luís Vieira; João Paulo Gomes. "Dissecting whole-genome sequencing-based online tools for predicting resistance in Mycobacterium tuberculosis : can we use them for clinical decision guidance?". Tuberculosis 110 (2018): 44-51. https://doi.org/10.1016/j.tube.2018.03.009.
    10.1016/j.tube.2018.03.009
  97. Gomes, João. "Imipenem Resistance in Clostridium difficile Ribotype 017, Portugal". Emerg Infect Dis (2018):
    10.3201/eid2404.170095
  98. Pardos de la Gandara, Maria; Borges, Vitor; Chung, Marilyn; Milheiriço, Catarina; Gomes, João Paulo; de Lencastre, Herminia; Tomasz, Alexander. "Genetic Determinants of High-Level Oxacillin Resistance in Methicillin-Resistant Staphylococcus aureus". Antimicrobial Agents and Chemotherapy 62 6 (2018): e002016. http://dx.doi.org/10.1128/aac.00206-18.
    Published • 10.1128/aac.00206-18
  99. Gomes, João. "Genetic determinants of high-level oxacillin resistance in MRSA". Antimicrob Agents Chemother (2018):
    10.1128/AAC.00206-18
  100. Pardos de la Gandara, M.; Borges, V.; Chung, M.; Milheiriço, C.; Gomes, J.P.; de Lencastre, H.; Tomasz, A.. "Erratum: Correction for Pardos de la Gandara et al., "Genetic Determinants of High-Level Oxacillin Resistance in Methicillin-Resistant Staphylococcus aureus" (Antimicrobial agents and chemotherapy (2018) 62 6 PII: e01096-18)". Antimicrobial agents and chemotherapy 62 7 (2018): http://www.scopus.com/inward/record.url?eid=2-s2.0-85060370698&partnerID=MN8TOARS.
    10.1128/AAC.01096-18
  101. Macedo, Rita; Pinto, Miguel; Borges, Vítor; Nunes, Alexandra; Isidro, Joana; Duarte, Sílvia; Vieira, Luís; Gomes, João Paulo. "Nova era na vigilância da tuberculose multirresistente em Portugal: sequenciação do genoma completo". (2018): http://hdl.handle.net/10400.18/5693.
  102. Isidro, Joana; Santos, Andrea; Nunes, Alexandra; Borges, Vítor; Silva, Catarina; Vieira, Luís; Mendes, Aristides L; et al. "Resistência de Clostridium difficile do ribotipo 017 ao imipenemo: contributo da sequenciação do genoma completo". (2018): http://hdl.handle.net/10400.18/5692.
  103. Pinto, Miguel; Borges, Vítor; Antelo, Minia; Pinheiro, Miguel; Nunes, Alexandra; Azevedo, Jacinta; Borrego, Maria José; et al. "Nova abordagem genómica para a investigação da sífilis". (2018): http://hdl.handle.net/10400.18/5690.
  104. Pechirra, Pedro; Borges, Vítor; Cristóvão, Paula; Costa, Inês; Conde, Patrícia; Machado, Ausenda; Rodrigues, Ana Paula; et al. "Sequenciação de nova geração e efetividade da vacina antigripal: um estudo sobre o vírus da gripe A(H3), em doentes com síndroma gripal, épocas 2016/2017 e 2017/2018". (2018): http://hdl.handle.net/10400.18/5694.
  105. Vilares, Anabela; Borges, Vítor; Sampaio, Daniel; Vieira, Luis; Martins, Susana; Reis, Tânia; Gomes, João Paulo; Gargate, MJ. "Sequenciação de nova geração: o paradigma dos parasitas". Boletim Epidemiológico - Observações 7 10 (2018): 34-37.
    Published
  106. Gomes, João. "The Environmental Acinetobacter baumannii Isolate DSM30011 Reveals Clues into the Preantibiotic Era Genome Diversity, Virulence Potential, and Niche Range of a Predominant Nosocomial Pathogen". Genome Biol Evol (2017):
    10.1093/gbe/evx162
  107. Gomes, João. "Insights on Klebsiella pneumoniae Biofilms Assembled on Different Surfaces Using Phenotypic and Genotypic Approaches". Microorganisms (2017): http://www.mdpi.com/2076-2607/5/2/16.
    10.3390/microorganisms5020016
  108. Pinto M; Antelo M; Ferreira R; Azevedo J; Santo I; Borrego MJ; Gomes JP. "A retrospective cross-sectional quantitative molecular approach in biological samples from patients with syphilis.". (2017): http://europepmc.org/abstract/med/28161356.
    10.1016/j.micpath.2017.01.059
  109. Vilares A; Gargaté MJ; Ferreira I; Martins S; Gomes JP. "Molecular and virulence characterization of Toxoplasma gondii strains isolated from humans in Portugal.". (2017): http://europepmc.org/abstract/med/28138769.
    10.1007/s00436-017-5374-5
  110. Vale FF; Nunes A; Oleastro M; Gomes JP; Sampaio DA; Rocha R; Vítor JM; et al. "Genomic structure and insertion sites of Helicobacter pylori prophages from various geographical origins.". (2017): http://europepmc.org/abstract/med/28205536.
    10.1038/srep42471
  111. Silva, B.; Nunes, A.; Vale, F.F.; Rocha, R.; Gomes, J.P.; Dias, R.; Oleastro, M.. "The expression of Helicobacter pylori tfs plasticity zone cluster is regulated by pH and adherence, and its composition is associated with differential gastric IL-8 secretion". Helicobacter 22 4 (2017): http://www.scopus.com/inward/record.url?eid=2-s2.0-85018921135&partnerID=MN8TOARS.
    10.1111/hel.12390
  112. Ferreira, R.; Borges, V.; Borrego, M.J.; Gomes, J.P.. "Global survey of mRNA levels and decay rates of Chlamydia trachomatis trachoma and lymphogranuloma venereum biovars". Heliyon 3 7 (2017): http://www.scopus.com/inward/record.url?eid=2-s2.0-85025705502&partnerID=MN8TOARS.
    10.1016/j.heliyon.2017.e00364
  113. Gomes, João. "Genome-scale analysis of the non-cultivable Treponema pallidum reveals extensive within-patient genetic variation.". Nature Microbiology (2016): http://europepmc.org/abstract/med/27748767.
    10.1038/nmicrobiol.2016.190
  114. Gomes, João. "Toxoplasma gondii seroprevalence in the Portuguese population: comparison of three cross-sectional studies spanning three decades.". BMJ Open (2016): http://europepmc.org/abstract/med/27707823.
    10.1136/bmjopen-2016-011648
  115. Gomes, João. "In Vitro Activity of Quaternary Ammonium Surfactants against Streptococcal, Chlamydial, and Gonococcal Infective Agents.". Antimicrobial Agents and Chemotherapy (2016): http://europepmc.org/abstract/med/26976875.
    10.1128/AAC.00166-16
  116. Gomes, João. "The inhibition of the apoptosis pathway by the Coxiella burnetii effector protein CaeA requires the EK repetition motif, but is independent of survivin.". Virulence (2016): http://europepmc.org/abstract/med/26760129.
    10.1080/21505594.2016.1139280
  117. Gomes, João. "Probable Person-to-Person Transmission of Legionnaires' Disease.". New England Journal of Medicine (2016): http://europepmc.org/abstract/med/26840151.
    10.1056/NEJMc1505356
  118. George, F.; Shivaji, T.; Pinto, C.S.; Serra, L.A.O.; Valente, J.; Albuquerque, M.J.; Vicêncio, P.C.O.; et al. "A large outbreak of Legionnaires’ Disease in an industrial town in Portugal | Um grande surto da Doença dos Legionários numa cidade industrial em Portugal". Revista Portuguesa de Saude Publica 34 3 (2016): 199-208. http://www.scopus.com/inward/record.url?eid=2-s2.0-85002428359&partnerID=MN8TOARS.
    10.1016/j.rpsp.2016.10.001
  119. Gomes, João. "A Multi-Component Prime-Boost Vaccination Regimen with a Consensus MOMP Antigen Enhances Chlamydia trachomatis Clearance.". Front Immunol (2016): http://europepmc.org/abstract/med/27199987.
    10.3389/fimmu.2016.00162
  120. Gomes, João. "Legionella pneumophila strain associated with the first evidence of person-to-person transmission of Legionnaires' disease: a unique mosaic genetic backbone.". Scientific Reports (2016): http://europepmc.org/abstract/med/27196677.
    10.1038/srep26261
  121. Gomes, João. "Burkholderia pseudomallei: First case of melioidosis in Portugal.". ID Cases (2016): http://europepmc.org/abstract/med/26962474.
