Mattia Prosperi

Mattia Prosperi

ASO PROF

Department: PHHP-COM EPIDEMIOLOGY
Business Phone: (352) 273-5860
Business Email: m.prosperi@ufl.edu

Research Profile

Open Researcher and Contributor ID (ORCID)

0000-0002-9021-5595

Publications

2021
Bagged random causal networks for interventional queries on observational biomedical datasets.
Journal of biomedical informatics. 115 [DOI] 10.1016/j.jbi.2021.103689. [PMID] 33548542.
2021
Transmitted drug resistance to NRTIs and risk of virological failure in naïve patients treated with integrase inhibitors.
HIV medicine. 22(1):22-27 [DOI] 10.1111/hiv.12956. [PMID] 32964671.
2021
Brain tissue transcriptomic analysis of SIV-infected macaques identifies several altered metabolic pathways linked to neuropathogenesis and poly (ADP-ribose) polymerases (PARPs) as potential therapeutic targets.
Journal of neurovirology. [DOI] 10.1007/s13365-020-00927-z. [PMID] 33405206.
2021
Exploring Prediction of Antimicrobial Resistance Based on Protein Solvent Accessibility Variation.
Frontiers in genetics. 12 [DOI] 10.3389/fgene.2021.564186. [PMID] 33552147.
2020
A Snapshot of SARS-CoV-2 Genome Availability up to April 2020 and its Implications: Data Analysis.
JMIR public health and surveillance. 6(2) [DOI] 10.2196/19170. [PMID] 32412415.
2020
Under-the-Radar Dengue Virus Infections in Natural Populations of Aedes aegypti Mosquitoes.
mSphere. 5(2) [DOI] 10.1128/mSphere.00316-20. [PMID] 32350095.
2020
The global spread of 2019-nCoV: a molecular evolutionary analysis.
Pathogens and global health. 114(2):64-67 [DOI] 10.1080/20477724.2020.1725339. [PMID] 32048560.
2020
Sociodemographic, ecological, and spatiotemporal factors associated with HIV drug resistance in Florida: a retrospective analysis.
The Journal of infectious diseases. [DOI] 10.1093/infdis/jiaa413. [PMID] 32644119.
2020
Sampling bias and incorrect rooting make phylogenetic network tracing of SARS-COV-2 infections unreliable.
Proceedings of the National Academy of Sciences of the United States of America. 117(23):12522-12523 [DOI] 10.1073/pnas.2007295117. [PMID] 32381734.
2020
Re: A Call for Deep-learning Healthcare.
Epidemiology (Cambridge, Mass.). 31(2) [DOI] 10.1097/EDE.0000000000001155. [PMID] 31856141.
2020
Prodromal clinical, demographic, and socio-ecological correlates of asthma in adults: a 10-year statewide big data multi-domain analysis.
The Journal of asthma : official journal of the Association for the Care of Asthma. 57(11):1155-1167 [DOI] 10.1080/02770903.2019.1642352. [PMID] 31288571.
2020
Precision Health Analytics With Predictive Analytics and Implementation Research: JACC State-of-the-Art Review.
Journal of the American College of Cardiology. 76(3):306-320 [DOI] 10.1016/j.jacc.2020.05.043. [PMID] 32674794.
2020
Portable nanopore analytics: are we there yet?
Bioinformatics (Oxford, England). 36(16):4399-4405 [DOI] 10.1093/bioinformatics/btaa237. [PMID] 32277811.
2020
Mining Twitter to Assess the Determinants of Health Behavior towards Palliative Care in the United States.
AMIA Joint Summits on Translational Science proceedings. AMIA Joint Summits on Translational Science. 2020:730-739 [PMID] 32477696.
View on: PubMed
2020
Mining Twitter to assess the determinants of health behavior toward human papillomavirus vaccination in the United States.
Journal of the American Medical Informatics Association : JAMIA. 27(2):225-235 [DOI] 10.1093/jamia/ocz191. [PMID] 31711186.
2020
Identification of important factors in an inpatient fall risk prediction model to improve the quality of care using EHR and electronic administrative data: A machine-learning approach.
International journal of medical informatics. 143 [DOI] 10.1016/j.ijmedinf.2020.104272. [PMID] 32980667.
2020
Prevalence and hospital charges from firearm injuries treated in US emergency departments from 2006 to 2016
Surgery. [DOI] 10.1016/j.surg.2020.11.009. [PMID] 33384161.
2020
Differing impacts of global and regional responses on SARS-CoV-2 transmission cluster dynamics.
bioRxiv : the preprint server for biology. [DOI] 10.1101/2020.11.06.370999. [PMID] 33173870.
2020
Design and methodology challenges of environment-wide association studies: A systematic review.
Environmental research. 183 [DOI] 10.1016/j.envres.2020.109275. [PMID] 32105887.
2020
Correction: A Snapshot of SARS-CoV-2 Genome Availability up to April 2020 and its Implications: Data Analysis.
JMIR public health and surveillance. 6(3) [DOI] 10.2196/22853. [PMID] 32776889.
2020
Authors’ Reply to: Errors in Tracing Coronavirus SARS-CoV-2 Transmission Using a Maximum Likelihood Tree. Comment on “A Snapshot of SARS-CoV-2 Genome Availability up to April 2020 and its Implications: Data Analysis”.
JMIR public health and surveillance. 6(4) [DOI] 10.2196/24661. [PMID] 33174844.
