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Inês Mendes
Inês Mendes
Theiagen Genomics
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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
712018
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
422019
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
262016
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
232022
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
152019
The PHA4GE SARS-CoV-2 contextual data specification for open genomic epidemiology
EJ Griffiths, RE Timme, AJ Page, N Alikhan, D Fornika, F Maguire, ...
142020
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
92019
Accelerating bioinformatics implementation in public health
KG Libuit, EL Doughty, JR Otieno, F Ambrosio, CJ Kapsak, EA Smith, ...
Microbial Genomics 9 (7), 001051, 2023
62023
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, ...
62018
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
42023
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
42019
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
12023
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, ...
12023
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
12022
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
12022
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
12020
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
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