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Rafael Fresca Mamede. Completed the Mestrado in Bioinformática e Biologia Computacional in 2019/02/15 by Universidade de Lisboa Faculdade de Ciências and Licenciatura in Biologia in 2016/07/21 by Universidade de Lisboa Faculdade de Ciências. Attends the Doutoramento in Doctorate Degree (PhD) in Doctoral Programme of the Academic Medical Centre of Lisbon by Universidade de Lisboa Faculdade de Medicina since 2021/01/01. Is Researcher in Instituto de Medicina Molecular João Lobo Antunes. Published 7 articles in journals. Participated in 8 event(s). Participates and/or participated as PhD Student Fellow in 1 project(s) and Researcher in 1 project(s). Works in the area(s) of Exact Sciences with emphasis on Computer and Information Sciences with emphasis on Bioinformatics, Natural sciences with emphasis on Biological Sciences with emphasis on Biology, Natural sciences with emphasis on Biological Sciences with emphasis on Molecular Biology and Natural sciences with emphasis on Biological Sciences with emphasis on Microbiology. In his curriculum Ciência Vitae the most frequent terms in the context of scientific, technological and artistic-cultural output are: Metagenomics; Metataxonomics; Graph matching; Taxonomic classification; 16S rRNA gene; Bacterial typing; Bioinformatics; Pangenome; Public health; Whole Genome Sequencing; Outbreak investigation; .
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Identification

Personal identification

Full name
Rafael Fresca Mamede

Citation names

  • Mamede, Rafael

Author identifiers

Ciência ID
8010-DA91-FC9D
ORCID iD
0000-0002-8691-0771
Google Scholar ID
8uAfOnIAAAAJ&hl

Email addresses

  • rmamede@medicina.ulisboa.pt (Professional)
  • rfm.1991.cas@gmail.com (Personal)

Telephones

Mobile phone
  • (+351) 916069963 (Personal)
Telephone
  • (+351) 217999411 (Professional)

Addresses

  • Faculdade de Medicina da Universidade de Lisboa, Av. Professor Egas Moniz, 1649-028, Lisboa, Lisboa, Portugal (Professional)

Websites

Knowledge fields

  • Exact Sciences - Computer and Information Sciences - Bioinformatics
  • Natural sciences - Biological Sciences - Biology
  • Natural sciences - Biological Sciences - Molecular Biology
  • Natural sciences - Biological Sciences - Microbiology

Languages

Language Speaking Reading Writing Listening Peer-review
Portuguese (Mother tongue)
English Advanced (C1) Proficiency (C2) Advanced (C1) Proficiency (C2)
Education
Degree Classification
2021/01/01 - 2025/01/01
Ongoing
 Doctorate Degree (PhD) in Doctoral Programme of the Academic Medical Centre of Lisbon (Doutoramento)
Major in Bioinformatics and Computational Biology
Universidade de Lisboa Faculdade de Medicina, Portugal

Instituto de Medicina Molecular João Lobo Antunes, Portugal
"Inter-laboratory reproducibility and expansion of the gene-by-gene typing approach in an era of whole genome sequencing" (THESIS/DISSERTATION)
2017/09 - 2019/02/15
Concluded
 Bioinformática e Biologia Computacional (Mestrado)
Major in Área de especialização: Bioinformática
Universidade de Lisboa Faculdade de Ciências, Portugal
"New approaches for taxonomic identification and profiling of polyclonal samples based on Next Generation Sequencing" (THESIS/DISSERTATION)
 18 valores
2009/09 - 2016/07/21
Concluded
 Biologia (Licenciatura)
Major in Biologia Molecular e Genética
Universidade de Lisboa Faculdade de Ciências, Portugal
 13
Affiliation

Science

Category
Host institution 		Employer
2024/10 - Current Researcher (Research) Gulbenkian Institute for Molecular Medicine, Portugal
Gulbenkian Institute for Molecular Medicine, Portugal
(...)
2019/07 - 2024/09 Researcher (Research) Instituto de Medicina Molecular João Lobo Antunes, Portugal
Instituto de Medicina Molecular João Lobo Antunes, Portugal
(...)
2019/04/08 - 2019/07/08 Researcher (Research) Associação para a Investigação e Desenvolvimento da Faculdade de Medicina, Portugal
Instituto de Medicina Molecular João Lobo Antunes, Portugal
Projects

Grant

Designation Funders
2023/11/01 - 2025/06/30 CENTAUR: Creating and refining whole-genome and core-genome typing schemas for pathogen surveillance
ISID_JRA_gun1
Researcher
Instituto de Medicina Molecular João Lobo Antunes, Portugal

