HIV-1 Coreceptor Usage Prediction via Indexed Local Kernel Smoothing Methods and Grid-Based Multiple Statistical Validation. - Iuri Fanti; Mattia C. F. Prosperi; Giovanni Ulivi; Alessandro Micarelli (CBMS, 2007)

Statistical Comparison of Machine Learning Techniques for Treatment Optimisation of Drug-Resistant HIV-1. - Mattia C. F. Prosperi; Giovanni Ulivi; Maurizio Zazzi (CBMS, 2007)

A bacterial colony growth framework for collaborative multi-robot localization. - Andrea Gasparri; Mattia Prosperi (ICRA, 2008)

Selecting anti-HIV therapies based on a variety of genomic and clinical factors. - Michal Rosen-Zvi; André Altmann; Mattia Prosperi; Ehud Aharoni; Hani Neuvirth; Anders Sönnerborg; Eugen Schülter; Daniel Struck; Yardena Peres; Francesca Incardona; Rolf Kaiser; Maurizio Zazzi; et al. (ISMB, 2008)

A bacterial colony growth algorithm for mobile robot localization. - Andrea Gasparri; Mattia Prosperi (Auton. Robots, 2008)

Evolutionary Fuzzy Modelling for Drug Resistant HIV-1 Treatment Optimization. - Mattia Prosperi; Giovanni Ulivi (Engineering Evolutionary Intelligent Systems, 2008)

Stochastic modelling of genotypic drug-resistance for human immunodeficiency virus towards long-term combination therapy optimization. - Mattia C. F. Prosperi; Roberto D'Autilia; Francesca Incardona; Andrea De Luca; Maurizio Zazzi; Giovanni Ulivi (Bioinform., 2009)

Combinatorial analysis and algorithms for quasispecies reconstruction using next-generation sequencing. - Mattia C. F. Prosperi; Luciano Prosperi; Alessandro Bruselles; Isabella Abbate; Gabriella Rozera; Donatella Vincenti; Maria Carmela Solmone; Maria Rosaria Capobianchi; Giovanni Ulivi (BMC Bioinform., 2011)

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; Simona Di Giambenedetto; Iuri Fanti; Genny Meini; Bianca Bruzzone; Annapaola Callegaro; Giovanni Penco; Patrizia Bagnarelli; Valeria Micheli; Elisabetta Paolini; Antonio Di Biagio; Valeria Ghisetti; et al. (BMC Medical Informatics Decis. Mak., 2011)

QuRe: software for viral quasispecies reconstruction from next-generation sequencing data. - Mattia C. F. Prosperi; Marco Salemi (Bioinform., 2012)

Using String Metrics to Identify Patient Journeys through Care Pathways. - Richard Williams 001; Iain E. Buchan; Mattia Prosperi; John D. Ainsworth (AMIA, 2014)

HErCoOl: High-Throughput Error Correction by Oligomers. - Franco Milicchio; Mattia C. F. Prosperi (CBMS, 2014)

Can multiple SNP testing in BRCA2 and BRCA1 female carriers be used to improve risk prediction models in conjunction with clinical assessment? - Mattia C. F. Prosperi; Sarah L. Ingham; Anthony Howell; Fiona Lalloo; Iain E. Buchan; Dafydd Gareth Evans (BMC Medical Informatics Decis. Mak., 2014)

Baseline CD4+ T Cell Counts Correlates with HIV-1 Synonymous Rate in HLA-B*5701 Subjects with Different Risk of Disease Progression. - Melissa M. Norström; Nazle M. Veras; Wei Huang; Mattia C. F. Prosperi; Jennifer Cook; Wendy Hartogensis; Frederick M. Hecht; Annika C. Karlsoon; Marco Salemi (PLoS Comput. Biol., 2014)

Development and preliminary validation of a dynamic, patient-tailored method to detect abnormal laboratory test results. - Paolo Fraccaro; Benjamin Brown 001; Mattia Prosperi; Matthew Sperrin; Iain E. Buchan; Niels Peek (MedInfo, 2015)