    10.1016/j.idcr.2016.01.004
  122. George, Francisco; Shivaji, Tara; Pinto, Catia Sousa; Serra, Luis Antonio Oliveira; Valente, João; Albuquerque, Maria João; Vicêncio, Paula Cristina Olivença; et al. "A large outbreak of Legionnaires¿ Disease in an industrial town in Portugal". (2016): http://hdl.handle.net/10362/22882.
  123. Gomes, João. "Quaternary ammonium surfactant structure determines selective toxicity towards bacteria: mechanisms of action and clinical implications in antibacterial prophylaxis.". J Antimicrob Chemother (2015):
    10.1093/jac/dkv405
  124. Gomes, João. "Bioinformatic Analysis of Chlamydia trachomatis Polymorphic Membrane Proteins PmpE, PmpF, PmpG and PmpH as Potential Vaccine Antigens.". PLoS One (2015): http://europepmc.org/abstract/med/26131720.
    10.1371/journal.pone.0131695
  125. Gomes, João. "Chlamydia trachomatis In Vivo to In Vitro Transition Reveals Mechanisms of Phase Variation and Down-Regulation of Virulence Factors.". PLoS One (2015): http://europepmc.org/abstract/med/26207372.
    10.1371/journal.pone.0133420
  126. Gomes, João. "In silico scrutiny of genes revealing phylogenetic congruence with clinical prevalence or tropism properties of Chlamydia trachomatis strains". G3 (Bethesda) (2015): http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4291473/pdf/9.pdf.
    10.1534/g3.114.015354
  127. Gomes, João; Nunes A; Rocha R; Vale FF; Vieira L; Sampaio DA; Dias R; Gomes JP; Oleastro M. "Genome Sequencing of 10 Helicobacter pylori Pediatric Strains from Patients with Nonulcer Dyspepsia and Peptic Ulcer Disease". Genome Announc (2015): http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4319599/pdf/e01488-14.pdf.
    10.1128/genomeA.01488-14.
  128. Gomes, João; Borges, V.; Gomes, J.P.. "Deep comparative genomics among Chlamydia trachomatis lymphogranuloma venereum isolates highlights genes potentially involved in pathoadaptation". Infect Genet Evol 32 (2015): 74-88. http://ac.els-cdn.com/S1567134815000696/1-s2.0-S1567134815000696-main.pdf?_tid=994b7552-f4e1-11e4-aa98-00000aacb360&acdnat=1431021230_7cfa4a5e37f4fbeaf021f382ce91ca5e.
    10.1016/j.meegid.2015.02.026.
  129. Borges, V.; Santos, A.; Correia, C.B.; Saraiva, M.; Ménard, A.; Vieira, L.; Sampaio, D.A.; et al. "Helicobacter pullorum isolated from fresh chicken meat: Antibiotic resistance and genomic traits of an emerging foodborne pathogen". Applied and Environmental Microbiology 81 23 (2015): 8155-8163. http://www.scopus.com/inward/record.url?eid=2-s2.0-84946043264&partnerID=MN8TOARS.
    10.1128/AEM.02394-15
  130. Repizo, G.D.; Gagné, S.; Foucault-Grunenwald, M.-L.; Borges, V.; Charpentier, X.; Limansky, A.S.; Gomes, J.P.; Viale, A.M.; Salcedo, S.P.. "Differential role of the T6SS in acinetobacter baumannii virulence". PLoS ONE 10 9 (2015): http://www.scopus.com/inward/record.url?eid=2-s2.0-84946906380&partnerID=MN8TOARS.
    10.1371/journal.pone.0138265
  131. Vítor, Borges; Santos, Andrea; Correia, Cristina Belo; Saraiva, Margarida; Vieira, Luís; Sampaio, Daniel A.; Gomes, João Paulo; Oleastro, Mónica. "Isolamento de Helicobacter pullorum de carne de frango: características de um patogénio emergente de origem alimentar". (2015): http://hdl.handle.net/10400.18/3238.
  132. Silveira, Leonor; Casimiro, Ana; Pinto, Margarida; Borges, Vítor; Gomes, João Paulo; Oleastro, Mónica. "Sequenciação de Nova Geração no apoio à decisão de transplante pulmonar num doente com fibrose quística". (2015): http://hdl.handle.net/10400.18/3235.
  133. Gomes, João. "Accuracy of prenatal culture in predicting intrapartum group B streptococcus colonization status". J Matern Fetal Neonatal Med (2014):
    10.3109/14767058.2013.820700
  134. Da Cunha, M.; Milho, C.; Almeida, F.; Pais, S.V.; Borges, V.; Maurício, R.; Borrego, M.J.; Gomes, J.P.; Mota, L.J.. "Identification of type III secretion substrates of Chlamydia trachomatis using Yersinia enterocolitica as a heterologous system". BMC Microbiol 14 1 (2014): http://www.scopus.com/inward/record.url?eid=2-s2.0-84894609856&partnerID=MN8TOARS.
    10.1186/1471-2180-14-40
  135. Nunes, A.; Gomes, J.P.. "Evolution, phylogeny, and molecular epidemiology of Chlamydia". Infect Genet Evol 23 (2014): 49-64. http://www.scopus.com/inward/record.url?eid=2-s2.0-84894045050&partnerID=MN8TOARS.
    10.1016/j.meegid.2014.01.029
  136. Gomes, João. "Isolation and molecular characterization of Toxoplasma gondii isolated from pigeons and stray cats in Lisbon, Portugal". Vet Parasitol (2014):
    10.1016/j.vetpar.2014.08.006
  137. Waap, H.; Gomes, J.; Nunes, T.. "Parasite communities in stray cat populations from Lisbon, Portugal". Journal of Helminthology 88 4 (2014): 389-395. http://www.scopus.com/inward/record.url?eid=2-s2.0-84908576606&partnerID=MN8TOARS.
    10.1017/S0022149X1300031X
  138. Borges, V.; Pinheiro, M.; Vieira, L.; Sampaio, D.A.; Nunes, A.; Borrego, M.J.; Gomes, J.P.; et al. "Complete genome sequence of Chlamydia trachomatis ocular serovar C strain TW-3". Genome Announcements 2 1 (2014): http://www.scopus.com/inward/record.url?eid=2-s2.0-84999040426&partnerID=MN8TOARS.
    10.1128/genomeA.e01204-13
  139. Gomes, João. "Optimization of fluorescent tools for cell biology studies in Gram-positive bacteria.". PLoS One (2014): http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4252051/pdf/pone.0113796.pdf.
    10.1371/journal.pone.0113796
  140. Henriques, M.X.; Catalão, M.J.; Figueiredo, J.; Gomes, J.P.; Filipe, S.R.. "Construction of Improved Tools for Protein Localization Studies in Streptococcus pneumoniae". PLoS One 8 1 (2013): http://www.scopus.com/inward/record.url?eid=2-s2.0-84872819538&partnerID=MN8TOARS.
    10.1371/journal.pone.0055049
  141. Silva, S.; Henriques, R.; Borrego, M.J.; Gomes, J.P.; Afonso, E.. "Congenital neurosyphilis - Authors' reply". Lancet Infect Dis 13 6 (2013): 475-476. http://www.scopus.com/inward/record.url?eid=2-s2.0-84878434756&partnerID=MN8TOARS.
    10.1016/S1473-3099(13)70123-3
  142. Borges, V.; Ferreira, R.; Nunes, A.; Sousa-Uva, M.; Abreu, M.; Borrego, M.J.; Gomes, J.P.. "Effect of long-term laboratory propagation on Chlamydia trachomatis genome dynamics". Infect Genet Evol 17 (2013): 23-32. http://www.scopus.com/inward/record.url?eid=2-s2.0-84876718480&partnerID=MN8TOARS.
    10.1016/j.meegid.2013.03.035
  143. Nunes, A.; Borrego, M.J.; Gomes, J.P.. "Genomic features beyond Chlamydia trachomatis phenotypes: What do we think we know?". Infect Genet Evol 16 (2013): 392-400. http://www.scopus.com/inward/record.url?eid=2-s2.0-84876332372&partnerID=MN8TOARS.
    10.1016/j.meegid.2013.03.018
  144. Ferreira, R.; Borges, V.; Nunes, A.; Borrego, M.J.; Gomes, J.P.. "Assessment of the load and transcriptional dynamics of Chlamydia trachomatis plasmid according to strains' tissue tropism". Microbiol Res 168 6 (2013): 333-339. http://www.scopus.com/inward/record.url?eid=2-s2.0-84878116662&partnerID=MN8TOARS.
    10.1016/j.micres.2013.02.001
  145. Filipe Almeida, F.; Borges, V.; Ferreira, R.; Borrego, M.J.; Gomes, J.P.; Jaime Motaa, L.J.. "Polymorphisms in inc proteins and differential expression of inc genes among Chlamydia trachomatis strains correlate with invasiveness and tropism of Lymphogranuloma venereum isolates". J Bacteriol 194 23 (2012): 6574-6585. http://www.scopus.com/inward/record.url?eid=2-s2.0-84871046599&partnerID=MN8TOARS.
