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[EN] I am a research and education professional in the general discipline of Computational Biology, focusing specifically on the Population Biology of Pathogens (viruses & bacteria). My expertise is on antigenically diverse and mosquito-borne pathogens of humans and other animals. My skills are on computational and mathematical approaches that can be applied to multi-level biological data (from genes to the environment). My interests are to answer questions regarding pathogen evolution, population genetics & dynamics, epidemiology and ecology. My goal is to contribute with a combination of hypothesis-driven and data-driven research outputs towards better solutions for surveillance, control and population health. In the last 5 years I have been translating expertise into practical solutions beyond research output. I have (e.g.) developed and made freely available online, computational tools and databases related to predicting/measuring how climate dictates the epidemic activity of multiple mosquito-borne viruses across the globe (e.g. dengue, Zika, West Nile viruses). In 2021 after 12 years abroad, I returned to Portugal in search of research and education opportunities to contribute to the nationally underdeveloped discipline of Computational Biology applied to the Population Biology of Pathogens. I already have successful research outputs and projects on a few pathogens/topics of national interest (e.g. West Nile virus, Bovine tuberculosis, antimicrobial resistance in farms). Given the recent urgency of the emergence of the dengue virus in Europe (Spain, France, Italy), I am now looking for funding opportunities to transfer 25 years of expertise in dengue mathematical modelling towards developing a quantitative assessment of its risk of emergence in Portugal. With the output of this assessment, I plan to inform better national surveillance, as well as to inform the first contingency plan for the emerge of dengue in Portugal. [PT] Sou um profissional de pesquisa e educação na área geral da Biologia Computacional, com foco específico na Biologia Populacional de Patógenos (vírus e bactérias). A minha experiência é em patógenos humanos e de outros animais que são antigenicamente diversos e-ou transmitidos por mosquitos. As minhas habilidades são em abordagens computacionais e matemáticas que podem ser aplicadas a dados biológicos de vários níveis (desde os genes ao ambiente). Os meus interesses são em responder a perguntas sobre a evolução, genética e dinâmica populacionais, epidemiologia e ecologia de patógenos. O meu objetivo é contribuir com uma combinação de pesquisas orientadas por hipóteses e baseadas em dados para soluções de vigilância, controle e saúde populacional. Nos últimos 5 anos desenvolvi e tornei disponíveis (online) ferramentas computacionais e bancos de dados gratuitos, relacionados à previsão/quantificação de como o clima local dita a atividade epidémica de múltiplos vírus transmitidos por mosquitos em todo o mundo (por exemplo, os vírus dengue, Zika, Nilo Ocidental). Em 2021, depois de 12 anos no estrangeiro, voltei para Portugal em busca de oportunidades de pesquisa e educação para contribuir para a disciplina de Biologia Computacional aplicada à Biologia Populacional de Patógenos (que se encontra subdesenvolvida no país). Já tenho pesquisas bem-sucedidas e projetos em curso sobre patógenos/tópicos de interesse nacional (e.g. vírus do Nilo Ocidental, tuberculose bovina, resistência aos antimicrobianos na industria). Dada a urgência recente do surgimento do vírus da dengue na Europa (Espanha, França, Itália), estou interessado em oportunidades de financiamento para transferir 25 anos de experiência em modelação matemática do vírus dengue, no sentido de desenvolver uma avaliação quantitativa do seu risco de surgimento em Portugal. Com esta avaliação, pretendo informar a vigilância nacional, assim como informar o primeiro plano de contingência nacional contra a emergência do vírus dengue.
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Identification

Personal identification

Full name
José Miguel Lima de Aguiar Graça Lourenço

Citation names

  • Lourenço, José

Author identifiers

Ciência ID
D01E-3305-71B8
ORCID iD
0000-0002-9318-2581
Google Scholar ID
A4y9Yw8AAAAJ

Email addresses

  • jolourenco@ucp.pt (Professional)

Websites

Knowledge fields

  • Medical and Health Sciences - Health Sciences - Epidemiology
  • Natural sciences - Biological Sciences - Ecology

Languages

Language Speaking Reading Writing Listening Peer-review
Portuguese (Mother tongue)
English Proficiency (C2) Proficiency (C2) Proficiency (C2) Proficiency (C2) Proficiency (C2)
Education
Degree Classification
2018/12/04 - 2020/02/28
Concluded
 Teaching and Learning in Higher Education (Postgraduate Certificate)
University of Oxford Department for Continuing Education, United Kingdom
2015/01/01
Concluded
 Postgraduate Award in Public Health (Postgraduate Certificate)
Oxford Brookes University, United Kingdom
2013/08/10
Concluded
 DPhil in Infectious Disease Modelling (Doctor of Philosophy)
Major in Population dynamics of dengue viruses
University of Oxford Department of Zoology, United Kingdom
1999 - 2006/10/01
Concluded
 Licenciatura em engenharia informática e de computadores (Licenciatura)
Universidade de Lisboa Instituto Superior Técnico, Portugal
Affiliation

Science

Category
Host institution 		Employer
2023/09/01 - Current Principal Investigator (Research) Universidade Católica Portuguesa, Portugal
Biomedical Research Center, Portugal
2021/12/01 - 2023/09/01 Principal Investigator (Research) Universidade de Lisboa Faculdade de Ciências, Portugal
Universidade de Lisboa Instituto de Biossistemas e Ciências Integrativas, Portugal
2018/09/01 - 2021/12/01 Principal Investigator (Research) University of Oxford Department of Zoology, United Kingdom
2014/04/01 - 2018/09/01 Auxiliary Researcher (Research) University of Oxford Department of Zoology, United Kingdom
2013/03/01 - 2014/03/01 Auxiliary Researcher (Research) Imperial College London - St Mary's Campus, United Kingdom
2007/12/31 - 2008/12/31 Auxiliary Researcher (Research) Instituto Gulbenkian de Ciência, Portugal
2005/01/01 - 2007/12/31 Science and Technology Management Instituto Gulbenkian de Ciência, Portugal

Teaching in Higher Education

Category
Host institution 		Employer
2023/09/01 - Current Assistant Professor (University Teacher) Universidade Católica Portuguesa, Portugal
Biomedical Research Center, Portugal
2018/09/01 - 2021/12/01 Associate Professor (University Teacher) Universidade de Oxford, United Kingdom
Universidade de Oxford, Departamento de Zoologia, United Kingdom

Others

Category
Host institution 		Employer
2009/09/01 - 2013/03/01 Aluno DPhil University of Oxford Department of Zoology, United Kingdom
Projects

Grant

Designation Funders
2011/06 - 2017/06 ERC 268904 - DIVERSITY
ERC 268904 - DIVERSITY
 European Research Council
2009/01/01 - 2013/01/01 DPhil in Theoretical Epidemiology
SFRH / BD / 33855 / 2009
PhD Student Fellow
Universidade de Oxford, United Kingdom
 Fundação para a Ciência e a Tecnologia
Concluded
2009/01 - 2013/01 DPhil in Theoretical Epidemiology
SFRH / BD / 33855 / 2009
 Fundação para a Ciência e a Tecnologia
2004 - 2008 MEXT-CT-2004-14338
MEXT-CT-2004-14338
 European Commission
Concluded

Contract

Designation Funders
2020/03 - Current Impact of vaccines on antimicrobial resistance
219900/Z/19/Z
GB-CHC-210183
Researcher
University College London Division of Infection and Immunity, United Kingdom
 Wellcome Trust
Ongoing
2020/01/01 - Current Improving scientific and public health decision making by developing technologies to increase use of robust methods to calibrate and analyse complex mathematical models
218261/Z/19/Z
Supervisor
London School of Hygiene & Tropical Medicine, United Kingdom
 Wellcome Trust
Ongoing
2020 - Current One Health International Network for SARS-CoV-2 real time genomic monitoring
IOC-009-FEX-21-2-1
Researcher
International Centre for Genetic Engineering and Biotechnology
Ongoing
2020 - Current Global Alliance for Zika Virus Control and Prevention
734548
Researcher
European Union’s Horizon 2020
Ongoing
2019/01/01 - Current GCRF One Health Poultry Hub
BB/S011269/1
Researcher
Universidade de Oxford, United Kingdom
 Biotechnology and Biological Sciences Research Council
Ongoing
2018/09 - Current To investigate the relationship between the profile of anti-pneumococcal antibodies at a population level, and pneumococcal colonisation in Malawi.
opp1185516
Researcher
University College London Division of Infection and Immunity, United Kingdom
 Bill & Melinda Gates Foundation
Ongoing
2018/09 - Current To evaluate the immunogenicity and impact of a reduced 13 valent pneumococcal conjugate vaccine (PCV13) dosing schedule
opp1126431
Researcher
University College London Division of Infection and Immunity, United Kingdom
 Bill & Melinda Gates Foundation
Concluded
2018 - Current Genomic monitoring and rapid detection of new circulating and co-circulating arboviruses in Brazil
421598/2018-2
Researcher
Ongoing
2016 - Current ZIBRA 2: Análise em Tempo Real, no Brasil, do Vírus ZIKA: Segunda etapa, funded by Conselho Nacional de Desenvolvimento Científico
440685/2016-8
88887.130716/2016-00
Researcher
Conselho Nacional de Desenvolvimento Científico e Tecnológico

