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Items: 1 to 50 of 57

1.

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

van der Linden M, Mamede R, Levina N, Helwig P, Vila-Cerqueira P, Carriço JA, Melo-Cristino J, Ramirez M, Martins ER.

J Antimicrob Chemother. 2019 Nov 18. pii: dkz465. doi: 10.1093/jac/dkz465. [Epub ahead of print]

PMID:
31740946
2.

Natural Occurrence of Escherichia coli-Infecting Bacteriophages in Clinical Samples.

Pacífico C, Hilbert M, Sofka D, Dinhopl N, Pap IJ, Aspöck C, Carriço JA, Hilbert F.

Front Microbiol. 2019 Oct 31;10:2484. doi: 10.3389/fmicb.2019.02484. eCollection 2019.

3.

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

Pacífico C, Sofka D, Carriço JA, Hilbert F.

Microbiol Resour Announc. 2019 Sep 19;8(38). pii: e00953-19. doi: 10.1128/MRA.00953-19.

4.

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

Espadinha D, Sobral RG, Mendes CI, Méric G, Sheppard SK, Carriço JA, de Lencastre H, Miragaia M.

Front Microbiol. 2019 Aug 27;10:1971. doi: 10.3389/fmicb.2019.01971. eCollection 2019.

5.

Author Correction: Critical steps in clinical shotgun metagenomics for the concomitant detection and typing of microbial pathogens.

Couto N, Schuele L, Raangs EC, Machado MP, Mendes CI, Jesus TF, Chlebowicz M, Rosema S, Ramirez M, Carriço JA, Autenrieth IB, Friedrich AW, Peter S, Rossen JW.

Sci Rep. 2019 Apr 17;9(1):6406. doi: 10.1038/s41598-019-42134-9.

6.

The Association of Patient Satisfaction-Based Incentives with Primary Care Physician Opioid Prescribing.

Carrico JA, Mahoney K, Raymond KM, Mims L, Smith PC, Sakai JT, Mikulich-Gilbertson SK, Hopfer CJ, Bartels K.

J Am Board Fam Med. 2018 Nov-Dec;31(6):941-943. doi: 10.3122/jabfm.2018.06.180067.

7.

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

Echániz-Aviles G, Guerreiro SI, Silva-Costa C, Mendes CI, Carriço JA, Carnalla-Barajas MN, Soto-Noguerón A, Velazquez-Meza ME, Melo-Cristino J, Luévanos-Velazquez A, Martínez-Medina L, Vázquez-Larios MDR, Ramirez M.

J Clin Microbiol. 2019 Jan 2;57(1). pii: e01354-18. doi: 10.1128/JCM.01354-18. Print 2019 Jan.

8.

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

Jesus TF, Ribeiro-Gonçalves B, Silva DN, Bortolaia V, Ramirez M, Carriço JA.

Nucleic Acids Res. 2019 Jan 8;47(D1):D188-D194. doi: 10.1093/nar/gky1073.

9.

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

Pinto M, González-Díaz A, Machado MP, Duarte S, Vieira L, Carriço JA, Marti S, Bajanca-Lavado MP, Gomes JP.

Infect Genet Evol. 2019 Jan;67:126-135. doi: 10.1016/j.meegid.2018.10.025. Epub 2018 Oct 31.

PMID:
30391557
10.

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

Couto N, Schuele L, Raangs EC, Machado MP, Mendes CI, Jesus TF, Chlebowicz M, Rosema S, Ramirez M, Carriço JA, Autenrieth IB, Friedrich AW, Peter S, Rossen JW.

Sci Rep. 2018 Sep 13;8(1):13767. doi: 10.1038/s41598-018-31873-w. Erratum in: Sci Rep. 2019 Apr 17;9(1):6406.

11.

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

Zhou Z, Alikhan NF, Sergeant MJ, Luhmann N, Vaz C, Francisco AP, Carriço JA, Achtman M.

Genome Res. 2018 Sep;28(9):1395-1404. doi: 10.1101/gr.232397.117. Epub 2018 Jul 26.

12.

Large-Scale Simulations of Bacterial Populations Over Complex Networks.

Teixeira AS, Monteiro PT, Carriço JA, Santos FC, Francisco AP.

J Comput Biol. 2018 Aug;25(8):850-861. doi: 10.1089/cmb.2018.0083. Epub 2018 Jul 9.

PMID:
29985650
13.

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.

Lopes E, Fernandes T, Machado MP, Carriço JA, Melo-Cristino J, Ramirez M, Martins ER; The Portuguese Group For The Study Of Streptococcal Infections.

Euro Surveill. 2018 May;23(21). doi: 10.2807/1560-7917.ES.2018.23.21.1700473.

14.

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

Motro Y, Carriço JA, Friedrich AW, Rossen JWA, Moran-Gilad J.

Microbes Infect. 2018 May;20(5):275-280. doi: 10.1016/j.micinf.2018.02.006. Epub 2018 Mar 17. No abstract available.

PMID:
29555344
15.