    10.1128/JB.01428-12
  146. Florindo, C.; Ferreira, R.; Borges, V.; Spellerberg, B.; Gomes, J.P.; Borrego, M.J.. "Selection of reference genes for real-time expression studies in Streptococcus agalactiae". J Microbiol Methods 90 3 (2012): 220-227. http://www.scopus.com/inward/record.url?eid=2-s2.0-84864107293&partnerID=MN8TOARS.
    10.1016/j.mimet.2012.05.011
  147. Gomes, J.P.; Gomes JP. "Genomic stability of genotyping markers in Chlamydia trachomatis.". Front Cell Infect Microbiol 2 (2012): http://www.scopus.com/inward/record.url?eid=2-s2.0-84890560903&partnerID=MN8TOARS.
    10.3389/fcimb.2012.00077
  148. Ferreira, R.; Borges, V.; Nunes, A.; Nogueira, P.J.; Borrego, M.J.; Gomes, J.P.. "Impact of loci nature on estimating recombination and mutation rates in Chlamydia trachomatis.". G3 (Bethesda, Md.) 2 7 (2012): 761-768. http://www.scopus.com/inward/record.url?eid=2-s2.0-84870496314&partnerID=MN8TOARS.
    10.1534/g3.112.002923
  149. Silva, S.; Henriques, R.; Gomes, J.P.; Borrego, M.J.; Afonso, E.. "Could we miss congenital neurosyphilis?". Lancet Infect Dis 12 10 (2012): http://www.scopus.com/inward/record.url?eid=2-s2.0-84866596761&partnerID=MN8TOARS.
    10.1016/S1473-3099(12)70059-2
  150. Borges, V.; Nunes, A.; Ferreira, R.; Borrego, M.J.; Gomes, J.P.. "Directional evolution of chlamydia trachomatis towards niche-specific adaptation". J Bacteriol 194 22 (2012): 6143-6153. http://www.scopus.com/inward/record.url?eid=2-s2.0-84869132655&partnerID=MN8TOARS.
    10.1128/JB.01291-12
  151. Jorge, A.M.; Hoiczyk, E.; Gomes, J.P.; Pinho, M.G.. "EzrA contributes to the regulation of cell size in Staphylococcus aureus". PLoS One 6 11 (2011): http://www.scopus.com/inward/record.url?eid=2-s2.0-81055124808&partnerID=MN8TOARS.
    10.1371/journal.pone.0027542
  152. Santo, I.; Azevedo, J.; Nunes, B.; Gomes, J.P.; Borrego, M.J.. "Partner notification for chlamydia trachomatis urogenital infections: Eight years of patient referral experience in the major Portuguese sexually transmitted infections clinic, 2000-07". Int J STD AIDS 22 10 (2011): 548-551. http://www.scopus.com/inward/record.url?eid=2-s2.0-80054739545&partnerID=MN8TOARS.
    10.1258/ijsa.2011.010268
  153. Florindo, C.; Gomes, J.P.; Rato, M.G.; Bernardino, L.; Spellerberg, B.; Santos-Sanches, I.; Borrego, M.J.. "Molecular epidemiology of group B streptococcal meningitis in children beyond the neonatal period from Angola". J Med Microbiol 60 9 (2011): 1276-1280. http://www.scopus.com/inward/record.url?eid=2-s2.0-80051774001&partnerID=MN8TOARS.
    10.1099/jmm.0.031674-0
  154. Florindo, C.; Viegas, S.; Paulino, A.; Rodrigues, E.; Gomes, J.P.; Borrego, M.J.. "Molecular characterization and antimicrobial susceptibility profiles in Streptococcus agalactiae colonizing strains: Association of erythromycin resistance with subtype III-1 genetic clone family". Clin Microbiol Infect 16 9 (2010): 1458-1463. http://www.scopus.com/inward/record.url?eid=2-s2.0-77956104971&partnerID=MN8TOARS.
    10.1111/j.1469-0691.2010.03106.x
  155. Florindo, C.; Pereira, R.; Boura, M.; Nunes, B.; Paulino, A.; Gomes, J.P.; Borrego, M.J.. "Genotypes and antimicrobial-resistant phenotypes of Neisseria gonorrhoeae in Portugal (2004-2009)". Sex Transm Infect 86 6 (2010): 449-453. http://www.scopus.com/inward/record.url?eid=2-s2.0-78449256736&partnerID=MN8TOARS.
    10.1136/sti.2010.044321
  156. Borges, V.; Ferreira, R.; Nunes, A.; Nogueira, P.; Borrego, M.J.; Gomes, J.P.. "Normalization strategies for real-time expression data in Chlamydia trachomatis". J Microbiol Methods 82 3 (2010): 256-264. http://www.scopus.com/inward/record.url?eid=2-s2.0-77955664179&partnerID=MN8TOARS.
    10.1016/j.mimet.2010.06.013
  157. Oleastro, M.; Cordeiro, R.; Ménard, A.; Gomes, J.P.. "Allelic diversity among helicobacter pylori outer membrane protein genes homB and homA generated by recombination". J Bacteriol 192 15 (2010): 3961-3968. http://www.scopus.com/inward/record.url?eid=2-s2.0-77955294797&partnerID=MN8TOARS.
    10.1128/JB.00395-10
  158. Nunes, A.; Nogueira, P.J.; Borrego, M.J.; Gomes, J.P.. "Adaptive evolution of the Chlamydia trachomatis dominant antigen reveals distinct evolutionary scenarios for B- and T-cell epitopes: Worldwide survey". PLoS One 5 10 (2010): http://www.scopus.com/inward/record.url?eid=2-s2.0-78049304748&partnerID=MN8TOARS.
    10.1371/journal.pone.0013171
  159. Santos, A.M.; Oliver, M.J.; Sánchez, A.M.; Payton, P.R.; Gomes, J.P.; Miguel, C.; Oliveira, M.M.. "An integrated strategy to identify key genes in almond adventitious shoot regeneration". J Exp Bot 60 14 (2009): 4159-4173. http://www.scopus.com/inward/record.url?eid=2-s2.0-70349667462&partnerID=MN8TOARS.
    10.1093/jxb/erp250
  160. Dean, D.; Bruno, W.J.; Wan, R.; Gomes, J.P.; Devignot, S.; Mehari, T.; De Vries, H.J.C.; et al. "Predicting phenotype and emerging strains among Chlamydia trachomatis infections". Emerg Infect Dis 15 9 (2009): 1385-1394. http://www.scopus.com/inward/record.url?eid=2-s2.0-70249142557&partnerID=MN8TOARS.
    10.3201/eid1509.090272
  161. Nunes, A.; Borrego, M.J.; Nunes, B.; Florindo, C.; Gomes, J.P.. "Evolutionary dynamics of ompA, the gene encoding the Chlamydia trachomatis key antigen". J Bacteriol 191 23 (2009): 7182-7192. http://www.scopus.com/inward/record.url?eid=2-s2.0-72249105320&partnerID=MN8TOARS.
    10.1128/JB.00895-09
  162. Gomes, J.P.; Nunes, A.; Florindo, C.; Ferreira, M.A.; Santo, I.; Azevedo, J.; Borrego, M.J.. "Lymphogranuloma venereum in Portugal: Unusual events and new variants during 2007". Sex Transm Dis 36 2 (2009): 88-91. http://www.scopus.com/inward/record.url?eid=2-s2.0-60749116915&partnerID=MN8TOARS.
    10.1097/OLQ.0b013e31818b1e27
  163. Nunes, A.; Nogueira, P.J.; Borrego, M.J.; Gomes, J.P.. "Chlamydia trachomatis diversity viewed as a tissue-specific coevolutionary arms race". Genome Biol 9 10 (2008): http://www.scopus.com/inward/record.url?eid=2-s2.0-55649084373&partnerID=MN8TOARS.
    10.1186/gb-2008-9-10-r153
  164. Florindo, C.; Reigado, V.; Gomes, J.P.; Azevedo, J.; Santo, I.; Borrego, M.J.. "Molecular typing of Treponema pallidum clinical strains from Lisbon, Portugal". J Clin Microbiol 46 11 (2008): 3802-3803. http://www.scopus.com/inward/record.url?eid=2-s2.0-55849093187&partnerID=MN8TOARS.
    10.1128/JCM.00128-08
  165. Nunez, A.; Gomes, J.P.; Mead, S.; Florindo, C.; Correia, H.; Borrego, M.J.; Dean, D.. "Comparative expression profiling of the Chlamydia trachomatis pmp gene family for clinical and reference strains". PLoS One 2 9 (2007): http://www.scopus.com/inward/record.url?eid=2-s2.0-41149101849&partnerID=MN8TOARS.
    10.1371/journal.pone.0000878
  166. Gomes, J.P.; Bruno, W.J.; Nunes, A.; Santos, N.; Florindo, C.; Borrego, M.J.; Dean, D.. "Evolution of Chlamydia trachomatis diversity occurs by widespread interstrain recombination involving hotspots". Genome Res 17 1 (2007): 50-60. http://www.scopus.com/inward/record.url?eid=2-s2.0-33845965685&partnerID=MN8TOARS.
    10.1101/gr.5674706