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior
Ongoing
2023/02/01 - 2026/01/31 AbOrdagens EmpiriCo-MEcanísticas na ModeLaçãO da Resistência a AnTimicrobianos sob o Paradigma de Uma Só Saúde
2022.01539.PTDC
10.54499/2022.01539.PTDC
FCiênciasID Associação para a Investigação e Desenvolvimento de Ciências, Portugal

Direcção-Geral de Alimentação e Veterinária, Portugal
Fundação para a Ciência e a Tecnologia
Ongoing
2021 - 2025 United World Antiviral Research Network (UWARN) – CREID
UWSC12067
Researcher
National Institutes of Health
Ongoing
2022/07/01 - 2023/07/01 Transferring methodological experience from the UK’s One Health Poultry Hub into the Portuguese ecological and farming contexts.
PARSUK/BRF22/JLFP
Universidade de Lisboa, Portugal
 PARSUK
Concluded
2018/09 - 2020/04 Shifts in the metabolic and virulence profiles of Streptococcus pneumoniae following the introduction of conjugate-polysaccharide vaccine in Malawi
GB-GOV-13-FUND--GCRF-MR_N023129_1
Researcher
University College London Division of Infection and Immunity, United Kingdom
 UK - Department for Business, Energy and Industrial Strategy
Concluded
Outputs

