Publications

Umberto Perron, Elena Grassi, Aikaterini Chatzipli, Marco Viviani, Emre Karakoc, Lucia Trastulla, Claudio Isella, Eugenia R Zanella, Hagen Klett, Ivan Molineris, Julia Schueler, Manel Esteller, Enzo Medico, Nathalie Conte, Ultan McDermott, Livio Trusolino, Andrea Bertotti, Francesco Iorio (2023). Integrative ensemble modelling of cetuximab sensitivity in colorectal cancer PDXs.

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Alessandro Vinceti, Riccardo Roberto De Lucia, Paolo Cremaschi, Umberto Perron, Emre Karakoc, Luca Mauri, Carlos Fernandez, Krzysztof Henryk Kluczynski, Daniel Stephen Anderson, Francesco Iorio (2023). An interactive web application for processing, correcting, and visualizing genome-wide pooled CRISPR-Cas9 screens. Cell Reports Methods.

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Alessandro Vinceti, Lucia Trastulla, Umberto Perron, Andrea Raiconi, Francesco Iorio (2023). A heuristic algorithm solving the mutual-exclusivity-sorting problem. Bioinformatics.

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Alessandro Vinceti, Umberto Perron, Lucia Trastulla, Francesco Iorio (2022). Reduced gene templates for supervised analysis of scale-limited CRISPR-Cas9 fitness screens. Cell Reports.

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Alessandro Vinceti, Emre Karakoc, Clare Pacini, Umberto Perron, Riccardo Roberto De Lucia, Mathew J. Garnett, Francesco Iorio (2021). CoRe: a robustly benchmarked R package for identifying core-fitness genes in genome-wide pooled CRISPR-Cas9 screens. BMC Genomics.

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Antanas Kalkauskas, Umberto Perron, Yuxuan Sun, Nick Goldman, Guy Baele, Stephane Guindon, Nicola De Maio (2021). Sampling bias and model choice in continuous phylogeography: getting lost on a random walk. PLOS Computational Biology.

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Hanna Najgebauer, Umberto Perron, Francesco Iorio (2021). Redefining false discoveries in cancer data. Nature Computational Science.

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Claudia C. Weber, Umberto Perron, Dearbhaile Casey, Ziheng Yang, Nick Goldman (2020). Ambiguity coding allows accurate inference of evolutionary parameters from alignments in an aggregated state-space. Systematic Biology.

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Umberto Perron, Alexey M. Kozlov, Alexandros Stamatakis, Nick Goldman, Iain H. Moal (2019). Modelling structural constraints on protein evolution via side-chain conformational states. Molecular Biology and Evolution.

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Umberto Perron, Paolo Provero, Ivan Molineris (2017). In silico prediction of lncRNA function using tissue specific and evolutionary conserved expression. BMC Bioinformatics.

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