2020
Assessing the practice of data quality evaluation in a national clinical data research network through a systematic scoping review in the era of real-world data.
Journal of the American Medical Informatics Association : JAMIA. 27(12):1999-2010 [DOI] 10.1093/jamia/ocaa245. [PMID] 33166397.
2020
Assessing the effect of data integration on predictive ability of cancer survival models.
Health informatics journal. 26(1):8-20 [DOI] 10.1177/1460458218824692. [PMID] 30672356.
2020
Assessing mental health signals among sexual and gender minorities using Twitter data.
Health informatics journal. 26(2):765-786 [DOI] 10.1177/1460458219839621. [PMID] 30969146.
2020
Are Preregistration and Registered Reports Vulnerable to Hacking?
Epidemiology (Cambridge, Mass.). 31(3) [DOI] 10.1097/EDE.0000000000001162. [PMID] 31985501.
2020
An ontology-based documentation of data discovery and integration process in cancer outcomes research.
BMC medical informatics and decision making. 20(Suppl 4) [DOI] 10.1186/s12911-020-01270-3. [PMID] 33317497.
2020
An external exposome-wide association study of hypertensive disorders of pregnancy.
Environment international. 141 [DOI] 10.1016/j.envint.2020.105797. [PMID] 32413622.
2020
Employing Molecular Phylodynamic Methods to Identify and Forecast HIV Transmission Clusters in Public Health Settings: A Qualitative Study.
Viruses. 12(9) [DOI] 10.3390/v12090921. [PMID] 32842636.
2019
Injury Burden in the United States: Accurate, Reliable, and Timely Surveillance Using Electronic Health Care Data.
American journal of public health. 109(12):1702-1706 [DOI] 10.2105/AJPH.2019.305306. [PMID] 31622141.
2019
Potential Impact of Interventions to Enhance Retention in Care During Real-World HIV Pre-Exposure Prophylaxis Implementation.
AIDS patient care and STDs. 33(10):434-439 [DOI] 10.1089/apc.2019.0064. [PMID] 31584857.
2019
Psychiatric disorders’ paradoxical protective effect on cardiovascular procedures and mortality.
Psychiatry research. 273 [DOI] 10.1016/j.psychres.2018.06.030. [PMID] 30642652.
2019
Response to letter.
Journal of psychiatric research. 116 [DOI] 10.1016/j.jpsychires.2018.12.011. [PMID] 30558836.
2019
Unexpected Predictors of Antibiotic Resistance in Housekeeping Genes of Staphylococcus Aureus.
ACM-BCB … … : the … ACM Conference on Bioinformatics, Computational Biology and Biomedicine. ACM Conference on Bioinformatics, Computational Biology and Biomedicine. 2019:259-268 [DOI] 10.1145/3307339.3342138. [PMID] 31592520.
2019
Statistical thinking, machine learning.
Journal of clinical epidemiology. 116:136-137 [DOI] 10.1016/j.jclinepi.2019.08.003. [PMID] 31425737.
2019
The Common Antidiabetic Drug Metformin Reduces Odds of Developing Age-Related Macular Degeneration.
Investigative ophthalmology & visual science. 60(5):1470-1477 [DOI] 10.1167/iovs.18-26422. [PMID] 30973575.
2019
Understanding Perceptions and Attitudes in Breast Cancer Discussions on Twitter.
Studies in health technology and informatics. 264:1293-1297 [DOI] 10.3233/SHTI190435. [PMID] 31438134.
2019
Risk of health morbidity for the uninsured: 10-year evidence from a large hospital center in Boston, Massachusetts.
International journal for quality in health care : journal of the International Society for Quality in Health Care. 31(5):325-330 [DOI] 10.1093/intqhc/mzy175. [PMID] 30137334.
2019
G-quadruplex – Characterization of Functions and Potential Therapeutic Uses of Non-canonical DNA Structures.
Current medicinal chemistry. 26(16):2879-2880 [DOI] 10.2174/092986732616190820105842. [PMID] 31526337.
2019
Hierarchical Hidden Markov models enable accurate and diverse detection of antimicrobial resistance sequences.
Communications biology. 2 [DOI] 10.1038/s42003-019-0545-9. [PMID] 31396574.
2019
Flexible design of multiple metagenomics classification pipelines with UGENE.
Bioinformatics (Oxford, England). 35(11):1963-1965 [DOI] 10.1093/bioinformatics/bty901. [PMID] 30358807.
2019
A data-driven and practice-based approach to identify risk factors associated with hospital-acquired falls: Applying manual and semi- and fully-automated methods.
International journal of medical informatics. 122:63-69 [DOI] 10.1016/j.ijmedinf.2018.11.006. [PMID] 30623785.
2019
ALOHA: developing an interactive graph-based visualization for dietary supplement knowledge graph through user-centered design.
BMC medical informatics and decision making. 19(Suppl 4) [DOI] 10.1186/s12911-019-0857-1. [PMID] 31391091.
2019
An Integrated Approach for Efficient Multi-Omics Joint Analysis.
ACM-BCB … … : the … ACM Conference on Bioinformatics, Computational Biology and Biomedicine. ACM Conference on Bioinformatics, Computational Biology and Biomedicine. 2019:619-625 [DOI] 10.1145/3307339.3343476. [PMID] 31588431.
2019
Association of Long-Term Dynamics in Circulating Testosterone with Serum PSA in Prostate Cancer-Free Men with Initial-PSA
Hormones & cancer. 10(4-6):168-176 [DOI] 10.1007/s12672-019-00369-y. [PMID] 31621000.