Publications

Journal article
  1. Pinotti, Francesco; Giovanetti, Marta; de Lima, Maricelia Maia; de Cerqueira, Erenilde Marques; Alcantara, Luiz C. J.; Gupta, Sunetra; Recker, Mario; Lourenço, José. "Shifting patterns of dengue three years after Zika virus emergence in Brazil". Nature Communications 15 1 (2024): http://dx.doi.org/10.1038/s41467-024-44799-x.
    10.1038/s41467-024-44799-x
  2. Teresa Nazareth; Gonçalo Seixas; Lourenço, José; Paulo Bettencourt. "Aedes albopictus arrives in Lisbon". Frontiers in Public Health 11 (2023): https://ciencia.ucp.pt/en/publications/e8875ced-679e-49bb-8201-8e0fcff5b37b.
    10.3389/fpubh.2023.1332334
  3. Uri Obolski; Todd D. Swarthout; Akuzike Kalizang’oma; Thandie S. Mwalukomo; Jia Mun Chan; Caroline M. Weight; Comfort Brown; et al. "The metabolic, virulence and antimicrobial resistance profiles of colonising Streptococcus pneumoniae shift after PCV13 introduction in urban Malawi". Nature Communications 14 1 (2023): https://ciencia.ucp.pt/en/publications/e65e40fb-7f4c-4e14-9ac3-9275235c2177.
    10.1038/s41467-023-43160-y
  4. Taishi Nakase; Marta Giovanetti; Uri Obolski; Lourenço, José. "Global transmission suitability maps for dengue virus transmitted by Aedes aegypti from 1981 to 2019". Scientific data 10 1 (2023): https://ciencia.ucp.pt/en/publications/9011661a-5138-44bf-8fce-1270de511fb6.
    10.1038/s41597-023-02170-7
  5. Marta Giovanetti; Cynthia Vazquez; Mauricio Lima; Emerson Castro; Analia Rojas; Andrea Gomez de la Fuente; Carolina Aquino; et al. "Rapid epidemic expansion of Chikungunya Virus East/Central/South African Lineage, Paraguay". Emerging Infectious Diseases 29 9 (2023): 1859-1863. https://ciencia.ucp.pt/en/publications/44640eee-a832-49e2-bd99-713b1faf57d6.
    10.3201/eid2909.230523
  6. Giovanetti, Marta; Pinotti, Francesco; Zanluca, Camila; Fonseca, Vagner; Nakase, Taishi; Koishi, Andrea C.; Tscha, Marcel; et al. "Genomic epidemiology unveils the dynamics and spatial corridor behind the Yellow Fever virus outbreak in Southern Brazil". Science Advances 9 35 (2023): http://dx.doi.org/10.1126/sciadv.adg9204.
    10.1126/sciadv.adg9204
  7. Cynthia Vazquez; Luiz Carlos Junior Alcantara; Vagner Fonseca; Mauricio Teixeira Lima; Joilson Xavier; Talita Adelino; Hegger Machado Fritsch; et al. "Retrospective Spatio-Temporal Dynamics of Dengue Virus 1, 2 and 4 in Paraguay". Viruses (2023): https://www.mdpi.com/1999-4915/15/6/1275.
    10.3390/v15061275
  8. Stephane Tosta; Keldenn Moreno; Gabriel Schuab; Vagner Fonseca; Fátima María Cardozo Segovia; Simone Kashima; Maria Carolina Elias; et al. "Global SARS-CoV-2 genomic surveillance". Infection, Genetics and Evolution 108 (2023): https://ciencia.ucp.pt/en/publications/14ace760-108e-40c7-89ce-4ceee9707b05.
    10.1016/j.meegid.2023.105405
  9. Lourenço, José; Anna L. McNaughton; Caitlin Pley; Uri Obolski; Sunetra Gupta; Philippa C. Matthews. "Polymorphisms predicting phylogeny in hepatitis B virus". Virus Evolution 9 1 (2023): https://ciencia.ucp.pt/en/publications/db013ae4-91bf-4cf4-b7a4-e04b072da055.
    10.1093/ve/veac116
  10. José Lourenço; Sílvia C. Barros; Líbia Zé-Zé; Daniel S. C. Damineli; Marta Giovanetti; Hugo C. Osório; Fátima Amaro; et al. "West Nile virus transmission potential in Portugal". Communications Biology (2022): https://doi.org/10.1038/s42003-021-02969-3.
    10.1038/s42003-021-02969-3
  11. Álvaro Salgado; Raquel C. de Melo-Minardi; Marta Giovanetti; Adriano Veloso; Francielly Morais-Rodrigues; Talita Adelino; Ronaldo de Jesus; et al. "Machine learning models exploring characteristic single-nucleotide signatures in yellow fever virus". PLoS one 17 12 Decembe (2022): https://ciencia.ucp.pt/en/publications/7e9d813e-0176-4c40-ae3d-9c91e72894ce.
    10.1371/journal.pone.0278982
  12. Zengmiao Wang; Peiyi Wu; Jingyuan Wang; José Lourenço; Bingying Li; Benjamin Rader; Marko Laine; et al. "Assessing the asymptomatic proportion of SARS-CoV-2 infection with age in China before mass vaccination". Journal of The Royal Society Interface (2022): https://doi.org/10.1098/rsif.2022.0498.
    10.1098/rsif.2022.0498
  13. Marta Giovanetti; Svetoslav Nanev Slavov; Vagner Fonseca; Eduan Wilkinson; Houriiyah Tegally; José Salvatore Leister Patané; Vincent Louis Viala; et al. "Genomic epidemiology of the SARS-CoV-2 epidemic in Brazil". Nature Microbiology 7 9 (2022): 1490-1500. https://ciencia.ucp.pt/en/publications/66b0a6ec-eb3a-453e-a0b1-af135d770184.
    10.1038/s41564-022-01191-z
  14. José Lourenço; Francesco Pinotti; Taishi Nakase; Marta Giovanetti; Uri Obolski. "Letter to the editor: Atypical weather is associated with the 2022 early start of West Nile virus transmission in Italy". Eurosurveillance (2022): https://doi.org/10.2807/1560-7917.ES.2022.27.34.2200662.
    10.2807/1560-7917.ES.2022.27.34.2200662
  15. Oxford Protective T Cell Immunology for COVID-19 (OPTIC) consortium; Scottish National Blood Transfusion Service (SNBTS) consortium; International Severe Acute Respiratory and emerging Infection Consortium Coronavirus Clinical Characterisation Consortiu; Anna L. McNaughton; Robert S. Paton; Matthew Edmans; Jonathan Youngs; et al. "Fatal COVID-19 outcomes are associated with an antibody response targeting epitopes shared with endemic coronaviruses". JCI insight 7 13 (2022): https://ciencia.ucp.pt/en/publications/12851f35-bce4-45ad-9cd4-a81e72268c87.
    10.1172/jci.insight.156372
  16. Felicidade Mota Pereira; Aline Salomão de Araujo; Ana Catarina Martins Reis; Anadilton Santos da Hora; Francesco Pinotti; Robert S. Paton; Camylla Vilas Boas Figueiredo; et al. "Dynamics and determinants of SARS-CoV-2 RT-PCR testing on symptomatic individuals attending healthcare centers during 2020 in Bahia, Brazil". Viruses 14 7 (2022): https://ciencia.ucp.pt/en/publications/7c2619d2-724e-4831-9a50-880977774baa.
    10.3390/v14071549
  17. Alcantara, Luiz Carlos Junior; Nogueira, Elisson; Shuab, Gabriel; Tosta, Stephane; Fristch, Hegger; Pimentel, Victor; Souza-Neto, Jayme A.; et al. "SARS-CoV-2 epidemic in Brazil: how the displacement of variants has driven distinct epidemic waves". Virus Research 315 (2022): 198785. http://dx.doi.org/10.1016/j.virusres.2022.198785.
    10.1016/j.virusres.2022.198785
  18. Caitlin Pley; José Lourenço; Anna L. McNaughton; Philippa C. Matthews; Hector C. Aguilar. "Spacer Domain in Hepatitis B Virus Polymerase: Plugging a Hole or Performing a Role?". Journal of Virology (2022): https://doi.org/10.1128/jvi.00051-22.
    10.1128/jvi.00051-22
  19. Chen, Yuyang; Li, Naizhe; Lourenço, José; Wang, Lin; Cazelles, Bernard; Dong, Lu; Li, Bingying; et al. "Measuring the effects of COVID-19-related disruption on dengue transmission in southeast Asia and Latin America: a statistical modelling study". The Lancet Infectious Diseases 22 5 (2022): 657-667. http://dx.doi.org/10.1016/s1473-3099(22)00025-1.
    Open access • 10.1016/s1473-3099(22)00025-1
  20. Marta Giovanetti; Luiz Augusto Pereira; Talita Emile Ribeiro Adelino; Vagner Fonseca; Joilson Xavier; Allison de Araújo Fabri; Svetoslav Nanev Slavov; et al. "A retrospective overview of Zika virus evolution in the Midwest of Brazil". Microbiology spectrum 10 2 (2022): https://ciencia.ucp.pt/en/publications/9e488a6d-4c80-4fd0-8fc0-307396758a9b.
    10.1128/spectrum.00155-22
  21. Zengmiao Wang; Yonghong Liu; Yuchun Li; Guangze Wang; Lourenço, José; Moritz Kraemer; Qixin He; et al. "The relationship between rising temperatures and malaria incidence in Hainan, China, from 1984 to 2010". The Lancet Planetary Health 6 4 (2022): e350-e358. https://ciencia.ucp.pt/en/publications/34a05020-d808-4677-980d-7dfa3d67c33f.
    10.1016/S2542-5196(22)00039-0
  22. Líbia Zé-Zé; Fátima Amaro; Hugo Costa Osório; Marta Giovanetti; José Lourenço; Maria João Alves. Corresponding author: Fátima Amaro. "Molecular Identification and Ecology of Portuguese Wild-Caught Phlebotomine Sandfly Specimens". Zoonotic Diseases 2 (2022): 19-31. https://www.mdpi.com/2813-0227/2/1/3/htm.
    Open access • Published
  23. Tian, Huaiyu; Li, Naizhe; Li, Yapin; Kraemer, Moritz U. G.; Tan, Hua; Liu, Yonghong; Li, Yidan; et al. "Malaria elimination on Hainan Island despite climate change". Communications Medicine 2 1 (2022): http://dx.doi.org/10.1038/s43856-022-00073-z.
    Open access • Published • 10.1038/s43856-022-00073-z
  24. Kamau, Alice; Paton, Robert S.; Akech, Samuel; Mpimbaza, Arthur; Khazenzi, Cynthia; Ogero, Morris; Mumo, Eda; et al. "Malaria hospitalisation in East Africa: age, phenotype and transmission intensity". BMC Medicine 20 1 (2022): http://dx.doi.org/10.1186/s12916-021-02224-w.
    Open access • 10.1186/s12916-021-02224-w
  25. Marta Giovanetti; Vagner Fonseca; Eduan Wilkinson; Houriiyah Tegally; Emmanuel James San; Christian L. Althaus; Joilson Xavier; et al. "Replacement of the Gamma by the Delta variant in Brazil". Virus Evolution 8 1 (2022): https://ciencia.ucp.pt/en/publications/933373ec-041e-476c-8234-3a314158fb06.
    10.1093/ve/veac024
  26. Mary E. Petrone; Rebecca Earnest; José Lourenço; Moritz U. G. Kraemer; Robert Paulino-Ramirez; Nathan D. Grubaugh; Leandro Tapia. "Asynchronicity of endemic and emerging mosquito-borne disease outbreaks in the Dominican Republic". Nature Communications 12 1 (2021): https://doi.org/10.1038/s41467-020-20391-x.
    10.1038/s41467-020-20391-x
  27. Martin, Darren P.; Weaver, Steven; Tegally, Houriiyah; San, James Emmanuel; Shank, Stephen D.; Wilkinson, Eduan; Lucaci, Alexander G.; et al. "The emergence and ongoing convergent evolution of the SARS-CoV-2 N501Y lineages". Cell 184 20 (2021): 5189-5200.e7. http://dx.doi.org/10.1016/j.cell.2021.09.003.
    Published • 10.1016/j.cell.2021.09.003
  28. Lourenço, José. "Malaria infection and severe disease risks in Africa.". Science (New York, N.Y.) (2021): https://europepmc.org/articles/PMC7611598.
    10.1126/science.abj0089
  29. Lourenço, José. "Phylogenetic Analysis of Massilia phlebovirus in Portugal.". Viruses (2021): https://europepmc.org/articles/PMC8310352.
    10.3390/v13071412
  30. Lourenço, José. "Short Report: Early genomic detection of SARS-CoV-2 P.1 variant in Northeast Brazil.". PLoS neglected tropical diseases (2021): https://europepmc.org/articles/PMC8321350.
    10.1371/journal.pntd.0009591
