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Chewie Nomenclature Server (chewie-NS): a deployable nomenclature server for easy sharing of core and whole genome MLST schemas

Nucleic acids research, 2021-01, Vol.49 (D1), p.D660-D666

2021

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Analysis of Typing Methods for Epidemiological Surveillance of both Methicillin-Resistant and Methicillin-Susceptible Staphylococcus aureus Strains

Journal of Clinical Microbiology, 2008-01, Vol.46 (1), p.136-144

2008

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Distance-based phylogenetic inference from typing data: a unifying view

Briefings in bioinformatics, 2021-05, Vol.22 (3), p.1-16

2021

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Scarlet fever is caused by a limited number of Streptococcus pyogenes lineages and is associated with the exotoxin genes ssa, speA and speC

The Pediatric infectious disease journal, 2014-03, Vol.33 (3), p.306-310

2014

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Large-Scale Simulations of Bacterial Populations Over Complex Networks

Journal of computational biology, 2018-08, Vol.25 (8), p.850-861

2018

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Polymerase Chain Reaction for the in vitro detection of the pESI plasmid associated with the globally circulating Salmonella Infantis outbreak strain

Letters in applied microbiology, 2023-08, Vol.76 (8)

2023

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Clinical and molecular epidemiology of Acinetobacter baumannii bloodstream infections in an endemic setting

Future microbiology, 2017-03, Vol.12 (4), p.271-283

2017

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PHYLOViZ 2.0: providing scalable data integration and visualization for multiple phylogenetic inference methods

Bioinformatics (Oxford, England), 2017-01, Vol.33 (1), p.128-129

2017

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Prognostic Prediction through Biclustering-Based Classification of Clinical Gene Expression Time Series

Journal of integrative bioinformatics, 2011-12, Vol.8 (3), p.73-89

2011

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PHYLOViZ: phylogenetic inference and data visualization for sequence based typing methods

BMC bioinformatics, 2012-05, Vol.13 (1), p.87-87, Article 87

2012

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Global optimal eBURST analysis of multilocus typing data using a graphic matroid approach

BMC bioinformatics, 2009-05, Vol.10 (152), p.152-152, Article 152

2009

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Adjusted Wallace Coefficient as a Measure of Congruence between Typing Methods

Journal of Clinical Microbiology, 2011-11, Vol.49 (11), p.3997-4000

2011

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Analysis of Invasiveness of Pneumococcal Serotypes and Clones Circulating in Portugal before Widespread Use of Conjugate Vaccines Reveals Heterogeneous Behavior of Clones Expressing the Same Serotype

Journal of Clinical Microbiology, 2011-04, Vol.49 (4), p.1369-1375

2011

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Critical steps in clinical shotgun metagenomics for the concomitant detection and typing of microbial pathogens

Scientific reports, 2018-09, Vol.8 (1), p.13767-13, Article 13767

2018

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Using Spark and GraphX to Parallelize Large-Scale Simulations of Bacterial Populations over Host Contact Networks

Algorithms and Architectures for Parallel Processing, p.591-600

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Plasmid ATLAS: plasmid visual analytics and identification in high-throughput sequencing data

Nucleic acids research, 2019-01, Vol.47 (D1), p.D188-D194

2019

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Phylogenetic and clonality analysis of Bacillus pumilus isolates uncovered a highly heterogeneous population of different closely related species and clones

FEMS microbiology ecology, 2014-12, Vol.90 (3), p.689-698

2014

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Food Safety in the Age of Next Generation Sequencing, Bioinformatics, and Open Data Access

Frontiers in microbiology, 2017-05, Vol.8, p.909-909

2017

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Distinct phenotypic and genomic signatures underlie contrasting pathogenic potential of Staphylococcus epidermidis clonal lineages

Frontiers in microbiology, 2019, Vol.10, p.1971

2019

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High Rates of Transmission of and Colonization by Streptococcus pneumoniae and Haemophilus influenzae within a Day Care Center Revealed in a Longitudinal Study