  167. Gomes, J.P.; Borrego, M.J.; Atik, B.; Santo, I.; Azevedo, J.; Brito De Sá, A.; Nogueira, P.; Dean, D.. "Correlating Chlamydia trachomatis infectious load with urogenital ecological success and disease pathogenesis". Microbes Infect 8 1 (2006): 16-26. http://www.scopus.com/inward/record.url?eid=2-s2.0-31344431835&partnerID=MN8TOARS.
    10.1016/j.micinf.2005.05.014
  168. Gomes, J.P.; Nunes, A.; Bruno, W.J.; Borrego, M.J.; Florindo, C.; Dean, D.. "Polymorphisms in the nine polymorphic membrane proteins of Chlamydia trachomatis across all serovars: Evidence for serovar da recombination and correlation with tissue tropism". J Bacteriol 188 1 (2006): 275-286. http://www.scopus.com/inward/record.url?eid=2-s2.0-33644880273&partnerID=MN8TOARS.
    10.1128/JB.188.1.275-286.2006
  169. Gomes, J.P.; Hsia, R.-C.; Mead, S.; Borrego, M.J.; Dean, D.. "Immunoreactivity and differential developmental expression of known and putative Chlamydia trachomatis membrane proteins for biologically variant serovars representing distinct disease groups". Microbes Infect 7 3 (2005): 410-420. http://www.scopus.com/inward/record.url?eid=2-s2.0-18044381715&partnerID=MN8TOARS.
    10.1016/j.micinf.2004.11.014
  170. Gomes, J.P.; Bruno, W.J.; Borrego, M.J.; Dean, D.. "Recombination in the genome of Chlamydia trachomatis involving the polymorphic membrane protein C gene relative to ompA and evidence for horizontal gene transfer". J Bacteriol 186 13 (2004): 4295-4306. http://www.scopus.com/inward/record.url?eid=2-s2.0-3042565597&partnerID=MN8TOARS.
    10.1128/JB.186.13.4295-4306.2004
  171. De Sá, A.B.; Gomes, J.P.; Viegas, S.; Ferreira, M.A.; Paulino, A.; Catry, M.D.A.; Brito de Sá A; et al. "Genital infection by Chlamydia trachomatis in Lisbon: Prevalence and risk markers". Fam Pract 19 4 (2002): 362-364. http://www.scopus.com/inward/record.url?eid=2-s2.0-0036331175&partnerID=MN8TOARS.
    10.1093/fampra/19.4.362
  172. Gomes, J.P.; Viegas, S.; Paulino, A.; Catry, M.A.. "Sensitivity evaluation of the Gen-Probe AMP-CT assay by pooling urine samples for the screening of Chlamydia trachomatis urogenital infection". Int J STD AIDS 13 8 (2002): 540-542. http://www.scopus.com/inward/record.url?eid=2-s2.0-0036312871&partnerID=MN8TOARS.
    10.1258/095646202760159648
  173. Gomes, J.P.; Tavira, L.; Exposto, F.; Prieto, E.; Catry, M.A.. "Neisseria gonorrhoeae and Chlamydia trachomatis infections in patients attending STD and family planning clinics in Bissau, Guinea-Bissau". Acta Trop 80 3 (2001): 261-264. http://www.scopus.com/inward/record.url?eid=2-s2.0-0035930383&partnerID=MN8TOARS.
    10.1016/S0001-706X(01)00182-6
  174. Gomes, J.P.; Ferreira, M.A.; De Sá, A.B.; Catry, M.A.; Gomes JP; Ferreira MA; De Sá AB; Catry MA. "Pooling urine samples for PCR screening of C trachomatis urogenital infection in women [4]". Sex Transm Infect 77 1 (2001): 76-77. http://www.scopus.com/inward/record.url?eid=2-s2.0-0035136731&partnerID=MN8TOARS.
    10.1136/sti.77.1.76
  175. Borrego, M.J.; Gomes, J.P.; Lefebvre, J.F.; Eb, F.; Orfila, J.; Catry, M.A.; Borrego MJ; et al. "Genotyping of Portuguese Chlamydia trachomatis urogenital isolates". Genitourin Med 73 6 (1997): 561-563. http://www.scopus.com/inward/record.url?eid=2-s2.0-79959945890&partnerID=MN8TOARS.
    10.1136/sti.73.6.561
  176. Ferreira, E.; Louro, D.; Gomes, J.P.; Catry, M.A.; Vaz Pato, M.V.; Ferreira E; Louro D; et al. "High-level tetracycline resistant Neisseria gonorrhoeae isolated in Portugal". Pathol Biol 45 5 (1997): 371-375. http://www.scopus.com/inward/record.url?eid=2-s2.0-0030790505&partnerID=MN8TOARS.
Magazine article
  1. Campana, Sara; Fernandes, Gonçalo; Patrício, Rui; Alves, Margarida; Lecis, Roberta; Ropio, Joana; Valença, Andreia; et al. Corresponding author: Belas, Adriana. "Salmonella spp. serovars isolated from healthy Leopard geckos (Eublepharis macularius) in Lisbon, Portugal.", II FMVet Research Meetings 2023, 2024, https://doi.org/10.60543/rlcmv.v15i.9246.
Online resource
  1. Ribeiro, Miguel; Sousa, Margarida; Borges, Vítor; Gomes, João Paulo; Duarte, Sílvia; Isidro, Joana; Vieira, Luís; et al. Genomic, transcriptomic and proteomic comparison of MRSA CC398 isolates collected from human and wild animal samples (Genome assembly and annotation dataset). 2022. https://doi.org/10.5281/zenodo.6359891.
    10.5281/zenodo.6359891
Preprint
  1. Ferreira, Rita; Coelho, Luís; Santos, João Dourado; Sobral, Daniel; Isidro, Joana; Mixão, Verónica; Pinto, Miguel; et al. "Probe-based metagenomic pathogen detection: an added-value for complex diagnosis". 2025. https://doi.org/10.21203/rs.3.rs-6172021/v1.
    10.21203/rs.3.rs-6172021/v1
  2. Ana Balau; Daniel Sobral; Patrícia Abrantes; Inês Santos; Verónica Mixão; João Paulo Gomes; Sandra Antunes; Ana Paula Arez. "Differential Gene Expression of Malaria Parasite in Response to Red Blood Cell-Specific Glycolytic Intermediate 2,3-Diphosphoglycerate (2,3-DPG)". 2023. https://doi.org/10.20944/preprints202311.0790.v1.
    10.20944/preprints202311.0790.v1
  3. Áine O’Toole; Richard A. Neher; Nnaemeka Ndodo; Vitor Borges; Ben Gannon; João Paulo Gomes; Natalie Groves; et al. "Putative APOBEC3 deaminase editing in MPXV as evidence for sustained human transmission since at least 2016". 2023. https://doi.org/10.1101/2023.01.23.525187.
    10.1101/2023.01.23.525187
  4. Santos, João Dourado; Sobral, Daniel; Pinheiro, Miguel; Isidro, Joana; Bogaardt, Carlijn; Pinto, Miguel; Eusébio, Rodrigo; et al. "INSaFLU-TELEVIR: an open web-based bioinformatics suite for viral metagenomic detection and routine genomic surveillance". 2023. http://dx.doi.org/10.21203/rs.3.rs-3556988/v1.
    10.21203/rs.3.rs-3556988/v1
  5. Irina Kislaya; André Peralta-Santos; Vítor Borges; Luís Vieira; Carlos Sousa; Bibiana Ferreira; Ana Pelerito; et al. "Comparative complete scheme and booster effectiveness of COVID-19 vaccines in preventing SARS-CoV-2 infections with SARS-CoV-2 Omicron (BA.1) and Delta (B.1.617.2) variants". 2022. https://doi.org/10.1101/2022.01.31.22270200.
    10.1101/2022.01.31.22270200
  6. André Peralta-Santos; Eduardo Freire Rodrigues; Joana Moreno; Vasco Ricoca; Pedro Casaca; Eugenia Fernandes; João Paulo Gomes; et al. "Omicron (BA.1) SARS-CoV-2 variant is associated with reduced risk of hospitalization and length of stay compared with Delta (B.1.617.2)". 2022. https://doi.org/10.1101/2022.01.20.22269406.
    10.1101/2022.01.20.22269406
  7. Verónica Mixão; Miguel Pinto; Daniel Sobral; Adriano Di Pasquale; João Paulo Gomes; Vitor Borges. "ReporTree: a surveillance-oriented tool to strengthen the linkage between pathogen genetic clusters and epidemiological data". 2022. https://doi.org/10.21203/rs.3.rs-1404655/v2.
    10.21203/rs.3.rs-1404655/v2
  8. João Paulo Gomes; Joana Isidro; Vitor Borges; Miguel Pinto; Daniel Sobral; João Santos; Verónica Mixão; et al. "Multi-country outbreak of monkeypox virus: phylogenomic characterization and signs of microevolution". 2022. https://doi.org/10.21203/rs.3.rs-1700947/v1.
    10.21203/rs.3.rs-1700947/v1
Report
  1. Llarena, Ann-Katrin; Ribeiro-Gonçalves, Bruno Filipe; Nuno Silva, Diogo; Halkilahti, Jani; Machado, Miguel Paulo; Da Silva, Mickael Santos; Jaakkonen, Anniina; et al. 2018. INNUENDO: A cross-sectoral platform for the integration of genomics in the surveillance of food-borne pathogens. http://dx.doi.org/10.2903/sp.efsa.2018.en-1498.
    10.2903/sp.efsa.2018.en-1498