  31. Network for Genomic Surveillance in South Africa (NGS-SA); Will Fischer; Elena E. Giorgi; Srirupa Chakraborty; Kien Nguyen; Tanmoy Bhattacharya; James Theiler; et al. "HIV-1 and SARS-CoV-2". Cell Host and Microbe 29 7 (2021): 1093-1110. https://ciencia.ucp.pt/en/publications/e4993893-8560-4fb4-a2f8-e336f756db7e.
    10.1016/j.chom.2021.05.012
  32. Érica Azevedo Costa; Marta Giovanetti; Lilian Catenacci; Vagner Fonseca; Flavia Figueira Aburjaile; Flávia L. L. Chalhoub; Joilson Xavier; et al. "West Nile Virus in Brazil". Pathogens (2021): https://www.mdpi.com/2076-0817/10/7/896.
    10.3390/pathogens10070896
  33. Lourenço, José. "Genomic surveillance activities unveil the introduction of the SARS-CoV-2 B.1.525 variant of interest in Brazil: Case report.". Journal of medical virology (2021): https://europepmc.org/articles/PMC8242367.
    10.1002/jmv.27086
  34. Lourenço, José. "Genomic evidence of SARS-CoV-2 reinfection case with the emerging B.1.2 variant in Brazil.". The Journal of infection (2021): https://europepmc.org/articles/PMC8139330.
    10.1016/j.jinf.2021.05.014
  35. Network for Genomic Surveillance in South Africa; COMMIT-KZN Team; Sandile Cele; Inbal Gazy; Laurelle Jackson; Shi Hsia Hwa; Houriiyah Tegally; et al. "Escape of SARS-CoV-2 501Y.V2 from neutralization by convalescent plasma". Nature 593 7857 (2021): 142-146. https://ciencia.ucp.pt/en/publications/b65dffca-0d25-43ce-8e35-1dd63ce2d093.
    10.1038/s41586-021-03471-w
  36. Brazil-UK CADDE Genomic Network; Network for Genomic Surveillance in South Africa; Chantal B.F. Vogels; Mallery I. Breban; Isabel M. Ott; Tara Alpert; Mary E. Petrone; et al. "Multiplex qPCR discriminates variants of concern to enhance global surveillance of SARS-CoV-2". PLoS Biology 19 5 May (2021): https://ciencia.ucp.pt/en/publications/bbe830e8-0318-4708-b933-116b1b723d65.
    10.1371/journal.pbio.3001236
  37. Lourenço, José. "SARS-CoV-2 shifting transmission dynamics and hidden reservoirs potentially limit efficacy of public health interventions in Italy.". Communications biology (2021): https://europepmc.org/articles/PMC8060392.
    10.1038/s42003-021-02025-0
  38. Lourenço, José. "Short report: Introduction of chikungunya virus ECSA genotype into the Brazilian Midwest and its dispersion through the Americas.". PLoS neglected tropical diseases (2021): https://europepmc.org/articles/PMC8051810.
    10.1371/journal.pntd.0009290
  39. Lourenço, José. "Field and classroom initiatives for portable sequence-based monitoring of dengue virus in Brazil.". Nature communications (2021): https://europepmc.org/articles/PMC8052316.
    10.1038/s41467-021-22607-0
  40. José Lourenço; Yair Daon; Andrea Gori; Uri Obolski. "Pneumococcal Competition Modulates Antibiotic Resistance in the Pre-Vaccination Era: A Modelling Study". Vaccines (2021): https://doi.org/10.3390/vaccines9030265.
    10.3390/vaccines9030265
  41. Lourenço, José. "Real-time seroprevalence and exposure levels of emerging pathogens in infection-naive host populations.". Scientific reports (2021): https://europepmc.org/articles/PMC7954847.
    10.1038/s41598-021-84672-1
  42. Lourenço, José. "Detection of a SARS-CoV-2 variant of concern in South Africa.". Nature (2021): https://doi.org/10.1038/s41586-021-03402-9.
    10.1038/s41586-021-03402-9
  43. Lourenço, José. "Sixteen novel lineages of SARS-CoV-2 in South Africa.". Nature medicine (2021): https://doi.org/10.1038/s41591-021-01255-3.
    10.1038/s41591-021-01255-3
  44. Pinotti, Francesco; Wikramaratna, Paul S.; Obolski, Uri; Paton, Robert S.; Damineli, Daniel S. C.; Alcantara, Luiz C. J.; Giovanetti, Marta; Gupta, Sunetra; Lourenço, José. "Potential impact of individual exposure histories to endemic human coronaviruses on age-dependent severity of COVID-19". BMC Medicine 19 1 (2021): http://dx.doi.org/10.1186/s12916-020-01887-1.
    10.1186/s12916-020-01887-1
  45. Caitlin M Pley; Anna L McNaughton; Philippa C Matthews; José Lourenço. "The global impact of the COVID-19 pandemic on the prevention, diagnosis and treatment of hepatitis B virus (HBV) infection". BMJ Global Health (2021): https://doi.org/10.1136/bmjgh-2020-004275.
    10.1136/bmjgh-2020-004275
  46. Paul S Wikramaratna; Robert S Paton; Mahan Ghafari; José Lourenço. "Estimating the false-negative test probability of SARS-CoV-2 by RT-PCR". Eurosurveillance 25 50 (2020): https://doi.org/10.2807/1560-7917.ES.2020.25.50.2000568.
    10.2807/1560-7917.ES.2020.25.50.2000568
  47. Lourenço, José. "The ongoing COVID-19 epidemic in Minas Gerais, Brazil: insights from epidemiological data and SARS-CoV-2 whole genome sequencing.". Emerging microbes & infections (2020): https://europepmc.org/articles/PMC7473129.
    10.1080/22221751.2020.1803146
  48. Todd D. Swarthout; Claudio Fronterre; José Lourenço; Uri Obolski; Andrea Gori; Naor Bar-Zeev; Dean Everett; et al. "High residual carriage of vaccine-serotype Streptococcus pneumoniae after introduction of pneumococcal conjugate vaccine in Malawi". Nature Communications 11 1 (2020): https://doi.org/10.1038/s41467-020-15786-9.
    10.1038/s41467-020-15786-9
  49. Lourenço, José. "Early transmission of SARS-CoV-2 in South Africa: An epidemiological and phylogenetic report.". International journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases (2020): https://europepmc.org/articles/PMC7658561.
    10.1016/j.ijid.2020.11.128
  50. Lourenço, José. "Characterising West Nile virus epidemiology in Israel using a transmission suitability index.". Euro surveillance : bulletin Europeen sur les maladies transmissibles = European communicable disease bulletin (2020): https://europepmc.org/articles/PMC7678037.
    10.2807/1560-7917.es.2020.25.46.1900629
  51. Lourenço, José. "Detection of neutralising antibodies to SARS-CoV-2 to determine population exposure in Scottish blood donors between March and May 2020.". Euro surveillance : bulletin Europeen sur les maladies transmissibles = European communicable disease bulletin (2020): https://europepmc.org/articles/PMC7651873.
    10.2807/1560-7917.es.2020.25.42.2000685
  52. Lourenço, José. "Hepatitis B virus seroepidemiology data for Africa: Modelling intervention strategies based on a systematic review and meta-analysis.". PLoS medicine (2020): https://europepmc.org/articles/PMC7173646.
    10.1371/journal.pmed.1003068
  53. Marta Giovanetti; Nuno Rodrigues Faria; Lourenço, José; Jaqueline Goes de Jesus; Joilson Xavier; Ingra Morales Claro; Moritz U.G. Kraemer; et al. "Genomic and epidemiological surveillance of Zika virus in the Amazon region". Cell reports 30 7 (2020): 2275-2283.e7. https://ciencia.ucp.pt/en/publications/fb7c9c73-a339-43d5-96d8-3e57028b7aef.
    10.1016/j.celrep.2020.01.085
  54. Lourenço, José. "Hospital discharges in urban sanitation systems: Long-term monitoring of wastewater resistome and microbiota in relationship to their eco-exposome.". Water research X (2020): https://europepmc.org/articles/PMC7013138.
    10.1016/j.wroa.2020.100045
  55. Lourenço, José. "Return of the founder Chikungunya virus to its place of introduction into Brazil is revealed by genomic characterization of exanthematic disease cases.". Emerging microbes & infections (2019): https://europepmc.org/articles/PMC6968431.
    10.1080/22221751.2019.1701954
  56. Nuno R. Faria; Ronald Swanstrom; Nicole Vidal; José Lourenco; Jayna Raghwani; Kim C. E. Sigaloff; Andy J. Tatem; et al. "Distinct rates and patterns of spread of the major HIV-1 subtypes in Central and East Africa". PLOS Pathogens (2019): https://doi.org/10.1371/journal.ppat.1007976.
    10.1371/journal.ppat.1007976
  57. Uri Obolski; Andrea Gori; José Lourenço; Craig Thompson; Robin Thompson; Neil French; Robert S. Heyderman; Sunetra Gupta. "Identifying genes associated with invasive disease in S. pneumoniae by applying a machine learning approach to whole genome sequence typing data". Scientific Reports 9 1 (2019): https://doi.org/10.1038/s41598-019-40346-7.
    10.1038/s41598-019-40346-7
  58. Lourenço, J.; Obolski, U.; Swarthout, T. D.; Gori, A.; Bar-Zeev, N.; Everett, D.; Kamng’ona, A. W.; et al. "Determinants of high residual post-PCV13 pneumococcal vaccine-type carriage in Blantyre, Malawi: a modelling study". BMC Medicine 17 1 (2019): http://dx.doi.org/10.1186/s12916-019-1450-2.
    10.1186/s12916-019-1450-2
  59. Uri Obolski; Pablo N. Perez; Christian J. Villabona-Arenas; Julien Thézé; Nuno R. Faria; José Lourenço; Timothée Poisot. "MVSE : An R-package that estimates a climate-driven mosquito-borne viral suitability index". Methods in Ecology and Evolution 10 8 (2019): 1357-1370. https://doi.org/10.1111/2041-210X.13205.
    10.1111/2041-210X.13205
  60. Lourenço, José. "First detection of human T-lymphotropic virus in blood donors in Benin shows that testing is required to improve blood safety". ISBT Science Series 14 2 (2019): 163-168. http://dx.doi.org/10.1111/voxs.12441.
    10.1111/voxs.12441
  61. Felipe Gomes Naveca; Rebecca C. Christofferson; Ingra Claro; Marta Giovanetti; Jaqueline Goes de Jesus; Joilson Xavier; Felipe Campos de Melo Iani; et al. "Genomic, epidemiological and digital surveillance of Chikungunya virus in the Brazilian Amazon". PLOS Neglected Tropical Diseases 13 3 (2019): e0007065-e0007065. https://doi.org/10.1371/journal.pntd.0007065.
    10.1371/journal.pntd.0007065
  62. Lourenço, José. "HBV vaccination and PMTCT as elimination tools in the presence of HIV: insights from a clinical cohort and dynamic model.". BMC medicine (2019): https://europepmc.org/articles/PMC6383254.
    10.1186/s12916-019-1269-x
  63. Spensley, Katrina J.; Wikramaratna, Paul S.; Penman, Bridget S.; Walker, Andrew; Smith, Adrian L.; Pybus, Oliver G.; Jean, Létitia; et al. "Reverse immunodynamics: a new method for identifying targets of protective immunity". Scientific Reports 9 1 (2019): http://dx.doi.org/10.1038/s41598-018-37288-x.
    10.1038/s41598-018-37288-x
  64. Craig P. Thompson; José Lourenço; Adam A. Walters; Uri Obolski; Matthew Edmans; Duncan S. Palmer; Kreepa Kooblall; et al. "A naturally protective epitope of limited variability as an influenza vaccine target". Nature Communications 9 1 (2018): https://doi.org/10.1038/s41467-018-06228-8.
    10.1038/s41467-018-06228-8
  65. Lourenço, José. "Genomic and epidemiological monitoring of yellow fever virus transmission potential.". Science (New York, N.Y.) (2018): https://europepmc.org/articles/PMC6874500.
