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Items: 34


Phylodynamic applications in 21st century global infectious disease research.

Rife BD, Mavian C, Chen X, Ciccozzi M, Salemi M, Min J, Prosperi MC.

Glob Health Res Policy. 2017 May 8;2:13. doi: 10.1186/s41256-017-0034-y. eCollection 2017.


Emergence of recombinant Mayaro virus strains from the Amazon basin.

Mavian C, Rife BD, Dollar JJ, Cella E, Ciccozzi M, Prosperi MCF, Lednicky J, Morris JG, Capua I, Salemi M.

Sci Rep. 2017 Aug 18;7(1):8718. doi: 10.1038/s41598-017-07152-5.


Relationship between cytokine expression patterns and clinical outcomes: two population-based birth cohorts.

Wu J, Prosperi MC, Simpson A, Hollams EM, Sly PD, Custovic A, Holt PG.

Clin Exp Allergy. 2015 Dec;45(12):1801-11. doi: 10.1111/cea.12579.


Evolution pathways of IgE responses to grass and mite allergens throughout childhood.

Custovic A, Sonntag HJ, Buchan IE, Belgrave D, Simpson A, Prosperi MCF.

J Allergy Clin Immunol. 2015 Dec;136(6):1645-1652.e8. doi: 10.1016/j.jaci.2015.03.041. Epub 2015 May 8.


Can multiple SNP testing in BRCA2 and BRCA1 female carriers be used to improve risk prediction models in conjunction with clinical assessment?

Prosperi MC, Ingham SL, Howell A, Lalloo F, Buchan IE, Evans DG.

BMC Med Inform Decis Mak. 2014 Oct 1;14:87. doi: 10.1186/1472-6947-14-87.


Spatiotemporal dynamics of simian immunodeficiency virus brain infection in CD8+ lymphocyte-depleted rhesus macaques with neuroAIDS.

Strickland SL, Rife BD, Lamers SL, Nolan DJ, Veras NM, Prosperi MC, Burdo TH, Autissier P, Nowlin B, Goodenow MM, Suchard MA, Williams KC, Salemi M.

J Gen Virol. 2014 Dec;95(Pt 12):2784-95. doi: 10.1099/vir.0.070318-0. Epub 2014 Sep 9.


Predicting phenotypes of asthma and eczema with machine learning.

Prosperi MC, Marinho S, Simpson A, Custovic A, Buchan IE.

BMC Med Genomics. 2014;7 Suppl 1:S7. doi: 10.1186/1755-8794-7-S1-S7. Epub 2014 May 8.


Challenges in identifying asthma subgroups using unsupervised statistical learning techniques.

Prosperi MC, Sahiner UM, Belgrave D, Sackesen C, Buchan IE, Simpson A, Yavuz TS, Kalayci O, Custovic A.

Am J Respir Crit Care Med. 2013 Dec 1;188(11):1303-12. doi: 10.1164/rccm.201304-0694OC.


Challenges in interpreting allergen microarrays in relation to clinical symptoms: a machine learning approach.

Prosperi MC, Belgrave D, Buchan I, Simpson A, Custovic A.

Pediatr Allergy Immunol. 2014 Feb;25(1):71-9. doi: 10.1111/pai.12139. Epub 2013 Oct 16.


Empirical validation of viral quasispecies assembly algorithms: state-of-the-art and challenges.

Prosperi MC, Yin L, Nolan DJ, Lowe AD, Goodenow MM, Salemi M.

Sci Rep. 2013 Oct 3;3:2837. doi: 10.1038/srep02837.


Declining prevalence of HIV-1 drug resistance in antiretroviral treatment-exposed individuals in Western Europe.

De Luca A, Dunn D, Zazzi M, Camacho R, Torti C, Fanti I, Kaiser R, Sönnerborg A, Codoñer FM, Van Laethem K, Vandamme AM, Bansi L, Ghisetti V, van de Vijver DA, Asboe D, Prosperi MC, Di Giambenedetto S; SEHERE collaboration in Chain.

J Infect Dis. 2013 Apr 15;207(8):1216-20. doi: 10.1093/infdis/jit017. Epub 2013 Jan 11.


Predictors of first-line antiretroviral therapy discontinuation due to drug-related adverse events in HIV-infected patients: a retrospective cohort study.

Prosperi MC, Fabbiani M, Fanti I, Zaccarelli M, Colafigli M, Mondi A, D'Avino A, Borghetti A, Cauda R, Di Giambenedetto S.

