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Items: 19

1.

SNAPPy: A snakemake pipeline for scalable HIV-1 subtyping by phylogenetic pairing.

Araújo PMM, Martins JS, Osório NS.

Virus Evol. 2019 Nov 19;5(2):vez050. doi: 10.1093/ve/vez050. eCollection 2019 Jul.

2.

Machine Learning-Enhanced T Cell Neoepitope Discovery for Immunotherapy Design.

Martins J, Magalhães C, Rocha M, Osório NS.

Cancer Inform. 2019 May 23;18:1176935119852081. doi: 10.1177/1176935119852081. eCollection 2019. Review.

3.

Characterization of a large cluster of HIV-1 A1 infections detected in Portugal and connected to several Western European countries.

Araújo PMM, Carvalho A, Pingarilho M; BEST-HOPE study group, Abecasis AB, Osório NS.

Sci Rep. 2019 May 10;9(1):7223. doi: 10.1038/s41598-019-43420-2.

4.

Predictors and outcomes of disseminated tuberculosis in an intermediate burden setting.

Meira L, Chaves C, Araújo D, Almeida L, Boaventura R, Ramos A, Carvalho T, Osório NS, Castro AG, Rodrigues F, Guimarães JT, Saraiva M, Bastos HN.

Pulmonology. 2019 Nov - Dec;25(6):320-327. doi: 10.1016/j.pulmoe.2018.11.001. Epub 2019 Feb 26.

5.

A Nonribosomal Peptide Synthase Gene Driving Virulence in Mycobacterium tuberculosis.

Bhatt K, Machado H, Osório NS, Sousa J, Cardoso F, Magalhães C, Chen B, Chen M, Kim J, Singh A, Ferreira CM, Castro AG, Torrado E, Jacobs WR Jr, Bhatt A, Saraiva M.

mSphere. 2018 Oct 31;3(5). pii: e00352-18. doi: 10.1128/mSphere.00352-18.

6.

The Troika Host-Pathogen-Extrinsic Factors in Tuberculosis: Modulating Inflammation and Clinical Outcomes.

Bastos HN, Osório NS, Gagneux S, Comas I, Saraiva M.

Front Immunol. 2018 Jan 9;8:1948. doi: 10.3389/fimmu.2017.01948. eCollection 2017. Review.

7.

Mycobacterium tuberculosis Complex Exhibits Lineage-Specific Variations Affecting Protein Ductility and Epitope Recognition.

Yruela I, Contreras-Moreira B, Magalhães C, Osório NS, Gonzalo-Asensio J.

Genome Biol Evol. 2016 Dec 1;8(12):3751-3764. doi: 10.1093/gbe/evw279.

8.

A Prediction Rule to Stratify Mortality Risk of Patients with Pulmonary Tuberculosis.

Bastos HN, Osório NS, Castro AG, Ramos A, Carvalho T, Meira L, Araújo D, Almeida L, Boaventura R, Fragata P, Chaves C, Costa P, Portela M, Ferreira I, Magalhães SP, Rodrigues F, Sarmento-Castro R, Duarte R, Guimarães JT, Saraiva M.

PLoS One. 2016 Sep 16;11(9):e0162797. doi: 10.1371/journal.pone.0162797. eCollection 2016.

9.

Analysis of a local HIV-1 epidemic in portugal highlights established transmission of non-B and non-G subtypes.

Carvalho A, Costa P, Triunfante V, Branca F, Rodrigues F, Santos CL, Correia-Neves M, Saraiva M, Lecour H, Castro AG, Pedrosa J, Osório NS.

J Clin Microbiol. 2015 May;53(5):1506-14. doi: 10.1128/JCM.03611-14. Epub 2015 Feb 18.

10.

Complex polymorphisms in the Plasmodium falciparum multidrug resistance protein 2 gene and its contribution to antimalarial response.

Veiga MI, Osório NS, Ferreira PE, Franzén O, Dahlstrom S, Lum JK, Nosten F, Gil JP.

Antimicrob Agents Chemother. 2014 Dec;58(12):7390-7. doi: 10.1128/AAC.03337-14. Epub 2014 Sep 29.

11.

Drawings as snapshots of student cellular anatomy understanding.