2019
Association of statin use with risk of Gleason score-specific prostate cancer: A hospital-based cohort study.
Cancer medicine. 8(17):7399-7407 [DOI] 10.1002/cam4.2500. [PMID] 31595713.
2019
Genomic Comparison Reveals Natural Occurrence of Clinically Relevant Multidrug-Resistant Extended-Spectrum-β-Lactamase-Producing Escherichia coli Strains.
Applied and environmental microbiology. 85(13) [DOI] 10.1128/AEM.03030-18. [PMID] 31053578.
2019
Clinical correlates of workplace injury occurrence and recurrence in adults.
PloS one. 14(9) [DOI] 10.1371/journal.pone.0222603. [PMID] 31513669.
2019
Cost-Effectiveness of a Statewide Pre-Exposure Prophylaxis Program for Gay, Bisexual, and Other Men Who Have Sex with Men.
Rhode Island medical journal (2013). 102(9):36-39 [PMID] 31675786.
View on: PubMed
2019
Exploring Lung Cancer Screening Discussions on Twitter.
Studies in health technology and informatics. 264:2011-2012 [DOI] 10.3233/SHTI190760. [PMID] 31438454.
2019
Changes in patterns of mortality rates and years of life lost due to firearms in the United States, 1999 to 2016: A joinpoint analysis.
PloS one. 14(11) [DOI] 10.1371/journal.pone.0225223. [PMID] 31756227.
2018
The global burden of HIV-1 drug resistance in the past 20 years.
PeerJ. 6 [DOI] 10.7717/peerj.4848. [PMID] 29844989.
2018
Prototyping an Interactive Visualization of Dietary Supplement Knowledge Graph.
Proceedings. IEEE International Conference on Bioinformatics and Biomedicine. 2018:1649-1652 [DOI] 10.1109/BIBM.2018.8621340. [PMID] 31667004.
2018
Multi-drug resistant Pseudomonas aeruginosa nosocomial strains: Molecular epidemiology and evolution.
Microbial pathogenesis. 123:233-241 [DOI] 10.1016/j.micpath.2018.07.020. [PMID] 30031889.
2018
Improving the impact of HIV pre-exposure prophylaxis implementation in small urban centers among men who have sex with men: An agent-based modelling study.
PloS one. 13(7) [DOI] 10.1371/journal.pone.0199915. [PMID] 29985949.
2018
Reported Adverse Events with Painkillers: Data Mining of the US Food and Drug Administration Adverse Events Reporting System.
Drug safety. 41(3):313-320 [DOI] 10.1007/s40264-017-0611-5. [PMID] 29098610.
2018
Computable Eligibility Criteria through Ontology-driven Data Access: A Case Study of Hepatitis C Virus Trials.
AMIA … Annual Symposium proceedings. AMIA Symposium. 2018:1601-1610 [PMID] 30815206.
View on: PubMed
2018
BMI trajectories and risk of overall and grade-specific prostate cancer: An observational cohort study among men seen for prostatic conditions.
Cancer medicine. 7(10):5272-5280 [DOI] 10.1002/cam4.1747. [PMID] 30207080.
2018
Big data hurdles in precision medicine and precision public health.
BMC medical informatics and decision making. 18(1) [DOI] 10.1186/s12911-018-0719-2. [PMID] 30594159.
2018
Development of a personalized diagnostic model for kidney stone disease tailored to acute care by integrating large clinical, demographics and laboratory data: the diagnostic acute care algorithm – kidney stones (DACA-KS).
BMC medical informatics and decision making. 18(1) [DOI] 10.1186/s12911-018-0652-4. [PMID] 30119627.
2018
A systematic review of the effectiveness of mobile apps for monitoring and management of mental health symptoms or disorders.
Journal of psychiatric research. 107:73-78 [DOI] 10.1016/j.jpsychires.2018.10.006. [PMID] 30347316.
2017
Using Social Media Data to Understand the Impact of Promotional Information on Laypeople’s Discussions: A Case Study of Lynch Syndrome.
Journal of medical Internet research. 19(12) [DOI] 10.2196/jmir.9266. [PMID] 29237586.
2017
Trends in Gene Expression Profiling for Prostate Cancer Risk Assessment: A Systematic Review.
Biomedicine hub. 2(2):1-15 [DOI] 10.1159/000472146. [PMID] 31988908.
2017
Phylodynamic applications in 21st century global infectious disease research.
Global health research and policy. 2 [DOI] 10.1186/s41256-017-0034-y. [PMID] 29202081.
2017
Multi-drug resistant Klebsiella pneumoniae strains circulating in hospital setting: whole-genome sequencing and Bayesian phylogenetic analysis for outbreak investigations.
Scientific reports. 7(1) [DOI] 10.1038/s41598-017-03581-4. [PMID] 28615687.
2017
Role of systemic inflammation scores for prediction of clinical outcomes in patients treated with atazanavir not boosted by ritonavir in the Italian MASTER cohort.
BMC infectious diseases. 17(1) [DOI] 10.1186/s12879-017-2322-z. [PMID] 28298195.
2017
Association between age-related reductions in testosterone and risk of prostate cancer-An analysis of patients’ data with prostatic diseases.
International journal of cancer. 141(9):1783-1793 [DOI] 10.1002/ijc.30882. [PMID] 28699177.
2017
A new approach to disentangle genetic and epigenetic components on disease comorbidities: studying correlation between genotypic and phenotypic disease networks.
