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people:ramirez [2014/11/21 11:01]
ramirez [Publications]
people:ramirez [2022/07/12 15:22] (current)
ramirez
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-<span id='​badgeCont708855'​ style='​width:​126px'​><​script src='http://labs.researcherid.com/​mashlets?​el=badgeCont708855&​mashlet=badge&​showTitle=false&​className=a&​rid=B-4993-2008'></​script></​span>​+<span id="​badgeCont652"​><​script ​type="​text/​javascript" ​src="https://publons.com/​mashlets?​el=badgeCont652&​rid=B-4993-2008"></​script></​span>​
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 [[http://​orcid.org/​0000-0002-4084-6233|{{:​people:​orcid-logo.png?​150|0000-0002-4084-6233}}]] [[http://​orcid.org/​0000-0002-4084-6233|{{:​people:​orcid-logo.png?​150|0000-0002-4084-6233}}]]
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 ===== Current Position ===== ===== Current Position =====
-**Associate Professor**\\ ​+**Associate Professor** ​("com agregação"​)\\ 
 Instituto de Microbiologia,​[[http://​www.fm.ul.pt/​|Faculdade de Medicina de Lisboa]], [[http://​www.ul.pt/​|Universidade de Lisboa]], Lisboa, Portugal\\ ​ Instituto de Microbiologia,​[[http://​www.fm.ul.pt/​|Faculdade de Medicina de Lisboa]], [[http://​www.ul.pt/​|Universidade de Lisboa]], Lisboa, Portugal\\ ​
  
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 **Mathematical and computational biology** : Univariate/​Multivariate Statistics for Data Analysis, Graph theory, Resampling Methods, Congruence Measurements,​ Evolutionary Models\\ **Mathematical and computational biology** : Univariate/​Multivariate Statistics for Data Analysis, Graph theory, Resampling Methods, Congruence Measurements,​ Evolutionary Models\\
 ===== Websites ===== ===== Websites =====
-[[http://www.phyloviz.net|PHYLOViZ]] - a software allowing ​the visualization ​of accessory epidemiological ​data together with evolutionary hypothesis derived ​from MLST, MLVA or SNP data developed in the lab in collaboration with INESC.+[[https://chewbbaca.online/|chewBBACA online]] - A whole genome/core genome multilocus sequence typing (wg/cgMLST) database developed facilitate ​the comparison ​of wg/cgMLST typing ​data obtained ​from high-throughput sequencing.
  
-[[http://www.comparingpartitions.info|Comparing Partitions]] - a site developed in the lab for comparing classification schemes\\+[[http://patlas.site|pAtlas]] - A plasmid database ​developed in the lab to facilitate plasmid detection in high-throughput data and the exploration of plasmid space.
  
-[[http://goeburst.phyloviz.net/|goeBURST]] - a globally optimized implementation of the eBURST algorithm for the analysis ​of MLST data developed in the lab in collaboration with INESC.+[[http://www.phyloviz.net|PHYLOViZ]] - a software allowing ​the visualization ​of accessory epidemiological data together with evolutionary hypothesis derived from MLST, MLVA or SNP data developed in the lab in collaboration with INESC. ​PHYLOViZ uses the goeBURST algorithm, a globally optimized implementation of the eBURST algorithm, to create minimum spanning tree like representations of the data. Both a desktop JAVA implementation and an online version are available. 
 + 
 +[[http://​www.comparingpartitions.info|Comparing Partitions]] - a site developed in the lab for comparing classification schemes\\
  
 ===== Contacts ===== ===== Contacts =====
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 ===== Publications ===== ===== Publications =====
  
