Author

João André Carriço

University of LisbonORCID 0000-0002-5274-2722Unclaimed ORCID profile · follow to get notified of new preprints

Biology Disciplines

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Signature Assays, Organisms & Methods

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Organism:bacteria (other)· 3 Approach:statistical model· 3 Assay:whole-genome sequencing· 3 Approach:experimental assay· 2 Research Focus:software / tool· 2 Research Focus:clustering· 1 Research Focus:database / resource· 1 Research Focus:gene regulatory network inference· 1

Frequent Co-Authors

Diogo Nuno SilvaiD· 2 shared Mário RamireziD· 2 shared Miguel P. MachadoiD· 2 shared Mirko RossiiD· 2 shared Adriana TamiiD· 1 shared Alexandre P. FranciscoiD· 1 shared Catarina Inês MendesiD· 1 shared Cátia VaziD· 1 shared

Activity by Year

2018-2019 · peak 3/yr

Co-Author Collaboration Network

10 top collaborators · 17 mutual co-author links

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2 shared papersBioinformatics

Diogo Nuno SilvaORCID

Mutual co-authors in cluster

Author profile →

4 papers

Recent·Most cited

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

GrapeTree: Visualization of core genomic relationships among 100,000 bacterial pathogens

Zhemin Zhou, Nabil-Fareed Alikhan, Martin J. Sergeant, Nina Luhmann, Cátia Vaz, Alexandre P. Francisco, João André Carriço, Mark Achtman

GrapeTree visualizes genomic relationships among 100,000 bacterial pathogens using a minimum spanning tree algorithm and interactive layouts.

Genome Research · Sep 1, 2018Peer-reviewedBioinformatics

Rapid Identification of Stable Clusters in Bacterial Populations Using the Adjusted Wallace Coefficient

Dillon Oliver Reese Barker, João André Carriço, Peter Kruczkiewicz, Féderica Palma, Mirko Rossi, Eduardo Napoleon Taboada

The paper introduces nAWC to identify stable clusters in bacterial populations using WGS data, showing it produces robust clusters that reflect population structure.

bioRxiv · Apr 16, 2018 · PreprintGenomics

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