Publications Papers

Papers

Our research sits at the intersection of computational biology, long-read sequencing, and precision medicine. Below is a curated selection of our group's most impactful publications, featuring innovative software frameworks, novel genomic algorithms, and translational biomedical discoveries. For a complete and up-to-date list of our research outputs, you can look up our team members’ profiles on Google Scholar.

Intermediate Layers Encode Optimal Biological Representations in Single-Cell Foundation Models

Authors: Civale, V. Y., Semeraro, R., Bagdanov, A. D., & Magi, A.
Journal: arXiv preprint (2026)
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PoreMeth2 for decoding the evolution of methylome alterations with nanopore sequencing

Authors: Mattei, G., Baragli, M., Gega, B., Mingrino, A., Chieca, M., Ducci, T., ... & Magi, A.
Journal: Genome Research (2025)
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Benchmarking DNA Foundation Models for zero-shot variant effect prediction: the role of context, training, and architecture

Authors: Alfisi, I., Ciapi, F., Baragli, M., & Magi, A.
Journal: bioRxiv (2025)
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GASOLINE: detecting germline and somatic structural variants from long-reads data

Authors: Magi, A., Mattei, G., Mingrino, A., Caprioli, C., Ronchini, C., Frigè, G., Semeraro, R., Baragli, M., Bolognini, D., Colombo, E., Mazzarella, L., & Pelicci, P. G.
Journal: Scientific Reports (2023)
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High-resolution Nanopore methylome-maps reveal random hyper-methylation at CpG-poor regions as driver of chemoresistance in leukemias

Authors: Magi, A., Mattei, G., Mingrino, A., Caprioli, C., Ronchini, C., Frigè, G., Semeraro, R., Bolognini, D., Rambaldi, A., Candoni, A., Colombo, E., Mazzarella, L., & Pelicci, P. G.
Journal: Communications Biology (2023)
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Nano-GLADIATOR: real-time detection of copy number alterations from nanopore sequencing data

Authors: Magi, A., Bolognini, D., Bartalucci, N., Mingrino, A., Semeraro, R., Giovannini, L., Bonifacio, S., Parrini, D., Pelo, E., Mannelli, F., Guglielmelli, P., & Vannucchi, A. M.
Journal: Bioinformatics (2019)
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Nanopore sequencing data analysis: state of the art, applications and challenges

Authors: Magi, A., Semeraro, R., Mingrino, A., Giusti, B., & D’Aurizio, R.
Journal: Briefings in Bioinformatics (2018)
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Enhanced copy number variants detection from whole-exome sequencing data using EXCAVATOR2

Authors: D’Aurizio, R., Pippucci, T., Tattini, L., Giusti, B., Pellegrini, M., & Magi, A.
Journal: Nucleic Acids Research (2016)
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EXCAVATOR: detecting copy number variants from whole-exome sequencing data

Authors: Magi, A., Tattini, L., Cifola, I., D’Aurizio, R., Benelli, M., Mangano, E., Battaglia, C., Bonora, E., Kurg, A., Seri, M., Magini, P., Giusti, B., Romeo, G., Pippucci, T., Bellis, G. D., Abbate, R., & Gensini, G. GF.
Journal: Genome Biology (2013)
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