-[[http://​orcid.org/​0000-0002-4084-6233|{{:​people:​orcid-icon.png}}]]ORCID 0000-0002-4084-6233 ​[[http://​www.scopus.com/​inward/​authorDetails.url?​authorID=7201568476&​partnerID=MN8TOARS|{{:​people:​scopus.ico}}]]Scopus 7201568476 ​[[http://​www.researcherid.com/​rid/​B-4993-2008!{{:​people:​researcherid.ico}}]]ResearcherID B-4993-2008 +[[http://​orcid.org/​0000-0002-4084-6233|{{:​people:​orcid-icon.png}}]][[http://​www.scopus.com/​inward/​authorDetails.url?​authorID=7201568476&​partnerID=MN8TOARS|{{:​people:​scopus.ico}}]][[http://​www.researcherid.com/​rid/​B-4993-2008|{{:​people:​researcherid.ico}}]][[http://​scholar.google.com/​citations?​user=EWHFzOAAAAAJ&​hl=en|{{:​people:​googlescholar.jpg?​100}}]] 
- +[[https://​www.ncbi.nlm.nih.gov/​pubmed?​term=ramirez+m+AND+(de+lencastre+OR+tomasz+a+OR+melo-cristino+OR+carrico+ja+OR+carri%C3%A7o+ja+OR+pinto+f+OR+aguiar+s+OR+frias+mj+OR+margarit+i+OR+mota+mm)&​sort=date|{{:​people:​pubmedimage1.jpg?​100|}}]][[https://​www.cienciavitae.pt/​9C1C-F2A2-4226|{{:​people:​cienciavitae.jpg?​200|}}]]
-[[http://​www.ncbi.nlm.nih.gov/​pubmed?​term=ramirez+m+AND+%28de+lencastre+OR+tomasz+a+OR+melo-cristino+OR+carrico+j+OR+pinto+fr+OR+aguiar+s+OR+frias%29|{{:​people:​pubmedimage1.jpg?​100|}}]]+
  
 **Publications after 2003:** **Publications after 2003:**
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 **Publications before 2003:** **Publications before 2003:**
  
-**J. Melo-Cristino,​ J., Ramirez, M., N. Serrano, T. Hänscheid and the Portuguese Surveillance Group for the Study of Respiratory Pathogens**. 2002. Macrolide resistance in //​Streptococcus pneumoniae//​ isolated from patients with community-acquired lower respiratory tract infections in Portugal: Results of a 3-year (1999 – 2001) multicenter surveillance study. Microb. Drug Resist. 9: 73-80. [[http://​www.ncbi.nlm.nih.gov/​pubmed/​12705685|(PMID:​ 12705685)]]+**J. Melo-Cristino,​ J., __Ramirez, M.__, N. Serrano, T. Hänscheid and the Portuguese Surveillance Group for the Study of Respiratory Pathogens**. 2002. Macrolide resistance in //​Streptococcus pneumoniae//​ isolated from patients with community-acquired lower respiratory tract infections in Portugal: Results of a 3-year (1999 – 2001) multicenter surveillance study. Microb. Drug Resist. 9: 73-80. [[http://​www.ncbi.nlm.nih.gov/​pubmed/​12705685|(PMID:​ 12705685)]]
  
-**Alou, L., Ramirez, M., García-Rey,​ C., Prieto, J. and H. de Lencastre**. 2001. //​Streptococcus pneumoniae//​ isolates with reduced susceptibility to ciprofloxacin in Spain: clonal diversity and appearance of ciprofloxacin resistant epidemic clones. Antimicrob. Agents Chemother. 45:2955-7. [[http://​www.ncbi.nlm.nih.gov/​pubmed/​11557501|(PMID:​ 11557501)]]+**Alou, L., __Ramirez, M.__, García-Rey,​ C., Prieto, J. and H. de Lencastre**. 2001. //​Streptococcus pneumoniae//​ isolates with reduced susceptibility to ciprofloxacin in Spain: clonal diversity and appearance of ciprofloxacin resistant epidemic clones. Antimicrob. Agents Chemother. 45:2955-7. [[http://​www.ncbi.nlm.nih.gov/​pubmed/​11557501|(PMID:​ 11557501)]]
  
-**Ramirez, M., and A. Tomasz**. 1999. Acquisition of new capsular genes among clinical isolates of antibiotic- resistant //​Streptococcus pneumoniae//​. Microb. Drug Resist. 5:241-6. [[http://​www.ncbi.nlm.nih.gov/​pubmed/​10647080|(PMID:​ 10647080)]]+**__Ramirez, M.__, and A. Tomasz**. 1999. Acquisition of new capsular genes among clinical isolates of antibiotic- resistant //​Streptococcus pneumoniae//​. Microb. Drug Resist. 5:241-6. [[http://​www.ncbi.nlm.nih.gov/​pubmed/​10647080|(PMID:​ 10647080)]]
  
-**Severina, E., MRamirez, and A. Tomasz**. 1999. Prophage carriage as a molecular epidemiological marker in //​Streptococcus pneumoniae//​. J. Clin. Microbiol. 37:3308-15. [[http://​www.ncbi.nlm.nih.gov/​pubmed/​10488197|(PMID:​ 10488197)]]+**Severina, E., __MRamirez__, and A. Tomasz**. 1999. Prophage carriage as a molecular epidemiological marker in //​Streptococcus pneumoniae//​. J. Clin. Microbiol. 37:3308-15. [[http://​www.ncbi.nlm.nih.gov/​pubmed/​10488197|(PMID:​ 10488197)]]
  