Instituto Nacional de Saúde Doutor Ricardo Jorge, Portugal

Institut Pasteur, France
European Union
Ongoing
2021/01/01 - 2025/01/01 Inter-laboratory reproducibility and expansion of the gene-by-gene typing approach in an era of whole genome sequencing
2020.08493.BD
PhD Student Fellow
Instituto de Medicina Molecular João Lobo Antunes, Portugal

Universidade de Lisboa Faculdade de Medicina, Portugal
Fundação para a Ciência e a Tecnologia
Ongoing
Outputs

Publications

Conference abstract
  1. Riche, C.V.W.; Mamede, Rafael; Pereira, R.I.; Carriço, J.A.; Dias, C.A.G.; Ramirez, Mário. "Decline of the Brazilian endemic clone and dominance of internationally disseminated lineages among MRSA from bacteraemic patients in Porto Alegre, Brazil". Paper presented in ECCMID, 2020.
    Accepted • 10.1190/sbgf2017-101
  2. Mamede, Rafael; Melo-Cristino, José; Ramirez, Mário; Martins, Elisabete. "Emergence of penicillin non-susceptible group B streptococci within the hypervirulent CC17 clone colonizing pregnant women in Portugal – a genomic analysis". Paper presented in ECCMID, 2020.
    Accepted
Conference poster
  1. Friães, Ana; Gouveia, Catarina; Bajanca-Lavado, Maria Paula; Mamede, Rafael; Melo-Cristino, José; Ramirez, Mário. "Paediatric invasive group A streptococcal infections in Portugal: post-pandemic expansion of the M1UK sub-lineage circulating since 2014/15". Paper presented in ECCMID, 2024.
  2. Friães, Ana; Santos, B; Mamede, Rafael; Marrão, G; Melo-Cristino, José; Ramirez, Mário. "Increasing macrolide resistance among pharyngeal Streptococcus pyogenes in a Portuguese hospital due to emm2-ST55 lineage carrying mef(A)-msr(D)". Paper presented in ECCMID, 2024.
  3. Mamede, Rafael; Friães, Ana; Ferreira, Mariana; Melo-Cristino, José; Ramirez, Mário. "Enabling high resolution typing of Streptococcus pyogenes with a novel whole-genome multilocus sequence typing schema". Paper presented in 13th International Meeting on Microbial Epidemiological Markers (IMMEM XIII), 2022.
  4. Mamede, Rafael; Vila-Cerqueira, Pedro; Ramirez, Mário. "Optimizing the gene-by-gene approach for bacterial typing with chewBBACA 3". Paper presented in 13th International Meeting on Microbial Epidemiological Markers (IMMEM XIII), 2022.
  5. de Almeida, Inês; Forofontov, Mykyta; Mamede, Rafael; Ramirez, Mário. "Schema Refinery: a tool to assist in the creation of cg/wgMLST schemas with chewBBACA". Paper presented in 13th International Meeting on Microbial Epidemiological Markers (IMMEM XIII), 2022.
  6. Forofontov, Mykyta; de Almeida, Inês; Mamede, Rafael; Martins, Elisabete; Ramirez, Mário. "Creation of a schema for gene-by-gene typing of Streptococcus agalactiae". Paper presented in 13th International Meeting on Microbial Epidemiological Markers (IMMEM XIII), 2022.
  7. Friães, Ana; Mamede, Rafael; Melo-Cristino, José; Ramirez, Mário. "High resolution typing of Streptococcus pyogenes using a novel whole genome multilocus sequence typing (wgMLST) schema". Paper presented in 21st Lancefield International Symposium for Streptococci and Streptococcal Diseases (LISSSD), 2022.
  8. Mamede, Rafael; Vila-Cerqueira, Pedro; Ramirez, Mário. "Accelerating the gene-by-gene approach for bacterial genomics with chewBBACA 3.0". Paper presented in 13th International Meeting on Microbial Epidemiological Markers (IMMEM XIII), 2022.
  9. Mamede, Rafael; Vila-Cerqueira, Pedro; Ramirez, Mário. "Fast, faster, fastest: improving an allele calling algorithm for whole-genome multilocus sequence typing (wgMLST)". Paper presented in ECCMID 2021, 2021.
  10. Riche, C.V.W.; Mamede, Rafael; Falci, D.R.; Carriço, João André; Ramirez, Mário; Dias, C.A.G.. "MRSA invasive infections: epidemiology and risk-factors for mortality in bacteraemic patients in Porto Alegre, Brazil". Paper presented in ECCMID 2021, 2021.
  11. Vila-Cerqueira, Pedro; Mamede, Rafael; Friães, Ana; Ramirez, Mário. "Defining publicly available whole-genome multilocus sequence typing schemas - the example of Streptococcus pyogenes". Paper presented in ECCMID 2021, 2021.
  12. Mamede, Rafael; Vila-Cerqueira, Pedro; Friães, Ana; Ramirez, Mário. "Towards a framework for the definition of publicly available whole-genome multilocus sequence typing schemas - the example of Streptococcus pyogenes". Paper presented in GenomePT Symposium, 2021.