BMC Infect Dis. 2012 Nov 12;12:296. doi: 10.1186/1471-2334-12-296.


Combination of immune and viral factors distinguishes low-risk versus high-risk HIV-1 disease progression in HLA-B*5701 subjects.

Norström MM, Buggert M, Tauriainen J, Hartogensis W, Prosperi MC, Wallet MA, Hecht FM, Salemi M, Karlsson AC.

J Virol. 2012 Sep;86(18):9802-16. doi: 10.1128/JVI.01165-12. Epub 2012 Jul 3.


PhyloTempo: A Set of R Scripts for Assessing and Visualizing Temporal Clustering in Genealogies Inferred from Serially Sampled Viral Sequences.

Norström MM, Prosperi MC, Gray RR, Karlsson AC, Salemi M.

Evol Bioinform Online. 2012;8:261-9. doi: 10.4137/EBO.S9738. Epub 2012 Jun 11.


Computational models for prediction of response to antiretroviral therapies.

Prosperi MC, De Luca A.

AIDS Rev. 2012 Apr-Jun;14(2):145-53. Review.


Prognostic value of virological and immunological responses after 6 months of antiretroviral treatment in adults with HIV-1 infection in sub-Saharan Africa.

De Luca A, Marazzi MC, Mancinelli S, Ceffa S, Altan AM, Buonomo E, Prosperi MC, Pedruzzi B, Noorjehan AM, Scarcella P, Liotta G, Palombi L.

J Acquir Immune Defic Syndr. 2012 Mar 1;59(3):236-44. doi: 10.1097/QAI.0b013e31824276e9.


Can linear regression modeling help clinicians in the interpretation of genotypic resistance data? An application to derive a lopinavir-score.

Cozzi-Lepri A, Prosperi MC, Kjær J, Dunn D, Paredes R, Sabin CA, Lundgren JD, Phillips AN, Pillay D; EuroSIDA Study; United Kingdom CHIC/United Kingdom HDRD Study.

PLoS One. 2011;6(11):e25665. doi: 10.1371/journal.pone.0025665. Epub 2011 Nov 16.


QuRe: software for viral quasispecies reconstruction from next-generation sequencing data.

Prosperi MC, Salemi M.

Bioinformatics. 2012 Jan 1;28(1):132-3. doi: 10.1093/bioinformatics/btr627. Epub 2011 Nov 15.


Interpretation of genotypic HIV-1 resistance to darunavir and virological response: validation of available systems and of a new score.

De Luca A, Di Giambenedetto S, Maserati R, Gianotti N, Narciso P, Antinori A, Di Perri G, Prosperi MC, Baldanti F, Micheli V, Zazzi M, Perno CF, Santoro MM; TMC114-C226 study group; ARCA study group.

Antivir Ther. 2011;16(4):489-97. doi: 10.3851/IMP1799.


A prognostic model for estimating the time to virologic failure in HIV-1 infected patients undergoing a new combination antiretroviral therapy regimen.

Prosperi MC, Di Giambenedetto S, Fanti I, Meini G, Bruzzone B, Callegaro A, Penco G, Bagnarelli P, Micheli V, Paolini E, Di Biagio A, Ghisetti V, Di Pietro M, Zazzi M, De Luca A; ARCA cohort.

BMC Med Inform Decis Mak. 2011 Jun 14;11:40. doi: 10.1186/1472-6947-11-40.


Detection of drug resistance mutations at low plasma HIV-1 RNA load in a European multicentre cohort study.

Prosperi MC, Mackie N, Di Giambenedetto S, Zazzi M, Camacho R, Fanti I, Torti C, Sönnerborg A, Kaiser R, Codoñer FM, Van Laethem K, Bansi L, van de Vijver DA, Geretti AM, De Luca A; SEHERE consortium.

J Antimicrob Chemother. 2011 Aug;66(8):1886-96. doi: 10.1093/jac/dkr171. Epub 2011 May 30.


A novel methodology for large-scale phylogeny partition.

Prosperi MC, Ciccozzi M, Fanti I, Saladini F, Pecorari M, Borghi V, Di Giambenedetto S, Bruzzone B, Capetti A, Vivarelli A, Rusconi S, Re MC, Gismondo MR, Sighinolfi L, Gray RR, Salemi M, Zazzi M, De Luca A; ARCA collaborative group.

Nat Commun. 2011;2:321. doi: 10.1038/ncomms1325. Epub 2011 May 24.


