Mattia Prosperi

MedicineComputer ScienceBiochemistry, Genetics and Molecular Biology

Pilot corpus only

This score is computed over theSindex pilot corpus and does not cover the full scientific literature. Scores are relative to papers we have ingested — papers, authors, and institutions outside the pilot are not represented. Methodology.

Top 1%percentile

12.3Author DataRank

Indexed papers

11in pilot corpus

datarank_citation_only_1hop_v6· scope data_onlyMethodology

Why this DataRank?

An author's DataRank is the sum of the DataRanks of all 11 indexed papers attributed to them. A prolific author with many moderate-impact papers can outrank one with a single high-impact paper.

Author scores recompute whenever paper DataRanks are refreshed, so this number lags the underlying paper scores by at most one batch run.

Read the full methodology →

The highest-impact dataset this researcher has shared, ranked by DataRank — the single contribution doing the most to lift their data-sharing standing.

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

Nucleic Acids Research(2022)10.1093/nar/gkac1047

Top 7%

3.4DataRank

Top 7%206 citations

Enrique Doster, Hannah Worley, Lee J. Pinnell, Jonathan E. Bravo, Peter Ferm +6 more

Papers

Driven by 59 papers — median percentile 55. Top paper: “MEGARes and AMR++, v3.0: an updated comprehensive database of antimicrobial resistance determinants and an improved software pipeline for classification using high-throughput sequencing”.

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

Nucleic Acids Research(2022)10.1093/nar/gkac1047

Top 7%

3.4DataRank

Top 7%206 citations

Enrique Doster, Hannah Worley, Lee J. Pinnell, Jonathan E. Bravo, Peter Ferm +6 more

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(2020)10.1093/jamia/ocaa245

Top 7%

3.3DataRank

Top 7%95 citations

Tianchen Lyu, Alexander Loiacono, Tonatiuh Mendoza Viramontes, Gloria Lipori, Yi Guo +7 more

Exploring the feasibility of using real-world data from a large clinical data research network to simulate clinical trials of Alzheimer’s disease

npj Digital Medicine(2021)10.1038/s41746-021-00452-1

Top 11%

1.9DataRank

Top 11%40 citations

Hansi Zhang, Yi Guo, Thomas J. George, Mattia Prosperi, William R. Hogan +5 more

The application of artificial intelligence and data integration in COVID-19 studies: a scoping review

Journal of the American Medical Informatics Association(2021)10.1093/jamia/ocab098

Top 11%

1.9DataRank

Top 11%50 citations

Yahan Zhang, Tianchen Lyu, Mattia Prosperi, Fei Wang, Hua Xu +2 more

Portable nanopore analytics: are we there yet?

Bioinformatics(2020)10.1093/bioinformatics/btaa237

N/A

1.1DataRank · unranked

27 citations

Franco Milicchio, Kaden King, Grace Benson, Christina Boucher, Mattia Prosperi +1 more

A comparative study of antibiotic resistance patterns in Mycobacterium tuberculosis

Scientific Reports(2025)10.1038/s41598-025-89087-w

Top 28%

0.703DataRank

Top 28%22 citations

Conrad Testagrose, Mattia Prosperi, Christina Boucher, Mohammadali Serajian

Sampling bias and incorrect rooting make phylogenetic network tracing of SARS-COV-2 infections unreliable

Proceedings of the National Academy of Sciences(2020)10.1073/pnas.2007295117

N/A

0.665DataRank · unranked

83 citations

Sergei L. Kosakovsky Pond, Simone Marini, Brittany Rife Magalis, Anne–Mieke Vandamme, Simon Dellicour +31 more

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

Frontiers in Microbiology(2023)10.3389/fmicb.2023.1060891

Top 45%

0.413DataRank

Top 45%10 citations

Christina Boucher, Noelle Noyes, Mattia Prosperi, Simone Marini

SARITA: a large language model for generating the S1 subunit of the SARS-CoV-2 spike protein

Briefings in Bioinformatics(2025)10.1093/bib/bbaf384

N/A

0.330DataRank · unranked

8 citations

Giovanna Nicora, Laura Bergomi, Tommaso Mario Buonocore, Daniel M. Czyż, Enea Parimbelli +5 more

