João André Carriço

发表

Bioinformatics in bacterial molecular epidemiology and public health: databases, tools and the next-generation sequencing revolution.

João André Carriço, A. Sabat, A. Friedrich, 2013, Euro surveillance : bulletin Europeen sur les maladies transmissibles = European communicable disease bulletin.

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

Alexandre P. Francisco, M. Achtman, Zhemin Zhou, 2017, bioRxiv.

Not Seeing the Forest for the Trees: Size of the Minimum Spanning Trees (MSTs) Forest and Branch Significance in MST-Based Phylogenetic Analysis

Alexandre P. Francisco, Pedro T. Monteiro, Andreia Sofia Teixeira, 2015, PloS one.

Data integration gets 'Sloppy'

Helena F. Deus, G. Mills, Fan Zhang, 2006, Nature Biotechnology.

INNUENDO: A cross‐sectoral platform for the integration of genomics in the surveillance of food‐borne pathogens

Diogo N. Silva, João André Carriço, J. Lundén, 2018, EFSA Supporting Publications.

Expert opinion on whole genome sequencing for public health surveillance

Karin Johansson, Ivo Van Walle, Denis Coulombier, 2016 .

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

João André Carriço, N. Frazão, H. de Lencastre, 2005, Microbial drug resistance.

Analysis of Typing Results

João André Carriço, M. Ramirez, 2014 .

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

Mickael Silva, Mário Ramirez, Bruno Ribeiro-Gonçalves, 2017, Methods in molecular biology.

Adjusted Wallace Coefficient as a Measure of Congruence between Typing Methods

João André Carriço, M. Ramirez, Francisco R. Pinto, 2011, Journal of Clinical Microbiology.

Comparison of Molecular Typing Methods for Characterization of Staphylococcus epidermidis: Proposal for Clone Definition

João André Carriço, M. Enright, J. Thomas, 2007, Journal of Clinical Microbiology.

Properties of Novel International Drug-Resistant Pneumococcal Clones Identified in Day-Care Centers of Lisbon, Portugal

João André Carriço, N. Frazão, H. de Lencastre, 2005, Journal of Clinical Microbiology.

Natural Occurrence of Escherichia coli-Infecting Bacteriophages in Clinical Samples

João André Carriço, F. Hilbert, N. Dinhopl, 2019, Front. Microbiol..

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

A. B. Avô, João André Carriço, H. de Lencastre, 2005, Journal of Clinical Microbiology.

The Use of Machine Learning Methodologies to Analyse Antibiotic and Biocide Susceptibility in Staphylococcus aureus

A. T. Freitas, I. Morrissey, J. Martínez, 2013, PloS one.

Effect of the Seven-Valent Conjugate Pneumococcal Vaccine on Carriage and Drug Resistance of Streptococcus pneumoniae in Healthy Children Attending Day-Care Centers in Lisbon

João André Carriço, N. Frazão, H. de Lencastre, 2005, The Pediatric infectious disease journal.

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

João André Carriço, M. P. van der Linden, M. Ramirez, 2019, The Journal of antimicrobial chemotherapy.

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

João André Carriço, M. Ramirez, M. Machado, 2018, Euro surveillance : bulletin Europeen sur les maladies transmissibles = European communicable disease bulletin.

A widespread family of polymorphic toxins encoded by temperate phages

M. Touchon, E. Rocha, João André Carriço, 2017, BMC Biology.

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

Tiago F Jesus, A. Friedrich, João André Carriço, 2018, Scientific Reports.

Spontaneous genomic variation as a survival strategy of nosocomial S. haemolyticus

João André Carriço, H. de Lencastre, M. Miragaia, 2022, bioRxiv.

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

A. Friedrich, João André Carriço, J. Rossen, 2018, Microbes and infection.

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

J. Ferreira, João André Carriço, R. Chan, 2017, Parkinsonism & related disorders.

Scarlet Fever Is Caused By a Limited Number of Streptococcus pyogenes Lineages and Is Associated with the Exotoxin Genes ssa, speA and speC

João André Carriço, M. Ramirez, J. Melo-Cristino, 2014, The Pediatric infectious disease journal.

Pathogenesis and host ResPonse

João André Carriço, M. Ramirez, J. Melo-Cristino, 2022 .