Procedia computer science. 110:453-458 [DOI] 10.1016/j.procs.2017.06.119. [PMID] 32318124.
2017
Explore Care Pathways of Colorectal Cancer Patients with Social Network Analysis.
Studies in health technology and informatics. 245 [PMID] 29295355.
View on: PubMed
2017
Emergence of recombinant Mayaro virus strains from the Amazon basin.
Scientific reports. 7(1) [DOI] 10.1038/s41598-017-07152-5. [PMID] 28821712.
2016
Moving microbiota research toward establishing causal associations that represent viable targets for effective public health interventions.
Annals of epidemiology. 26(5):306-10 [DOI] 10.1016/j.annepidem.2016.03.011. [PMID] 27133768.
2016
An external validation of models to predict the onset of chronic kidney disease using population-based electronic health records from Salford, UK.
BMC medicine. 14 [DOI] 10.1186/s12916-016-0650-2. [PMID] 27401013.
2016
Challenges in the Analysis of Viral Metagenomes
Virus Evolution. 2(2) [DOI] 10.1093/ve/vew022. [PMID] 29492275.
2016
Computer-Aided Optimization of Combined Anti-Retroviral Therapy for HIV: New Drugs, New Drug Targets and Drug Resistance.
Current HIV research. 14(2):101-9 [PMID] 26511342.
View on: PubMed
2016
Incidence and predictors of cardiovascular disease, chronic kidney disease, and diabetes in HIV/HCV-coinfected patients who achieved sustained virological response.
European journal of clinical microbiology & infectious diseases : official publication of the European Society of Clinical Microbiology. 35(9):1511-20 [DOI] 10.1007/s10096-016-2692-y. [PMID] 27272121.
2016
Kin of coauthorship in five decades of health science literature.
Proceedings of the National Academy of Sciences of the United States of America. 113(32):8957-62 [DOI] 10.1073/pnas.1517745113. [PMID] 27457939.
2016
Liver fibrosis progression and clinical outcomes are intertwined: role of CD4+ T-cell count and NRTI exposure from a large cohort of HIV/HCV-coinfected patients with detectable HCV-RNA: A MASTER cohort study.
Medicine. 95(29) [DOI] 10.1097/MD.0000000000004091. [PMID] 27442636.
2016
Mining Twitter to Assess the Public Perception of the “Internet of Things”.
PloS one. 11(7) [DOI] 10.1371/journal.pone.0158450. [PMID] 27391760.
2016
The global spread of Middle East respiratory syndrome: an analysis fusing traditional epidemiological tracing and molecular phylodynamics.
Global health research and policy. 1 [DOI] 10.1186/s41256-016-0014-7. [PMID] 29202063.
2016
Visual programming for next-generation sequencing data analytics.
BioData mining. 9 [DOI] 10.1186/s13040-016-0095-3. [PMID] 27127540.
2015
Combining macula clinical signs and patient characteristics for age-related macular degeneration diagnosis: a machine learning approach.
BMC ophthalmology. 15 [DOI] 10.1186/1471-2415-15-10. [PMID] 25623470.
2015
Development and preliminary validation of a dynamic, patient-tailored method to detect abnormal laboratory test results.
Studies in health technology and informatics. 216:701-5 [PMID] 26262142.
View on: PubMed
2015
Distinguishing Asthma Phenotypes Using Machine Learning Approaches.
Current allergy and asthma reports. 15(7) [DOI] 10.1007/s11882-015-0542-0. [PMID] 26143394.
2015
Evolution pathways of IgE responses to grass and mite allergens throughout childhood.
The Journal of allergy and clinical immunology. 136(6):1645-1652.e8 [DOI] 10.1016/j.jaci.2015.03.041. [PMID] 25962900.
2015
Relationship between cytokine expression patterns and clinical outcomes: two population-based birth cohorts.
Clinical and experimental allergy : journal of the British Society for Allergy and Clinical Immunology. 45(12):1801-11 [DOI] 10.1111/cea.12579. [PMID] 26061524.
2015
Two Distinct Hepatitis C Virus Genotype 1a Clades Have Different Geographical Distribution and Association With Natural Resistance to NS3 Protease Inhibitors.
Open forum infectious diseases. 2(2) [DOI] 10.1093/ofid/ofv043. [PMID] 26213689.
2015
Use of efavirenz or atazanavir/ritonavir is associated with better clinical outcomes of HAART compared to other protease inhibitors: routine evidence from the Italian MASTER Cohort.
Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases. 21(4):386.e1-9 [DOI] 10.1016/j.cmi.2014.10.022. [PMID] 25595708.
2014
Using String Metrics to Identify Patient Journeys through Care Pathways.
AMIA … Annual Symposium proceedings. AMIA Symposium. 2014:1208-17 [PMID] 25954432.
View on: PubMed
2014
Spatiotemporal dynamics of simian immunodeficiency virus brain infection in CD8+ lymphocyte-depleted rhesus macaques with neuroAIDS.
The Journal of general virology. 95(Pt 12):2784-2795 [DOI] 10.1099/vir.0.070318-0. [PMID] 25205684.
2014
Single tablet regimens are associated with reduced Efavirenz withdrawal in antiretroviral therapy naïve or switching for simplification HIV-infected patients.
BMC infectious diseases. 14 [DOI] 10.1186/1471-2334-14-26. [PMID] 24418191.
2014
Predicting phenotypes of asthma and eczema with machine learning.