High-performance data structures for de novo assembly of genomes: cache oblivious generic programming. - Franco Milicchio; Giuseppe Tradigo; Pierangelo Veltri; Mattia Prosperi (BCB, 2016)

Predicting human-immunodeficiency virus rebound after therapy initiation/switch using genetic, laboratory, and clinical data. - Mattia Prosperi; Alejandro Pironti; Francesca Incardona; Giuseppe Tradigo; Maurizio Zazzi (BCB, 2016)

G-quadruplex Structure Prediction and integration in the GenData2020 data model. - Giuseppe Tradigo; Francesca Cristiano; Stefano Alcaro; Sergio Greco; Gianluca Pollastri; Pierangelo Veltri; Mattia Prosperi (BCB, 2016)

On the identification of long non-coding RNAs from RNA-seq. - Francesca Cristiano; Pierangelo Veltri; Mattia Prosperi; Giuseppe Tradigo (BIBM, 2016)

A* fast and scalable high-throughput sequencing data error correction via oligomers. - Franco Milicchio; Iain E. Buchan; Mattia C. F. Prosperi (CIBCB, 2016)

Accessible Tourism for the Deaf via Mobile Apps. - Franco Milicchio; Mattia Prosperi (PETRA, 2016)

Visual programming for next-generation sequencing data analytics. - Franco Milicchio; Rebecca Rose; Jiang Bian 001; Jae Min; Mattia Prosperi (BioData Min., 2016)

Efficient data structures for mobile de novo genome assembly by third-generation sequencing. - Franco Milicchio; Mattia Prosperi (FNC/MobiSPC, 2017)

A new approach to disentangle genetic and epigenetic components on disease comorbidities: studying correlation between genotypic and phenotypic disease networks. - Giuseppe Tradigo; Raffaele Vacca; Todd M. Manini; Victoria Y. Bird; Travis A. Gerke; Pierangelo Veltri; Mattia Prosperi (FNC/MobiSPC, 2017)

Explore Care Pathways of Colorectal Cancer Patients with Social Network Analysis. - Tianyao Huo; Thomas J. George Jr.; Yi Guo 005; Zhe He 001; Mattia Prosperi; François Modave; Jiang Bian 001 (MedInfo, 2017)

Computable Eligibility Criteria through Ontology-driven Data Access: A Case Study of Hepatitis C Virus Trials. - Hansi Zhang; Zhe He 001; Xing He 003; Yi Guo 005; David R. Nelson; François Modave; Yonghui Wu; William R. Hogan; Mattia Prosperi; Jiang Bian 001 (AMIA, 2018)

Prototyping an Interactive Visualization of Dietary Supplement Knowledge Graph. - Xing He 003; Rui Zhang 028; Rubina F. Rizvi; Jake Vasilakes; Xi Yang 015; Yi Guo 005; Zhe He 001; Mattia Prosperi; Jiang Bian 001 (BIBM, 2018)

Third-generation sequencing data analytics on mobile devices: cache oblivious and out-of-core approaches as a proof-of-concept. - Franco Milicchio; Marco Oliva; Christina Boucher 001; Mattia Prosperi (FNC/MobiSPC, 2018)

An Operational Deep Learning Pipeline for Classifying Life Events from Individual Tweets. - Xinsong Du; Jiang Bian 001; Mattia Prosperi (SIMBig, 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). - Zhaoyi Chen; Victoria Y. Bird; Rupam Ruchi; Mark S. Segal; Jiang Bian 001; Saeed R. Khan; Marie-Carmelle Elie; Mattia Prosperi (BMC Medical Informatics Decis. Mak., 2018)

Big data hurdles in precision medicine and precision public health. - Mattia Prosperi; Jae Min; Jiang Bian 001; François Modave (BMC Medical Informatics Decis. Mak., 2018)

Unexpected Predictors of Antibiotic Resistance in Housekeeping Genes of Staphylococcus Aureus. - Mattia Prosperi; Taj Azarian; Judith A. Johnson; Marco Salemi; Franco Milicchio; Marco Oliva (BCB, 2019)

