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 | 71 | 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, 463823, 2019 | 42 | 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 | 26 | 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 | 23 | 2022 |
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 | 15 | 2019 |
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 |
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 | 8 | 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 | 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 |
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 | 4 | 2023 |
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 |
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 |
PHA4GE quality control contextual data tags: standardized annotations for sharing public health sequence datasets with known quality issues to facilitate testing and training E Griffiths, CI Mendes, F Maguire, J Guthrie, L Chindelevitch, ... | 1 | 2023 |
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 | 1 | 2022 |
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 |
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 | 1 | 2020 |
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 | | 2023 |
Towards accreditation in metagenomics for clinical microbiology CI Mendes | | 2023 |
The PHA4GE SARS-CoV-2 Contextual Data Specification for Open Genomic Epidemiology (preprint) EJ Griffiths, RE Timme, AJ Page, NF Alikhan, D Fornika, F Maguire, ... | | 2020 |
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 |