Molecular Epidemiology of Streptococcus pneumoniae

João André Carriço, M. Ramirez, J. Melo-Cristino, 2015 .

Comparison of Molecular Typing Methods for Characterization of Staphylococcus epidermidis : Proposal for Clone Deﬁnition (cid:1) †

João André Carriço, M. Enright, J. Thomas, 2007 .

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

João André Carriço, P. Hermans, H. Bootsma, 2009, Journal of Clinical Microbiology.

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

João André Carriço, M. Ramirez, J. Melo-Cristino, 2017, PloS one.

Streptococcus pneumoniae Serotype 3 in Mexico (1994 to 2017): Decrease of the Unusual Clonal Complex 4909 Lineage following PCV13 Introduction

João André Carriço, Soraia I. Guerreiro, M. Ramirez, 2018, Journal of Clinical Microbiology.

EFSA and ECDC technical report on the collection and analysis of whole genome sequencing data from food‐borne pathogens and other relevant microorganisms isolated from human, animal, food, feed and food/feed environmental samples in the joint ECDC‐EFSA molecular typing database

G. Cochrane, T. Dallman, J. Mossong, 2019, EFSA Supporting Publications.

Highly Specific Blood-Brain Barrier Transmigrating Single-Domain Antibodies Selected by an In Vivo Phage Display Screening

C. Barbas, João André Carriço, J. Correia, 2021, Pharmaceutics.

DEN-IM: dengue virus genotyping from amplicon and shotgun metagenomic sequencing

Diogo N. Silva, João André Carriço, J. Rossen, 2020, Microbial genomics.

Molecular Characterization of Methicillin-Resistant Staphylococcus epidermidis Clones: Evidence of Geographic Dissemination

João André Carriço, S. Pereira, H. Westh, 2002, Journal of Clinical Microbiology.

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

Alexandre P. Francisco, Cátia Vaz, Pedro T. Monteiro, 2012, BMC Bioinformatics.

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

João André Carriço, M. Ramirez, J. Melo-Cristino, 2015, Journal of Clinical Microbiology.

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

Alexandre P. Francisco, João A. Carriço, Miguel Bugalho, 2009, BMC Bioinformatics.

Genome analysis of Legionella pneumophila ST23 from various countries reveals highly similar strains

M. Faccini, M. Scaturro, João André Carriço, 2022, Life Science Alliance.

Two multi-fragment recombination events resulted in the β-lactam-resistant serotype 11A-ST6521 related to Spain9V-ST156 pneumococcal clone spreading in south-western Europe, 2008 to 2016

João André Carriço, E. Cercenado, M. Ramirez, 2020, Euro surveillance : bulletin Europeen sur les maladies transmissibles = European communicable disease bulletin.

Insights into the population structure and pan-genome of Haemophilus influenzae.

João André Carriço, M. Machado, J. P. Gomes, 2019, Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases.

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

João André Carriço, H. de Lencastre, R. Sá-Leão, 2007, Journal of Clinical Microbiology.

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

J. Lopes, João André Carriço, G. Klein, 2014, International journal of systematic and evolutionary microbiology.

Analysis of genomic sequences by Chaos Game Representation

Jonas S. Almeida, João A. Carriço, António Maretzek, 2001, Bioinform..

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

Alexandre P. Francisco, Cátia Vaz, João A. Carriço, 2016, Nucleic Acids Res..

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

S. Sheppard, João André Carriço, G. Méric, 2019, Front. Microbiol..

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

Mickael Silva, Mário Ramirez, João A Carriço, 2020, Nucleic Acids Res..

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

João A. Carriço, Luis Pedro Coelho, Luís Pedro Coelho, 2015, Bioinform..

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

Alexandre P. Francisco, Cátia Vaz, João A. Carriço, 2017, Bioinform..

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

João A. Carriço, Mário Ramirez, Natacha Couto, 2019, bioRxiv.

A widespread family of polymorphic toxins encoded by temperate phages

M. Touchon, E. Rocha, João André Carriço, 2017, BMC Biology.

A primer on microbial bioinformatics for nonbioinformaticians.

J A Carriço, M Rossi, J Moran-Gilad, 2018, Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases.

Lactobacillus mulieris sp. nov., a new species of Lactobacillus delbrueckii group.