An Integrated Approach for Efficient Multi-Omics Joint Analysis. - Massimiliano S. Tagliamonte; Sheldon G. Waugh; Mattia Prosperi; Volker Mai (BCB, 2019)

Understanding Perceptions and Attitudes in Breast Cancer Discussions on Twitter. - François Modave; Yunpeng Zhao; Janice L. Krieger; Zhe He 001; Yi Guo 005; Jinhai Huo; Mattia Prosperi; Jiang Bian 001 (MedInfo, 2019)

Exploring Lung Cancer Screening Discussions on Twitter. - Yunpeng Zhao; Jinhai Huo; Mattia Prosperi; Yi Guo 005; Yongqiu Li; Jiang Bian 001 (MedInfo, 2019)

Flexible design of multiple metagenomics classification pipelines with UGENE. - Rebecca Rose; Olga Golosova; Dmitrii Sukhomlinov; Aleksey Tiunov; Mattia Prosperi (Bioinform., 2019)

Mining Twitter to Assess the Determinants of Health Behavior towards Human Papillomavirus Vaccination in the United States. - Hansi Zhang; Christopher Wheldon; Adam G. Dunn; Cui Tao; Jinhai Huo; Rui Zhang 028; Mattia Prosperi; Yi Guo 005; Jiang Bian 001 (CoRR, 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. - Robert James Lucero; David S. Lindberg; Elizabeth Fehlberg; Ragnhildur I. Bjarnadottir; Yin Li; Jeannie P. Cimiotti; Marsha Crane; Mattia Prosperi (Int. J. Medical Informatics, 2019)

ALOHA: developing an interactive graph-based visualization for dietary supplement knowledge graph through user-centered design. - Xing He 003; Rui Zhang 028; Rubina F. Rizvi; Jake Vasilakes; Xi Yang 015; Yi Guo 005; Zhe He 001; Mattia Prosperi; Jinhai Huo; Jordan Alpert; Jiang Bian 001 (BMC Medical Informatics Decis. Mak., 2019)

Is it time to rethink institutional review boards for the era of big data? - Mattia Prosperi; Jiang Bian 001 (Nat. Mach. Intell., 2019)

Multivariate Independence Set Search via Progressive Addition for Conditional Markov Acyclic Networks. - Mattia Prosperi; Jiang Bian 001; Mo Wang (BIBM, 2020)

On the use of clinical based infection data for pandemic case studies. - Giuseppe Tradigo; Patrizia Vizza; Gabriel Gabriele; Maria Mazzitelli; Carlo Torti; Mattia Prosperi; Pietro Hiram Guzzi; Pierangelo Veltri (BIBM, 2020)

Integrating Crowdsourcing and Active Learning for Classification of Work-Life Events from Tweets. - Yunpeng Zhao; Mattia Prosperi; Tianchen Lyu; Yi Guo 005; Le Zhou; Jiang Bian 001 (IEA/AIE, 2020)

Portable nanopore analytics: are we there yet? - Marco Oliva; Franco Milicchio; Kaden King; Grace Benson; Christina Boucher 001; Mattia Prosperi; Inanç Birol (Bioinform., 2020)

Integrating Crowdsourcing and Active Learning for Classification of Work-Life Events from Tweets. - Yunpeng Zhao; Mattia Prosperi; Tianchen Lyu; Yi Guo 005; Jiang Bian 001 (CoRR, 2020)

Assessing the effect of data integration on predictive ability of cancer survival models. - Yi Guo 005; Jiang Bian 001; François Modave; Qian Li 034; Thomas J. George; Mattia Prosperi; Elizabeth Shenkman (Health Informatics J., 2020)

Assessing mental health signals among sexual and gender minorities using Twitter data. - Yunpeng Zhao; Yi Guo 005; Xing He 003; Yonghui Wu; Xi Yang 015; Mattia Prosperi; Yanghua Jin; Jiang Bian 001 (Health Informatics J., 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. - David S. Lindberg; Mattia Prosperi; Ragnhildur I. Bjarnadottir; Jaime Thomas; Marsha Crane; Zhaoyi Chen; Kristen Shear; Laurence M. Solberg; Urszula Alina Snigurska; Yonghui Wu; Yunpeng Xia; Robert J. Lucero (Int. J. Medical Informatics, 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. - Jiang Bian 001; Tianchen Lyu; Alexander T. Loiacono; Tonatiuh Mendoza Viramontes; Gloria P. Lipori; Yi Guo 005; Yonghui Wu; Mattia Prosperi; Thomas J. George; Christopher A. Harle; Elizabeth A. Shenkman; William R. Hogan (J. Am. Medical Informatics Assoc., 2020)

