| 2025 | AIME | 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, Christina Boucher, Yonghui Wu, Mattia Prosperi |
| 2025 | AIME | 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 |
| 2022 | AMIA | DR-VIDAL - Doubly Robust Variational Information-theoretic Deep Adversarial Learning for Counterfactual Prediction and Treatment Effect Estimation. | Shantanu Ghosh, Zheng Feng, Jiang Bian, Kevin Butler, Mattia Prosperi |
| 2022 | AMIA | 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 |
| 2021 | AMIA | Data and Model Biases in Social Media Analyses: A Case Study of COVID-19 Tweets. | Yunpeng Zhao, Pengfei Yin, Yongqiu Li, Xing He, Jingcheng Du, Cui Tao, Yi Guo, Mattia Prosperi, Pierangelo Veltri, Xi Yang, Yonghui Wu, Jiang Bian |
| 2018 | AMIA | Computable Eligibility Criteria through Ontology-driven Data Access: A Case Study of Hepatitis C Virus Trials. | Hansi Zhang, Zhe He, Xing He, Yi Guo, David R. Nelson, Franois Modave, Yonghui Wu, William R. Hogan, Mattia Prosperi, Jiang Bian |
| 2018 | FNC | 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, Mattia Prosperi |
| 2017 | FNC | Efficient data structures for mobile de novo genome assembly by third-generation sequencing. | Franco Milicchio, Mattia Prosperi |
| 2017 | FNC | 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 |
| 2014 | AMIA | Using String Metrics to Identify Patient Journeys through Care Pathways. | Richard Williams, Iain E. Buchan, Mattia Prosperi, John D. Ainsworth |
| 2008 | ICRA | A bacterial colony growth framework for collaborative multi-robot localization. | Andrea Gasparri, Mattia Prosperi |
| 2008 | ISMB | Selecting anti-HIV therapies based on a variety of genomic and clinical factors. | Michal Rosen-Zvi, Andr Altmann, Mattia Prosperi, Ehud Aharoni, Hani Neuvirth, Anders Snnerborg, Eugen Schlter, Daniel Struck, Yardena Peres, Francesca Incardona, Rolf Kaiser, Maurizio Zazzi, Thomas Lengauer |