BMC medical genomics. 7 Suppl 1 [DOI] 10.1186/1755-8794-7-S1-S7. [PMID] 25077568.
2014
Pharmacy refill adherence outperforms self-reported methods in predicting HIV therapy outcome in resource-limited settings.
BMC public health. 14 [DOI] 10.1186/1471-2458-14-1035. [PMID] 25280535.
2014
Intra-Host Bayesian Phylogeography Infers Tempo and Mode of Neuropathogenesis in Sivmac251 Infected Cd8-Lymphocyte Depleted Rhesus Macaques
Journal of Medical Primatology. 43(5)
2014
Challenges in interpreting allergen microarrays in relation to clinical symptoms: a machine learning approach.
Pediatric allergy and immunology : official publication of the European Society of Pediatric Allergy and Immunology. 25(1):71-9 [DOI] 10.1111/pai.12139. [PMID] 24131308.
2014
Can multiple SNP testing in BRCA2 and BRCA1 female carriers be used to improve risk prediction models in conjunction with clinical assessment?
BMC medical informatics and decision making. 14 [DOI] 10.1186/1472-6947-14-87. [PMID] 25274085.
2014
Phylodynamic analysis of clinical and environmental Vibrio cholerae isolates from Haiti reveals diversification driven by positive selection.
mBio. 5(6) [DOI] 10.1128/mBio.01824-14. [PMID] 25538191.
2013
Longitudinal analysis of intra-host simian immunodeficiency virus recombination in varied tissues of the rhesus macaque model for neuroAIDS.
The Journal of general virology. 94(Pt 11):2469-2479 [DOI] 10.1099/vir.0.055335-0. [PMID] 23963535.
2013
Transmission of Hiv in Sexual Networks in Sub-Saharan Africa and Europe
European Physical Journal-Special Topics. 222(6):1403-1411 [DOI] 10.1140/epjst/e2013-01934-8.
2013
Molecular epidemiology of community-associated methicillin-resistant Staphylococcus aureus in the genomic era: a cross-sectional study.
Scientific reports. 3 [DOI] 10.1038/srep01902. [PMID] 23712667.
2013
Declining prevalence of HIV-1 drug resistance in antiretroviral treatment-exposed individuals in Western Europe.
The Journal of infectious diseases. 207(8):1216-20 [DOI] 10.1093/infdis/jit017. [PMID] 23315324.
2013
Empirical validation of viral quasispecies assembly algorithms: state-of-the-art and challenges.
Scientific reports. 3 [DOI] 10.1038/srep02837. [PMID] 24089188.
2013
Combining Social and Genetic Networks To Study Hiv Transmission in Mixing Risk Groups
European Physical Journal-Special Topics. 222(6):1377-1387 [DOI] 10.1140/epjst/e2013-01932-x.
2013
Clinical evaluation of Rega 8: an updated genotypic interpretation system that significantly predicts HIV-therapy response.
PloS one. 8(4) [DOI] 10.1371/journal.pone.0061436. [PMID] 23613852.
2013
Challenges in identifying asthma subgroups using unsupervised statistical learning techniques.
American journal of respiratory and critical care medicine. 188(11):1303-12 [DOI] 10.1164/rccm.201304-0694OC. [PMID] 24180417.
2013
A single early introduction of HIV-1 subtype B into Central America accounts for most current cases.
Journal of virology. 87(13):7463-70 [DOI] 10.1128/JVI.01602-12. [PMID] 23616665.
2012
Single-Tablet Regimen Is Associated With Reduced Efavirenz Withdrawal in Antiretroviral Na Ve Or Switching for Simplification Hiv-Infected Patients
Journal of the International Aids Society. 15 [DOI] 10.7448/IAS.15.6.18094.
2012
QuRe: software for viral quasispecies reconstruction from next-generation sequencing data.
Bioinformatics (Oxford, England). 28(1):132-3 [DOI] 10.1093/bioinformatics/btr627. [PMID] 22088846.
2012
Prognostic value of virological and immunological responses after 6 months of antiretroviral treatment in adults with HIV-1 infection in sub-Saharan Africa.
Journal of acquired immune deficiency syndromes (1999). 59(3):236-44 [DOI] 10.1097/QAI.0b013e31824276e9. [PMID] 22327246.
2012
Predicting response to antiretroviral treatment by machine learning: the EuResist project.
Intervirology. 55(2):123-7 [DOI] 10.1159/000332008. [PMID] 22286881.
2012
PhyloTempo: A Set of R Scripts for Assessing and Visualizing Temporal Clustering in Genealogies Inferred from Serially Sampled Viral Sequences.
Evolutionary bioinformatics online. 8:261-9 [DOI] 10.4137/EBO.S9738. [PMID] 22745529.
2012
Predictors of first-line antiretroviral therapy discontinuation due to drug-related adverse events in HIV-infected patients: a retrospective cohort study.
BMC infectious diseases. 12 [DOI] 10.1186/1471-2334-12-296. [PMID] 23145925.
2012
Factors influencing the normalization of CD4+ T-cell count, percentage and CD4+/CD8+ T-cell ratio in HIV-infected patients on long-term suppressive antiretroviral therapy.
Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases. 18(5):449-58 [DOI] 10.1111/j.1469-0691.2011.03650.x. [PMID] 21919996.
2012
Computational models for prediction of response to antiretroviral therapies.
AIDS reviews. 14(2):145-53 [PMID] 22627610.