Other

Dataset
  1. Mixão, Verónica; Brendebach, Holger; Pinto, Miguel; Sobral, Daniel; Gomes, João Paulo; Deneke, Carlus; Tausch, Simon; Borges, Vítor. Genome assemblies and respective wg/cgMLST profiles of a diverse dataset comprising 1,999 Escherichia coli isolates. https://zenodo.org/record/7230102#.Y-fuTi0qJQI.
    https://doi.org/10.5281/zenodo.7120057
  2. Mixão, Verónica; Brendebach, Holger; Pinto, Miguel; Sobral, Daniel; Gomes, João Paulo; Deneke, Carlus; Tausch, Simon; Borges, Vítor. Genome assemblies and respective wg/cgMLST profiles of a diverse dataset comprising 1,434 Salmonella enterica isolates. https://zenodo.org/record/7230091#.Y-fvrC0qJQI.
    https://doi.org/10.5281/zenodo.7119735
  3. Mixão, Verónica; Brendebach, Holger; Pinto, Miguel; Sobral, Daniel; Gomes, João Paulo; Deneke, Carlus; Tausch, Simon; Borges, Vítor. Genome assemblies and respective wg/cgMLST profiles of a diverse dataset comprising 3,076 Campylobacter jejuni isolates. https://zenodo.org/record/7230105#.Y-ftJi0qJQI.
    https://doi.org/10.5281/zenodo.7120166
Other output
  1. SARS-CoV-2 BA.5 vaccine breakthrough risk and severity compared with BA.2: a case-case and cohort study using Electronic Health Records in Portugal. 2022. Kislaya, I.; Casaca, P.; Borges, V.; Sousa, C.; Ferreira, B.I.; Fernandes, E.; Dias, C.M.; et al. http://www.scopus.com/inward/record.url?eid=2-s2.0-85135818426&partnerID=MN8TOARS.
    10.1101/2022.07.25.22277996
  2. B.1.617.2 SARS-CoV-2 (Delta) variant is associated with increased risk of hospitalization and death compared with B.1.1.7 SARS-CoV-2 (Alpha) variant. 2022. Rodrigues, E.F.; Moreno, J.; Leite, P.P.; Casaca, P.; Nunes, B.; Gomes, J.P.; Ferreira, R.; et al. http://www.scopus.com/inward/record.url?eid=2-s2.0-85125200512&partnerID=MN8TOARS.
    10.1101/2022.01.21.22268602
  3. Development of an amplicon-based sequencing approach in response to the global emergence of human monkeypox virus. 2022. Chen, N.F.G.; Chaguza, C.; Gagne, L.; Doucette, M.; Smole, S.; Buzby, E.; Hall, J.; et al. http://www.scopus.com/inward/record.url?eid=2-s2.0-85147725054&partnerID=MN8TOARS.
    10.1101/2022.10.14.22280783
  4. Delta variant and mRNA Covid-19 vaccines effectiveness: higher odds of vaccine infection breakthroughs. 2021. Irina Kislaya; Eduardo Freire Rodrigues; Vítor Borges; João Paulo Gomes; Carlos Sousa; José Pedro Almeida; André Peralta-Santos; Baltazar Nunes. https://doi.org/10.1101/2021.08.14.21262020.
    10.1101/2021.08.14.21262020
  5. Increased Antibacterial Properties of Indoline-Derived Phenolic Mannich Bases. European Journal of Medicinal Chemistry. 2021. Tatu Rimpilainen; Alexandra Nunes; Rita Calado; Ana Fernandes; Joana Andrade; Epole Ngolle; Gabriella Spengler; et al. https://doi.org/10.26434/chemrxiv.14184929.
    10.26434/chemrxiv.14184929.v1
  6. The early dynamics of the SARS-CoV-2 epidemic in Portugal. 2021. Borges, V.; Isidro, J.; Trovão, N.S.; Duarte, S.; Cortes-Martins, H.; Martiniano, H.; Gordo, I.; et al. http://www.scopus.com/inward/record.url?eid=2-s2.0-85104089441&partnerID=MN8TOARS.
    10.1101/2021.02.22.21252216
  7. Nosocomial outbreak of SARS-CoV-2 in a “non-COVID-19” hospital ward: Virus genome sequencing as a key tool to understand cryptic transmission. 2021. Borges, V.; Isidro, J.; Macedo, F.; Neves, J.; Silva, L.; Paiva, M.; Barata, J.; et al. http://www.scopus.com/inward/record.url?eid=2-s2.0-85102362538&partnerID=MN8TOARS.
    10.1101/2021.02.20.20248421
  8. Genomic insights on DNase production in Streptococcus agalactiae ST17 and ST19 strains. 2020. Inês Silvestre; Alexandra Nunes; Vítor Borges; Joana Isidro; Catarina Silva; Luís Vieira; João Paulo Gomes; Maria José Borrego. https://doi.org/10.1101/2020.12.09.418327.
    10.1101/2020.12.09.418327
  9. Global gene expression analysis of Streptococcus agalactiae at exponential growth phase. 2020. Inês Silvestre; Vítor Borges; Sílvia Duarte; Alexandra Nunes; Rita Sobral; Luís Vieira; João Paulo Gomes; Maria José Borrego. https://doi.org/10.1101/2020.11.13.381939.
    10.1101/2020.11.13.381939
  10. On the track of the D839Y mutation in the SARS-CoV-2 Spike fusion peptide: Emergence and geotemporal spread of a highly prevalent variant in Portugal. 2020. Borges, V.; Isidro, J.; Cortes-Martins, H.; Duarte, S.; Vieira, L.; Leite, R.; Gordo, I.; et al. http://www.scopus.com/inward/record.url?eid=2-s2.0-85098615611&partnerID=MN8TOARS.
    10.1101/2020.08.10.20171884
  11. Virulence and antibiotic resistance plasticity of Arcobacter butzleri: Insights on the genomic diversity of an emerging human pathogen. 2019. Isidro, J.; Ferreira, S.; Pinto, M.; Domingues, F.; Oleastro, M.; Gomes, J.P.; Borges, V.. http://www.scopus.com/inward/record.url?eid=2-s2.0-85095498643&partnerID=MN8TOARS.
    10.1101/775932
  12. Chlamydia trachomatis outbreak: When the virulence-associated genome backbone imports a prevalence-associated major antigen signature. 2019. Borges, V.; Cordeiro, D.; Salas, A.I.; Lodhia, Z.; Correia, C.; Isidro, J.; Fernandes, C.; et al. http://www.scopus.com/inward/record.url?eid=2-s2.0-85095498809&partnerID=MN8TOARS.
    10.1101/622324
  13. INSaFLU: An automated open web-based bioinformatics suite “from-reads” for influenza whole-genome-sequencing-based surveillance. 2018. Borges, V.; Pinheiro, M.; Pechirra, P.; Guiomar, R.; Gomes, J.P.. http://www.scopus.com/inward/record.url?eid=2-s2.0-85095541592&partnerID=MN8TOARS.
    10.1101/253161
  14. Whole genome analysis of influenza A(H3) viruses detected between 2016-2018 in the scope of EuroEVA/I-MOVE vaccine effectiveness study. Abstract publicado em: https://www.escaide.eu/sites/escaide/files/documents/book_escaide2018_updated-dec-2018.pdf. Background: NGS techniques, allow a much deeper genetic analysis of influenza viruses, compared to traditional Sanger sequencing of hemagglutinin gene. The present study aims to perform phylogenetic and mutational analysis at whole-genome level in order to search for genetic features. 2018. Pechirra, Pedro; Borges, Vítor; Cristóvão, Paula; Costa, Inês; Conde, Patrícia; Machado, Ausenda; Rodrigues, Ana Paula; et al. http://hdl.handle.net/10400.18/5856.
Software
  1. Mixão, Verónica; Pinto, Miguel; Sobral, Daniel; Di Pasquale, Adriano; Gomes, João Paulo; Borges, Vitor. "ReporTree". https://github.com/insapathogenomics/ReporTree. Instituto Nacional de Saúde Doutor Ricardo Jorge. Unix and Windows WSL. Available in Docker. 2023.
Activities