Mining Twitter to assess the determinants of health behavior toward human papillomavirus vaccination in the United States. - Hansi Zhang; Christopher Wheldon; Adam G. Dunn; Cui Tao; Jinhai Huo; Rui Zhang 028; Mattia Prosperi; Yi Guo 005; Jiang Bian 001 (J. Am. Medical Informatics Assoc., 2020)

An ontology-based documentation of data discovery and integration process in cancer outcomes research. - Hansi Zhang; Yi Guo 005; Mattia Prosperi; Jiang Bian 001 (BMC Medical Informatics Decis. Mak., 2020)

Causal inference and counterfactual prediction in machine learning for actionable healthcare. - Mattia Prosperi; Yi Guo 005; Matthew Sperrin; James S. Koopman; Jae S. Min; Xing He 003; Shannan N. Rich; Mo Wang; Iain E. Buchan; Jiang Bian 001 (Nat. Mach. Intell., 2020)

Data and Model Biases in Social Media Analyses: A Case Study of COVID-19 Tweets. - Yunpeng Zhao; Pengfei Yin; Yongqiu Li; Xing He 003; Jingcheng Du; Cui Tao; Yi Guo 005; Mattia Prosperi; Pierangelo Veltri; Xi Yang 015; Yonghui Wu; Jiang Bian 001 (AMIA, 2021)

KARGA: Multi-platform Toolkit for k-mer-based Antibiotic Resistance Gene Analysis of High-throughput Sequencing Data. - Mattia Prosperi; Simone Marini (BHI, 2021)

Experimental Survey on Power Dissipation of k-mer-Handling Data Structures for Mobile Bioinformatics. - Franco Milicchio; Mattia Prosperi (BIBM, 2021)

Causal AI with Real World Data: Do Statins Protect from Alzheimer's Disease Onset? - Mattia Prosperi; Shantanu Ghosh; Zhaoyi Chen; Marco Salemi; Tianchen Lyu; Jinying Zhao; Jiang Bian 001 (ICMHI, 2021)

Fast and exact quantification of motif occurrences in biological sequences. - Mattia Prosperi; Simone Marini; Christina Boucher 001 (BMC Bioinform., 2021)

Challenges in replicating secondary analysis of electronic health records data with multiple computable phenotypes: A case study on methicillin-resistant Staphylococcus aureus bacteremia infections. - Inyoung Jun; Shannan N. Rich; Zhaoyi Chen; Jiang Bian 001; Mattia Prosperi (Int. J. Medical Informatics, 2021)

The application of artificial intelligence and data integration in COVID-19 studies: a scoping review. - Yi Guo 005; Yahan Zhang; Tianchen Lyu; Mattia Prosperi; Fei Wang 001; Hua Xu 001; Jiang Bian 001 (J. Am. Medical Informatics Assoc., 2021)

Deep propensity network using a sparse autoencoder for estimation of treatment effects. - Shantanu Ghosh; Jiang Bian 001; Yi Guo 005; Mattia Prosperi (J. Am. Medical Informatics Assoc., 2021)

Bagged random causal networks for interventional queries on observational biomedical datasets. - Mattia Prosperi; Yi Guo 005; Jiang Bian 001 (J. Biomed. Informatics, 2021)

Exploring the feasibility of using real-world data from a large clinical data research network to simulate clinical trials of Alzheimer's disease. - Zhaoyi Chen; Hansi Zhang; Yi Guo 005; Thomas J. George; Mattia Prosperi; William R. Hogan; Zhe He 001; Elizabeth A. Shenkman; Fei Wang 001; Jiang Bian 001 (npj Digit. Medicine, 2021)