  13. Mamede, Rafael; Vila-Cerqueira, Pedro; Ramirez, Mário. "The need for speed: improving an allele calling algorithm for whole-genome multilocus sequence typing (wgMLST)". Paper presented in Applied Bioinformatics & Public Health Microbiology 2021, 2021.
  14. Vila-Cerqueira, Pedro; Mamede, Rafael; Friães, Ana; Ramirez, Mário. "Tracking strains is simpler if you use common schemas from public repositories". Paper presented in Applied Bioinformatics & Public Health Microbiology 2021, 2021.
  15. Mamede, Rafael; Vila-Cerqueira, Pedro; Silva, Mickael; Carriço, João André; Ramirez, Mário. "Enabling easy sharing of gene-by-gene typing schemas and results based on a common allelic nomenclature". Paper presented in iMM Computational Biology and Bioinformatics Day, 2020.
  16. Mamede, Rafael; Melo-Cristino, José; Ramirez, Mário; Martins, Elisabete. "Genomic characterization of emerging penicillin non-susceptibility among group B streptococci". Paper presented in Bioinformatics Open Days, 2020.
  17. Vila-Cerqueira, Pedro; Mamede, Rafael; Silva, Mickael; Carriço, João André; Ramirez, Mário. "Chewie-NS: Enabling the use of gene-by-gene typing methods through a public and centralized service". Paper presented in Bioinformatics Open Days, 2020.
  18. Sim-Sim, Maria; Garcia, César; Martins, Anabela; Fontinha, Susana; Sérgio, Cecília; Mamede, Rafael; Belém, Cláudia (2A13-EE87-B7C6); Matos, Ana Rita; Stech, Michael. "Biogeographic inference of early land plants. Disentangle the evolutionary patterns in the natural forests of Atlantic Archipelagos". Paper presented in 2nd cE3c Annual Meeting, 2016.
Journal article
  1. Catarina Gouveia; Maria Paula Bajanca-Lavado; Rafael Mamede; Ana Araújo Carvalho; Fernanda Rodrigues; José Melo-Cristino; Mario Ramirez; Ana Friães. "Sustained increase of paediatric invasive Streptococcus pyogenes infections dominated by M1UK and diverse emm12 isolates, Portugal, September 2022 to May 2023". Eurosurveillance (2023): https://doi.org/10.2807/1560-7917.ES.2023.28.36.2300427.
    10.2807/1560-7917.ES.2023.28.36.2300427
  2. A. Friães; R. Mamede; M. Ferreira; J. Melo-Cristino; Mario Ramirez. "Annotated Whole-Genome Multilocus Sequence Typing Schema for Scalable High-Resolution Typing of Streptococcus pyogenes". Journal of Clinical Microbiology (2022): http://dx.doi.org/10.1128/jcm.00315-22.
    10.1128/jcm.00315-22
  3. Boas C.L. van der Putten; C. I. Mendes; Brooke M. Talbot; Jolinda de Korne-Elenbaas; Rafael Mamede; Pedro Vila-Cerqueira; Luis Pedro Coelho; Christopher A. Gulvik; Lee S. Katz. "Software testing in microbial bioinformatics: a call to action". Microbial Genomics (2022): https://doi.org/10.1099/mgen.0.000790.
    Published • 10.1099/mgen.0.000790
  4. Cezar Vinícius Würdig Riche; Rafael Mamede; Renato Cassol; Diego Rodrigues Falci; João André Carriço; Mario Ramirez. "EPIDEMIOLOGIA E FATORES DE RISCO PARA MORTALIDADE EM BACTEREMIAS OCASIONADAS POR MRSA DE PORTO ALEGRE, RS". The Brazilian Journal of Infectious Diseases (2022): http://dx.doi.org/10.1016/j.bjid.2021.102239.
    10.1016/j.bjid.2021.102239
  5. Mihkel Mäesaar; Rafael Mamede; Terje Elias; Mati Roasto; João Paulo Gomes. "Retrospective Use of Whole-Genome Sequencing Expands the Multicountry Outbreak Cluster of Listeria monocytogenes ST1247". International Journal of Genomics 2021 (2021): 1-5. https://doi.org/10.1155/2021/6636138.
    Published • 10.1155/2021/6636138
  6. Mamede, Rafael; Vila-Cerqueira, Pedro; Silva, Mickael; Carriço, João André; Ramirez, Mário. "Chewie Nomenclature Server (chewie-NS): a deployable nomenclature server for easy sharing of core and whole genome MLST schemas". Nucleic Acids Research (2020): http://dx.doi.org/10.1093/nar/gkaa889.
    Published • 10.1093/nar/gkaa889
  7. van der Linden, Mark; Mamede, Rafael; Levina, Natascha; Helwig, Peter; Vila-Cerqueira, Pedro; Carriço, João André; Melo-Cristino, José; Ramirez, Mário; Martins, Elisabete. "Heterogeneity of penicillin-non-susceptible group B streptococci isolated from a single patient in Germany". Journal of Antimicrobial Chemotherapy (2019): http://dx.doi.org/10.1093/jac/dkz465.
    10.1093/jac/dkz465
Preprint
  1. 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
Thesis / Dissertation
  1. Mamede, Rafael. "New approaches for taxonomic identification and profiling of polyclonal samples based on next generation sequencing". Master, Universidade de Lisboa Faculdade de Ciências, 2019. http://hdl.handle.net/10451/37740.
Activities