View on: PubMed
2012
Combining epidemiological and genetic networks signifies the importance of early treatment in HIV-1 transmission.
PloS one. 7(9) [DOI] 10.1371/journal.pone.0046156. [PMID] 23029421.
2012
Combination of immune and viral factors distinguishes low-risk versus high-risk HIV-1 disease progression in HLA-B*5701 subjects.
Journal of virology. 86(18):9802-16 [DOI] 10.1128/JVI.01165-12. [PMID] 22761389.
2012
On Counting the Frequency Distribution of String Motifs in Molecular Sequences
International Journal of Biomathematics. 5 [DOI] 10.1142/S1793524512500556.
2011
Detection of drug resistance mutations at low plasma HIV-1 RNA load in a European multicentre cohort study.
The Journal of antimicrobial chemotherapy. 66(8):1886-96 [DOI] 10.1093/jac/dkr171. [PMID] 21624929.
2011
Update on emergence of HIV-1 resistance to antiretroviral drug classes in an Italian national database: 2007-2009.
Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases. 17(9):1352-5 [DOI] 10.1111/j.1469-0691.2011.03563.x. [PMID] 21635664.
2011
Prediction of response to antiretroviral therapy by human experts and by the EuResist data-driven expert system (the EVE study).
HIV medicine. 12(4):211-8 [DOI] 10.1111/j.1468-1293.2010.00871.x. [PMID] 20731728.
2011
Interpretation of genotypic HIV-1 resistance to darunavir and virological response: validation of available systems and of a new score.
Antiviral therapy. 16(4):489-97 [DOI] 10.3851/IMP1799. [PMID] 21685536.
2011
Favourable evolution of virological and immunological profiles in treated and untreated patients in Italy in the period 1998-2008.
HIV medicine. 12(3):174-82 [DOI] 10.1111/j.1468-1293.2010.00866.x. [PMID] 20726904.
2011
Darunavir/ritonavir and raltegravir coadministered in routine clinical practice: potential role for an unexpected drug interaction.
Pharmacological research. 63(3):249-53 [DOI] 10.1016/j.phrs.2010.11.009. [PMID] 21130167.
2011
A novel methodology for large-scale phylogeny partition.
Nature communications. 2 [DOI] 10.1038/ncomms1325. [PMID] 21610724.
2011
Clinical presentation, microbiological features and correlates of disease severity of 2009 pandemic influenza A (H1N1) infection.
European journal of clinical microbiology & infectious diseases : official publication of the European Society of Clinical Microbiology. 30(4):541-9 [DOI] 10.1007/s10096-010-1116-7. [PMID] 21104285.
2011
Can linear regression modeling help clinicians in the interpretation of genotypic resistance data? An application to derive a lopinavir-score.
PloS one. 6(11) [DOI] 10.1371/journal.pone.0025665. [PMID] 22110581.
2011
A prognostic model for estimating the time to virologic failure in HIV-1 infected patients undergoing a new combination antiretroviral therapy regimen.
BMC medical informatics and decision making. 11 [DOI] 10.1186/1472-6947-11-40. [PMID] 21672248.
2011
A computational approach to identify point mutations associated with occult hepatitis B: significant mutations affect coding regions but not regulative elements of HBV.
Virology journal. 8 [DOI] 10.1186/1743-422X-8-394. [PMID] 21824402.
2011
Combinatorial analysis and algorithms for quasispecies reconstruction using next-generation sequencing.
BMC bioinformatics. 12 [DOI] 10.1186/1471-2105-12-5. [PMID] 21208435.
2010
The threshold bootstrap clustering: a new approach to find families or transmission clusters within molecular quasispecies.
PloS one. 5(10) [DOI] 10.1371/journal.pone.0013619. [PMID] 21049051.
2010
Resistance considerations in sequencing of antiretroviral therapy in low-middle income countries with currently available options.
Current opinion in HIV and AIDS. 5(1):27-37 [DOI] 10.1097/COH.0b013e328333ad45. [PMID] 20046145.
2010
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.
Journal of medical virology. 82(12):1996-2003 [DOI] 10.1002/jmv.21927. [PMID] 20981785.
2010
Mid-dosing interval concentration of atazanavir and virological outcome in patients treated for HIV-1 infection.
HIV medicine. 11(5):326-33 [DOI] 10.1111/j.1468-1293.2009.00785.x. [PMID] 20070407.
2010
Comparison of HIV-1 genotypic resistance test interpretation systems in predicting virological outcomes over time.
PloS one. 5(7) [DOI] 10.1371/journal.pone.0011505. [PMID] 20634893.
2010
Comparative determination of HIV-1 co-receptor tropism by Enhanced Sensitivity Trofile, gp120 V3-loop RNA and DNA genotyping.
Retrovirology. 7 [DOI] 10.1186/1742-4690-7-56. [PMID] 20591141.
2010
Antiretroviral therapy optimisation without genotype resistance testing: a perspective on treatment history based models.
PloS one. 5(10) [DOI] 10.1371/journal.pone.0013753. [PMID] 21060792.
2010
Incidence of malignancies in HIV-infected patients and prognostic role of current CD4 cell count: evidence from a large Italian cohort study.
Clinical infectious diseases : an official publication of the Infectious Diseases Society of America. 50(9):1316-21 [DOI] 10.1086/651688. [PMID] 20297953.
2009
Robust supervised and unsupervised statistical learning for HIV type 1 coreceptor usage analysis.
