✎ people:ramirez [Molecular Microbiology and Infection Unit]

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====== Mário Ramirez ======
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[[http://orcid.org/0000-0002-4084-6233|{{:people:orcid-logo.png?150|0000-0002-4084-6233}}]]
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===== Current Position =====
**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\\ 

**Laboratory Head**\\ 
[[http://www.imm.fm.ul.pt/web/imm/molecularmicrobiologyandinfection|Molecular Microbiology and Infection Unit]], [[http://www.imm.fm.ul.pt/web/imm/home|Instituto de Medicina Molecular]], Lisboa, Portugal\\

===== Previous Positions =====
**Assistant Professor of Microbiology**, Instituto de Microbiologia,[[http://www.medicina.ulisboa.pt/|Faculdade de Medicina de Lisboa]], [[http://www.ulisboa.pt//|Universidade de Lisboa]], Lisboa, Portugal\\
**Post-Doc**, [[http://www.itqb.unl.pt/|Instituto de Tecnologia Química e Biológica]], Oeiras, Portugal\\
**Guest Investigator**, [[http://www.rockefeller.edu/|The Rockefeller University]], NY, USA

===== Research Interests =====
**Biology** : Clinical Microbiology, Microbial Evolution, Population Biology, Molecular Epidemiology, Microbial Typing methods\\
**Mathematical and computational biology** : Univariate/Multivariate Statistics for Data Analysis, Graph theory, Resampling Methods, Congruence Measurements, Evolutionary Models\\
===== Websites =====
[[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://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://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 =====

**Email**: 
  * ramirez_at_fm.ul.pt (replace _at_ by @)\\

**Telephone**: 
  * +351217999458

===== Publications =====

[[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|}}]]

**Publications after 2003:**

See the [[:publications|UMMI publications]].

**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)]]

**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)]]

**Severina, E., __M. Ramirez__, 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.__ 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., __M. Ramirez__, 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)]]

**__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)]]