Variant calling from scRNA-seq data allows the assessment of cellular identity in patient-derived cell lines von Ramazzotti, Daniele, Angaroni, Fabrizio, Maspero, Davide, Ascolani, Gianluca, Castiglioni, Isabella, Piazza, Rocco, Antoniotti, Marco, Graudenzi, Alex

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Mutational signatures and heterogeneous host response revealed via large-scale characterization of SARS-CoV-2 genomic diversity von Graudenzi, Alex, Maspero, Davide, Angaroni, Fabrizio, Piazza, Rocco, Ramazzotti, Daniele

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Integration of single-cell RNA-seq data into population models to characterize cancer metabolism von Damiani, Chiara, Maspero, Davide, Di Filippo, Marzia, Colombo, Riccardo, Pescini, Dario, Graudenzi, Alex, Westerhoff, Hans Victor, Alberghina, Lilia, Vanoni, Marco, Mauri, Giancarlo

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LACE 2.0: an interactive R tool for the inference and visualization of longitudinal cancer evolution von Ascolani, Gianluca, Angaroni, Fabrizio, Maspero, Davide, Craighero, Francesco, Bhavesh, Narra Lakshmi Sai, Piazza, Rocco, Damiani, Chiara, Ramazzotti, Daniele, Antoniotti, Marco, Graudenzi, Alex

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On the Use of Topological Features of Metabolic Networks for the Classification of Cancer Samples von Machicao, Jeaneth, Craighero, Francesco, Maspero, Davide, Angaroni, Fabrizio, Damiani, Chiara, Graudenzi, Alex, Antoniotti, Marco, Bruno, Odemir M.

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Early detection and improved genomic surveillance of SARS-CoV-2 variants from deep sequencing data von Ramazzotti, Daniele, Maspero, Davide, Angaroni, Fabrizio, Spinelli, Silvia, Antoniotti, Marco, Piazza, Rocco, Graudenzi, Alex

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VirMutSig: Discovery and assignment of viral mutational signatures from sequencing data von Maspero, Davide, Angaroni, Fabrizio, Porro, Danilo, Piazza, Rocco, Graudenzi, Alex, Ramazzotti, Daniele

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An Optimal Control Framework for the Automated Design of Personalized Cancer Treatments von Angaroni, Fabrizio, Graudenzi, Alex, Rossignolo, Marco, Maspero, Davide, Calarco, Tommaso, Piazza, Rocco, Montangero, Simone, Antoniotti, Marco

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SparseSignatures: An R package using LASSO-regularized non-negative matrix factorization to identify mutational signatures from human tumor samples von Mella, Lorenzo, Lal, Avantika, Angaroni, Fabrizio, Maspero, Davide, Piazza, Rocco, Sidow, Arend, Antoniotti, Marco, Graudenzi, Alex, Ramazzotti, Daniele

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MaREA4Galaxy: Metabolic reaction enrichment analysis and visualization of RNA-seq data within Galaxy von Damiani, Chiara, Rovida, Lorenzo, Maspero, Davide, Sala, Irene, Rosato, Luca, Di Filippo, Marzia, Pescini, Dario, Graudenzi, Alex, Antoniotti, Marco, Mauri, Giancarlo

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A review of computational strategies for denoising and imputation of single-cell transcriptomic data von Patruno, Lucrezia, Maspero, Davide, Craighero, Francesco, Angaroni, Fabrizio, Antoniotti, Marco, Graudenzi, Alex

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Combining multi-target regression deep neural networks and kinetic modeling to predict relative fluxes in reaction systems von Patruno, Lucrezia, Craighero, Francesco, Maspero, Davide, Graudenzi, Alex, Damiani, Chiara

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popFBA: tackling intratumour heterogeneity with Flux Balance Analysis von Damiani, Chiara, Di Filippo, Marzia, Pescini, Dario, Maspero, Davide, Colombo, Riccardo, Mauri, Giancarlo

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Single-cell Digital Twins for Cancer Preclinical Investigation von Filippo, Marzia Di, Damiani, Chiara, Vanoni, Marco, Maspero, Davide, Mauri, Giancarlo, Alberghina, Lilia, Pescini, Dario

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Cigarette smoke alters the transcriptome of non-involved lung tissue in lung adenocarcinoma patients von Pintarelli, Giulia, Noci, Sara, Maspero, Davide, Pettinicchio, Angela, Dugo, Matteo, De Cecco, Loris, Incarbone, Matteo, Tosi, Davide, Santambrogio, Luigi, Dragani, Tommaso A., Colombo, Francesca

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Chemotherapy after PD‐1 inhibitors in relapsed/refractory Hodgkin lymphoma: Outcomes and clonal evolution dynamics von Calabretta, Eleonora, Guidetti, Anna, Ricci, Francesca, Di Trani, Martina, Monfrini, Chiara, Magagnoli, Massimo, Bramanti, Stefania, Maspero, Davide, Morello, Lucia, Merli, Michele, Di Rocco, Alice, Graudenzi, Alex, Derenzini, Enrico, Antoniotti, Marco, Rossi, Davide, Corradini, Paolo, Santoro, Armando, Carlo‐Stella, Carmelo

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Integration of transcriptomic data and metabolic networks in cancer samples reveals highly significant prognostic power von Graudenzi, Alex, Maspero, Davide, Di Filippo, Marzia, Gnugnoli, Marco, Isella, Claudio, Mauri, Giancarlo, Medico, Enzo, Antoniotti, Marco, Damiani, Chiara

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Read-through transcripts in lung: germline genetic regulation and correlation with the expression of other genes von Maspero, Davide, Dassano, Alice, Pintarelli, Giulia, Noci, Sara, De Cecco, Loris, Incarbone, Matteo, Tosi, Davide, Santambrogio, Luigi, Dragani, Tommaso A, Colombo, Francesca

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VERSO: A comprehensive framework for the inference of robust phylogenies and the quantification of intra-host genomic diversity of viral samples von Ramazzotti, Daniele, Angaroni, Fabrizio, Maspero, Davide, Gambacorti-Passerini, Carlo, Antoniotti, Marco, Graudenzi, Alex, Piazza, Rocco

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LACE: Inference of cancer evolution models from longitudinal single-cell sequencing data von Ramazzotti, Daniele, Angaroni, Fabrizio, Maspero, Davide, Ascolani, Gianluca, Castiglioni, Isabella, Piazza, Rocco, Antoniotti, Marco, Graudenzi, Alex

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