    10.1126/science.aat7115
  66. José Lourenço; Warren Tennant; Nuno R. Faria; Andrew Walker; Sunetra Gupta; Mario Recker. "Challenges in dengue research: A computational perspective". Evolutionary Applications 11 4 (2018): 516-533. https://doi.org/10.1111/eva.12554.
    10.1111/eva.12554
  67. Jung-Seok Lee; José Lourenço; Sunetra Gupta; Andrew Farlow. "A multi-country study of dengue vaccination strategies with Dengvaxia and a future vaccine candidate in three dengue-endemic countries: Vietnam, Thailand, and Colombia". Vaccine (2018): https://app.dimensions.ai/details/publication/pub.1101678538.
    10.1016/j.vaccine.2018.03.002
  68. Uri Obolski; José Lourenço; Craig Thompson; Robin Thompson; Andrea Gori; Sunetra Gupta. "Vaccination can drive an increase in frequencies of antibiotic resistance among nonvaccine serotypes of Streptococcus pneumoniae". Proceedings of the National Academy of Sciences 115 12 (2018): 3102-3107. https://doi.org/10.1073/pnas.1718712115.
    10.1073/pnas.1718712115
  69. José Lourenço; Maria de Lourdes Monteiro; Tomás Valdez; Júlio Monteiro Rodrigues; Oliver Pybus; Nuno Rodrigues Faria. "Epidemiology of the Zika Virus Outbreak in the Cabo Verde Islands, West Africa". PLoS Currents (2018): https://app.dimensions.ai/details/publication/pub.1101537054.
    10.1371/currents.outbreaks.19433b1e4d007451c691f138e1e67e8c
  70. von Delft, A.; Donnison, T.A.; Lourenço, J.; Hutchings, C.; Mullarkey, C.E.; Brown, A.; Pybus, O.G.; et al. "The generation of a simian adenoviral vectored HCV vaccine encoding genetically conserved gene segments to target multiple HCV genotypes". Vaccine 36 2 (2018): 313-321. http://www.scopus.com/inward/record.url?eid=2-s2.0-85035339163&partnerID=MN8TOARS.
    10.1016/j.vaccine.2017.10.079
  71. Perez-Guzman, Pablo Noel; Carlos Junior Alcantara, Luiz; Obolski, Uri; de Lima, Maricelia M.; Ashley, Elizabeth A.; Smithuis, Frank; Horby, Peter; et al. "Measuring Mosquito-borne Viral Suitability in Myanmar and Implications for Local Zika Virus Transmission". PLoS Currents (2018): http://dx.doi.org/10.1371/currents.outbreaks.7a6c64436a3085ebba37e5329ba169e6.
    10.1371/currents.outbreaks.7a6c64436a3085ebba37e5329ba169e6
  72. Nuno R. Faria; Antonio Charlys da Costa; José Lourenço; Paula Loureiro; Maria Esther Lopes; Roberto Ribeiro; Cecilia Salete Alencar; et al. "Genomic and epidemiological characterisation of a dengue virus outbreak among blood donors in Brazil". Scientific Reports 7 1 (2017): https://doi.org/10.1038/s41598-017-15152-8.
    10.1038/s41598-017-15152-8
  73. José Lourenço; Eleanor R. Watkins; Uri Obolski; Samuel J. Peacock; Callum Morris; Martin C. J. Maiden; Sunetra Gupta; et al. "Lineage structure of Streptococcus pneumoniae may be driven by immune selection on the groEL heat-shock protein". Scientific Reports 7 1 (2017): http://dx.doi.org/10.1038/s41598-017-08990-z.
    10.1038/s41598-017-08990-z
  74. Ben Ashby; Eleanor Watkins; José Lourenço; Sunetra Gupta; Kevin R. Foster. "Competing species leave many potential niches unfilled". Nature Ecology & Evolution 1 10 (2017): 1495-1501. https://doi.org/10.1038/s41559-017-0295-3.
    10.1038/s41559-017-0295-3
  75. José Lourenço; Maricelia Maia de Lima; Nuno Rodrigues Faria; Andrew Walker; Moritz UG Kraemer; Christian Julian Villabona-Arenas; Ben Lambert; et al. "Epidemiological and ecological determinants of Zika virus transmission in an urban setting". eLife 6 (2017): https://doi.org/10.7554/eLife.29820.
    10.7554/eLife.29820
  76. Da Costa, A.C.; Thézé, J.; Komninakis, S.C.V.; Sanz-Duro, R.L.; Felinto, M.R.L.; Moura, L.C.C.; De Oliveira Barroso, I.M.; et al. "Spread of chikungunya virus east/central/South African genotype in northeast Brazil". Emerging Infectious Diseases 23 10 (2017): 1742-1744. http://www.scopus.com/inward/record.url?eid=2-s2.0-85029760310&partnerID=MN8TOARS.
    10.3201/eid2310.170307
  77. Tetyana I. Vasylyeva; Samuel R. Friedman; Jose Lourenco; Sunetra Gupta; Angelos Hatzakis; Oliver G. Pybus; Aris Katzourakis; et al. "Reducing HIV infection in people who inject drugs is impossible without targeting recently-infected subjects". AIDS 30 18 (2016): 2885-2890. https://app.dimensions.ai/details/publication/pub.1043051317.
    10.1097/qad.0000000000001291
  78. Marta Giovanetti; Nuno Rodrigues Faria; Marcio Roberto Teixeira Nunes; Janaina Mota de Vasconcelos; José Lourenço; Sueli Guerreiro Rodrigues; Joao Lidio Vianez, Jr; et al. "Zika virus complete genome from Salvador, Bahia, Brazil". Infection, Genetics and Evolution 41 (2016): 142-145. https://doi.org/10.1016/j.meegid.2016.03.030.
    10.1016/j.meegid.2016.03.030
  79. Faria, Nuno Rodrigues; Lourenço, José; Marques de Cerqueira, Erenilde; Maia de Lima, Maricélia; Carlos Junior Alcantara, Luiz. "Epidemiology of Chikungunya Virus in Bahia, Brazil, 2014-2015". PLoS Currents (2016): http://dx.doi.org/10.1371/currents.outbreaks.c97507e3e48efb946401755d468c28b2.
    10.1371/currents.outbreaks.c97507e3e48efb946401755d468c28b2
  80. A. Von Delft; T. Donnison; S. Chinnakannan; J. Lourenco; C. Hutchings; A. Brown; P. Klenerman; E. Barnes. "FRI-209 The Generation of an Immunogenic Second-Generation Conserved Segment HCV T Cell Vaccine to Target Multiple HCV Genotypes". Journal of Hepatology (2016): https://app.dimensions.ai/details/publication/pub.1051209410.
    10.1016/s0168-8278(16)00877-1
  81. Flasche, S.; Jit, M.; Rodríguez-Barraquer, I.; Coudeville, L.; Recker, M.; Koelle, K.; Milne, G.; et al. "The Long-Term Safety, Public Health Impact, and Cost-Effectiveness of Routine Vaccination with a Recombinant, Live-Attenuated Dengue Vaccine (Dengvaxia): A Model Comparison Study". PLoS Medicine 13 11 (2016): http://www.scopus.com/inward/record.url?eid=2-s2.0-84999670040&partnerID=MN8TOARS.
    10.1371/journal.pmed.1002181
  82. Faria, N.R.; Do Socorro Da Silva Azevedo, R.; Kraemer, M.U.G.; Souza, R.; Cunha, M.S.; Hill, S.C.; Thézé, J.; et al. "Zika virus in the Americas: Early epidemiological and genetic findings". Science 352 6283 (2016): 345-349. http://www.scopus.com/inward/record.url?eid=2-s2.0-84961653991&partnerID=MN8TOARS.
    10.1126/science.aaf5036
  83. Lourenço, J.; Recker, M.. "Dengue serotype immune-interactions and their consequences for vaccine impact predictions". Epidemics 16 (2016): 40-48. http://www.scopus.com/inward/record.url?eid=2-s2.0-84971413858&partnerID=MN8TOARS.
    10.1016/j.epidem.2016.05.003
  84. Walker AS; Lourenço J; Hill AV; Gupta S. "Modeling Combinations of Pre-erythrocytic Plasmodium falciparum Malaria Vaccines.". (2015): http://europepmc.org/abstract/med/26503278.
    10.4269/ajtmh.14-0767
  85. Paul S. Wikramaratna; José Lourenço; Paul Klenerman; Oliver G. Pybus; Sunetra Gupta. "Effects of neutralizing antibodies on escape from CD8 + T-cell responses in HIV-1 infection". Philosophical Transactions of the Royal Society B: Biological Sciences 370 1675 (2015): 20140290-20140290. https://doi.org/10.1098/rstb.2014.0290.
    10.1098/rstb.2014.0290
  86. Watkins ER; Penman BS; Lourenço J; Buckee CO; Maiden MC; Gupta S. "Vaccination Drives Changes in Metabolic and Virulence Profiles of Streptococcus pneumoniae.". (2015): http://europepmc.org/abstract/med/26181911.
    10.1371/journal.ppat.1005034
  87. Lourenço J; Wikramaratna PS; Gupta S. "MANTIS: an R package that simulates multilocus models of pathogen evolution.". (2015): http://europepmc.org/abstract/med/26017358.
    10.1186/s12859-015-0598-9
  88. Lourenço J; Recker M. "The 2012 Madeira dengue outbreak: epidemiological determinants and future epidemic potential.". (2014): http://europepmc.org/abstract/med/25144749.
    10.1371/journal.pntd.0003083
  89. Lourenço, J.; Recker, M.. "Natural, Persistent Oscillations in a Spatial Multi-Strain Disease System with Application to Dengue". PLoS Computational Biology 9 10 (2013): http://www.scopus.com/inward/record.url?eid=2-s2.0-84887294358&partnerID=MN8TOARS.
    10.1371/journal.pcbi.1003308
  90. Lourenço, J.; Recker, M.. "Viral and epidemiological determinants of the invasion dynamics of Novel Dengue Genotypes". PLoS Neglected Tropical Diseases 4 11 (2010): http://www.scopus.com/inward/record.url?eid=2-s2.0-78649772319&partnerID=MN8TOARS.
    10.1371/journal.pntd.0000894
  91. Águas, R.; Lourenço, J.M.L.; Gomes, M.G.M.; White, L.J.. "The impact of IPTi and IPTc interventions on malaria clinical burden - In Silico perspectives". PLoS ONE 4 8 (2009): http://www.scopus.com/inward/record.url?eid=2-s2.0-68949155477&partnerID=MN8TOARS.
    10.1371/journal.pone.0006627
  92. van Noort, S.P.; Muehlen, M.; Rebelo de Andrade, H.; Koppeschaar, C.; Lima Lourenço, J.M.; Gomes, M.G.. "Gripenet: an internet-based system to monitor influenza-like illness uniformly across Europe.". Euro surveillance : bulletin européen sur les maladies transmissibles = European communicable disease bulletin 12 7 (2007): http://www.scopus.com/inward/record.url?eid=2-s2.0-38449104486&partnerID=MN8TOARS.
    10.2807/esm.12.07.00722-en
Preprint
  1. Martim Afonso Geraldes; Mónica V. Cunha; Carlos Godinho; Ricardo Faustino de Lima; Marta Giovanetti; José Lourenço. "The historical ecological background of West Nile virus in Portugal provides One Health opportunities into the future". 2023. https://doi.org/10.1101/2023.11.30.569416.
    10.1101/2023.11.30.569416
  2. Branda, Francesco; Nakase, Taishi; Maruotti, Antonello; Scarpa, Fabio; Ciccozzi, Alessandra; Romano, Chiara; Peletto, Simone; et al. "Dengue virus transmission in Italy: surveillance and epidemiological trends up to 2023". 2023. http://dx.doi.org/10.1101/2023.12.19.23300208.
    10.1101/2023.12.19.23300208
  3. Pereira, André C.; Lourenço, José; Themudo, Gonçalo; Botelho, Ana; Cunha, Mónica V.. "Population structure and history ofMycobacterium bovisEuropean 3 clonal complex reveal transmission across ecological corridors of unrecognised importance in Portugal". 2023. http://dx.doi.org/10.1101/2023.11.01.564909.
    10.1101/2023.11.01.564909
  4. Nakase, Taishi; Giovanetti, Marta; Obolski, Uri; Lourenço, José. "A retrospective analysis of climate-based dengue virus transmission suitability and demographic changes over the last four decades". 2023. http://dx.doi.org/10.1101/2023.11.21.23298791.
    10.1101/2023.11.21.23298791