DR-VIDAL - Doubly Robust Variational Information-theoretic Deep Adversarial Learning for Counterfactual Prediction and Treatment Effect Estimation. - Shantanu Ghosh; Zheng Feng; Jiang Bian 001; Kevin Butler; Mattia Prosperi (AMIA, 2022)

Complementing ICD Codes with Nurses' Assessment Data Can Improve the Identification of Patients with Hearing and Visual Impairments. - Urszula Alina Snigurska; Sarah E. Ser; Mattia Prosperi; Ragnhildur I. Bjarnadottir; Robert Lucero (AMIA, 2022)

An interleaved hardware-accelerated k-mer parser. - Franco Milicchio; Marco Oliva; Mattia Prosperi (BIBM, 2022)

Transmission cluster characteristics of global, regional, and lineage-specific SARS-CoV-2 phylogenies. - Mattia Prosperi; Brittany Rife Magalis; Simone Marini; Marco Salemi (BIBM, 2022)

Identification of Social and Racial Disparities in Risk of HIV Infection in Florida using Causal AI Methods. - Mattia Prosperi; Jie Xu 012; Jingchuan Serena Guo; Jiang Bian 001; Wei-Han William Chen; Shantrel Canidate; Simone Marini; Mo Wang (BIBM, 2022)

Annotations of Virus Data for Knowledge Enrichment. - Patrizia Vizza; Giuseppe Tradigo; Pietro H. Guzzi; Barbara Puccio; Mattia Prosperi; Carlo Torti; Pierangelo Veltri (ICHI, 2022)

Assessing putative bias in prediction of anti-microbial resistance from real-world genotyping data under explicit causal assumptions. - Mattia Prosperi; Christina Boucher 001; Jiang Bian 001; Simone Marini (Artif. Intell. Medicine, 2022)

Towards routine employment of computational tools for antimicrobial resistance determination via high-throughput sequencing. - Simone Marini; Rodrigo A. Mora; Christina Boucher 001; Noelle Robertson Noyes; Mattia Prosperi (Briefings Bioinform., 2022)

Optimizing viral genome subsampling by genetic diversity and temporal distribution (TARDiS) for phylogenetics. - Simone Marini; Carla Mavian; Alberto Riva; Mattia Prosperi; Marco Salemi; Brittany Rife Magalis (Bioinform., 2022)

Joint Application of the Target Trial Causal Framework and Machine Learning Modeling to Optimize Antibiotic Therapy: Use Case on Acute Bacterial Skin and Skin Structure Infections due to Methicillin-resistant Staphylococcus aureus. - Inyoung Jun; Simone Marini; Christina Boucher 001; J. Glenn Morris; Jiang Bian 001; Mattia Prosperi (CoRR, 2022)

Variational Temporal Deconfounder for Individualized Treatment Effect Estimation from Longitudinal Observational Data. - Zheng Feng; Mattia Prosperi; Jiang Bian 001 (CoRR, 2022)

A scoping review of semantic integration of health data and information. - Hansi Zhang; Tianchen Lyu; Pengfei Yin; Sarah Bost; Xing He 003; Yi Guo 005; Mattia Prosperi; William R. Hogan; Jiang Bian 001 (Int. J. Medical Informatics, 2022)

Biases in using social media data for public health surveillance: A scoping review. - Yunpeng Zhao; Xing He 003; Zheng Feng; Sarah Bost; Mattia Prosperi; Yonghui Wu; Yi Guo 005; Jiang Bian 001 (Int. J. Medical Informatics, 2022)

Finding Overlapping Rmaps via Clustering. - Kingshuk Mukherjee; Daniel Dole-Muinos; Massimiliano Rossi 001; Ayomide Ajayi; Mattia Prosperi; Christina Boucher 001 (IEEE ACM Trans. Comput. Biol. Bioinform., 2022)

Quantification of Racial Disparity on Urinary Tract Infection Recurrence and Treatment Resistance in Florida using Algorithmic Fairness Methods. - Inyoung Jun; Sarah E. S. Leary; Jie Xu 012; Jiang Bian 001; Mattia Prosperi (ICHI, 2023)