João André Carriço, L. Peixe, M. Pintado, 2020, International journal of systematic and evolutionary microbiology.

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

João André Carriço, M. Machado, M. Rossi, 2017, bioRxiv.

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

João A. Carriço, Gary Van Domselaar, Eduardo N. Taboada, 2017, Front. Microbiol..

Assessment of Band-Based Similarity Coefficients for Automatic Type and Subtype Classification of Microbial Isolates Analyzed by Pulsed-Field Gel Electrophoresis

J A Carriço, João André Carriço, N. Frazão, 2005, Journal of Clinical Microbiology.

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

João André Carriço, M. Ramirez, H. de Lencastre, 2007, Journal of Clinical Microbiology.

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

Alexandre P. Francisco, Cátia Vaz, João A. Carriço, 2010, JBI.

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

Jonas S. Almeida, João A. Carriço, Mário Ramirez, 2007, BMC Bioinformatics.

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

João A. Carriço, Valeria Bortolaia, Mário Ramirez, 2018, Nucleic Acids Res..

Evaluation of Jackknife and Bootstrap for Defining Confidence Intervals for Pairwise Agreement Measures

João A. Carriço, Mário Ramirez, João André Carriço, 2011, PloS one.

Illustration of a Common Framework for Relating Multiple Typing Methods by Application to Macrolide-Resistant Streptococcus pyogenes

J A Carriço, M Ramirez, João André Carriço, 2006, Journal of Clinical Microbiology.

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

João Carriço, Catarina Pato, João André Carriço, 2015, mBio.

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

João A Carriço, Mário Ramirez, João André Carriço, 2011, Journal of Clinical Microbiology.

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

S. Madeira, João André Carriço, A. Carreiro, 2011, J. Integr. Bioinform..

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

V. Chalifa-Caspi, João André Carriço, J. Moran-Gilad, 2017, Future microbiology.

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

João André Carriço, L. Peixe, M. Pintado, 2014, FEMS microbiology ecology.

Citrobacter portucalensis sp. nov., isolated from an aquatic sample.

João André Carriço, L. Peixe, T. Ribeiro, 2017, International journal of systematic and evolutionary microbiology.

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

João André Carriço, L. Wieler, S. Preziuso, 2016, Scientific Reports.

Characterization of the Genetic Lineages Responsible for Pneumococcal Invasive Disease in Portugal

J A Carriço, M Ramirez, João André Carriço, 2005, Journal of Clinical Microbiology.

The Integrated Rapid Infectious Disease Analysis (IRIDA) Platform

Cedric Chauve, Geoffrey L. Winsor, Fiona S. L. Brinkman, 2018, bioRxiv.

BacPipe: A Rapid, User-Friendly Whole-Genome Sequencing Pipeline for Clinical Diagnostic Bacteriology

Herman Goossens, Blaise T. F. Alako, Peter W. Harrison, 2019, iScience.

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

Eduardo N. Taboada, João André Carriço, Peter Kruczkiewicz, 2018, bioRxiv.

Invasiveness of pneumococcal serotypes and clones circulating in Portugal before widespread use of conjugate vaccines revealing heterogeneous behavior of clones expressing the same serotype

João André Carriço, N. Frazão, S. Nunes, 2011 .

CcrB typing tool: an online resource for staphylococci ccrB sequence typing.

Arlindo L. Oliveira, S. Vinga, João André Carriço, 2008, The Journal of antimicrobial chemotherapy.

Large-Scale Simulations of Bacterial Populations Over Complex Networks

Alexandre P. Francisco, F. C. Santos, Pedro T. Monteiro, 2018, J. Comput. Biol..

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

Francisco C. Santos, Alexandre P. Francisco, F. C. Santos, 2017, ICA3PP.

BacPipe: A Rapid, User-Friendly Whole-Genome Sequencing Pipeline for Clinical Diagnostic Bacteriology

Blaise T. F. Alako, Peter W. Harrison, G. Cochrane, 2019, iScience.

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

João André Carriço, M. Machado, M. Rossi, 2017, Scientific Reports.

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

Alexandre P. Francisco, Pedro T. Monteiro, João André Carriço, 2012, BMC Bioinformatics.

TypOn: the microbial typing ontology

Keith A. Jolley, James E. Bray, Alexandre P. Francisco, 2014, Journal of Biomedical Semantics.