List of works by Joao Andre Carrico

A Primer on Microbial Bioinformatics for non-bioinformaticians

scientific article published on 5 January 2018

A widespread family of polymorphic toxins encoded by temperate phages.

scientific article published on 29 August 2017

Adjusted Wallace coefficient as a measure of congruence between typing methods.

scientific article published on 14 September 2011

An Ontology and a REST API for Sequence Based Microbial Typing Data

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. ⬇️

scientific article published on 26 January 2011

Analysis of typing methods for epidemiological surveillance of both methicillin-resistant and methicillin-susceptible Staphylococcus aureus strains.

scientific article published on 7 November 2007

Assessment of band-based similarity coefficients for automatic type and subtype classification of microbial isolates analyzed by pulsed-field gel electrophoresis

scientific article

Automatic determination of NET (neutrophil extracellular traps) coverage in fluorescent microscopy images.

scientific article published on 19 March 2015

Bacillus invictae sp. nov., isolated from a health product

scientific article

Baiacu: A Tool for the Visual Analysis of the Saccharomyces Cerevisiae Regulatory Network

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

scientific article

Biclustering-Based Classification of Clinical Expression Time Series: A Case Study in Patients with Multiple Sclerosis

scientific article published in 2011

Building the national health information infrastructure for personal health, health care services, public health, and research

scientific article

Characterization of the genetic lineages responsible for pneumococcal invasive disease in Portugal

scientific article published on April 2005

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

scientific article published on 24 February 2017

Clonal and serotype dynamics of serogroup 6 isolates causing invasive pneumococcal disease in Portugal: 1999-2012.

scientific article

Comparing Matrix-Assisted Laser Desorption Ionization-Time of Flight Mass Spectrometry and Phenotypic and Molecular Methods for Identification of Species within the Streptococcus anginosus Group.

scientific article published on 9 September 2015

Comparison of molecular typing methods for characterization of Staphylococcus epidermidis: proposal for clone definition.

scientific article published on 7 November 2007

Data integration gets 'Sloppy'

scientific article

Distinct Phenotypic and Genomic Signatures Underlie Contrasting Pathogenic Potential of Staphylococcus epidermidis Clonal Lineages

scientific article published on 27 August 2019

Draft Genome Sequence of Escherichia coli DSM 12242, a Highly Efficient Host Strain for the Isolation of Somatic Coliphages

scientific article published on 19 September 2019

ESCMID postgraduate education course: regional capacity building for integration of next-generation sequencing in the clinical microlab

scientific article published on 17 March 2018

Emergence of the Same Successful Clade among Distinct Populations of emm89 Streptococcus pyogenes in Multiple Geographic Regions.

scientific article published in December 2015

Epidemiological Surveillance and Typing Methods to Track Antibiotic Resistant Strains Using High Throughput Sequencing

scientific article published on January 2017

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

scientific article (publication date: 2011)

Fast phylogenetic inference from typing data.

scientific article published on 15 February 2018

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

scientific article

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

scientific article published on 26 July 2018

Heterogeneity of penicillin-non-susceptible group B streptococci isolated from a single patient in Germany

scientific article published on 01 February 2020

High rates of transmission of and colonization by Streptococcus pneumoniae and Haemophilus influenzae within a day care center revealed in a longitudinal study

scientific article

Highly penicillin-resistant multidrug-resistant pneumococcus-like strains colonizing children in Oeiras, Portugal: genomic characteristics and implications for surveillance

scientific article

Illustration of a common framework for relating multiple typing methods by application to macrolide-resistant Streptococcus pyogenes.

scientific article published on July 2006

Increasing macrolide resistance among Streptococcus agalactiae causing invasive disease in non-pregnant adults was driven by a single capsular-transformed lineage, Portugal, 2009 to 2015

article

Large-Scale Simulations of Bacterial Populations Over Complex Networks

scientific article published on 09 July 2018

Molecular characterization of methicillin-resistant Staphylococcus epidermidis clones: evidence of geographic dissemination

scientific article

Natural history of drug-resistant clones of Streptococcus pneumoniae colonizing healthy children in Portugal.

scientific article published in January 2005

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

scientific article published on 23 March 2015

Origin, evolution, and distribution of the molecular machinery for biosynthesis of sialylated lipooligosaccharide structures in Campylobacter coli

scientific article published on 14 February 2018

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

scientific article

PHYLOViZ Online: web-based tool for visualization, phylogenetic inference, analysis and sharing of minimum spanning trees

scientific article

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

scientific article

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

scientific article published on 6 October 2014

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

scientific article published on 01 January 2019

Properties of novel international drug-resistant pneumococcal clones identified in day-care centers of Lisbon, Portugal.

scientific article

Ranked Adjusted Rand: integrating distance and partition information in a measure of clustering agreement

scientific article

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

scientific article published on March 2014

Serum lipid alterations in GBA-associated Parkinson's disease.

scientific article

The use of machine learning methodologies to analyse antibiotic and biocide susceptibility in Staphylococcus aureus.

scientific article

Trends in drug resistance, serotypes, and molecular types of Streptococcus pneumoniae colonizing preschool-age children attending day care centers in Lisbon, Portugal: a summary of 4 years of annual surveillance

scientific article

TypOn: the microbial typing ontology

scientific article

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

serotype 3 in Mexico (1994-2017): decrease of the unusual CC4909 lineage post-PCV13 introduction

scientific article published on 02 January 2019

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