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List of works by Mario Ramirez

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

Analysis of group B streptococcal isolates from infants and pregnant women in Portugal revealing two lineages with enhanced invasiveness. ⬇️

scientific article

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

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

scientific article published on 19 March 2015

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

scientific article

Capsular Transformation of a Multidrug‐ResistantStreptococcus pneumoniaeIn Vivo ⬇️

scientific article published on March 1, 1998

Capsule impairs efficient adherence of Streptococcus agalactiae to intestinal epithelium in tilapias Oreochromis sp.

scientific article

Changes in Streptococcus pneumoniae serotypes causing invasive disease with non-universal vaccination coverage of the seven-valent conjugate vaccine

scientific article

Changes in emm types and superantigen gene content of Streptococcus pyogenes causing invasive infections in Portugal

scientific article published on 02 December 2019

Changing epidemiology of group B streptococcal infections among adults in Iceland: 1975-2014.

scientific article published on 12 December 2015

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

scientific article published on April 2005

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 alternative mixture model methods to analyze bacterial CGH experiments with multi-genome arrays.

scientific article

Conjugate vaccine serotypes persist as major causes of non-invasive pneumococcal pneumonia in Portugal despite declines in serotypes 3 and 19A (2012-2015)

scientific article published in PLoS ONE

DNA methylase activity as a marker for the presence of a family of phage-like elements conferring efflux-mediated macrolide resistance in streptococci.

scientific article published on 5 September 2006

Decrease in macrolide resistance and clonal instability among Streptococcus pyogenes in Portugal.

scientific article published on 21 November 2008

Denmark14-230 clone as an increasing cause of pneumococcal infection in Portugal within a background of diverse serotype 19A lineages.

scientific article

Distribution of pilus islands in Streptococcus agalactiae that cause human infections: insights into evolution and implication for vaccine development

scientific article published on 26 December 2012

Dominance of vaccine serotypes in pediatric invasive pneumococcal infections in Portugal (2012-2015)

scientific article published in Scientific Reports

Emergence of optochin resistance among Streptococcus pneumoniae in Portugal.

scientific article published in January 2006

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

scientific article published in December 2015

Epidemiological survey of the first case of vancomycin-resistant Staphylococcus aureus infection in Europe

scientific article published on 5 June 2014

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

scientific article (publication date: 2011)

Expanding the diagnosis of pediatric bacteremic pneumococcal pneumonia from blood cultures to molecular methods: advantages and caveats.

scientific article

Export of the pneumococcal phage SV1 lysin requires choline‐containing teichoic acids and is holin‐independent ⬇️

scientific article published on December 11, 2012

First case of infection with vancomycin-resistant Staphylococcus aureus in Europe

scientific article published on 21 June 2013

Fluoroquinolone resistance in Streptococcus dysgalactiae subsp. equisimilis and evidence for a shared global gene pool with Streptococcus pyogenes.

scientific article published on 9 February 2010

Genomic analysis reveals the molecular basis for capsule loss in the group B Streptococcus population

scientific article

Group B streptococci causing neonatal infections in barcelona are a stable clonal population: 18-year surveillance.

scientific article

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

scientific article published on 01 February 2020

Heterogeneity of pneumococcal phase variants in invasive human infections.

scientific article published on 26 July 2006

Identification of immunoreactive extracellular proteins of Streptococcus agalactiae in bovine mastitis

scientific article published on 01 November 2008

Identification of macrolide-resistant clones of Streptococcus pyogenes in Portugal

scientific article published in June 2006

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

Induction of prophages by fluoroquinolones in Streptococcus pneumoniae: implications for emergence of resistance in genetically-related clones

scientific article

Invasive Streptococcus pneumoniae from Portugal: implications for vaccination and antimicrobial therapy

scientific article

Macrolide-resistant Streptococcus pyogenes: prevalence and treatment strategies.

scientific article

Molecular Characterization of the Complete 23F Capsular Polysaccharide Locus of Streptococcus pneumoniae ⬇️

scientific article published on October 1, 1998

Molecular Epidemiology of Penicillin-Resistant Streptococcus pneumoniae Isolates Recovered in Italy from 1993 to 1996 ⬇️

scientific article published on October 1, 1998

Non-invasive pneumococcal pneumonia in Portugal--serotype distribution and antimicrobial resistance

scientific article

Nonoutbreak surveillance of group A streptococci causing invasive disease in Portugal identified internationally disseminated clones among members of a genetically heterogeneous population

scientific article published on 25 April 2007

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

PCR based differentiation between Streptococcus dysgalactiae subsp. equisimilis strains isolated from humans and horses.

scientific article published on 26 April 2014

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

Pediatric Complicated Pneumonia Caused by Streptococcus pneumoniae Serotype 3 in 13-Valent Pneumococcal Conjugate Vaccinees, Portugal, 2010-2015

scientific article published in July 2018

Pherotype influences biofilm growth and recombination in Streptococcus pneumoniae

scientific article

Pherotypes are driving genetic differentiation within Streptococcus pneumoniae.

scientific article published on 7 September 2009

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

scientific article published on 01 January 2019

Population Structure of Streptococcus pneumoniae Causing Invasive Disease in Adults in Portugal before PCV13 Availability for Adults: 2008-2011.

scientific article

Prophage spontaneous activation promotes DNA release enhancing biofilm formation in Streptococcus pneumoniae

scientific article (publication date: 20 December 2010)

Rapid inversion of the prevalences of macrolide resistance phenotypes paralleled by a diversification of T and emm types among Streptococcus pyogenes in Portugal

scientific article published on May 2005

Reevaluating the serotype II capsular locus of Streptococcus agalactiae

scientific article published on 22 August 2007

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

Serotype 3 Remains the Leading Cause of Invasive Pneumococcal Disease in Adults in Portugal (2012-2014) Despite Continued Reductions in Other 13-Valent Conjugate Vaccine Serotypes

scientific article

Serotype discrimination of encapsulated Streptococcus pneumoniae strains by Fourier-transform infrared spectroscopy and chemometrics.

scientific article published on 13 March 2013

Serotypes 1, 7F and 19A became the leading causes of pediatric invasive pneumococcal infections in Portugal after 7 years of heptavalent conjugate vaccine use.

scientific article published on 15 June 2010

Streptococcus agalactiae in a large Portuguese teaching hospital: antimicrobial susceptibility, serotype distribution, and clonal analysis of macrolide-resistant isolates

scientific article

Streptococcus agalactiae serotype Ib as an agent of meningitis in two adult nonpregnant women

scientific article

Superantigen gene complement of Streptococcus pyogenes--relationship with other typing methods and short-term stability

scientific article published on 31 August 2012

The autolysin LytA contributes to efficient bacteriophage progeny release in Streptococcus pneumoniae

scientific article published on 6 July 2009

The presence of the pilus locus is a clonal property among pneumococcal invasive isolates. ⬇️

scientific article

Use of the 13-valent conjugate vaccine has the potential to eliminate pilus carrying isolates as causes of invasive pneumococcal disease

scientific article published on 29 June 2012

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

scientific article published on 15 March 2018

miR-363-5p regulates endothelial cell properties and their communication with hematopoietic precursor cells

scientific article

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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