Oral presentation

Presentation title Event name
Host (Event location)
2025/05 Metagenomics: an added value for clinical decision in infectious diseases? 8th Luxembourg Microbiology Day
Luxembourg Institute of Health / Luxembourg Society for Microbiology
2025/04 METAGENÓMICA CLÍNICA: FERRAMENTA DE APOIO AO DIAGNÓSTICO COMPLEXO 17ª Reunião Científica da Sociedade Portuguesa de Medicina Laboratorial
Sociedade Portuguesa de Medicina Laboratorial
2025/02 Metagenómica: aplicação ao diagnóstico complexo Jornadas científicas de neurologia do Centro Hospitalar de Lisboa Ocidental
CHLO - Hospital Egas Moniz
2024/12 O papel da sequenciação genómica microbiana no conceito One Health JORNADAS DE INTERAÇÃO CIENTÍFICA
CECAV - UTAD (Portugal)
2024/11/13 Microbial genomics as a public health borderless compass for the detection and monitoring of emerging infectious agents and outbreak control 7th INTERNATIONAL CONFERENCE NOVA Health -“Tackling Pandemics: Strategies for Prevention, Preparedness and Response”
NOVA University (Portugal)
2024/09 A genómica dos micróbios como guia para a decisão em saúde Dia Internacional do Microrganismo
Instituto Superior Técnico (Portugal)
2024/09 O papel da genómica na caracterização e monitorização dos surtos do vírus mpox Mestrado
FCUL
2024/06/29 O papel da genómica na caracterização da 1ª e 2ª vaga do surto do vírus mpox em Portugal Reunião do Verão
Sociedade Portuguesa de Dermatologia e Venereologia (Évora, Portugal)
2024/05/10 Novas investigações: A metagenómica na procura do microrganismo escondido Reunião Temática de Vírus Respiratórios
Sociedade de Infeciologia Pediátrica (Aveiro, Portugal)
2024/05/02 Microbial genomics: the borderless compass of the One Health concept One Health TOXRUN International Congress
IUCS-CESPU (Portugal)
2024/05 Metagenómica: perspectivas de aplicação clínica Mestrado
Faculdade de Farmácia da Universidade de Coímbra (Portugal)
2024/04 Genotyping and its contributions for public health surveillance PUBLIC HEALTH DAYS OF DGS
Direção Geral da Saúde (Portugal)
2024/03 Os micróbios que há em nós. A metagenómica na procura do microrganismo escondido Microbioma Humano
Academia das Ciências de Lisboa (Portugal)
2023/03 Multi-country outbreak of mpox virus: genomics as a tool to identify genetic clustering, transmission dynamics and the role of Portugal in the international virus spread Bioinformatics Open Day
Universidade do Minho
2023 Variantes de SARS-CoV-2 e seu impacto: passado, presente e futuro Congresso Saúde Pública 23 – Uma Nova Era
(Portugal)
2023 Metagenómica: perspectivas de aplicação clínica Sessões Clínicas Hospitalares
Centro Hospitalar de Setúbal (Portugal)
2023 Epidemiologia molecular do vírus mpox em Portugal VI Congresso Nacional de Virologia
Sociedade Portuguesa de Virologia (Portugal)
2023 Metagenómica em controlo de infecção Encontro do Dia Mundial da Higiene das Mãos
Unidade Regional do Programa de Prevenção e Controlo de Infeções e de Resistência aos Antimicrobianos (UR PPCIRA) (Portugal)
2023 Papel da investigação do genoma viral na gestão do surto de mpox Fórum dos Conselhos Científicos dos Laboratórios de Estado
(Portugal)
2023 Multi-country outbreak of mpox virus: genomics as a tool to identify genetic clustering, transmission dynamics and the role of Portugal in the international virus spread Bioinformatics Open Days
UTAD (Portugal)
2022/12 Invited speaker by Astrazeneca. Presentation title: "The evolutionary pathway of SARS-CoV-2", on behalf of the "COVID-19 and Immunosupression" event.
Astrazeneca
2022/11 Metagenómica clínica – O futuro hoje? XV Congresso Nacional de Doenças Infeciosas e Microbiologia Clínica
2022/11 Evolução do SARS-CoV-2 e seu impacto na infecciosidade e doença 38º Congresso de Pneumologia
(Vilamoura)
2022/11 Pathogenomics e o seu papel na vigilância e investigação epidemiológica 3º Congresso Nacional da Unidade de Saúde Pública do ACES Baixo Vouga
(Ílhavo)
2022/04 Invited speaker by "Sociedade Portuguesa de Medicina Laboratorial". Presentation entitled: "Variantes do SARS-CoV-2: como lidar com uma evolução “sem rumo”? ", on behalf of the "14ª Reunião Científica da Sociedade Portuguesa de Medicina Laboratorial" 14ª Reunião Científica da Sociedade Portuguesa de Medicina Laboratorial
Sociedade Portuguesa de Medicina Laboratorial (Tomar)
2022/03 Invited speaker by Merck Sharp & Dohme and the Portuguese Society of Diabetes. Presentation entitled: "¿SARS-CoV-2 variants and their impact: past, present and future", on behalf of the National Congress of the Portuguese Society of Diabetes Congresso Nacional da Sociedade Portuguesa de Diabetologia.
Merck Sharp & Dohme and the Portuguese Society of Diabetes
2022/02 Invites speaker by "Ordem dos Médicos". Presentation entitled: “Caracterização genética do SARS-CoV-2 – impacto em Saúde Pública e decisão política”, on behalf of the III START PATOLOGIA CLÍNICA 2022. III START PATOLOGIA CLÍNICA 2022
Ordem dos Médicos
2022/02 Invited speaker by "Centro Hospitalar de Lisboa Central". Presentation entitled: "Viral variants and global distribution", on behalf of the "13.as Jornadas de Atualização em Doenças Infecciosas. 13.as Jornadas de Atualização em Doenças Infecciosas
CHLC
2022/01 Invited speaker by the University of Aveiro. Presentation entitled: “Two years of COVID-19 in Portugal: the impact of monitoring SARS-CoV-2 genetic diversity on Public Health and policy makers”, on behalf of the 1st Epiviral symposium. 1st Epiviral symposium
Universidade de Aveiro
2021/11 Invited speaker by the Portuguese Society of Pneumology. Presentation entitled: “Evolução do SARS-CoV-2 e seu impacto na infecciosidade e doença” on behalf of the 37º Congresso da Sociedade Portuguesa de Pneumologia, Praia da falésia. 37º Congresso da Sociedade Portuguesa de Pneumologia
2021/11 Invited speaker by the Portuguese Society of Microbiology. Presentation entitled: “SARS-CoV-2 variants - the steering wheel of public health and governments”, on behalf of Microbiotec2021 Meeting, Microbiotech in Health & Disease Section Microbiotec2021 Meeting
Portuguese Society of Microbiology
2021/07 Invited speaker by the Consortium Genome PT. Presentation entitled: “Genetic characterization of SARS-CoV-2: impact on public health and policy decision”. Genome PT symposium
2021/06 Invited speaker by the Universidade de Trás-os-Montes e Alto Douro. Presentation entitled: “SARS-COV-2 SEQUENCING: A Tool for Public Health and to Decipher Viral Adaptation to New Species”, on behalf of the International Conference NEW INSIGHTS AND CHALLENGES ONE HEALTH OF ZOONOTIC DISEASES International Conference NEW INSIGHTS AND CHALLENGES ONE HEALTH OF ZOONOTIC DISEASES
2021/05 Invited speaker by the "Ordem dos Médicos". Presentation entitled; " “Estudo da diversidade genética do SARS-CoV-2 (COVID-19) em Portugal”, on behalf of the 23º Congresso Nacional de Medicina (23CNMOM) 23º Congresso Nacional de Medicina (23CNMOM)
2021/04 Invited speaker by the European Molecular Biology Laboratory (EMBL). Presentation entitled: “Impact of monitoring SARS-CoV-2 variants in policy making”, on behalf of the International Conference “Emerging Infectious diseases and related environmental, clinical and translational challenges”. Emerging Infectious diseases and related environmental, clinical and translational challenges
European Molecular Biology Laboratory
2020 Invited speaker by the AICIB Agência de Investigação Clínica e Inovação Biomédica. Presentation entitled: ¿Study of SARS COV2 genetic diversity in Portugal", on behalf of the programme The Challenges for Clinical Research and Biomedical Innovation in a Time of Pandemic. The Challenges for Clinical Research and Biomedical Innovation in a Time of Pandemic
Agência de Investigação Clínica e Inovação Biomédica.
2020 Invited speaker by the Federation of European Microbiological Societies. Presentation entitled "Genomic diversity of the new coronavírus SARS-CoV-2 (COVID-19) in Portugal" on behalf of the International Microrganism Day 2020. International Microrganism Day 2020
Federation of European Microbiological Societies
2020 Invited speaker by the Genetics Portuguese Society. Presentation entitled: “SARS-CoV-2 genetic diversity as a tool to characterize the COVID-19 early epidemic in Portugal”.
Sociedade Portuguesa de Genética
2019/04 Invited speaker by the Iberian Nanotechnology Laboratory. Presentation entitled: “Novel approaches to better understand infectious diseases”, on behalf of the Health Cluster 2019 Meeting. Encontros com a Inovação em Saúde
2019 Invited speaker by the Faculty of Pharmacy (FFUP- AEICBAS). Presentation entitled: " The infectious diseases in the genomics era”, on behalf of the Biomedical Congress - Day of the microbiology laboratory. Biomedical Congress - Day of the microbiology laboratory.
FFUP- AEICBAS
2017 Invited speaker by the Portuguese Society of Microbiology. Presentation entitled: “Host-pathogen arms-race: the within-patient genetic variation of microbial pathogens on the course of infection”. on behalf of Microbiotec2017 Meeting. Microbiotec2017 Meeting.
2017 Invited speaker by agilent and Hospital Clinico de Barcelona. Presentation entitled: “Genome-scale analysis of Treponema pallidum reveals extensive within-patient genetic variation during syphilis"
Hospital Clínico de Barcelona
2016 Invited speaker by CEDOC (Center for the Study of Chronic Diseases). Presentation entitled: “Application of Next-Generation Sequencing (NGS) to the study of infectious diseases”, on behalf of Seminars promoted by CEDOC.
CEDOC