Clinical Prediction Models for Hospital-Induced Delirium Using Structured and Unstructured Electronic Health Record Data: Protocol for a Development and Validation Study

JMIR Research Protocols(2023)10.2196/48521

N/A

0.292DataRank · unranked

6 citations

Kristen Shear, Urszula A Snigurska, Mattia Prosperi, Yonghui Wu, Tanja Magoč +3 more

Exploring the Feasibility of Using Real-World Data from a Large Clinical Data Research Network to Simulate Clinical Trials of Alzheimer’s Disease

medRxiv(2020)10.1101/2020.06.03.20121491

Top 65%

0.208DataRank

Top 65%3 citations

Hansi Zhang, Yi Guo, Thomas J. George, Mattia Prosperi, William R. Hogan +5 more

Demographics, Trends, and Clinical Characteristics of HIV Pre-Exposure Prophylaxis Recipients and People Newly Diagnosed with HIV from Large Electronic Health Records in Florida

AIDS Patient Care and STDs(2024)10.1089/apc.2023.0220

Top 65%

0.208DataRank

Top 65%3 citations

Khairul A. Siddiqi, Hwayoung Cho, Haesuk Park, Mattia Prosperi, Robert L. Cook +1 more

Novel insights on unraveling dynamics of transmission clusters in outbreaks using phylogeny-based methods

Infection Genetics and Evolution(2024)10.1016/j.meegid.2024.105661

N/A

0.208DataRank · unranked

3 citations

Alberto Riva, Simone Marini, Marco Salemi, Mattia Prosperi, Brittany Rife Magalis

The Burden of Cancer and Pre-cancerous Conditions Among Transgender Individuals in a Large Healthcare Network

medRxiv(2024)10.1101/2024.03.24.24304777

N/A

0.130DataRank · unranked

1 citations

Yongqiu Li, Christopher W. Wheldon, Mattia Prosperi, Thomas J. George, Elizabeth Shenkman +4 more

Developing an automated algorithm for identification of children and adolescents with diabetes using electronic health records from the OneFlorida + clinical research network

Diabetes Obesity and Metabolism(2024)10.1111/dom.15987

Top 78%

0.104DataRank

Top 78%1 citations

Eliot Spector, Khalid Alkhuzam, Rahul Patel, William T. Donahoo, Sarah Bost +18 more

Predicting HIV Diagnosis Among Emerging Adults Using Electronic Health Records and Health Survey Data in All of Us Research Program

PubMed(2024)10.1109/bibm62325.2024.10822296

N/A

0.104DataRank · unranked

1 citations

Yiyang Liu, Mattia Prosperi, Karen Kolmodin MacDonell, Sylvie Naar, Zhe He +1 more

The K -mer Antibiotic Resistance Gene Variant Analyzer (KARGVA)

bioRxiv (Cold Spring Harbor Laboratory)(2022)10.1101/2022.08.12.503773

Top 78%

0.104DataRank

Top 78%1 citations

Christina Boucher, Noelle Noyes, Mattia Prosperi, Simone Marini

Forecasting dominance of SARS-CoV-2 lineages by anomaly detection using deep AutoEncoders

bioRxiv (Cold Spring Harbor Laboratory)(2023)10.1101/2023.10.24.563721

N/A

0.104DataRank · unranked

1 citations

Giovanna Nicora, Mattia Prosperi, Riccardo Bellazzi, Marco Salemi, Simone Marini +1 more

The Burden of Cancer and Precancerous Conditions Among Transgender Individuals in a Large Health Care Network: Retrospective Cohort Study

JMIR Cancer(2025)10.2196/73843

N/A

0.104DataRank · unranked

1 citations

Yongqiu Li, Christopher W. Wheldon, Jessica Y. Islam, Mattia Prosperi, Thomas J. George +5 more

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

Microbiome(2022)10.1186/s40168-022-01368-y

N/A

0DataRank · unranked

26 citations

Marco Antônio Oliva, Jonathen Settle, Lidiya V. Zyskina, Mattia Prosperi, Christina Boucher +2 more

Assess the documentation of cognitive tests and biomarkers in electronic health records via natural language processing for Alzheimer’s disease and related dementias