Intellectual property

Copyright registration
  1. 2019. "MVSE - mosquito-vector suitability estimator (R-package)".
    Registered
  2. 2015. "MANTIS - multi-locus antigenic simulator (R-package)".
    Registered
Patent
  1. Lourenço, José. 2018. "HCV Vaccines / Project 10355 / Serial 16/087,352". United States.
    Pending
Provisional application for patent
  1. 2023. "Polypeptides and immunogenic compositions, particularly vaccine compositions, for the prevention or treatment of influenza A".
    Disclosed
  2. 2022. "Polypeptides and immunogenic compositions, particularly vaccine compositions, for the prevention or treatment of influenza B".
    Disclosed

Other

Other output
  1. Preventing future pandemics and epidemics through a North-South collaboration on genomic surveillance in Africa. 2022. Vittorio Colizzi; Claudia Alteri; Stefano D'amelio; Ibrahim Hassan Garba; Marta Giovanetti; Florence Komurian-Pradel; Lourenço, José; et al. https://ciencia.ucp.pt/en/publications/0fd446d8-8328-436a-b309-8c8bd7e3f8a3.
    10.4081/jphia.2022.2319
  2. Analysis and visualization of epidemics on the timescale of burden: derivation and application of Epidemic Resistance Lines (ERLs) to COVID-19 outbreaks in the US. 2021. Alex Washburne; Justin Silverman; Jose Lourenco; Nathaniel Hupert. https://doi.org/10.1101/2021.05.03.21256542.
    10.1101/2021.05.03.21256542
  3. Chikungunya virus outbreak in the Amazon region: replacement of the Asian genotype by an ECSA lineage. 2018. Felipe Gomes Naveca; Ingra Claro; Marta Giovanetti; Jaqueline Goes de Jesus; Joilson Xavier; Felipe Campos de Melo Iani; Valdinete Alves do Nascimento; et al. https://doi.org/10.1101/492595.
    10.1101/492595
  4. Determinants of high residual post-PCV13 pneumococcal vaccine type carriage in Blantyre, Malawi: a modelling study. 2018. J. Lourenço; U. Obolski; T.D. Swarthout; A. Gori; N. Bar-Zeev; D. Everett; A.W. Kamng’ona; et al. https://doi.org/10.1101/477695.
    10.1101/477695
  5. Lineage structure of Streptococcus pneumoniae is driven by immune selection on the groEL heat-shock protein. 2016. José Lourenço; Eleanor R. Watkins; Uri Obolski; Samuel J. Peacock; Callum Morris; Martin C. J. Maiden; Sunetra Gupta. https://doi.org/10.1101/082990.
    10.1101/082990
Activities

Oral presentation

Presentation title Event name
Host (Event location)
2021/12 Seminar/talk "Theoretical epidemiology at BioISI" BioISI Research Seminar
BioISI, FCUL, UL (Lisboa, Portugal)
2021/08 Plenary/keynote talk "Predicting mosquito-borne transmission using climate data" at the workshop VEME 2021 (BIOINFORMATICS WORKSHOP ON VIRUS EVOLUTION AND MOLECULAR EPIDEMIOLOGY).
(Minas Gerais, Brazil)
2021/02 Seminar/talk "Characterising West Nile virus epidemiology in Israel using a transmission suitability index" Dynamical Systems Applied To Biology And Natural Sciences
(Online, Portugal)
2020/12 Seminar/talk "Characterising West Nile virus epidemiology in Israel using a transmission suitability index " Mathematical Biology seminar series
University of Bath (Bath, United Kingdom)
2020/08 Seminar/talk "Characterising West Nile virus epidemiology in Israel using a transmission suitability index " VIRES : Virus Research and Surveillance: Bioinformatics, Genetics and Public Health
(Belo Horizonte, Brazil)
2020/03 "Reunião/capacitação sobre Modelagem de Dados Epidemiológicos" organized by Governo do Estado da Bahia, Brazil. Talk on "Modelagem epidemiológica para predição de risco das arboviroses: Análises preditivas sobre epidemia de Dengue na Ilha da Madeira e sobre epidemia de Zika em Feira de Santana-BA." Reunião/capacitação sobre Modelagem de Dados Epidemiológicos
Governo do Estado da Bahia, Diretoria de Vigilância Epidemiológica (Brazil)
2020/03 Seminar/talk "Population structure of the pneumococcus is driven by selection on the GROEL protein"
INSTITUTO NACIONAL DE TECNOLOGÍA AGROPECUARIA (Buenos Aires, Argentina)
2019/09 Seminar/talk "Applications of the mosquito-borne viral suitability index P" IDD conference
University of Cumbria (Ambleside, United Kingdom)
2019/02 Seminar/talk "Mathematical modelling: from theory to practice" MSc course on mathematical modelling
MSc Modelling for Global Health, Nuffield Department of Medicine (Oxford, United Kingdom)
2018/10 Seminar/talk "The role of HBV vaccination and prevention of mother to child transmission as tools for elimination in the presence of HIV" Peter Medawar day
Peter Medawar Building for Pathogen Research (Oxford, United Kingdom)
2018/06 Seminar/talk "POPULATION STRUCTURE OF THE PNEUMOCOCCUS IS DRIVEN BY SELECTION ON THE GROEL HEAT-SHOCK PROTEIN" at Instituto de tecnologia quimica e biologica (ITQB Nova), Oeiras, Portugal.
Instituto de tecnologia quimica e biologica (ITQB Nova) (Oeiras, Portugal)

