Modeling biological systems with delays in Bio-PEPA by Giulio Caravagna, Jane Hillston

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The interplay of intrinsic and extrinsic bounded noises in biomolecular networks. by Giulio Caravagna, Giancarlo Mauri, Alberto d'Onofrio

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Cancer genomes tolerate deleterious coding mutations through somatic copy number amplifications of wild-type regions by Fabio Alfieri, Giulio Caravagna, Martin H. Schaefer

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Distributed delays in a hybrid model of tumor-Immune system interplay by Giulio Caravagna, Alex Graudenzi, Alberto d’Onofrio

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Author Correction: Cancer genomes tolerate deleterious coding mutations through somatic copy number amplifications of wild-type regions by Fabio Alfieri, Giulio Caravagna, Martin H. Schaefer

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The MOBSTER R package for tumour subclonal deconvolution from bulk DNA whole-genome sequencing data by Giulio Caravagna, Guido Sanguinetti, Trevor A. Graham, Andrea Sottoriva

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On the Interpretation of Delays in Delay Stochastic Simulation of Biological Systems by Andrea Maggiolo-Schettini, Paolo Milazzo, Giulio Caravagna, Roberto Barbuti

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Analysis of the spatial and dynamical properties of a multiscale model of intestinal crypts by Marco Antoniotti, Giulio Caravagna, Alex Graudenzi, Giovanni de Matteis

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Learning mutational graphs of individual tumour evolution from single-cell and multi-region sequencing data by Daniele Ramazzotti, Alex Graudenzi, Luca De Sano, Marco Antoniotti, Giulio Caravagna

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Aspects of multiscale modelling in a process algebra for biological systems by Roberto Barbuti, Giulio Caravagna, Paolo Milazzo, Andrea Maggiolo-Schettini, Simone Tini

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Effects of delayed immune-response in tumor immune-system interplay by Alberto d'Onofrio, Giancarlo Mauri, Marco Antoniotti, Alex Graudenzi, Giulio Caravagna

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GPU-powered Simulation Methodologies for Biological Systems by Dario Pescini, Marco Nobile, Paolo Cazzaniga, Giulio Caravagna, Daniela Besozzi, Alessandro Re

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Deep Learning-Informed Bayesian Model-Based Analysis to Estimate Superspreading Events in Epidemic Outbreaks by Arianna Tasciotti, Federico Urban, Federica de Dea, Luca Bortolussi, Giulio Caravagna, Alberto D'Onofrio

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CoGNaC: A Chaste Plugin for the Multiscale Simulation of Gene Regulatory Networks Driving the Spatial Dynamics of Tissues and Cancer by Simone Rubinacci, Alex Graudenzi, Giulio Caravagna, Giancarlo Mauri, James Osborne, Joe Pitt-Francis, Marco Antoniotti

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Data Symmetries and Learning in Fully Connected Neural Networks by Fabio Anselmi, Luca Manzoni, Alberto D'onofrio, Alex Rodriguez, Giulio Caravagna, Luca Bortolussi, Francesca Cairoli

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Inferring tree causal models of cancer progression with probability raising. by Loes Olde Loohuis, Giulio Caravagna, Alex Graudenzi, Daniele Ramazzotti, Giancarlo Mauri, Marco Antoniotti, Bud Mishra

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CoGNaC: A Chaste Plugin for the Multiscale Simulation of Gene Regulatory Networks Driving the Spatial Dynamics of Tissues and Cancer by Simone Rubinacci, Alex Graudenzi, Giulio Caravagna, Giancarlo Mauri, James Osborne, Joe Pitt-Francis, Marco Antoniotti

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Spatially constrained tumour growth affects the patterns of clonal selection and neutral drift in cancer genomic data. by Ketevan Chkhaidze, Timon Heide, Benjamin Werner, Marc J Williams, Weini Huang, Giulio Caravagna, Trevor A Graham, Andrea Sottoriva

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A Bayesian method to infer copy number clones from single-cell RNA and ATAC sequencing. by Lucrezia Patruno, Salvatore Milite, Riccardo Bergamin, Nicola Calonaci, Alberto D'Onofrio, Fabio Anselmi, Marco Antoniotti, Alex Graudenzi, Giulio Caravagna

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Clinical application of tumour-in-normal contamination assessment from whole genome sequencing by Jonathan Mitchell, Salvatore Milite, Jack Bartram, Susan Walker, Nadezda Volkova, Olena Yavorska, Magdalena Zarowiecki, Jane Chalker, Rebecca Thomas, Luca Vago, Alona Sosinsky, Giulio Caravagna

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