Author

Mário Ramirez

University of LisbonORCID 0000-0002-4084-6233Unclaimed ORCID profile · follow to get notified of new preprints

Biology Disciplines

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Bioinformatics· 2 Microbiology· 2

Signature Assays, Organisms & Methods

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Approach:experimental assay· 3 Research Focus:software / tool· 2 Approach:statistical model· 2 Organism:bacteria (other)· 1 Research Focus:clustering· 1 Assay:DNA methylation· 1 Research Focus:gene regulatory network inference· 1 Research Focus:host-pathogen & immune response· 1

Frequent Co-Authors

Diogo Nuno SilvaiD· 2 shared João André CarriçoiD· 2 shared Miguel P. MachadoiD· 2 shared Adriana TamiiD· 1 shared Alberto J. Martín‐RodrígueziD· 1 shared Ana FriãesiD· 1 shared Ariane NeumanniD· 1 shared Catarina Inês MendesiD· 1 shared

Activity by Year

2018-2025 · peak 2/yr

Co-Author Collaboration Network

10 top collaborators · 17 mutual co-author links

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2 shared papersBioinformatics

Diogo Nuno SilvaORCID

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Author profile →

4 papers

Recent·Most cited

Streptococcus pyogenes nuclease A interferes with host complement functions

Isabella Andersson Bennig, Joel Ströbaek, Rafael Mamede, Ariane Neumann, Ana Friães, Mário Ramirez, Michael Hall, Mattias Collin, Lars Malmström, Simon Ekström, Inga-Maria Frick, Lars Björck, Lotta Happonen

This study identifies SpnA's role in inhibiting the complement system by interacting with C5b67, preventing membrane attack complex assembly.

bioRxiv · Aug 25, 2025 · PreprintMicrobiology

Polyphasic discrimination of Shewanella seohaensis from closely related species and a whole-genome multilocus (wgMLST) scheme for the evaluation of diversity within this Shewanella clade

Maria O. Firmino, Mykyta Forofontov, Ricardo Soares, Ricardo O. Louro, Alberto J. Martín‐Rodríguez, Mário Ramirez, Catarina M. Paquete

This paper develops a whole-genome multilocus sequence typing (wgMLST) scheme to accurately discriminate Shewanella seohaensis from closely related species and assess their diversity.

Applied and Environmental Microbiology · Aug 13, 2025Peer-reviewedMicrobiology

DEN-IM: Dengue Virus identification from shotgun and targeted metagenomics

Catarina Inês Mendes, Erley Lizarazo, Miguel P. Machado, Diogo Nuno Silva, Adriana Tami, Mário Ramirez, Natacha Couto, John W. A. Rossen, João André Carriço

DEN-IM is a workflow for analyzing DENV sequencing data from shotgun and targeted metagenomics, enabling CDS inference, serotype/genotype identification, and phylogenetic tree generation.

bioRxiv · May 6, 2019 · PreprintBioinformatics

chewBBACA: A complete suite for gene-by-gene schema creation and strain identification

Mickael Silva, Miguel P. Machado, Diogo Nuno Silva, Mirko Rossi, Jacob Moran‐Gilad, Sérgio M. Santos, Mário Ramirez, João André Carriço

The paper introduces chewBBACA, a software suite for creating gene-by-gene schemas and identifying bacterial strains, offering scalable and open-source solutions for genomic epidemiology.

Microbial Genomics · Mar 1, 2018Peer-reviewedBioinformatics