Automatising the analysis of stochastic biochemical time-series. - Giulio Caravagna; Luca De Sano; Marco Antoniotti (BMC Bioinform., 2015)

TRONCO: an R package for the inference of cancer progression models from heterogeneous genomic data. - Luca De Sano; Giulio Caravagna; Daniele Ramazzotti; Alex Graudenzi; Giancarlo Mauri; Bud Mishra; Marco Antoniotti (Bioinform., 2016)

Design of the TRONCO BioConductor Package for TRanslational ONCOlogy. - Marco Antoniotti; Giulio Caravagna; Luca De Sano; Alex Graudenzi; Giancarlo Mauri; Bud Mishra; Daniele Ramazzotti (R J., 2016)

SIMLR: a tool for large-scale single-cell analysis by multi-kernel learning. - Bo Wang 044; Daniele Ramazzotti; Luca De Sano; Junjie Zhu; Emma Pierson; Serafim Batzoglou (CoRR, 2017)

Learning mutational graphs of individual tumor evolution from multi-sample sequencing data. - Daniele Ramazzotti; Alex Graudenzi; Luca De Sano; Marco Antoniotti; Giulio Caravagna (CoRR, 2017)

cyTRON and cyTRON/JS: Two Cytoscape-Based Applications for the Inference of Cancer Evolution Models. - Lucrezia Patruno; Edoardo Galimberti; Daniele Ramazzotti; Giulio Caravagna; Luca De Sano; Marco Antoniotti; Alex Graudenzi (CIBB, 2019)

Learning mutational graphs of individual tumour evolution from single-cell and multi-region sequencing data. - Daniele Ramazzotti; Alex Graudenzi; Luca De Sano; Marco Antoniotti; Giulio Caravagna (BMC Bioinform., 2019)