AIDS research and human retroviruses. 25(3):305-14 [DOI] 10.1089/aid.2008.0039. [PMID] 19327050.
2009
Virological suppression reduces clinical progression in patients with multiclass-resistant HIV type 1.
AIDS research and human retroviruses. 25(3):261-7 [DOI] 10.1089/aid.2008.0136. [PMID] 19292594.
2009
Use of massively parallel ultradeep pyrosequencing to characterize the genetic diversity of hepatitis B virus in drug-resistant and drug-naive patients and to detect minor variants in reverse transcriptase and hepatitis B S antigen.
Journal of virology. 83(4):1718-26 [DOI] 10.1128/JVI.02011-08. [PMID] 19073746.
2009
Use of massive parallel pyrosequencing for near full-length characterization of a unique HIV Type 1 BF recombinant associated with a fatal primary infection.
AIDS research and human retroviruses. 25(9):937-42 [DOI] 10.1089/aid.2009.0083. [PMID] 19751146.
2009
Stochastic modelling of genotypic drug-resistance for human immunodeficiency virus towards long-term combination therapy optimization.
Bioinformatics (Oxford, England). 25(8):1040-7 [DOI] 10.1093/bioinformatics/btn568. [PMID] 18977781.
2009
Rules-based HIV-1 genotypic resistance interpretation systems predict 8 week and 24 week virological antiretroviral treatment outcome and benefit from drug potency weighting.
The Journal of antimicrobial chemotherapy. 64(3):616-24 [DOI] 10.1093/jac/dkp252. [PMID] 19620134.
2009
Predictors of successful genotype-guided antiretroviral therapy in treatment-experienced individuals over calendar years: a cohort study.
Journal of clinical virology : the official publication of the Pan American Society for Clinical Virology. 46(3):290-4 [DOI] 10.1016/j.jcv.2009.07.013. [PMID] 19699675.
2009
Effectiveness of antiretroviral regimens containing abacavir with tenofovir in treatment-experienced patients: predictors of virological response and drug resistance evolution in a multi-cohort study.
Infection. 37(5):438-44 [DOI] 10.1007/s15010-009-8237-x. [PMID] 19669091.
2009
Long-term follow-up of nevirapine-treated patients in a single-centre cohort.
HIV medicine. 10(8):461-9 [DOI] 10.1111/j.1468-1293.2009.00713.x. [PMID] 19459991.
2009
Investigation of expert rule bases, logistic regression, and non-linear machine learning techniques for predicting response to antiretroviral treatment.
Antiviral therapy. 14(3):433-42 [PMID] 19474477.
View on: PubMed
2009
Determinants of survival in progressive multifocal leukoencephalopathy.
Neurology. 73(19):1551-8 [DOI] 10.1212/WNL.0b013e3181c0d4a1. [PMID] 19901246.
2009
Are mutations in HIV type-1 reverse transcriptase 245 codon predictive of abacavir hypersensitivity reaction?
Antiviral therapy. 14(1):99-101 [PMID] 19320242.
View on: PubMed
2009
Archived HIV-1 minority variants detected by ultra-deep pyrosequencing in provirus may be fully replication competent.
AIDS (London, England). 23(18):2541-3 [DOI] 10.1097/QAD.0b013e32832fd2e1. [PMID] 19907212.
2009
Massively parallel pyrosequencing highlights minority variants in the HIV-1 env quasispecies deriving from lymphomonocyte sub-populations.
Retrovirology. 6 [DOI] 10.1186/1742-4690-6-15. [PMID] 19216757.
2008
Comparison of classifier fusion methods for predicting response to anti HIV-1 therapy.
PloS one. 3(10) [DOI] 10.1371/journal.pone.0003470. [PMID] 18941628.
2008
Selecting anti-HIV therapies based on a variety of genomic and clinical factors.
Bioinformatics (Oxford, England). 24(13):i399-406 [DOI] 10.1093/bioinformatics/btn141. [PMID] 18586740.
2007
Declining prevalence of HIV-1 drug resistance in treatment-failing patients: a clinical cohort study.
Antiviral therapy. 12(5):835-9 [PMID] 17713168.
View on: PubMed
2007
Genotypic resistance to lopinavir and fosamprenavir with or without ritonavir of clinical isolates from patients failing protease inhibitors-containing HAART regimens: prevalence and predictors.
Scandinavian journal of infectious diseases. 39(9):813-8 [PMID] 17701721.
View on: PubMed
2007
Improved interpretation of genotypic changes in the HIV-1 reverse transcriptase coding region that determine the virological response to didanosine.
The Journal of infectious diseases. 196(11):1645-53 [PMID] 18008248.