International Journal of Medical Informatics(2022)10.1016/j.ijmedinf.2022.104973

N/A

0DataRank · unranked

21 citations

Hansi Zhang, Xi Yang, Songzi Wu, Xing He, Jie Xu +12 more

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

Artificial Intelligence in Medicine(2022)10.1016/j.artmed.2022.102326

N/A

0DataRank · unranked

9 citations

Christina Boucher, Jiang Bian, Simone Marini, Mattia Prosperi

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

GigaScience(2022)10.1093/gigascience/giac029

N/A

0DataRank · unranked

18 citations

Marco Antônio Oliva, Ilya B. Slizovskiy, Rishabh A Das, Noelle Noyes, Tamer Kahveci +3 more

Syndromic Surveillance Systems for Mass Gatherings: A Scoping Review

International Journal of Environmental Research and Public Health(2022)10.3390/ijerph19084673

N/A

0DataRank · unranked

13 citations

Yahan Zhang, Yi Guo, Sarah Bost, Xi Yang, Mattia Prosperi +4 more

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

Frontiers in Bioengineering and Biotechnology(2022)10.3389/fbioe.2022.1016408

N/A

0DataRank · unranked

7 citations

Simone Marini, Christina Boucher, Jaimé Ruiz, Mattia Prosperi, Alexander Barquero

Protocol for the development of a reporting guideline for causal and counterfactual prediction models in biomedicine

BMJ Open(2022)10.1136/bmjopen-2021-059715

N/A

0DataRank · unranked

6 citations

Yi Guo, Fei Wang, Hua Xu, Robert Lucero, Jiang Bian +2 more

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(2020)10.1016/j.ijmedinf.2020.104272

N/A

0DataRank · unranked

96 citations

Mattia Prosperi, Ragnhildur I. Bjarnadóttir, Jaime Thomas, Marsha Crane, Zhaoyi Chen +7 more

Variational Temporal Deconfounder for Individualized Treatment Effect Estimation with Longitudinal Observational Data

Research Square(2023)10.21203/rs.3.rs-2536079/v1

N/A

0DataRank · unranked

1 citations

Mattia Prosperi, Yi Guo, Jiang Bian, Zheng Feng

Identifying Symptoms of Delirium from Clinical Narratives Using Natural Language Processing

arXiv (Cornell University)(2023)10.48550/arxiv.2304.00111

N/A

0DataRank · unranked

1 citations

Daniel Paredes, Zehao Yu, Xiwei Lou, Roberta Brunson, Jamie N. Thomas +11 more

DR-VIDAL -- Doubly Robust Variational Information-theoretic Deep Adversarial Learning for Counterfactual Prediction and Treatment Effect Estimation on Real World Data

arXiv (Cornell University)(2023)10.48550/arxiv.2303.04201

N/A

0DataRank · unranked

0 citations

Feng, Zheng, Jiang Bian, Kevin Butler, Mattia Prosperi, Shantanu Ghosh

Scalable de novo classification of antibiotic resistance of Mycobacterium tuberculosis

Bioinformatics(2024)10.1093/bioinformatics/btae243

N/A

0DataRank · unranked

17 citations

Simone Marini, Jarno Alanko, Noelle Noyes, Mattia Prosperi, Christina Boucher +1 more

Forecasting dominance of SARS-CoV-2 lineages by anomaly detection using deep AutoEncoders

Briefings in Bioinformatics(2024)10.1093/bib/bbae535

N/A

0DataRank · unranked

14 citations

Giovanna Nicora, Mattia Prosperi, Riccardo Bellazzi, Marco Salemi, Simone Marini +1 more

Comorbidity Burden and Health Care Utilization by Substance use Disorder Patterns among People with HIV in Florida

AIDS and Behavior(2024)10.1007/s10461-024-04325-y

N/A

0DataRank · unranked

8 citations

Preeti Manavalan, Khairul A. Siddiqi, Robert L. Cook, Mattia Prosperi, Yiyang Liu

OCTOPUS: Disk-based, Multiplatform, Mobile-friendly Metagenomics Classifier

bioRxiv (Cold Spring Harbor Laboratory)(2024)10.1101/2024.03.15.585215

N/A

0DataRank · unranked

4 citations

Alexander Barquero, Anisha Ashok Wadhwani, Jiang Bian, Jaime Ruiz, Christina Boucher +2 more

