Mattia C F Prosperi

Summary

Affiliation: University of Florida
Country: USA

Publications

  1. ncbi request reprint Computational models for prediction of response to antiretroviral therapies
    Mattia C F Prosperi
    Department of Pathology, Immunology and Laboratory Medicine, College of Medicine, Emerging Pathogens Institute, University of Florida, Gainesville, FL 32610, USA
    AIDS Rev 14:145-53. 2012
  2. doi request reprint A novel methodology for large-scale phylogeny partition
    Mattia C F Prosperi
    Clinic of Infectious Diseases, Catholic University of the Sacred Heart, Rome, Italy
    Nat Commun 2:321. 2011
  3. doi request reprint Declining prevalence of HIV-1 drug resistance in antiretroviral treatment-exposed individuals in Western Europe
    Andrea De Luca
    Catholic University of the Sacred Heart, Rome, Italy
    J Infect Dis 207:1216-20. 2013
  4. doi request reprint Detection of drug resistance mutations at low plasma HIV-1 RNA load in a European multicentre cohort study
    Mattia C F Prosperi
    Clinic of Infectious Diseases, Catholic University of Sacred Heart, Rome, Italy
    J Antimicrob Chemother 66:1886-96. 2011
  5. pmc A prognostic model for estimating the time to virologic failure in HIV-1 infected patients undergoing a new combination antiretroviral therapy regimen
    Mattia C F Prosperi
    Infectious Diseases Clinic, Catholic University of the Sacred Heart, Rome, Italy
    BMC Med Inform Decis Mak 11:40. 2011
  6. pmc Antiretroviral therapy optimisation without genotype resistance testing: a perspective on treatment history based models
    Mattia C F Prosperi
    Clinic of Infectious Diseases, Catholic University of Sacred Heart, Rome, Italy
    PLoS ONE 5:e13753. 2010
  7. pmc Comparative determination of HIV-1 co-receptor tropism by Enhanced Sensitivity Trofile, gp120 V3-loop RNA and DNA genotyping
    Mattia C F Prosperi
    Infectious Diseases Clinic, Catholic University of Sacred Heart, Rome, Italy
    Retrovirology 7:56. 2010
  8. pmc Predictors of first-line antiretroviral therapy discontinuation due to drug-related adverse events in HIV-infected patients: a retrospective cohort study
    Mattia C F Prosperi
    Viral Immunodeficiency Unit, National Institute for Infectious Diseases Lazzaro Spallanzani, Rome, Italy
    BMC Infect Dis 12:296. 2012
  9. doi request reprint Interpretation of genotypic HIV-1 resistance to darunavir and virological response: validation of available systems and of a new score
    Andrea De Luca
    Institute of Clinical Infectious Diseases, Catholic University, Rome, Italy
    Antivir Ther 16:489-97. 2011
  10. pmc Combinatorial analysis and algorithms for quasispecies reconstruction using next-generation sequencing
    Mattia C F Prosperi
    Clinic of Infectious Diseases, Catholic University of Sacred Heart, Rome, Italy
    BMC Bioinformatics 12:5. 2011