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

Silva M, Machado MP, Silva DN, Rossi M, Moran-Gilad J, Santos S, Ramirez M, Carriço JA.

Microb Genom. 2018 Mar;4(3). doi: 10.1099/mgen.0.000166. Epub 2018 Mar 15.

16.

Fast phylogenetic inference from typing data.

Carriço JA, Crochemore M, Francisco AP, Pissis SP, Ribeiro-Gonçalves B, Vaz C.

Algorithms Mol Biol. 2018 Feb 15;13:4. doi: 10.1186/s13015-017-0119-7. eCollection 2018.

17.

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

Culebro A, Machado MP, Carriço JA, Rossi M.

Sci Rep. 2018 Feb 14;8(1):3028. doi: 10.1038/s41598-018-21438-2.

18.

A primer on microbial bioinformatics for nonbioinformaticians.

Carriço JA, Rossi M, Moran-Gilad J, Van Domselaar G, Ramirez M.

Clin Microbiol Infect. 2018 Apr;24(4):342-349. doi: 10.1016/j.cmi.2017.12.015. Epub 2018 Jan 5. Review.

19.

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

Guedes LC, Chan RB, Gomes MA, Conceição VA, Machado RB, Soares T, Xu Y, Gaspar P, Carriço JA, Alcalay RN, Ferreira JJ, Outeiro TF, Miltenberger-Miltenyi G.

Parkinsonism Relat Disord. 2017 Nov;44:58-65. doi: 10.1016/j.parkreldis.2017.08.026. Epub 2017 Sep 1.

PMID:
28890071
20.

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

Ribeiro TG, Gonçalves BR, da Silva MS, Novais Â, Machado E, Carriço JA, Peixe L.

Int J Syst Evol Microbiol. 2017 Sep;67(9):3513-3517. doi: 10.1099/ijsem.0.002154. Epub 2017 Aug 31.

PMID:
28857032
21.

A widespread family of polymorphic toxins encoded by temperate phages.

Jamet A, Touchon M, Ribeiro-Gonçalves B, Carriço JA, Charbit A, Nassif X, Ramirez M, Rocha EPC.

BMC Biol. 2017 Aug 29;15(1):75. doi: 10.1186/s12915-017-0415-1.

22.

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

Taboada EN, Graham MR, Carriço JA, Van Domselaar G.

Front Microbiol. 2017 May 23;8:909. doi: 10.3389/fmicb.2017.00909. eCollection 2017. Review.

23.

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

Marchaim D, Levit D, Zigron R, Gordon M, Lazarovitch T, Carrico JA, Chalifa-Caspi V, Moran-Gilad J.

Future Microbiol. 2017 Mar;12:271-283. doi: 10.2217/fmb-2016-0158. Epub 2017 Feb 24.

PMID:
28287300
24.

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

Diamantino-Miranda J, Aguiar SI, Carriço JA, Melo-Cristino J, Ramirez M.

PLoS One. 2017 Feb 2;12(2):e0170354. doi: 10.1371/journal.pone.0170354. eCollection 2017.

25.

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

Machado MP, Ribeiro-Gonçalves B, Silva M, Ramirez M, Carriço JA.

Methods Mol Biol. 2017;1520:331-356. doi: 10.1007/978-1-4939-6634-9_20. Erratum in: Methods Mol Biol. 2017;1520:E1-E3.

PMID:
27873262
26.

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

Nascimento M, Sousa A, Ramirez M, Francisco AP, Carriço JA, Vaz C.

Bioinformatics. 2017 Jan 1;33(1):128-129. doi: 10.1093/bioinformatics/btw582. Epub 2016 Sep 6.

PMID:
27605102
27.

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

Pinho MD, Erol E, Ribeiro-Gonçalves B, Mendes CI, Carriço JA, Matos SC, Preziuso S, Luebke-Becker A, Wieler LH, Melo-Cristino J, Ramirez M.

Sci Rep. 2016 Aug 17;6:31736. doi: 10.1038/srep31736.

28.

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

Ribeiro-Gonçalves B, Francisco AP, Vaz C, Ramirez M, Carriço JA.

Nucleic Acids Res. 2016 Jul 8;44(W1):W246-51. doi: 10.1093/nar/gkw359. Epub 2016 Apr 29.

29.

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.

Arinto-Garcia R, Pinho MD, Carriço JA, Melo-Cristino J, Ramirez M.

J Clin Microbiol. 2015 Nov;53(11):3580-8. doi: 10.1128/JCM.01892-15. Epub 2015 Sep 9.

30.

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

Teixeira AS, Monteiro PT, Carriço JA, Ramirez M, Francisco AP.

PLoS One. 2015 Mar 23;10(3):e0119315. doi: 10.1371/journal.pone.0119315. eCollection 2015.

31.

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

Coelho LP, Pato C, Friães A, Neumann A, von Köckritz-Blickwede M, Ramirez M, Carriço JA.

Bioinformatics. 2015 Jul 15;31(14):2364-70. doi: 10.1093/bioinformatics/btv156. Epub 2015 Mar 19.

PMID:
25792554
32.

