PhD student building interpretable ML pipelines for omics data analysis.

I'm a PhD student at the University of Bologna with a background in Physics. I work at the intersection of machine learning and biomedicine, building interpretable, reproducible, and scalable pipelines for omics data analysis. I'm part of the Multi-Omics and Health-Care Data Analytics Unit at Sant'Orsola Hospital in Bologna.

• ML & Deep Learning in Biomedicine - Feature engineering, multi-omics integration, and interpretable models for clinical and biological prediction tasks
• Algorithms for Biomedical Data - Building computational tools, statistical models, and network-based approaches to simulate and analyze biological systems
• Mass Spectrometry - ML methods for predicting antimicrobial resistance from MALDI-TOF mass spectra
• Metagenomics - Network-based modeling of microbial communities for microbiome profiling, simulation, and pathogen detection
• Genomics - Analyzing structural variants, APOBEC-style mutations, and computational approaches to CRISPR genome editing

• combatlearn - Scikit-learn compatible ComBat for batch effect correction in high-dimensional data. Useful for harmonizing data across studies.

• ResPredAI - ML pipeline for predicting antimicrobial resistance from demographic and clinical data.

• MaldiAMRKit - Toolkit to read and preprocess MALDI-TOF mass spectra for AMR analyses.

• CATS - Compare Cas9 nucleases by detecting overlapping PAM sites and enabling allele-specific targeting of disease mutations, with ClinVar integration.

• CAMISIM-BrokenStick - Extension of CAMISIM to simulate metagenomic sequencing data using a broken stick model.

• APOBECSeeker - Pipeline for identifying APOBEC-style mutations from multiple sequence alignment.

• Rocchi, E., Nicitra, E., Calvo, M., Cento, V., Peiretti, L., Asif, Z., Menchinelli, G., Posteraro, B., Sala, C., Colosimo, C., Cricca, M., Sambri, V., Sanguinetti, M., Castellani, G. & Stefani, S. Combining mass spectrometry and machine learning models for predicting Klebsiella pneumoniae antimicrobial resistance: a multicenter experience from clinical isolates in Italy. BMC Microbiology (2026).

• Bonazzetti, C., Rocchi, E., Toschi, A., Derus, N.R., Sala, C., Pascale, R., Rinaldi, M., Campoli, C., Pasquini, Z.A.I., Tazza, B., Amicucci, A., Gatti, M., Ambretti, S., Viale, P., Castellani, G. & Giannella, M. Artificial Intelligence model to predict resistances in Gram-negative bloodstream infections. npj Digital Medicine 8, 319 (2025).

• Rocchi, E., Magnani, F., Castellani, G., Carusillo, A. & Tarozzi, M. CATS: a bioinformatic tool for automated Cas9 nucleases activity comparison in clinically relevant contexts. Frontiers in Genome Editing 7, 1571023 (2025).

• De Pascali, A.M., Ingletto, L., Brandolini, M., Rocchi, E., Tarozzi, M., Turba, M.E., Casadio, R., Gentilini, F., Gatti, G., Dionisi, L., Colosimo, C., Guerra, M., Zannoli, S., Dirani, G., Montanari, M.S., Marzucco, A., Grumiro, L., Rossini, G., Lazzarotto, T., Cricca, M., Castellani, G., Sambri, V. & Scagliarini, A. Understanding the evolutionary dynamics of Monkeypox virus through less explored pathways. Scientific Reports 15, 25849 (2025).

I'm a member of Physics4MedicineLab, the Applied Physics group within the Department of Medicine at Alma Mater Studiorum - University of Bologna.

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