| Critical steps in clinical shotgun metagenomics for the concomitant detection and typing of microbial pathogens N Couto, L Schuele, EC Raangs, MP Machado, CI Mendes, TF Jesus, ... Scientific reports 8 (1), 13767, 2018 | 72 | 2018 |
| Distinct Phenotypic and Genomic Signatures Underlie Contrasting Pathogenic Potential of Staphylococcus epidermidis Clonal Lineages D Espadinha, RG Sobral, CI Mendes, G Méric, SK Sheppard, JA Carriço, ... Frontiers in Microbiology 10, 1971, 2019 | 47 | 2019 |
| Beta-hemolytic Streptococcus dysgalactiae strains isolated from horses are a genetically distinct population within the Streptococcus dysgalactiae taxon MD Pinho, E Erol, B Ribeiro-Gonçalves, CI Mendes, JA Carriço, SC Matos, ... Scientific reports 6 (1), 31736, 2016 | 28 | 2016 |
| Future-proofing and maximizing the utility of metadata: The PHA4GE SARS-CoV-2 contextual data specification package EJ Griffiths, RE Timme, CI Mendes, AJ Page, NF Alikhan, D Fornika, ... GigaScience 11, giac003, 2022 | 26 | 2022 |
| The PHA4GE SARS-CoV-2 contextual data specification for open genomic epidemiology EJ Griffiths, RE Timme, AJ Page, N Alikhan, D Fornika, F Maguire, ... | 14 | 2020 |
| Detection of a novel mcr-5.4 gene variant in hospital tap water by shotgun metagenomic sequencing G Fleres, N Couto, L Schuele, MA Chlebowicz, CI Mendes, ... Journal of Antimicrobial Chemotherapy 74 (12), 3626-3628, 2019 | 14 | 2019 |
| Accelerating bioinformatics implementation in public health KG Libuit, EL Doughty, JR Otieno, F Ambrosio, CJ Kapsak, EA Smith, ... Microbial Genomics 9 (7), 001051, 2023 | 10 | 2023 |
| Streptococcus pneumoniae serotype 3 in México (1994 to 2017): Decrease of the unusual clonal complex 4909 Lineage following PCV13 introduction G Echániz-Aviles, SI Guerreiro, C Silva-Costa, CI Mendes, JA Carriço, ... Journal of Clinical Microbiology 57 (1), 10.1128/jcm. 01354-18, 2019 | 9 | 2019 |
| LMAS: evaluating metagenomic short de novo assembly methods through defined communities CI Mendes, P Vila-Cerqueira, Y Motro, J Moran-Gilad, JA Carriço, ... GigaScience 12, giac122, 2023 | 6 | 2023 |
| Critical steps in clinical shotgun metagenomics for the concomitant detection and typing of microbial pathogens. Sci Rep 8: 13767 N Couto, L Schuele, EC Raangs, MP Machado, CI Mendes, TF Jesus, ... | 6 | 2018 |
| Author correction: critical steps in clinical shotgun metagenomics for the concomitant detection and typing of microbial pathogens N Couto, L Schuele, EC Raangs, MP Machado, CI Mendes, TF Jesus, ... Scientific Reports 9, 2019 | 4 | 2019 |
| Putting everything in its place: using the INSDC compliant Pathogen Data Object Model to better structure genomic data submitted for public health applications RE Timme, I Karsch-Mizrachi, Z Waheed, M Arita, D MacCannell, ... Microbial Genomics 9 (12), 001145, 2023 | 3 | 2023 |
| PHA4GE quality control contextual data tags: standardized annotations for sharing public health sequence datasets with known quality issues to facilitate testing and training EJ Griffiths, I Mendes, F Maguire, JL Guthrie, BA Wee, S Schmedes, ... Microbial Genomics 10 (6), 001260, 2024 | 2 | 2024 |
| hAMRonization: Enhancing antimicrobial resistance prediction using the PHA4GE AMR detection specification and tooling I Mendes, E Griffiths, A Manuele, D Fornika, SH Tausch, T Le Viet, ... bioRxiv, 2024.03. 07.583950, 2024 | 2 | 2024 |
| Software testing in microbial bioinformatics: a call to action BCL van der Putten, CI Mendes, BM Talbot, J de Korne-Elenbaas, ... Microbial Genomics 8 (3), 000790, 2022 | 2 | 2022 |
| DEN-IM: dengue virus genotyping from amplicon and shotgun metagenomic sequencing CI Mendes, E Lizarazo, MP Machado, DN Silva, A Tami, M Ramirez, ... Microbial genomics 6 (3), e000328, 2020 | 2 | 2020 |
| POS1426 Unraveling the mysteries of the connection between gut and the chronic activation of the immune system in systemic lupus erythematosus I Almada-Correia, M Castro, C Motta, CS Guerreiro, RA Moura, ... Annals of the Rheumatic Diseases 82 (Suppl 1), 1066-1067, 2023 | 1 | 2023 |
| Lessons learned in virulence factor identification and data management from a hackathon on microbial virulence BE Pickett, R Connor, T Berhanu-Denka, S Bhalla, V Brover, ... F1000Research 11, 160, 2022 | 1 | 2022 |
| Towards accreditation in metagenomics for clinical microbiology CI Mendes | | 2023 |
| DEN-IM: Dengue Virus identification from shotgun and targeted metagenomics CI Mendes, E Lizarazo, MP Machado, DN Silva, A Tami, M Ramirez, ... bioRxiv, 628073, 2019 | | 2019 |
João André CarriçobioMérieux Industry and Researcher, Faculty of Medicine, University of LisbonPatvirtintas el. paštas fm.ul.pt