Detail Information

Publications15

  1. ncbi request reprint Computational models for prediction of response to antiretroviral therapies
    Mattia C F Prosperi
    Department of Pathology, Immunology and Laboratory Medicine, College of Medicine, Emerging Pathogens Institute, University of Florida, Gainesville, FL 32610, USA
    AIDS Rev 14:145-53. 2012
    ..Future perspectives in the field foresee the extension of therapy optimization systems to newly approved antiretroviral drug targets and the prediction of other clinical outcomes, rather than the sole virologic response...
  2. doi request reprint A novel methodology for large-scale phylogeny partition
    Mattia C F Prosperi
    Clinic of Infectious Diseases, Catholic University of the Sacred Heart, Rome, Italy
    Nat Commun 2:321. 2011
    ..Our method takes an advantage of a flexible notion of transmission cluster and can become a general framework to analyse other epidemics...
  3. doi request reprint Declining prevalence of HIV-1 drug resistance in antiretroviral treatment-exposed individuals in Western Europe
    Andrea De Luca
    Catholic University of the Sacred Heart, Rome, Italy
    J Infect Dis 207:1216-20. 2013
    ..5% in 2005, decreasing thereafter. The proportion of cases exhausting available drug options dropped from 32% in 2000 to 1% in 2008. Reduced risk of resistance over calendar years was confirmed by multivariable analysis...
  4. doi request reprint Detection of drug resistance mutations at low plasma HIV-1 RNA load in a European multicentre cohort study
    Mattia C F Prosperi
    Clinic of Infectious Diseases, Catholic University of Sacred Heart, Rome, Italy
    J Antimicrob Chemother 66:1886-96. 2011
    ....
  5. pmc A prognostic model for estimating the time to virologic failure in HIV-1 infected patients undergoing a new combination antiretroviral therapy regimen
    Mattia C F Prosperi
    Infectious Diseases Clinic, Catholic University of the Sacred Heart, Rome, Italy
    BMC Med Inform Decis Mak 11:40. 2011
    ..However, their relative-hazard for the time to virologic failure has not been thoroughly investigated, and an expert system that is able to predict how long a new cART regimen will remain effective has never been designed...
  6. pmc Antiretroviral therapy optimisation without genotype resistance testing: a perspective on treatment history based models
    Mattia C F Prosperi
    Clinic of Infectious Diseases, Catholic University of Sacred Heart, Rome, Italy
    PLoS ONE 5:e13753. 2010
    ..Since treatment history (TH) impacts response to subsequent therapy, we investigated a set of statistical learning models to optimise cART in the absence of GRT information...
  7. pmc Comparative determination of HIV-1 co-receptor tropism by Enhanced Sensitivity Trofile, gp120 V3-loop RNA and DNA genotyping
    Mattia C F Prosperi
    Infectious Diseases Clinic, Catholic University of Sacred Heart, Rome, Italy
    Retrovirology 7:56. 2010
    ..7% false positive rate cutoff were evaluated using viral DNA and RNA samples, compared against each other and ESTA, using Cohen's kappa, phylogenetic analysis, and area under the receiver operating characteristic (AUROC)...
  8. pmc Predictors of first-line antiretroviral therapy discontinuation due to drug-related adverse events in HIV-infected patients: a retrospective cohort study
    Mattia C F Prosperi
    Viral Immunodeficiency Unit, National Institute for Infectious Diseases Lazzaro Spallanzani, Rome, Italy
    BMC Infect Dis 12:296. 2012
    ..However, its determinants are not fully understood. Aim of this study was to investigate predictors of first-line antiretroviral therapy discontinuation due to adverse events and their evolution in recent years...
  9. doi request reprint Interpretation of genotypic HIV-1 resistance to darunavir and virological response: validation of available systems and of a new score
    Andrea De Luca
    Institute of Clinical Infectious Diseases, Catholic University, Rome, Italy
    Antivir Ther 16:489-97. 2011
    ..There is not yet consensus on interpretation of genotypic HIV-1 resistance to darunavir (DRV). We validated existing rules and a newly derived score...
  10. pmc Combinatorial analysis and algorithms for quasispecies reconstruction using next-generation sequencing
    Mattia C F Prosperi
    Clinic of Infectious Diseases, Catholic University of Sacred Heart, Rome, Italy
    BMC Bioinformatics 12:5. 2011
    ..The reconstruction algorithm is based on combinations of multinomial distributions and is designed to minimise the reconstruction of false variants, called in-silico recombinants...
  11. pmc QuRe: software for viral quasispecies reconstruction from next-generation sequencing data
    Mattia C F Prosperi
    Department of Pathology, Immunology and Laboratory Medicine, College of Medicine, Emerging Pathogens Institute, University of Florida, Gainesville, FL 32610 3633, USA
    Bioinformatics 28:132-3. 2012
    ..QuRe comes with a built-in Poisson error correction method and a post-reconstruction probabilistic clustering, both parameterized on given error rates in homopolymeric and non-homopolymeric regions...
  12. doi request reprint 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
    Mattia C F Prosperi
    Clinic of Infectious Diseases, Catholic University of Sacred Heart, Rome, Italy
    J Med Virol 82:1996-2003. 2010
    ..Despite the likely differences in patient population and adherence, both the low rate of virological failure and the lack of development of LPV/rtv resistance documented in clinical trials are thus confirmed in clinical practice...
  13. pmc The threshold bootstrap clustering: a new approach to find families or transmission clusters within molecular quasispecies
    Mattia C F Prosperi
    Infectious Diseases Clinic, Catholic University of the Sacred Heart, Rome, Italy
    PLoS ONE 5:e13619. 2010
    ..We introduce the threshold bootstrap clustering (TBC), a new methodology for partitioning molecular sequences, that does not require a phylogenetic tree estimation...
  14. doi request reprint Stochastic modelling of genotypic drug-resistance for human immunodeficiency virus towards long-term combination therapy optimization
    Mattia C F Prosperi
    Department of Computer Science and Automation, University of Roma Tre, Informa Contract Research Organisation, Infectious Disease Clinic, Catholic University of Sacred Heart, Rome, Italy
    Bioinformatics 25:1040-7. 2009
    ..The effect of limited adherence to therapy was also analyzed. Sequential treatment change episodes were also exploited with the aim to evaluate optimal synoptic treatment scenarios...
  15. ncbi request reprint Investigation of expert rule bases, logistic regression, and non-linear machine learning techniques for predicting response to antiretroviral treatment
    Mattia C F Prosperi
    Computer Science and Automation Department, Roma Tre University, Rome, Italy
    Antivir Ther 14:433-42. 2009
    ..Interpretation of HIV-1 genotypic drug resistance is evolving from rule-based systems guided by expert opinion to data-driven engines developed through machine learning methods...