J-SPACE: a Julia package for the simulation of spatial models of cancer evolution and of sequencing experiments
Angaroni, Fabrizio, Guidi, Alessandro, Ascolani, Gianluca, d'Onofrio, Alberto, Antoniotti, Marco, Graudenzi, Alex
Published in BMC bioinformatics (08.07.2022)
Published in BMC bioinformatics (08.07.2022)
Get full text
Journal Article
A Bayesian method to infer copy number clones from single-cell RNA and ATAC sequencing
Patruno, Lucrezia, Milite, Salvatore, Bergamin, Riccardo, Calonaci, Nicola, D'Onofrio, Alberto, Anselmi, Fabio, Antoniotti, Marco, Graudenzi, Alex, Caravagna, Giulio
Published in PLoS computational biology (02.11.2023)
Published in PLoS computational biology (02.11.2023)
Get full text
Journal Article
Evolutionary signatures of human cancers revealed via genomic analysis of over 35,000 patients
Fontana, Diletta, Crespiatico, Ilaria, Crippa, Valentina, Malighetti, Federica, Villa, Matteo, Angaroni, Fabrizio, De Sano, Luca, Aroldi, Andrea, Antoniotti, Marco, Caravagna, Giulio, Piazza, Rocco, Graudenzi, Alex, Mologni, Luca, Ramazzotti, Daniele
Published in Nature communications (25.09.2023)
Published in Nature communications (25.09.2023)
Get full text
Journal Article
Variant calling from scRNA-seq data allows the assessment of cellular identity in patient-derived cell lines
Ramazzotti, Daniele, Angaroni, Fabrizio, Maspero, Davide, Ascolani, Gianluca, Castiglioni, Isabella, Piazza, Rocco, Antoniotti, Marco, Graudenzi, Alex
Published in Nature communications (12.05.2022)
Published in Nature communications (12.05.2022)
Get full text
Journal Article
Inferring tree causal models of cancer progression with probability raising
Olde Loohuis, Loes, Loohuis, Loes Olde, Caravagna, Giulio, Graudenzi, Alex, Ramazzotti, Daniele, Mauri, Giancarlo, Antoniotti, Marco, Mishra, Bud
Published in PloS one (09.10.2014)
Published in PloS one (09.10.2014)
Get full text
Journal Article
LACE 2.0: an interactive R tool for the inference and visualization of longitudinal cancer evolution
Ascolani, Gianluca, Angaroni, Fabrizio, Maspero, Davide, Craighero, Francesco, Bhavesh, Narra Lakshmi Sai, Piazza, Rocco, Damiani, Chiara, Ramazzotti, Daniele, Antoniotti, Marco, Graudenzi, Alex
Published in BMC bioinformatics (17.03.2023)
Published in BMC bioinformatics (17.03.2023)
Get full text
Journal Article
On the Use of Topological Features of Metabolic Networks for the Classification of Cancer Samples
Machicao, Jeaneth, Craighero, Francesco, Maspero, Davide, Angaroni, Fabrizio, Damiani, Chiara, Graudenzi, Alex, Antoniotti, Marco, Bruno, Odemir M
Published in Current genomics (01.02.2021)
Published in Current genomics (01.02.2021)
Get full text
Journal Article
Early detection and improved genomic surveillance of SARS-CoV-2 variants from deep sequencing data
Ramazzotti, Daniele, Maspero, Davide, Angaroni, Fabrizio, Spinelli, Silvia, Antoniotti, Marco, Piazza, Rocco, Graudenzi, Alex
Published in iScience (17.06.2022)
Published in iScience (17.06.2022)
Get full text
Journal Article
Web Resource
An Optimal Control Framework for the Automated Design of Personalized Cancer Treatments
Angaroni, Fabrizio, Graudenzi, Alex, Rossignolo, Marco, Maspero, Davide, Calarco, Tommaso, Piazza, Rocco, Montangero, Simone, Antoniotti, Marco
Published in Frontiers in bioengineering and biotechnology (28.05.2020)
Published in Frontiers in bioengineering and biotechnology (28.05.2020)
Get full text
Journal Article
SparseSignatures: An R package using LASSO-regularized non-negative matrix factorization to identify mutational signatures from human tumor samples
Mella, Lorenzo, Lal, Avantika, Angaroni, Fabrizio, Maspero, Davide, Piazza, Rocco, Sidow, Arend, Antoniotti, Marco, Graudenzi, Alex, Ramazzotti, Daniele
Published in STAR protocols (16.09.2022)
Published in STAR protocols (16.09.2022)
Get full text
Journal Article
Modeling Cumulative Biological Phenomena with Suppes-Bayes Causal Networks
Ramazzotti, Daniele, Graudenzi, Alex, Caravagna, Giulio, Antoniotti, Marco
Published in Evolutionary Bioinformatics (2018)
Published in Evolutionary Bioinformatics (2018)
Get full text
Book Review
Journal Article
MaREA4Galaxy: Metabolic reaction enrichment analysis and visualization of RNA-seq data within Galaxy
Damiani, Chiara, Rovida, Lorenzo, Maspero, Davide, Sala, Irene, Rosato, Luca, Di Filippo, Marzia, Pescini, Dario, Graudenzi, Alex, Antoniotti, Marco, Mauri, Giancarlo
Published in Computational and structural biotechnology journal (01.01.2020)
Published in Computational and structural biotechnology journal (01.01.2020)
Get full text
Journal Article
Reverse engineering dynamic temporal models of biological processes and their relationships
Ramakrishnan, Naren, Tadepalli, Satish, Watson, Layne T., Helm, Richard F., Antoniotti, Marco, Mishra, Bud, Wigler, Michael H.
Published in Proceedings of the National Academy of Sciences - PNAS (13.07.2010)
Published in Proceedings of the National Academy of Sciences - PNAS (13.07.2010)
Get full text
Journal Article
CoGNaC: A Chaste Plugin for the Multiscale Simulation of Gene Regulatory Networks Driving the Spatial Dynamics of Tissues and Cancer
Rubinacci, Simone, Graudenzi, Alex, Caravagna, Giulio, Mauri, Giancarlo, Osborne, James, Pitt-Francis, Joe, Antoniotti, Marco
Published in Cancer informatics (01.01.2015)
Published in Cancer informatics (01.01.2015)
Get full text
Journal Article
From bytes to bedside: data integration and computational biology for translational cancer research
Mathew, Jomol P, Taylor, Barry S, Bader, Gary D, Pyarajan, Saiju, Antoniotti, Marco, Chinnaiyan, Arul M, Sander, Chris, Burakoff, Steven J, Mishra, Bud
Published in PLoS computational biology (01.02.2007)
Published in PLoS computational biology (01.02.2007)
Get full text
Journal Article
A Model of Colonic Crypts using SBML Spatial
Ramazzotti, Daniele, Maj, Carlo, Antoniotti, Marco
Published in Electronic proceedings in theoretical computer science (01.01.2013)
Published in Electronic proceedings in theoretical computer science (01.01.2013)
Get full text
Journal Article