Journal of Clinical Microbiology, 2008-01, Vol.46 (1), p.225-234

2008

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Not seeing the forest for the trees: size of the minimum spanning trees (MSTs) forest and branch significance in MST-based phylogenetic analysis

PloS one, 2015-03, Vol.10 (3), p.e0119315-e0119315

2015

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Evaluation of jackknife and bootstrap for defining confidence intervals for pairwise agreement measures

PloS one, 2011-05, Vol.6 (5), p.e19539-e19539

2011

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Highly Penicillin-Resistant Multidrug-Resistant Pneumococcus-Like Strains Colonizing Children in Oeiras, Portugal: Genomic Characteristics and Implications for Surveillance

Journal of Clinical Microbiology, 2010-01, Vol.48 (1), p.238-246

2010

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Beta-hemolytic Streptococcus dysgalactiae strains isolated from horses are a genetically distinct population within the Streptococcus dysgalactiae taxon

Scientific reports, 2016-08, Vol.6 (1), p.31736-31736, Article 31736

2016

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Fast phylogenetic inference from typing data

Algorithms for molecular biology, 2018-02, Vol.13 (1), p.4-4, Article 4

2018

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Chewie Nomenclature Server (chewie-NS): a deployable nomenclature server for easy sharing of core and whole genome MLST schemas

Analysis of Typing Methods for Epidemiological Surveillance of both Methicillin-Resistant and Methicillin-Susceptible Staphylococcus aureus Strains

Distance-based phylogenetic inference from typing data: a unifying view

Scarlet fever is caused by a limited number of Streptococcus pyogenes lineages and is associated with the exotoxin genes ssa, speA and speC

Large-Scale Simulations of Bacterial Populations Over Complex Networks

Polymerase Chain Reaction for the in vitro detection of the pESI plasmid associated with the globally circulating Salmonella Infantis outbreak strain

Clinical and molecular epidemiology of Acinetobacter baumannii bloodstream infections in an endemic setting

PHYLOViZ 2.0: providing scalable data integration and visualization for multiple phylogenetic inference methods

Prognostic Prediction through Biclustering-Based Classification of Clinical Gene Expression Time Series

PHYLOViZ: phylogenetic inference and data visualization for sequence based typing methods

Global optimal eBURST analysis of multilocus typing data using a graphic matroid approach

Adjusted Wallace Coefficient as a Measure of Congruence between Typing Methods

Analysis of Invasiveness of Pneumococcal Serotypes and Clones Circulating in Portugal before Widespread Use of Conjugate Vaccines Reveals Heterogeneous Behavior of Clones Expressing the Same Serotype

Critical steps in clinical shotgun metagenomics for the concomitant detection and typing of microbial pathogens

Using Spark and GraphX to Parallelize Large-Scale Simulations of Bacterial Populations over Host Contact Networks

Plasmid ATLAS: plasmid visual analytics and identification in high-throughput sequencing data

Phylogenetic and clonality analysis of Bacillus pumilus isolates uncovered a highly heterogeneous population of different closely related species and clones

Food Safety in the Age of Next Generation Sequencing, Bioinformatics, and Open Data Access

Distinct phenotypic and genomic signatures underlie contrasting pathogenic potential of Staphylococcus epidermidis clonal lineages

High Rates of Transmission of and Colonization by Streptococcus pneumoniae and Haemophilus influenzae within a Day Care Center Revealed in a Longitudinal Study

Not seeing the forest for the trees: size of the minimum spanning trees (MSTs) forest and branch significance in MST-based phylogenetic analysis

Evaluation of jackknife and bootstrap for defining confidence intervals for pairwise agreement measures

Highly Penicillin-Resistant Multidrug-Resistant Pneumococcus-Like Strains Colonizing Children in Oeiras, Portugal: Genomic Characteristics and Implications for Surveillance

Beta-hemolytic Streptococcus dysgalactiae strains isolated from horses are a genetically distinct population within the Streptococcus dysgalactiae taxon

Fast phylogenetic inference from typing data

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