Osório NS, Rodrigues F, Garcia EA, Costa MJ.

Med Educ. 2013 Nov;47(11):1120-1. doi: 10.1111/medu.12320. No abstract available.

PMID:
24117561
12.

Mycobacterium tuberculosis Strains Are Differentially Recognized by TLRs with an Impact on the Immune Response.

Carmona J, Cruz A, Moreira-Teixeira L, Sousa C, Sousa J, Osorio NS, Saraiva AL, Svenson S, Kallenius G, Pedrosa J, Rodrigues F, Castro AG, Saraiva M.

PLoS One. 2013 Jun 26;8(6):e67277. doi: 10.1371/journal.pone.0067277. Print 2013.

13.

Evidence for diversifying selection in a set of Mycobacterium tuberculosis genes in response to antibiotic- and nonantibiotic-related pressure.

Osório NS, Rodrigues F, Gagneux S, Pedrosa J, Pinto-Carbó M, Castro AG, Young D, Comas I, Saraiva M.

Mol Biol Evol. 2013 Jun;30(6):1326-36. doi: 10.1093/molbev/mst038. Epub 2013 Feb 28.

PMID:
23449927
14.

Morphological heterogeneity of Paracoccidioides brasiliensis: relevance of the Rho-like GTPase PbCDC42.

Menino JF, Osório NS, Sturme MH, Barros D, Gomes-Alves AG, Almeida AJ, Ludovico P, Costa P, Goldman GH, Rodrigues F.

Med Mycol. 2012 Oct;50(7):768-74. doi: 10.3109/13693786.2012.665614. Epub 2012 Apr 12.

PMID:
22493946
15.

The C allele of rs5743836 polymorphism in the human TLR9 promoter links IL-6 and TLR9 up-regulation and confers increased B-cell proliferation.

Carvalho A, Osório NS, Saraiva M, Cunha C, Almeida AJ, Teixeira-Coelho M, Ludovico P, Pedrosa J, Pitzurra L, Aversa F, Romani L, Castro AG, Rodrigues F.

PLoS One. 2011;6(11):e28256. doi: 10.1371/journal.pone.0028256. Epub 2011 Nov 23.

16.

The rs5743836 polymorphism in TLR9 confers a population-based increased risk of non-Hodgkin lymphoma.

Carvalho A, Cunha C, Almeida AJ, Osório NS, Saraiva M, Teixeira-Coelho M, Pedreiro S, Torrado E, Domingues N, Gomes-Alves AG, Marques A, Lacerda JF, da Silva MG, Gomes M, Pinto AC, Torres F, Rendeiro P, Tavares P, Di Ianni M, Medeiros R, Heutink P, Bracci PM, Conde L, Ludovico P, Pedrosa J, Maciel P, Pitzurra L, Aversa F, Marques H, Paiva A, Skibola CF, Romani L, Castro AG, Rodrigues F.

Genes Immun. 2012 Feb;13(2):197-201. doi: 10.1038/gene.2011.59. Epub 2011 Aug 25.

17.

Neurodevelopmental delay in the Cln3Deltaex7/8 mouse model for Batten disease.

Osório NS, Sampaio-Marques B, Chan CH, Oliveira P, Pearce DA, Sousa N, Rodrigues F.

Genes Brain Behav. 2009 Apr;8(3):337-45. doi: 10.1111/j.1601-183X.2009.00478.x. Epub 2009 Feb 19.

18.

NO-mediated apoptosis in yeast.

Almeida B, Buttner S, Ohlmeier S, Silva A, Mesquita A, Sampaio-Marques B, Osório NS, Kollau A, Mayer B, Leão C, Laranjinha J, Rodrigues F, Madeo F, Ludovico P.

J Cell Sci. 2007 Sep 15;120(Pt 18):3279-88. Epub 2007 Aug 28.

19.

Nitric oxide signaling is disrupted in the yeast model for Batten disease.

Osório NS, Carvalho A, Almeida AJ, Padilla-Lopez S, Leão C, Laranjinha J, Ludovico P, Pearce DA, Rodrigues F.

Mol Biol Cell. 2007 Jul;18(7):2755-67. Epub 2007 May 2.

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