Combinatorial analysis and algorithms for quasispecies reconstruction using next-generation sequencing.

Prosperi MC, Prosperi L, Bruselles A, Abbate I, Rozera G, Vincenti D, Solmone MC, Capobianchi MR, Ulivi G.

BMC Bioinformatics. 2011 Jan 5;12:5. doi: 10.1186/1471-2105-12-5.


Antiretroviral therapy optimisation without genotype resistance testing: a perspective on treatment history based models.

Prosperi MC, Rosen-Zvi M, Altmann A, Zazzi M, Di Giambenedetto S, Kaiser R, Schülter E, Struck D, Sloot P, van de Vijver DA, Vandamme AM, Sönnerborg A; EuResist study group; Virolab study group.

PLoS One. 2010 Oct 29;5(10):e13753. doi: 10.1371/journal.pone.0013753. Erratum in: PLoS One. 2011;6(4). doi:10.1371/annotation/d0254103-21b9-4078-836b-57ba5bd1c26a.


The threshold bootstrap clustering: a new approach to find families or transmission clusters within molecular quasispecies.

Prosperi MC, De Luca A, Di Giambenedetto S, Bracciale L, Fabbiani M, Cauda R, Salemi M.

PLoS One. 2010 Oct 25;5(10):e13619. doi: 10.1371/journal.pone.0013619.


Low rate of virological failure and maintenance of susceptibility to HIV-1 protease inhibitors with first-line lopinavir/ritonavir-based antiretroviral treatment in clinical practice.

Prosperi MC, Zazzi M, Punzi G, Monno L, Colao G, Corsi P, Di Giambenedetto S, Meini G, Ghisetti V, Bonora S, Pecorari M, Gismondo MR, Bagnarelli P, Carli T, De Luca A; ARCA Collaborative Group.

J Med Virol. 2010 Dec;82(12):1996-2003. doi: 10.1002/jmv.21927.


Favourable evolution of virological and immunological profiles in treated and untreated patients in Italy in the period 1998-2008.

Prosperi MC, Cozzi-Lepri A, Antinori A, Cassola G, Torti C, Ursitti MA, Pellizzer GP, Giacometti A, d'Arminio Monforte A, De Luca A; Icona Foundation Study Group.

HIV Med. 2011 Mar;12(3):174-82. doi: 10.1111/j.1468-1293.2010.00866.x. Epub 2010 Aug 18.


Comparative determination of HIV-1 co-receptor tropism by Enhanced Sensitivity Trofile, gp120 V3-loop RNA and DNA genotyping.

Prosperi MC, Bracciale L, Fabbiani M, Di Giambenedetto S, Razzolini F, Meini G, Colafigli M, Marzocchetti A, Cauda R, Zazzi M, De Luca A.

Retrovirology. 2010 Jun 30;7:56. doi: 10.1186/1742-4690-7-56.


Incidence of malignancies in HIV-infected patients and prognostic role of current CD4 cell count: evidence from a large Italian cohort study.

Prosperi MC, Cozzi-Lepri A, Castagna A, Mussini C, Murri R, Giacometti A, Torti C, Costantini A, Narciso P, Ghinelli F, Antinori A, d'Arminio Monforte A; Icona Foundation Study Group.

Clin Infect Dis. 2010 May 1;50(9):1316-21. doi: 10.1086/651688.


Investigation of expert rule bases, logistic regression, and non-linear machine learning techniques for predicting response to antiretroviral treatment.

Prosperi MC, Altmann A, Rosen-Zvi M, Aharoni E, Borgulya G, Bazso F, Sönnerborg A, Schülter E, Struck D, Ulivi G, Vandamme AM, Vercauteren J, Zazzi M; EuResist and Virolab study groups.

Antivir Ther. 2009;14(3):433-42.


Robust supervised and unsupervised statistical learning for HIV type 1 coreceptor usage analysis.

Prosperi MC, Fanti I, Ulivi G, Micarelli A, De Luca A, Zazzi M.

AIDS Res Hum Retroviruses. 2009 Mar;25(3):305-14. doi: 10.1089/aid.2008.0039.


Stochastic modelling of genotypic drug-resistance for human immunodeficiency virus towards long-term combination therapy optimization.

Prosperi MC, D'Autilia R, Incardona F, De Luca A, Zazzi M, Ulivi G.

Bioinformatics. 2009 Apr 15;25(8):1040-7. doi: 10.1093/bioinformatics/btn568. Epub 2008 Oct 31.


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