Optimizing Dynamic Antibiotic Treatment Strategies against Invasive Methicillin-Resistant Staphylococcus Aureus Infections using Causal Survival Forests and G-Formula on Statewide Electronic Health Record Data. - Inyoung Jun; Scott A. Cohen; Sarah E. Ser; Simone Marini; Robert J. Lucero; Jiang Bian 001; Mattia Prosperi (CDPD, 2023)

Preface: The 2023 ACM SIGKDD Workshop on Causal Discovery, Prediction and Decision. - Thuc Duy Le; Jiuyong Li; Robert Osazuwa Ness; Sofia Triantafillou; Shohei Shimizu; Peng Cui 001; Kun Kuang; Jian Pei 001; Fei Wang 001; Mattia Prosperi (CDPD, 2023)

Real-World Effectiveness of Lung Cancer Screening Using Deep Learning-Based Counterfactual Prediction. - Zheng Feng; Zhaoyi Chen; Yi Guo 005; Mattia Prosperi; Hiren J. Mehta; Dejana Braithwaite; Yonghui Wu; Jiang Bian 001 (MedInfo, 2023)

DR-VIDAL - Doubly Robust Variational Information-theoretic Deep Adversarial Learning for Counterfactual Prediction and Treatment Effect Estimation on Real World Data. - Shantanu Ghosh; Zheng Feng; Jiang Bian 001; Kevin Butler; Mattia Prosperi (CoRR, 2023)

Assess the documentation of cognitive tests and biomarkers in electronic health records via natural language processing for Alzheimer's disease and related dementias. - Zhaoyi Chen; Hansi Zhang; Xi Yang 015; Songzi Wu; Xing He 003; Jie Xu 012; Jingchuan Guo; Mattia Prosperi; Fei Wang 001; Hua Xu 001; Yong Chen 016; Hui Hu; et al. (Int. J. Medical Informatics, 2023)

MEGARes and AMR++, v3.0: an updated comprehensive database of antimicrobial resistance determinants and an improved software pipeline for classification using high-throughput sequencing. - Nathalie Bonin; Enrique Doster; Hannah Worley; Lee J. Pinnell; Jonathan E. Bravo; Peter Ferm; Simone Marini; Mattia Prosperi; Noelle R. Noyes; Paul S. Morley; Christina Boucher 001 (Nucleic Acids Res., 2023)

The role of health system penetration rate in estimating the prevalence of type 1 diabetes in children and adolescents using electronic health records. - Piaopiao Li; Tianchen Lyu; Khalid Alkhuzam; Eliot Spector; William T. Donahoo; Sarah Bost; Yonghui Wu; William R. Hogan; Mattia Prosperi; Desmond A. Schatz; Mark A Atkinson; Michael J. Haller; et al. (J. Am. Medical Informatics Assoc., 2023)

Application of a practice-based approach in variable selection for a prediction model development study of hospital-induced delirium. - Urszula Alina Snigurska; Sarah E. Ser; Laurence M. Solberg; Mattia Prosperi; Tanja Magoc; Zhaoyi Chen; Jiang Bian 001; Ragnhildur I. Bjarnadottir; Robert J. Lucero (BMC Medical Informatics Decis. Mak., 2023)

Predicting HIV Diagnosis Among Emerging Adults Using Electronic Health Records and Health Survey Data in All of Us Research Program. - Balu Bhasuran; Yiyang Liu; Mattia Prosperi; Karen MacDonell; Sylvie Naar; Zhe He 001 (BIBM, 2024)

Learning on Forecasting HIV Epidemic Based on Individuals' Contact Networks. - Chaoyue Sun; Yiyang Liu; Christina Parisi; Rebecca Fisk-Hoffman; Marco Salemi; Ruogu Fang; Brandi Danforth; Mattia Prosperi; Simone Marini (BIOSTEC (2), 2024)

Identifying Symptoms of Delirium from Clinical Narratives Using Natural Language Processing. - Aokun Chen; Daniel Paredes; Zehao Yu 001; Xiwei Lou; Roberta Brunson; Jamie N. Thomas; Kimberly A. Martinez; Robert J. Lucero; Tanja Magoc; Laurence M. Solberg; Urszula Alina Snigurska; Sarah E. Ser; et al. (ICHI, 2024)