Oral presentation

Presentation title Event name
Host (Event location)
2023/10/31 Data analysis pitfalls - The example of a cancer microbiome study Pizza Seminar
Instituto de Medicina Molecular João Lobo Antunes (Lisbon, Portugal)
2023/09/19 Scalable and reproducible wg/cgMLST analysis of bacterial pathogens iMM Scientific Retreat 2023
Instituto de Medicina Molecular João Lobo Antunes (Lisbon, Portugal)
2023/05 Scalable and detailed wg/cgMLST analysis of bacterial pathogens with chewBBACA XVI CAML PhD Students Meeting
Instituto de Medicina Molecular João Lobo Antunes (Lisbon, Portugal)
2023/03/28 (Not So) Fantastic Bacteria And How To Type Them Pizza Seminar
Instituto de Medicina Molecular João Lobo Antunes (Lisbon, Portugal)
2022/04/06 Break it to understand it - Sequence k-mers Computational Biology and Bioinformatics Seminars
Instituto de Medicina Molecular João Lobo Antunes (Lisbon, Portugal)
2021/05 Exploiting the complementary nature of alignment-based and alignment-free methods to enhance an allele calling algorithm for whole-genome multilocus sequence typing (wgMLST) XIV CAML · IV NeurULisboa PhD Students Virtual Meeting
Instituto de Medicina Molecular João Lobo Antunes (Lisbon, Portugal)
2020/10/21 Enabling easy sharing of gene-by-gene typing schemas and results based on a common allelic nomenclature Computational Biology and Bioinformatics Day
Instituto de Medicina Molecular João Lobo Antunes (Lisbon, Portugal)

Event participation

Activity description
Type of event 		Event name
Institution / Organization
2023/09/19 - 2023/09/19 iMM Scientific Retreat 2023
Meeting
 iMM Scientific Retreat 2023
Instituto de Medicina Molecular João Lobo Antunes, Portugal
2023/05 - 2023/05 XVI CAML PhD Students Meeting
Meeting
 XVI CAML PhD Students Meeting
Instituto de Medicina Molecular João Lobo Antunes, Portugal
2022/09/14 - 2022/09/17 13th International Meeting on Microbial Epidemiological Markers (IMMEM XIII)
Conference
 13th International Meeting on Microbial Epidemiological Markers (IMMEM XIII)
European Society of Clinical Microbiology and Infectious Diseases, Switzerland
2021/07/04 - 2021/07/04 GenomePT Symposium
Symposium
 GenomePT Symposium
2021/05/05 - 2021/05/07 Applied Bioinformatics & Public Health Microbiology 2021
Conference
 Applied Bioinformatics & Public Health Microbiology 2021
Wellcome Connecting Science, United Kingdom
2021/05 - 2021/05 XIV CAML · IV NeurULisboa PhD Students Virtual Meeting
Meeting
 XIV CAML · IV NeurULisboa PhD Students Virtual Meeting
Instituto de Medicina Molecular João Lobo Antunes, Portugal
2020/10/21 - 2020/10/21 Computational Biology and Bioinformatics Day
Conference
 Computational Biology and Bioinformatics Day
Instituto de Medicina Molecular João Lobo Antunes, Portugal
2020/02/19 - 2020/02/21 IX Bioinformatics Open Days
Congress
 IX Bioinformatics Open Days
Universidade do Minho, Portugal
Distinctions

Award

2024 Best Oral Presentation in Health Sciences and Technologies, XVII CAML PhD Students Meeting
Universidade de Lisboa Faculdade de Medicina, Portugal
2022 Travel Grant
Quadram Institute, United Kingdom