Supervision

Thesis Title
Role 		Degree Subject (Type)
Institution / Organization
2023/02/15 - 2025/12/15 Arthropods as transmission vectors of wound-infecting bacteria in a clinical setting
Co-supervisor of Kate Cook
 DPhil Biology - Ineos Oxford Institute (PhD)
Universidade de Oxford, United Kingdom
2021/09 - 2024/09 Understanding the spatio-temporal invasion and establishment process of SARS-CoV-2 in England
Supervisor
 Dphil Theoretical Epidemiology (PhD)
Universidade de Oxford, United Kingdom
2022/12/15 - 2023/12/15 Uncovering the ecological barriers of West Nile virus transmission in Portugal
Supervisor of Martim Afonso Geraldes
 Microbiologia Aplicada (Master)
Universidade de Lisboa, Portugal
2020/09 - 2023/09 Antimicrobial residues (AMD) and mathematical modelling.
Co-supervisor
 DPhil Epidemiology (PhD)
The Royal Veterinary College, United Kingdom
2022/09/15 - 2023/08/15 Predicting the Spatio-Temporal Reproductive Potential of Aedes aegypti
Supervisor of Tarek Alrefae
 Modelling for Global Health (Master)
Universidade de Oxford, United Kingdom
2022/09/15 - 2023/08/15 Predicting Viral Genome Sequencing Outcomes from Sample Variables
Supervisor of Andrea S. Rivera Diaz
 Modelling for Global Health (Master)
Universidade de Oxford, United Kingdom
2021/09 - 2022/09 Scaling up the development and analysis of a spatio-temporal transmission suitability measure for mosquito-borne viruses
Supervisor
 MSc Modelling for Global Health (Master)
Universidade de Oxford, United Kingdom
2021/09/15 - 2022/08/15 Mapping global climate-driven transmission suitability for dengue virus with validation and application in Brazil
Supervisor of Taishi Nakase
 Modelling for Global Health (Master)
Universidade de Oxford, United Kingdom
2020/09 - 2021/06 Developing a framework to analyse drivers of immunity and future outbreaks of Zika virus in Mexico
Supervisor
 Final year dissertation (project proposal), BSc Biology (Degree)
Universidade de Oxford, United Kingdom
2021 - 2021 A comparative review on non-pharmaceutical interventions for infectious respiratory disease outbreaks and their impact for endemic pathogen control
Supervisor
 Oral presentation final year, BSc Biology (Other)
Universidade de Oxford, United Kingdom
2021 - 2021 Mathematical modeling of the spread of Campylobacter in chicken flocks
Supervisor
 LIDo rotation 1 thesis, Royal Veterinary College (Scientific initiation)
The Royal Veterinary College, United Kingdom
2021 - 2021 Multi-locus models of antigenic evolution
Co-supervisor
 UKRI-BBSRC DTP for Interdisciplinary Bioscience, Second Rotation Project (Scientific initiation)
Universidade de Oxford, United Kingdom
2021 - 2021 Targeting disease spread: a game theory perspective
Supervisor
 Oral presentation final year, BSc Biology (Scientific initiation)
Universidade de Oxford, United Kingdom
2021 - 2021 The RTS,S vaccine as a game-changing but imperfect tool against Malaria.
Supervisor
 Oral presentation final year, BSc Biology (Scientific initiation)
Universidade de Oxford, United Kingdom
2020 - 2021 A universal Influenza A vaccine targeting epitopes of limited variability
Supervisor
 Final year dissertation (project proposal), BSc Biology (Degree)
Universidade de Oxford, United Kingdom
2018/09 - 2019/09 Caracterización de la estructura poblacional del virus del dengue serotipo 4 por inmunodinámica inversa
Supervisor
 BSc Biology (Degree)
Universidad Industrial de Santander, Colombia
2018 - 2019 Population-level effects of original antigenic sin in the context of influenza A virus antigenic thrift
Supervisor
 DTP rotation, University College, University of Oxford (Scientific initiation)
Universidade de Oxford, United Kingdom
2018 - 2019 Assessing the usefulness of the established index P and newly proposed index PQ as mosquito-viral suitability measures across multiple geographical regions
Supervisor
 Project dissertation, Hertford College, University of Oxford (Degree)
Universidade de Oxford, United Kingdom
2018 - 2019 Towards a better understanding of the eco-epidemiology of West Nile virus in Israel and Italy
Supervisor
 Project dissertation, New College, University of Oxford (Degree)
Universidade de Oxford, United Kingdom
2018 - 2019 Unravelling the evolution and maintenance of pneumococcal serotypes through their universal allelic profiles
Supervisor
 Project dissertation, St John's College, University of Oxford (Degree)
Universidade de Oxford, United Kingdom
2015/09 - 2018/09 A multi-country study of dengue vaccination modelling using econometric and GIS approaches in three dengue-endemic countries: Vietnam, Thailand, and Colombia
Supervisor
 Doctor of Philosophy, DPhil, Linacre College, Trinity 2018, University of Oxford (PhD)
Universidade de Oxford, United Kingdom
2017 - 2018 Applying Reverse Immunodynamics to the Dengue Virus
Supervisor
 Project dissertation, Jesus College, University of Oxford (Degree)
Universidade de Oxford, United Kingdom
2017 - 2018 What are the causes of the difference in pathogenesis between HIV­-1 and HIV­-2?
Supervisor
 Project dissertation, New College, University of Oxford (Degree)
Universidade de Oxford, United Kingdom
2017 - 2018 The effects of host-population profiles on multi-strain pathogen dynamics
Supervisor
 Project dissertation, St Hugh's College, University of Oxford (Degree)
Universidade de Oxford, United Kingdom
2017 - 2018 How do the sensitivity of CD4 and CD8 responses to HIV-1 affect within-host dynamics?
Supervisor
 Project dissertation, New College, University of Oxford (Degree)
Universidade de Oxford, United Kingdom
2016/09 - 2017/09 Modelling the risk of a Zika virus outbreak in Myanmar
Supervisor
 MSc in International Health and Tropical Medicine, Oriel College, 2017, University of Oxford (Master)
Universidade de Oxford, United Kingdom
2014/09 - 2017/09 The stability of host-pathogen multi-strain models
Supervisor
 Doctor of Philosophy, DPhil, Pembroke College, Trinity 2017, University of Oxford (PhD)
Universidade de Oxford, United Kingdom
2014/09 - 2017/09 Computational approaches to vaccine development for multi-strain pathogens
Supervisor
 Doctor of Philosophy, DPhil, Hertford College, Michaelmas 2017, University of Oxford (PhD)
Universidade de Oxford, United Kingdom
2016 - 2017 Modelling the in-host dynamics of Epstein-Barr virus
Supervisor
 Project dissertation, St Hilda's College, University of Oxford (Degree)
Universidade de Oxford, United Kingdom
2015 - 2016 The Antigenic Thrift hypothesis of influenza
Supervisor
 Project dissertation, St Hilda's College, University of Oxford (Degree)
Universidade de Oxford, United Kingdom
2015 - 2016 Literature evidence for Influenza antigenic thrift in the context of antigenic maps
Supervisor
 Extended Essay, Christ Church College, University of Oxford (Other)
Universidade de Oxford, United Kingdom
2014 - 2015 Drug decriminalisation and HIV: what can we learn from Portugal?
Supervisor
 Extended Essay, Pembroke College, University of Oxford (Other)
Universidade de Oxford, United Kingdom

Event participation

Activity description
Type of event 		Event name
Institution / Organization
2023/12/19 - 2023/12/19 I was one of the principal investigators participating in the Centre for Biomedical Research (CBR, Universidade Católica Portuguesa) Job Shadowing initiative, under which highschool students from the municipality of Oeiras visited my research laboratory, listening to personal & professional experiences, motivations, ambitions and day-to-day tasks of researchers
Meeting
 CBR Job Shadowing initiative
Universidade Católica Portuguesa, Portugal
2023/11/28 - 2023/12/01 Attendance and contribution with a poster to the EPIDEMICS 9 international conference on Infectious Diseases that took place in Bologna, Italy.
Conference
 Epidemics 9
Imperial College London, United Kingdom