An Average-Case Efficient Two-Stage Algorithm for Enumerating All Longest Common Substrings of Minimum Length $k$ Between Genome Pairs. - Mattia Prosperi; Simone Marini; Christina Boucher 001 (ICHI, 2024)

Prediction of A. Baumannii Amikacin Resistance in Clinical Metagenomics. - Michael Aaron G. Sy; Mattia Prosperi; Mohammadali Serajian; Christina Boucher 001; Panayotis Takis Benos; Simone Marini (MIE, 2024)

Forecasting dominance of SARS-CoV-2 lineages by anomaly detection using deep AutoEncoders. - Simone Rancati; Giovanna Nicora; Mattia Prosperi; Riccardo Bellazzi; Marco Salemi; Simone Marini (Briefings Bioinform., 2024)

Scalable de novo classification of antibiotic resistance of Mycobacterium tuberculosis. - Mohammadali Serajian; Simone Marini; Jarno N. Alanko; Noelle R. Noyes; Mattia Prosperi; Christina Boucher 001 (Bioinform., 2024)

DeepDynaForecast: Phylogenetic-informed graph deep learning for epidemic transmission dynamic prediction. - Chaoyue Sun; Ruogu Fang; Marco Salemi; Mattia Prosperi; Brittany Rife Magalis (PLoS Comput. Biol., 2024)

Comparative Evaluation of Clinical Large Language Models and Machine Learning to Predict Antimicrobial Resistance in Hospital-Onset Sepsis. - Scott A. Cohen; Ziyi Chen; Jiang Bian 001; Christina Boucher 001; Yonghui Wu; Mattia Prosperi (AIME (1), 2025)

Enabling Transcriptome Classification in Micro-cohorts with Pathway-Anchoring and Single-Subject Studies. - Mahdieh Shabanian; Nima Pouladi; Liam S. Wilson; Mattia Prosperi; Yves A. Lussier (AIME (2), 2025)

What to consider when developing a new molecular HIV surveillance tool: Perspectives of key stakeholders working in HIV prevention and treatment. - Shantrel S. Canidate; Hannah R. Gracy; Sean McIntosh; Yiyang Liu; Rebecca Fisk-Hoffman; Shannon Rich; Carla Mavian; Robert L. Cook 002; Mattia Prosperi; Marco Salemi (ICHI, 2025)

Causal machine learning to investigate the effectiveness of vancomycin as the empiric treatment choice in patients hospitalized with community acquired pneumonia. - Fabrizio Pecoraro; Scott A. Cohen; Mattia Prosperi (ICHI, 2025)

SARITA: a large language model for generating the S1 subunit of the SARS-CoV-2 spike protein. - Simone Rancati; Giovanna Nicora; Laura Bergomi; Tommaso Mario Buonocore; Daniel M. Czyz; Enea Parimbelli; Riccardo Bellazzi; Marco Salemi; Mattia Prosperi; Simone Marini (Briefings Bioinform., 2025)

Variational temporal deconfounder network for individualized treatment effect estimation with longitudinal observational data. - Hao Dai; Yu Huang 018; Yuxi Liu; Xing He 003; Jingchuan Guo; Mattia Prosperi; Jiang Bian 001 (J. Biomed. Informatics, 2025)

SDSL-Mobile: Enabling space-efficient data structures for mobile applications. - Alexander Barquero; Anisha Wadhwani; Tyler Pencinger; Aaron Hong; Jaime Ruiz; Mattia Prosperi; Christina Boucher 001 (SoftwareX, 2025)

A Topic Modeling Analysis of Stigma Dimensions, Social, and Related Behavioral Circumstances in Clinical Notes Among Patients with HIV. - Ziyi Chen; Yiyang Liu; Mattia Prosperi; Krishna Vaddiparti; Robert L. Cook 002; Jiang Bian 001; Yi Guo 005; Yonghui Wu (CoRR, 2025)