Supervision

Thesis Title
Role 		Degree Subject (Type)
Institution / Organization
2021 - 2023 Genomics of nontuberculous mycobacteria (NTM): development of a laboratory tool for rapid and precise diagnosis and surveillance of NTM infections
Co-supervisor of Sofia Carneiro
2019/07 - 2022/06 Decoding the Peptidoglycan Patterns associated with Beta-lactams Susceptibility and Host Immune Recognition in Drug-resistant Mycobacterium tuberculosis (SFRH/BD/136853/2018)
Co-supervisor of Francisco Olivença Miguel
Programa de doutoramento em medicação e inovação farmacêutica (I3DU) (PhD)
Universidade de Lisboa Faculdade de Farmácia, Portugal
2019 - 2022 Insights into the genomics features of invasive Neisseria meningitidis strains in Portugal
Co-supervisor of Célia Bettencourt
Instituto Nacional de Saúde Doutor Ricardo Jorge, Portugal
2016/10 - 2020/09 Genomics of Neisseria gonorrhoeae tropism and antimicrobial resistance (SFRH/BD/109264/2015)
Supervisor of Miguel Cascais Ferreira Pinto
 Biologia (PhD)
Instituto Nacional de Saúde Doutor Ricardo Jorge, Portugal
2015/10 - 2019/09 Phenotypic and genotypic characterization of Salmonella spp. isolates in Portugal
Supervisor of Leonor de Sousa Dâmaso da Silveira
Biologia (PhD)
Instituto Nacional de Saúde Doutor Ricardo Jorge, Portugal
2014/10 - 2019/09 Contribution for the knowledge of toxoplasmosis in Portugal
Supervisor of Maria João Gargaté
Biologia (PhD)
Instituto Nacional de Saúde Doutor Ricardo Jorge, Portugal
2014 - 2019/09 Genetic study of Toxoplasma gondii strains isolated from humans and animals
Supervisor of Anabela Barreiro Gomes Vilares Bendada Esteves
Biologia (PhD)
Universidade de Lisboa Faculdade de Ciências, Portugal

Instituto Nacional de Saúde Doutor Ricardo Jorge, Portugal
2015/10 - 2019/07 Tuberculosis: new era for diagnosis and surveillance using whole-genome sequencing-based approaches
Co-supervisor of Ana Rita Frazão Macedo Galésio
 Biologia (PhD)
Instituto Nacional de Saúde Doutor Ricardo Jorge, Portugal

Universidade Nova de Lisboa Faculdade de Ciências e Tecnologia, Portugal
2011/11 - 2015/09 Contribution for the understanding of the biological role of Chlamydia trachomatis plasmid (SFRH/BD/68532/2010)
Supervisor of Rita Susana Ferreira
Biologia (PhD)
Instituto Nacional de Saúde Doutor Ricardo Jorge, Portugal
2011/10 - 2015/07 Evolutionary dynamics of Chlamydia trachomatis genome and identification of the molecular patterns of hypothetical protein coding genes (SFRH/BD/68527/2010)
Supervisor of Vítor Monteiro Borges
Biologia (PhD)
Instituto Nacional de Saúde Doutor Ricardo Jorge, Portugal
2006/10 - 2010/09 Genomic and Transcriptomic Features of Chlamydia trachomatis (SFRH/BD/25651/2005)
Supervisor of Alexandra Isabel Cardoso Nunes
Biologia (PhD)
Instituto Nacional de Saúde Doutor Ricardo Jorge, Portugal