Jury of academic degree

Topic
Role 		Candidate name (Type of degree)
Institution / Organization
2021/12 Jury member of the "confirmation" exam for a DPhil/PhD, which takes place 2y post DPhil/PhD start. Failing the exam cancels the DPhil/PhD or transfers the student to another degree (e.g. MSc).
(Thesis) Main arguer
 Stefan Dascalu (PhD)
Universidade de Oxford, United Kingdom
2021/08 Jury member for "Banca Examinadora de Tese de Doutorado " at Universidade Federal de Minas Gerais, Brazil.
(Thesis) Main arguer
 Filipe Campos de Melo Iani (PhD)
Universidade Federal de Minas Gerais, Brazil
2021/05 Jury member of the "viva" exam for a DPhil/PhD, which takes place at the end of a DPhil/PhD. Only two individuals compose the jury (internal and external to the university). Failing the exam cancels the DPhil/PhD.
(Thesis) Main arguer
 Lam Ha (PhD)
Universidade de Oxford, United Kingdom
2021/01 Jury member of the "viva" exam for a DPhil/PhD, which takes place at the end of a DPhil/PhD. Only two individuals compose the jury (internal and external to the university). Failing the exam cancels the DPhil/PhD.
(Thesis) Main arguer
 Willem Bonnaffe (PhD)
Universidade de Oxford, United Kingdom
2020/05 Jury member of the "transfer" exam for a DPhil/PhD, which takes place 1y post DPhil/PhD start. Failing the exam cancels the DPhil/PhD or transfers the student to another degree (e.g. MSc).
(Thesis) Main arguer
 Thomas Rawson (PhD)
Universidade de Oxford, United Kingdom
2020/03 Jury member of the "viva" exam for a DPhil/PhD, which takes place at the end of a DPhil/PhD. Only two individuals compose the jury (internal and external to the university). Failing the exam cancels the DPhil/PhD.
(Thesis) Main arguer
 James Foley (PhD)
Universidade de Oxford, United Kingdom
2020/03 Jury member of "Banca Examinadora de Tese de Doutorado " for Universidade Estadual de Feira de Santana, Brazil.
(Thesis) Main arguer
 Maricélia Maia de Lima (PhD)
Universidade Estadual de Feira de Santana, Brazil
2020/01 Jury member of the "confirmation" exam for a DPhil/PhD, which takes place 2y post DPhil/PhD start. Failing the exam cancels the DPhil/PhD or transfers the student to another degree (e.g. MSc).
(Thesis) Main arguer
 Ming Shan Tsai (PhD)
Universidade de Oxford, United Kingdom
2019/11 Jury member of the "transfer" exam for a DPhil/PhD, which takes place 1y post DPhil/PhD start. Failing the exam cancels the DPhil/PhD or transfers the student to another degree (e.g. MSc).
(Thesis) Main arguer
 Willem Bonnaffe (PhD)
Universidade de Oxford, United Kingdom
2019/08 Jury member of "Banca Examinadora de Qualificação de Doutorado " at the Universidade Federal de Minas Gerais, Brazil. The "Qualificação" exam takes place midway on the PhD as confirmation of status for the student.
(Thesis) Main arguer
 Vagner de Souza Fonseca (PhD)
Universidade Federal de Minas Gerais, Brazil
2018/12 Jury member of the "transfer" exam for a DPhil/PhD, which takes place 1y post DPhil/PhD start. Failing the exam cancels the DPhil/PhD or transfers the student to another degree (e.g. MSc).
(Thesis) Main arguer
 Lam Ha (PhD)
Universidade de Oxford, United Kingdom

Committee member

Activity description
Role 		Institution / Organization
2023/01/01 - Current I am one of twelve members of the committee that evaluates projects submitted under the general topic of Infectious Diseases & Environment (IDE). We represent research experts from different subareas / disciplines related to the IDE topic, reviewing projects and deciding on funding.
Member
 Agence nationale de la recherche, France
2018/09 - 2021/12 Member of the Equality committee of the Department of Zoology, University of Oxford. Committee responsible for examining the performance of the department, as well as proposing changes towards Equality.
Member
 Universidade de Oxford, United Kingdom
2019/09 - 2021/09 Chair of the "Prelims" committee, dedicated to evaluate first year Biology students (BSc/MSc) at the Department of Zoology, University of Oxford. Committee responsible for creating the 3 final exams and their marking.
President / Vice-president
 Universidade de Oxford, United Kingdom

Consulting

Activity description Institution / Organization
2023/11/30 - 2023/12/13 As part of the international consortium CLIMATE (https://climade.health/), I help design and write the report "Epidemics and Climate" for the 2023 United Nations Climate Change Conference (COP2023). United Nations Framework Convention on Climate Change, Germany

Course / Discipline taught

Academic session Degree Subject (Type) Institution / Organization
2023/08/20 - 2023/08/25 Practical (computer lab) course "Epidemiological models: back to basics" at the workshop VEME 2023 (BIOINFORMATICS WORKSHOP ON VIRUS EVOLUTION AND MOLECULAR EPIDEMIOLOGY). Epidemiological models: back to basics (Postgraduate Certificate) Stellenbosch University, South Africa
2022/08/21 - 2022/08/25 Practical (computer lab) course "Epidemiological models: back to basics" at the workshop VEME 2022 (BIOINFORMATICS WORKSHOP ON VIRUS EVOLUTION AND MOLECULAR EPIDEMIOLOGY). Epidemiological models: back to basics (Postgraduate Certificate) Ciudad del Saber, Panama
2020/09 - 2021/12 "Advanced computational skills - data visualization" - curso para alunos de terceiro ano de biologia (BSc/MSc Biology) no Departamento de Zoologia, Universidade de Oxford. Curso inclui métodos avançados de visualização de dados e programação dos mesmos. Advanced computational skills - data visualization (Bachelor) Universidade de Oxford, United Kingdom
2020/09 - 2021/12 "Advanced computational skills - random forests" - curso para alunos de terceiro ano de biologia (BSc/MSc Biology) do Departamento de Zoologia, Universidade de Oxford. Curso inclui métodos de machine learning (random forests) e a sua programação. Advanced computational skills - random forests (Bachelor) Universidade de Oxford, United Kingdom
2019/09 - 2021/12 "Introduction to computation and programming" - course for first year students of Biology (BSc/MSc) at the Department of Zoology, University of Oxford. Introduction to computation and programming (Bachelor) Universidade de Oxford, United Kingdom
2014/09 - 2021/09 "Infectious disease modelling" - practical (computer lab) course with a total of 12 hours, for 2nd year students of Biology (BSc/MSc) at the Department of Zoology, University of Oxford. Infectious disease modelling (Bachelor) Universidade de Oxford, United Kingdom
2021/08 - 2021/08 Practical (computer lab) course "Epidemiological models: back to basics" at the workshop VEME 2021 (BIOINFORMATICS WORKSHOP ON VIRUS EVOLUTION AND MOLECULAR EPIDEMIOLOGY). Epidemiological models: back to basics (Postgraduate Certificate) Universidade Federal de Minas Gerais, Brazil

Journal scientific committee

Journal title (ISSN) Publisher
2019 - Current Nature Scientific Reports (Editor da área de Doenças Infeciosas)

Other jury / evaluation

Activity description Institution / Organization
2023/09/13 - 2023/09/13 Jury member for interviews for the post "recrutamento international de um investigador doutorado na carreira de investigação científica da FCiências.ID no âmbito do projecto OCELOT (call #4383)" from University of Lisbon, Ce3C Universidade de Lisboa, Portugal
2021/05 - 2021/05 Jury member for interviews for the post "Postdoctoral Research Associate – Microbiology and Antimicrobial Resistance / ID 150094" from Department of Zoology Universidade de Oxford, United Kingdom
2020/02 - 2020/02 Jury member for interviews for the post "Postdoctoral Researcher in Mathematical Modelling and Data Analysis / ID 145216" from Department of Zoology Universidade de Oxford, United Kingdom
2019/12 - 2019/12 Jury member for interviews for the post "Mathematical Modeller / ID 143831" from University of Oxford, The Wellcome Trust - Mahidol University - Oxford Tropical Medicine Research Programme (MORU) Universidade de Oxford, United Kingdom
2019/12 - 2019/12 Jury member for interviews for the post "Postdoctoral Research Assistant in Mathematical Modelling / ID 143020" from the Department of Zoology Universidade de Oxford, United Kingdom
2018/07 - 2018/07 Jury member for interviews for the post "Mathematical Modeller / ID 134979" from Centre for Tropical Medicine and Global Health, Peter Medawar Building, Nuffield Department of Medicine. Universidade de Oxford, United Kingdom
2018/04 - 2018/04 Jury member for interviews for the post "DPhil in Population Health / ID 1225414" from University of Oxford Universidade de Oxford, United Kingdom
2017/10 - 2017/10 Jury member for interviews for the post "Senior Health Economist / ID 131156" from Centre for Tropical Medicine and Global Health, Peter Medawar Building, Nuffield Department of Medicine Universidade de Oxford, United Kingdom
2017/10 - 2017/10 Jury member for interviews for the post "Mathematical Modeller / ID 131151" from Centre for Tropical Medicine and Global Health, Peter Medawar Building, Nuffield Department of Medicine Universidade de Oxford, United Kingdom
2016/10 - 2016/10 Jury member of interviews for the position "Research Associate in Bacterial Genomics & Evolutionary Biology / ID 398290" at University College London. University College London Division of Infection and Immunity, United Kingdom