M. Prosperi

发表

Massively parallel pyrosequencing highlights minority variants in the HIV-1 env quasispecies deriving from lymphomonocyte sub-populations

Giovanni Chillemi, Alessandro Bruselles, Isabella Abbate, 2009, Retrovirology.

UvA-DARE (Digital Academic Repository) Combining epidemiological and genetic networks signifies the importance of early treatment in HIV-1 transmission

P. Sloot, Narges Zarrabi, R. Belleman, 2012 .

AMR-meta: a k-mer and metafeature approach to classify antimicrobial resistance from high-throughput short-read metagenomics data

Tamer Kahveci, C. Boucher, I. Slizovskiy, 2022, GigaScience.

Archived HIV-1 minority variants detected by ultra-deep pyrosequencing in provirus may be fully replication competent.

G. D'offizi, P. Narciso, G. Ippolito, 2009, AIDS.

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

M. Salemi, M. Prosperi, 2011 .

Sequence analysis Portable nanopore analytics: are we there yet?

C. Boucher, M. Prosperi, F. Milicchio, 2020 .

Annotations of Virus Data for Knowledge Enrichment

P. Guzzi, P. Veltri, G. Tradigo, 2022, 2022 IEEE 10th International Conference on Healthcare Informatics (ICHI).

Severe Acute Respiratory Syndrome Coronavirus 2 Delta Vaccine Breakthrough Transmissibility in Alachua County, Florida

A. Riva, M. Salemi, P. Starostik, 2022, Clinical Infectious Diseases: An Official Publication of the Infectious Diseases Society of America.

Target-enriched long-read sequencing (TELSeq) contextualizes antimicrobial resistance genes in metagenomes

C. Boucher, I. Slizovskiy, N. Noyes, 2022, Microbiome.

The K-mer antibiotic resistance gene variant analyzer (KARGVA)

C. Boucher, N. Noyes, M. Prosperi, 2022, bioRxiv.

Analysis Regaining perspective on SARS-CoV-2 molecular tracing and its implications

M. Salemi, C. Mavian, I. Capua, 2020 .

MEGARes and AMR++, v3.0: an updated comprehensive database of antimicrobial resistance determinants and an improved software pipeline for classification using high-throughput sequencing

C. Boucher, N. Noyes, E. Doster, 2022, Nucleic Acids Res..

Finding Overlapping Rmaps via Clustering

C. Boucher, M. Prosperi, Kingshuk Mukherjee, 2021, IEEE/ACM Transactions on Computational Biology and Bioinformatics.

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

Alessandro Bruselles, Maria Rosaria Capobianchi, Donatella Vincenti, 2008, Journal of Virology.

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” (Preprint)

M. Salemi, C. Mavian, M. Prosperi, 2020 .

Transmission cluster characteristics of global, regional, and lineage-specific SARS-CoV-2 phylogenies

M. Salemi, M. Prosperi, S. Marini, 2022, 2022 IEEE International Conference on Bioinformatics and Biomedicine (BIBM).

Finding Overlapping Rmaps via Gaussian Mixture Model Clustering

C. Boucher, M. Prosperi, Kingshuk Mukherjee, 2021, bioRxiv.

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

Giovanni Ulivi, Mattia C. F. Prosperi, Alessandro Bruselles, 2011, BMC Bioinformatics.

KARGAMobile: Android app for portable, real-time, easily interpretable analysis of antibiotic resistance genes via nanopore sequencing

C. Boucher, M. Prosperi, Jaime Ruiz, 2022, Frontiers in Bioengineering and Biotechnology.

Towards routine employment of computational tools for antimicrobial resistance determination via high-throughput sequencing

C. Boucher, N. Noyes, M. Prosperi, 2021, bioRxiv.

SARS-CoV-2 Delta vaccine breakthrough transmissibility in Alachua, Florida

M. Salemi, P. Starostik, M. Pieretti, 2021, medRxiv.

Transmission of HIV in sexual networks in sub-Saharan Africa and Europe

J. Ramasco, D. A. van de Vijver, M. Prosperi, 2013, The European Physical Journal Special Topics.

Use of massive parallel pyrosequencing for near full-length characterization of a unique HIV Type 1 BF recombinant associated with a fatal primary infection.

P. Narciso, M. Capobianchi, A. Bruselles, 2009, AIDS research and human retroviruses.

Declining Prevalence of HIV-1 Drug Resistance in Treatment-Failing Patients: A Clinical Cohort Study

G. Fadda, A. De Luca, S. Giambenedetto, 2007, Antiviral Therapy.

Low-abundance drug resistance mutations: extending the HIV paradigm to hepatitis B virus.

M. Capobianchi, A. Bruselles, S. Menzo, 2009, The Journal of infectious diseases.

Molecular Epidemiology of HIV-1 Subtype B Infection across Florida Reveals Few Large Superclusters with Metropolitan Origin

Emma C Spencer, M. Salemi, C. Mavian, 2022, Microbiology spectrum.

Molecular Epidemiology of Community-Associated Methicillin-resistant Staphylococcus aureus in the genomic era: a Cross-Sectional Study

Nazle M. Veras, J. Morris, M. Salemi, 2013, Scientific Reports.

Phylodynamic Analysis of Clinical and Environmental Vibrio cholerae Isolates from Haiti Reveals Diversification Driven by Positive Selection

Rita R. Colwell, Lee S. Katz, J. Glenn Morris, 2014, mBio.

Assessing putative bias in prediction of anti-microbial resistance from real-world genotyping data under explicit causal assumptions pdf

Christina Boucher, Jiang Bian, Simone Marini, 2021, Artif. Intell. Medicine.

G. Ippolito, M. Capobianchi, A. Bruselles, 2008, Journal of Virology.