View on: PubMed

Grants

Jan 2021 ACTIVE
SCH: INT: Enabling real-time surveillance of antimicrobial resistance
Role: Co-Investigator
Funding: NATL SCIENCE FOU
Sep 2020 ACTIVE
Using Real-world Data to Assess the Burden of Diabetes in Children and Adolescents in Florida
Role: Co-Investigator
Funding: CTRS FOR DISEASE CONTROL AND PREVENTION
Aug 2020 ACTIVE
Using Electronic Health Records from a Large Clinical Data Research Network to Understand Cancer Burden and Cancer Risks Among Transgender and Gender Nonconforming (TGNC) Individuals
Role: Co-Investigator
Funding: NATL INST OF HLTH NCI
May 2020 ACTIVE
Forecasting trajectories of HIV transmission networks with a novel phylodynamic and deep learning framework
Role: Principal Investigator
Funding: NATL INST OF HLTH NIAID
May 2020 ACTIVE
Spatiotemporal analysis of HIV health and quality of life outcomes in Florida
Role: Principal Investigator
Funding: FL DEPT OF HLTH via US HLTH RESOURCES AND SERV ADMN HIV/AIDS
Apr 2020 ACTIVE
RAPID: Dynamic Identification of SARS-COV-2 Transmission Epicenters in Presence of Spatial Heterogeneity (COV-DYNAMITE)
Role: Principal Investigator
Funding: NATL SCIENCE FOU
Dec 2019 ACTIVE
Artificial Intelligence-aided Personalization on Dual Antiplatelet Therapy for Patients Underwent Coronary Stent Implantation Using Large-scale Electronic Health Records
Role: Co-Investigator
Funding: UNIV OF TEXAS HLTH SCI CTR HOUSTON via AMER HEART ASSOCIATION
Oct 2019 – May 2020
Miami Center for AIDS Research
Role: Principal Investigator
Funding: UNIV OF MIAMI via NATL INST OF HLTH NIAID
Apr 2019 ACTIVE
Advancing Interdisciplinary Science of Aging through Identification of Iatrogenic Complications: The UF EHR Clinical Data Infrastructure for Enhanced Patient Safety among the Elderly (UF-ECLIPSE)
Role: Co-Investigator
Funding: NATL INST OF HLTH NIA
Jan 2019 ACTIVE
Management of Standardized Evaluation of Retroviral HIV Infection
Role: Principal Investigator
Funding: FONDAZIONE M.I.S.I.
Nov 2018 ACTIVE
Developing Computational Methods for Surveillance of Antimicrobial Resistant Agents
Role: Principal Investigator
Funding: NATL INST OF HLTH NIAID
May 2018 – Mar 2020
Spatiotemporal analysis of HIV drug resistance in Florida
Role: Principal Investigator
Funding: FL DEPT OF HLTH via US HLTH RESOURCES AND SERV ADMN
Feb 2018 ACTIVE
HIV Dynamic Modelling for Identification of Transmission Epicenters (HIV-DYNAMITE)
Role: Principal Investigator
Funding: NATL INST OF HLTH NIAID
Sep 2017 ACTIVE
Viral evolution in peripheral macrophages and brain during progression to AIDS
Role: Co-Investigator
Funding: NATL INST OF HLTH NINDS
Sep 2017 ACTIVE
A Person-Centric Prediction Model of Job Loss based on Social Media Data and Linguistic and Linguistic Analytics
Role: Principal Investigator
Funding: NATL SCIENCE FOU
May 2017 – May 2020
Miscellaneous Donors
Role: Principal Investigator
Funding: MISCELLANEOUS DONORS
Mar 2017 – Dec 2018
Strengthening the UF Health Nursing Academic Partnership Phase IV: Generating Practice-Based Evidence for Quality Improvement (Stage 2)
Role: Co-Investigator
Funding: UF HEALTH SHANDS HOSPITAL
Jun 2016 – Oct 2017
Mapping and modeling Bacillus anthracis and Clostridiumbotulinum across North Africa and the Middle East with high resolutiongenetic sequencing and spatial analysis.
Role: Project Manager
Funding: US DEPT OF HOMELAND SECURITY
Apr 2016 – Mar 2018
Enhancing Population Impact of HIV Pre-Exposure Prophylaxis Implementation
Role: Principal Investigator
Funding: BROWN UNIV via NATL INST OF HLTH NIMH
Jan 2016 – Dec 2018
Big data approach for correlating gut microbiota with epithelial methylation pattern
Role: Principal Investigator
Funding: NATL INST OF HLTH NCI
Jan 2016 ACTIVE
ufhcc-ioa cancer-aging collaborative team grants
Role: Project Manager
Funding: UF HEALTH SHANDS HOSPITAL
Jul 2015 – Jul 2016
EuResist Engine retraining
Role: Principal Investigator
Funding: EURESIST NETWORK GEIE
Jun 2015 – May 2018
Virus discovery and epidemic tracing from high throughput metagenomic sequencing
Role: Principal Investigator
Funding: EUROPEAN COMMISSION
Mar 2015 – Mar 2018
Management of standardized evaluation of retroviral HIV infection
Role: Principal Investigator
Funding: FONDAZIONE M.I.S.I.
Dec 2011 – Jun 2016
Cholera Transmission in Gressier Region, Haiti
Role: Project Manager
Funding: NATL INST OF HLTH NIAID

Teaching Profile

Courses Taught
2018,2020-2021
PHC7918 Independent Study
2018,2020
PHC7083 Computational Epidemiology in Population Science
2020-2021
PHC7199 Topics in Precision Medicine and Public Health Informatics
2017,2019-2020
PHC6601 Seminar in Contemporary Public Health Issues
2018-2019
PHC7980 Research for Doctoral Dissertation
2016-2019
PHC6937 Special Topics in Public Health
2018
MAT7979 Advanced Research
2018
CIS7979 Advanced Research
2016-2018
PHC7979 Advanced Research
2017
PHC6946 Public Health Internship
2017
PHC4101 Public Health Concepts
2017
PHC7000 Epidemiology Seminar II: Critical Evaluation, Research Proposals, and Methods
2021
PHC6941 MPH Applied Practice Experience

Contact Details

Phones:
Business:
(352) 273-5860
Emails:
Business:
m.prosperi@ufl.edu