Jury of academic degree

Topic
Role 		Candidate name (Type of degree)
Institution / Organization
2024/12 Main arguer of the PhD dissertation: "Antimicrobial resistance phylodynamics and source attribution under a One Health framework".
(Thesis) Main arguer
 Beatriz Gameiro Ramos (PhD)
Universidade de Lisboa Faculdade de Ciências, Portugal
2019 Main arguer of the PhD dissertation entitled: Adaptation of Burkholderia cepacia complex bacteria to the cystic fibrosis lung: focus on lipopolysaccharide O-antigen and cell wall physical properties
(Thesis) Main arguer
 Ahmed Amir Elsayed Hassan (PhD)
Universidade de Lisboa Instituto Superior Técnico, Portugal
2018 Main arguer of the PhD dissertation: Carbapenemase producers of Pseudomonas aeruginosa: lights on new mobile genetic elements.
(Thesis) Main arguer
 João Francisco Tomaz Santos Botelho (PhD)
Universidade do Porto Faculdade de Farmácia, Portugal
2017 Member of the jury of the PhD dissertation: Biochemical and physiological insights into the bacterial cytochrome c peroxidases from Escherichia coli and Neisseria gonorrhoeae
(Thesis) Arguer
 Cláudia Nobrega (PhD)
Universidade Nova de Lisboa Faculdade de Ciências e Tecnologia, Portugal
2017 Main arguer of the PhD dissertation: Comparative genomics in Brucella suis: from intra-specific and inter-specific distinctive features to diagnostic molecular markers
(Thesis) Main arguer
 Ana Cristina Inácio (PhD)
Universidade de Lisboa Faculdade de Ciências, Portugal
2016 Member of the jury of the PhD dissertation: Functional analyses of inclusion membrane proteins of Chlamydia trachomatis.
(Thesis) Arguer
 Filipe Almeida (PhD)
Universidade Nova de Lisboa Faculdade de Ciências e Tecnologia, Portugal
2016 Member of the jury of the PhD dissertation: Evolution of the methicillin resistance determinant in staphylococci
(Thesis) Arguer
 Joana Rolo (PhD)
Universidade Nova de Lisboa Instituto de Tecnologia Química e Biológica, Portugal
2016 Main arguer of the PhD dissertation: Assessment of the genetic determinants involved in the expression of high-level of oxacillin resistance in contemporary clinical MRSA strains.
(Thesis) Main arguer
 Maria Gabriela Bento (PhD)
Universidade Nova de Lisboa Instituto de Tecnologia Química e Biológica, Portugal
2014 Main referee of the PhD dissertation: “Role of genetic diversity on the pathogenesis and evolution of community-associated methicillin-resistant Staphylococcus aureus (CA-MRSA)”
(Thesis) Main arguer
 Ana Lopes Tavares (PhD)
Universidade Nova de Lisboa Instituto de Tecnologia Química e Biológica, Portugal
2014 Referee of the PhD dissertation: “Molecular Epidemiology and Virulence Factors of Streptococcus agalactiae”
Thesis Member
 Carlos Florindo (PhD)
Universidade Nova de Lisboa Faculdade de Ciências e Tecnologia, Portugal
2012 Referee of the PhD dissertation: “Insights into cell Wall synthesis and cell division in Staphylococcus aureus”
(Thesis) Arguer
 Ana Maria R. Jorge (PhD)
Universidade Nova de Lisboa Instituto de Tecnologia Química e Biológica, Portugal
2009 Main referee of the Master dissertation: “Implementation and evaluation of new metodologies for early diagnosis of high risk Human Papillomavirus infection”.
(Thesis) Main arguer
 Cândida Delgado (Master)
Universidade de Lisboa Faculdade de Ciências, Portugal

Committee member

Activity description
Role 		Institution / Organization
2020/03 - Current National coordinator of the Task force in charge of monitoring the emergence and dissemination of SARS-CoV-2 genetic variants
Coordinator
 Instituto Nacional de Saúde Doutor Ricardo Jorge, Portugal
2013 - Current Invited co-chair for the Chlamydia Basic Research Society Congress - session: “membrane interactions” in San Antonio, Texas, USA.
Member
2022 - 2023 National coordinator of the genomic surveillance of the mpox virus on behalf of the 2022 multi-country outbreak
Coordinator

Evaluation committee

Activity description
Role 		Institution / Organization Funding entity
2022 - 2023 Member of the evaluation panel of the interdisciplinary platform "NOVAsaúde" from Universidade NOVA de Lisboa, in collaboration with Pfizer, on behalf of the “Bolsas de Investigação NOVAsaúde Chronic Disease and Infection”.
Evaluator
 Universidade Nova de Lisboa, Portugal Universidade Nova de Lisboa
2021 - 2022 Member of the evaluation panel of the 2021 Grants funded by Agência Nacional de Investigação (ANI) and Agência para o Investimento e Comércio Externo de Portugal (AICEP) on behalf of the Agendas Mobilizadoras do Plano de Recuperação e Resiliência (PRR).
Evaluator
 Agência para o Investimento e Comércio Externo de Portugal EPE, Portugal Agência para o Investimento e Comércio Externo de Portugal EPE
2021 - 2022 Member of the evaluation panel of the Grant proposals in the BMBF Call "Junior Research Groups in Infection Research", funded by the German Federal Ministry of Education and Research (BMBF).
Evaluator
 German Federal Ministry of Education and Research, Germany German Federal Ministry of Education and Research
2021 - 2022 Member of the evaluation panel of the 2021 Grants on behalf of the One Health European Joint Programme for STM applications in Foodborne Zoonoses, Antimicrobial Resistance, and Emerging Threats, funded by the European Union
Evaluator
 European Union, Belgium European Union
2020 - 2021 Member of the evaluation panel on behalf of the Call “Aviso/Convite 02/SAICT/2020 – Programa -Testar com Ciência e Solidariedade - COVID-19”.
Evaluator
 Fundação para a Ciência e a Tecnologia, Portugal Fundação para a Ciência e a Tecnologia
2020 - 2021 Member of the evaluation panel of the 2020 Grants on behalf of the One Health European Joint Programme for STM applications in Foodborne Zoonoses, Antimicrobial Resistance, and Emerging Threats, funded by the European Union.
Evaluator
 European Union, Belgium European Union
2020 - 2021 Member of the evaluation panel of the 2020 Grants on behalf of the "Research4COVID" programme, funded by Fundação para a Ciência e Tecnologia (FCT) e Agência para a Investigação Clínica e Inovação Biomédica (AICIB).
Evaluator
 Fundação para a Ciência e a Tecnologia, Portugal Fundação para a Ciência e a Tecnologia
2020 - 2020 Member of the evaluation panel of the 2020 Grants funded by the French Priority Research Programme on Antibiotic Resistance (PPR).
Evaluator
 Agence nationale de la recherche
2019 - 2019 Member of the evaluation panel of the FRDE-AMR-2019 (“2019 French-German call for projects on antimicrobial resistance”)
Evaluator
 French Ministry of Higher Education, Research and Innovation, France

German Federal Ministry of Education and Research, Germany 		French Ministry of Higher Education, Research and Innovation

German Federal Ministry of Education and Research
2019 - 2019 Member of the evaluation panel of the 2019 Grants funded by the “Czech Science Fund (FWF)
Evaluator
 Czech Science Fundation, Czech Republic Czech Science Fundation
2018 - 2018 Member of the evaluation panel of the 6ª Call of the “Joint Programming Initiative on Antimicrobial Resistance (JPI-AMR)”, funded by the European Union
Evaluator
 Agence nationale de la recherche, France European Union
2018 - 2018 Member of the evaluation panel of the PhD programme on behalf of the “WP6 One Health European Joint Programme-EJP”
Evaluator
 European Food Safety Authority, Italy European Food Safety Authority
2018 - 2018 Member of the evaluation panel of the Grants funded by the “Austrian Science Fund (FWF)
Evaluator
 Fonds zur Förderung der wissenschaftlichen Forschung, Austria Fonds zur Förderung der wissenschaftlichen Forschung
2017 - 2018 Member of the evaluation panel of the “Irish Research Council” on behalf of the “Irish Research Council Laureate Awards Programme 2017/18
Evaluator
 Irish Research Council, Ireland Irish Research Council
2016 - 2016 Member of the evaluation panel on behalf of the “Wellcome Trust Technology Development Grants"
Evaluator
 Wellcome Sanger Institute, United Kingdom Wellcome Sanger Institute
2016 - 2016 Member of the evaluation panel on behalf of the “Fourth Joint Transnational Call on human infectious diseases within the framework of the ERA-Net Infect-ERA
Evaluator
 European Commission Seventh Framework Programme for Research and Technological Development International Cooperation, Belgium European Commission Seventh Framework Programme for Research and Technological Development
2014 - 2014 Member of the evaluation panel of the “Fundação para a Ciência e Tecnologia” of Grants submitted on behalf of Bilateral Scientific Cooperation Protocols
Evaluator
 Fundação para a Ciência e a Tecnologia, Portugal Fundação para a Ciência e a Tecnologia
Distinctions

Award

2022 Gold Medal for Distinguished Services from the Ministry of Health
Ministério da Saúde, Portugal
2011 European PathoGenoMics PhD Award 2011 (This award recognizes up to three of the most remarkable and outstanding PhD theses in the field of genome research on human-pathogenic microorganisms). Supervisor of the PhD student that was awarded with this priz
European Commission, Belgium
2007 European PathoGenoMics PhD Award 2007 (This award recognizes up to three of the most remarkable and outstanding PhD theses in the field of genome research on human-pathogenic microorganisms) Its own PhD thesis was awarded.
European Commission, Belgium