TypOn: the microbial typing ontology.

Vaz C, Francisco AP, Silva M, Jolley KA, Bray JE, Pouseele H, Rothganger J, Ramirez M, Carriço JA.

J Biomed Semantics. 2014 Oct 18;5(1):43. doi: 10.1186/2041-1480-5-43. eCollection 2014.

33.

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

Branquinho R, Meirinhos-Soares L, Carriço JA, Pintado M, Peixe LV.

FEMS Microbiol Ecol. 2014 Dec;90(3):689-98. doi: 10.1111/1574-6941.12426. Epub 2014 Oct 6.

34.

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

Branquinho R, Sousa C, Osório H, Meirinhos-Soares L, Lopes J, Carriço JA, Busse HJ, Abdulmawjood A, Klein G, Kämpfer P, Pintado ME, Peixe LV.

Int J Syst Evol Microbiol. 2014 Nov;64(Pt 11):3867-76. doi: 10.1099/ijs.0.067850-0. Epub 2014 Aug 29.

PMID:
25171924
35.

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

Silva-Costa C, Carriço JA, Ramirez M, Melo-Cristino J.

Pediatr Infect Dis J. 2014 Mar;33(3):306-10. doi: 10.1097/INF.0000000000000088.

PMID:
24168973
36.

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

Coelho JR, Carriço JA, Knight D, Martínez JL, Morrissey I, Oggioni MR, Freitas AT.

PLoS One. 2013;8(2):e55582. doi: 10.1371/journal.pone.0055582. Epub 2013 Feb 19.

37.

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

Carriço JA, Sabat AJ, Friedrich AW, Ramirez M; ESCMID Study Group for Epidemiological Markers (ESGEM).

Euro Surveill. 2013 Jan 24;18(4):20382. Review.

38.

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

Francisco AP, Vaz C, Monteiro PT, Melo-Cristino J, Ramirez M, Carriço JA.

BMC Bioinformatics. 2012 May 8;13:87. doi: 10.1186/1471-2105-13-87.

39.

Prognostic prediction through biclustering-based classification of clinical gene expression time series.

Carreiro AV, Anunciação O, Carriço JA, Madeira SC.

J Integr Bioinform. 2011 Sep 15;8(3):175. doi: 10.2390/biecoll-jib-2011-175.

PMID:
21926438
40.

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

Severiano A, Pinto FR, Ramirez M, Carriço JA.

J Clin Microbiol. 2011 Nov;49(11):3997-4000. doi: 10.1128/JCM.00624-11. Epub 2011 Sep 14.

41.

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

Severiano A, Carriço JA, Robinson DA, Ramirez M, Pinto FR.

PLoS One. 2011;6(5):e19539. doi: 10.1371/journal.pone.0019539. Epub 2011 May 18.

42.

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.

Sá-Leão R, Pinto F, Aguiar S, Nunes S, Carriço JA, Frazão N, Gonçalves-Sousa N, Melo-Cristino J, de Lencastre H, Ramirez M.

J Clin Microbiol. 2011 Apr;49(4):1369-75. doi: 10.1128/JCM.01763-10. Epub 2011 Jan 26.

43.

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

Simões AS, Sá-Leão R, Eleveld MJ, Tavares DA, Carriço JA, Bootsma HJ, Hermans PW.

J Clin Microbiol. 2010 Jan;48(1):238-46. doi: 10.1128/JCM.01313-09. Epub 2009 Nov 11.

44.

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

Francisco AP, Bugalho M, Ramirez M, Carriço JA.

BMC Bioinformatics. 2009 May 18;10:152. doi: 10.1186/1471-2105-10-152.

45.

Adapting experimental ontologies for molecular epidemiology.

Deus HF, Sousa MA, Carrico JA, Lencastre Hd, Almeida JS.

AMIA Annu Symp Proc. 2007 Oct 11:935.

PMID:
18694035
46.

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

Oliveira DC, Santos M, Milheiriço C, Carriço JA, Vinga S, Oliveira AL, de Lencastre H.

J Antimicrob Chemother. 2008 Apr;61(4):959-60. doi: 10.1093/jac/dkn021. Epub 2008 Jan 27. No abstract available.

PMID:
18227085
47.

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

Sá-Leão R, Nunes S, Brito-Avô A, Alves CR, Carriço JA, Saldanha J, Almeida JS, Santos-Sanches I, de Lencastre H.

J Clin Microbiol. 2008 Jan;46(1):225-34. Epub 2007 Nov 14.

48.

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

Miragaia M, Carriço JA, Thomas JC, Couto I, Enright MC, de Lencastre H.

J Clin Microbiol. 2008 Jan;46(1):118-29. Epub 2007 Nov 7.

49.

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

Faria NA, Carrico JA, Oliveira DC, Ramirez M, de Lencastre H.

J Clin Microbiol. 2008 Jan;46(1):136-44. Epub 2007 Nov 7.

50.

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

Pinto FR, Carriço JA, Ramirez M, Almeida JS.

BMC Bioinformatics. 2007 Feb 7;8:44.

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