-**Ramirez, M., E. Severina, and A. Tomasz**. 1999. A high incidence of prophage carriage among natural isolates of //​Streptococcus pneumoniae//​. J. Bacteriol. 181:​3618-25. [[http://​www.ncbi.nlm.nih.gov/​pubmed/​10368133|(PMID:​ 10368133)]]+**__Ramirez, M.__, E. Severina, and A. Tomasz**. 1999. A high incidence of prophage carriage among natural isolates of //​Streptococcus pneumoniae//​. J. Bacteriol. 181:​3618-25. [[http://​www.ncbi.nlm.nih.gov/​pubmed/​10368133|(PMID:​ 10368133)]]
  
-**Ramirez, M. and A. Tomasz**. 1998. Molecular characterization of the complete 23F capsular polysaccharide locus of //​Streptococcus pneumoniae//​. J. Bacteriol. 180:5273-8. [[http://​www.ncbi.nlm.nih.gov/​pubmed/​9748469|(PMID:​ 9748469)]]+**__Ramirez, M.__ and A. Tomasz**. 1998. Molecular characterization of the complete 23F capsular polysaccharide locus of //​Streptococcus pneumoniae//​. J. Bacteriol. 180:5273-8. [[http://​www.ncbi.nlm.nih.gov/​pubmed/​9748469|(PMID:​ 9748469)]]
  
-**Marchese, A., MRamirez, G. C. Schito, Tomasz, A.**. 1998. Molecular epidemiology of penicillin-resistant //​Streptococcus pneumoniae//​ isolates recovered in Italy from 1993 to 1996. J. Clin. Microbiol. 36:2944-9. [[http://​www.ncbi.nlm.nih.gov/​pubmed/​9738048|(PMID:​ 9738048)]]+**Marchese, A., __MRamirez__, G. C. Schito, Tomasz, A.**. 1998. Molecular epidemiology of penicillin-resistant //​Streptococcus pneumoniae//​ isolates recovered in Italy from 1993 to 1996. J. Clin. Microbiol. 36:2944-9. [[http://​www.ncbi.nlm.nih.gov/​pubmed/​9738048|(PMID:​ 9738048)]]
  
-**Nesin, M., Ramirez, M., Tomasz, A.** 1998. Capsular transformation of a multidrug resistant //​Streptococcus pneumoniae//​ in vivo. J. Infect. Diseases, 177, 707-703. [[http://​www.ncbi.nlm.nih.gov/​pubmed/​9498451|(PMID:​ 9498451)]]+**Nesin, M., __Ramirez, M.__, Tomasz, A.** 1998. Capsular transformation of a multidrug resistant //​Streptococcus pneumoniae//​ in vivo. J. Infect. Diseases, 177, 707-703. [[http://​www.ncbi.nlm.nih.gov/​pubmed/​9498451|(PMID:​ 9498451)]]
  
-**Ramirez, M., Tomasz, A., Morrison, D.** 1996. Ubiquitous distribution of the competence related genes //comA// and //comC// among isolates of //​Streptococcus pneumoniae//​. Microbial Drug Resistance, 3, 39-52. [[http://​www.ncbi.nlm.nih.gov/​pubmed/​9109095|(PMID:​ 9109095)]]+**__Ramirez, M.__, Tomasz, A., Morrison, D.** 1996. Ubiquitous distribution of the competence related genes //comA// and //comC// among isolates of //​Streptococcus pneumoniae//​. Microbial Drug Resistance, 3, 39-52. [[http://​www.ncbi.nlm.nih.gov/​pubmed/​9109095|(PMID:​ 9109095)]]
  
-**Santos Sanches, I., Ramirez, M., Troni, H., Abecassis, M., Padua, M., Tomasz, A., De Lencastre, H.** 1995. Evidence for the geographic spread of a methicillin-resistant //​Staphylococcus aureus// clone between Portugal and Spain. J. Clin. Microbiol., 3, 1243-46. [[http://​www.ncbi.nlm.nih.gov/​pubmed/​7615735|(PMID:​ 7615735)]]+**Santos Sanches, I., __Ramirez, M.__, Troni, H., Abecassis, M., Padua, M., Tomasz, A., De Lencastre, H.** 1995. Evidence for the geographic spread of a methicillin-resistant //​Staphylococcus aureus// clone between Portugal and Spain. J. Clin. Microbiol., 3, 1243-46. [[http://​www.ncbi.nlm.nih.gov/​pubmed/​7615735|(PMID:​ 7615735)]]
  
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