Identifying Symptoms of Delirium from Clinical Narratives Using Natural Language Processing

PubMed(2024)10.1109/ichi61247.2024.00046

N/A

0DataRank · unranked

1 citations

Daniel Paredes, Zehao Yu, Xiwei Lou, Roberta Brunson, Jamie N. Thomas +11 more

An Average-Case Efficient Two-Stage Algorithm for Enumerating All Longest Common Substrings of Minimum Length $k$ Between Genome Pairs

PubMed(2024)10.1109/ichi61247.2024.00020

N/A

0DataRank · unranked

0 citations

Simone Marini, Christina Boucher, Mattia Prosperi

Leveraging large language models to predict antibiotic resistance in Mycobacterium tuberculosis

Bioinformatics(2025)10.1093/bioinformatics/btaf232

N/A

0DataRank · unranked

3 citations

Sakshi Pandey, Mohammadali Serajian, Simone Marini, Mattia Prosperi, Christina Boucher +1 more

Dynamic Networks of Methicillin-Resistant Staphylococcus aureus in Communities Drive Hospital Transmission

Open Forum Infectious Diseases(2025)10.1093/ofid/ofaf264

N/A

0DataRank · unranked

2 citations

Massimiliano S. Tagliamonte, Carla Mavian, Nicole M. Iovine, Yuting Zhai, Kwangcheol Casey Jeong +5 more

Variational temporal deconfounder network for individualized treatment effect estimation with longitudinal observational data

Journal of Biomedical Informatics(2025)10.1016/j.jbi.2025.104880

N/A

0DataRank · unranked

3 citations

Yu Huang, Yuxi Liu, Xing He, Jingchuan Guo, Mattia Prosperi +2 more

Receipt of long-acting injectable antiretroviral therapy among people with HIV in Southern US states: an assessment using electronic health records and claims data

AIDS Research and Therapy(2025)10.1186/s12981-024-00690-9

N/A

0DataRank · unranked

1 citations

Rebecca Fisk-Hoffman, Maitri Patel, Robert L. Cook, Mattia Prosperi, Yiyang Liu

Application of a practice-based approach in variable selection for a prediction model development study of hospital-induced delirium

BMC Medical Informatics and Decision Making(2023)10.1186/s12911-023-02278-1

N/A

0DataRank · unranked

1 citations

Sarah E Ser, Laurence M. Solberg, Mattia Prosperi, Tanja Magoč, Zhaoyi Chen +4 more

Deep propensity network using a sparse autoencoder for estimation of treatment effects

Journal of the American Medical Informatics Association(2020)10.1093/jamia/ocaa346

N/A

0DataRank · unranked

15 citations

Jiang Bian, Yi Guo, Mattia Prosperi, Shantanu Ghosh

An ontology-based documentation of data discovery and integration process in cancer outcomes research

BMC Medical Informatics and Decision Making(2020)10.1186/s12911-020-01270-3

N/A

0DataRank · unranked

9 citations

Yi Guo, Mattia Prosperi, Jiang Bian, Hansi Zhang

Mining Twitter to Assess the Determinants of Health Behavior towards Palliative Care in the United States

medRxiv(2020)10.1101/2020.03.26.20038372

N/A

0DataRank · unranked

7 citations

Hansi Zhang, Jinhai Huo, Yi Guo, Yonghui Wu, Mattia Prosperi +2 more

Differing impacts of global and regional responses on SARS-CoV-2 transmission cluster dynamics

bioRxiv (Cold Spring Harbor Laboratory)(2020)10.1101/2020.11.06.370999

N/A

0DataRank · unranked

7 citations

Andrea S. Ramirez-Mata, Anna Zhukova, Carla Mavian, Simone Marini, Frédéric Lemoine +4 more

Understanding Perceptions and Attitudes toward Genetically Modified Organisms on Twitter

(2020)10.1145/3400806.3400839

N/A

0DataRank · unranked

4 citations

Yunpeng Zhao, Xing He, Rania Gollakner, Christa D. Court, Olga Muñoz +4 more

Brain tissue transcriptomic analysis of SIV-infected macaques identifies Poly (ADP-ribose) polymerases (PARPs) as potential biomarkers for neuropathogenesis.

(2020)10.21203/rs.3.rs-30629/v1

N/A

0DataRank · unranked

0 citations

Andrea S. Ramirez-Mata, James J. Dollar, David J. Nolan, Shannan N. Rich, Kevin White +9 more

Exploring the Feasibility of Using Real-World Data from a Large Clinical Data Research Network to Simulate Clinical Trials of Alzheimer’s Disease

medRxiv(2020)10.1101/2020.08.16.20167577

Top 100%

0DataRank

Top 100%0 citations

Hansi Zhang, Yi Guo, Thomas J. George, Mattia Prosperi, William R. Hogan +5 more

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

bioRxiv (Cold Spring Harbor Laboratory)(2020)10.1101/2020.05.21.109140

N/A

0DataRank · unranked

0 citations

Andrea S. Ramirez-Mata, James J. Dollar, David J. Nolan, Kevin White, Shannan N. Rich +9 more

Semantic standards of external exposome data

Environmental Research(2021)10.1016/j.envres.2021.111185

N/A

0DataRank · unranked

25 citations

Hui Hu, Matthew Diller, William R. Hogan, Mattia Prosperi, Yi Guo +2 more

Propensity score synthetic augmentation matching using generative adversarial networks (PSSAM-GAN)

Computer Methods and Programs in Biomedicine Update(2021)10.1016/j.cmpbup.2021.100020

N/A

0DataRank · unranked

19 citations

Christina Boucher, Jiang Bian, Mattia Prosperi, Shantanu Ghosh

Optimizing viral genome subsampling by genetic diversity and temporal distribution (TARDiS) for phylogenetics

Bioinformatics(2021)10.1093/bioinformatics/btab725

N/A

0DataRank · unranked

17 citations

Carla Mavian, Alberto Riva, Mattia Prosperi, Marco Salemi, Brittany Rife Magalis +1 more

Fast and exact quantification of motif occurrences in biological sequences

BMC Bioinformatics(2021)10.1186/s12859-021-04355-6

N/A

0DataRank · unranked

5 citations

Simone Marini, Christina Boucher, Mattia Prosperi

Exploring Prediction of Antimicrobial Resistance Based on Protein Solvent Accessibility Variation

Frontiers in Genetics(2021)10.3389/fgene.2021.564186

N/A

0DataRank · unranked

5 citations

Marco Antônio Oliva, Ilya B. Slizovskiy, Noelle Noyes, Christina Boucher, Mattia Prosperi +1 more

Causal AI with Real World Data: Do Statins Protect from Alzheimer's Disease Onset?

PubMed(2021)10.1145/3472813.3473206

N/A

0DataRank · unranked

4 citations

Shantanu Ghosh, Zhaoyi Chen, Marco Salemi, Tianchen Lyu, Jinying Zhao +2 more

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

bioRxiv (Cold Spring Harbor Laboratory)(2021)10.1101/2021.11.03.467126

N/A

0DataRank · unranked

1 citations

Rodrígo Mora, Christina Boucher, Noelle Noyes, Mattia Prosperi, Simone Marini

Protocol for Development of a Reporting Guideline for Causal and Counterfactual Prediction Models

medRxiv(2021)10.1101/2021.11.19.21266604

N/A

0DataRank · unranked

0 citations

Yi Guo, Fei Wang, Hua Xu, Robert Lucero, Jiang Bian +2 more

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

Briefings in Bioinformatics(2022)10.1093/bib/bbac020

N/A

0DataRank · unranked

16 citations

Rodrígo Mora, Christina Boucher, Noelle Noyes, Mattia Prosperi, Simone Marini

Development of a Prediction Model for Antibiotic-Resistant Urinary Tract Infections Using Integrated Electronic Health Records from Multiple Clinics in North-Central Florida

Infectious Diseases and Therapy(2022)10.1007/s40121-022-00677-x

N/A

0DataRank · unranked

30 citations

Inyoung Jun, Jiang Bian, Christina Boucher, Kartikeya Cherabuddi, J. Glenn Morris +2 more

Mattia Prosperi

Indexed papers

Top data-sharing exemplar

Papers