Cell Size at S Phase Initiation: An Emergent Property of the G1/S Network. - Matteo Barberis; Edda Klipp; Marco Vanoni; Lilia Alberghina (PLoS Comput. Biol., 2007)

Towards a systems biology approach to mammalian cell cycle: modeling the entrance into S phase of quiescent fibroblasts after serum stimulation. - Roberta Alfieri; Matteo Barberis; Ferdinando Chiaradonna; Daniela Gaglio; Luciano Milanesi; Marco Vanoni; Edda Klipp; Lilia Alberghina (BMC Bioinform., 2009)

Data recovery and integration from public databases uncovers transformation-specific transcriptional downregulation of cAMP-PKA pathway-encoding genes. - Chiara Balestrieri; Lilia Alberghina; Marco Vanoni; Ferdinando Chiaradonna (BMC Bioinform., 2009)

Glucose Signaling-Mediated Coordination of Cell Growth and Cell Cycle in Saccharomyces Cerevisiae. - Stefano Busti; Paola Coccetti; Lilia Alberghina; Marco Vanoni (Sensors, 2010)

An Acidic Loop and Cognate Phosphorylation Sites Define a Molecular Switch That Modulates Ubiquitin Charging Activity in Cdc34-Like Enzymes. - Elena Papaleo; Valeria Ranzani; Farida Tripodi; Alessandro Vitriolo; Claudia Cirulli; Piercarlo Fantucci; Lilia Alberghina; Marco Vanoni; Luca De Gioia; Paola Coccetti (PLoS Comput. Biol., 2011)

An ensemble approach to the study of the emergence of metabolic and proliferative disorders via Flux Balance Analysis. - Chiara Damiani; Riccardo Colombo; Sara Molinari; Dario Pescini; Daniela Gaglio; Marco Vanoni; Lilia Alberghina; Giancarlo Mauri (WIVACE, 2013)

An ensemble evolutionary constraint-based approach to understand the emergence of metabolic phenotypes. - Chiara Damiani; Dario Pescini; Riccardo Colombo; Sara Molinari; Lilia Alberghina; Marco Vanoni; Giancarlo Mauri (Nat. Comput., 2014)

Zooming-in on cancer metabolic rewiring with tissue specific constraint-based models. - Marzia Di Filippo; Riccardo Colombo; Chiara Damiani; Dario Pescini; Daniela Gaglio; Marco Vanoni; Lilia Alberghina; Giancarlo Mauri (Comput. Biol. Chem., 2016)

An Integrated Model Quantitatively Describing Metabolism, Growth and Cell Cycle in Budding Yeast. - Pasquale Palumbo; Marco Vanoni; Federico Papa; Stefano Busti; Meike T. Wortel; Bas Teusink; Lilia Alberghina (WIVACE, 2017)

A metabolic core model elucidates how enhanced utilization of glucose and glutamine, with enhanced glutamine-dependent lactate production, promotes cancer cell growth: The WarburQ effect. - Chiara Damiani; Riccardo Colombo; Daniela Gaglio; Fabrizia Mastroianni; Dario Pescini; Hans V. Westerhoff; Giancarlo Mauri; Marco Vanoni; Lilia Alberghina (PLoS Comput. Biol., 2017)

Modeling Biological Timing and Synchronization Mechanisms by Means of Interconnections of Stochastic Switches. - Costanzo Manes; Pasquale Palumbo; Valerio Cusimano; Marco Vanoni; Lilia Alberghina (IEEE Control. Syst. Lett., 2018)

Whole yeast model: what and why. - Pasquale Palumbo; Marco Vanoni; Federico Papa; Stefano Busti; Lilia Alberghina (PeerJ Prepr., 2018)

Integration of Single-Cell RNA-Sequencing Data into Flux Balance Cellular Automata. - Davide Maspero; Marzia Di Filippo; Fabrizio Angaroni; Dario Pescini; Giancarlo Mauri; Marco Vanoni; Alex Graudenzi; Chiara Damiani (CIBB, 2019)

Integration of single-cell RNA-seq data into population models to characterize cancer metabolism. - Chiara Damiani; Davide Maspero; Marzia Di Filippo; Riccardo Colombo; Dario Pescini; Alex Graudenzi; Hans V. Westerhoff; Lilia Alberghina; Marco Vanoni; Giancarlo Mauri (PLoS Comput. Biol., 2019)

The Influence of Nutrients Diffusion on a Metabolism-driven Model of a Multi-cellular System. - Davide Maspero; Chiara Damiani; Marco Antoniotti; Alex Graudenzi; Marzia Di Filippo; Marco Vanoni; Giulio Caravagna; Riccardo Colombo; Daniele Ramazzotti; Dario Pescini (Fundam. Informaticae, 2020)

A framework for validating AI in precision medicine: considerations from the European ITFoC consortium. - Rosy Tsopra; Xosé M. Fernández; Claudio Luchinat; Lilia Alberghina; Hans Lehrach; Marco Vanoni; Felix Dreher 002; Osman Ugur Sezerman; Marc Cuggia; Marie de Tayrac; Edvins Miklasevics; Lucian Mihai Itu; et al. (BMC Medical Informatics Decis. Mak., 2021)

A coarse-grain model for cellular growth accounting for ribosome synthesis. - Massimiliano D'Angelo; Pasquale Palumbo; Stefano Busti; Marco Vanoni (CDC, 2022)

Combining denoising of RNA-seq data and flux balance analysis for cluster analysis of single cells. - Bruno G. Galuzzi; Marco Vanoni; Chiara Damiani (BMC Bioinform., 2022)

INTEGRATE: Model-based multi-omics data integration to characterize multi-level metabolic regulation. - Marzia Di Filippo; Dario Pescini; Bruno Giovanni Galuzzi; Marcella Bonanomi; Daniela Gaglio; Eleonora Mangano; Clarissa Consolandi; Lilia Alberghina; Marco Vanoni; Chiara Damiani (PLoS Comput. Biol., 2022)

Coupling constrained-based flux sampling and clustering to tackle cancer metabolic heterogeneity. - Bruno G. Galuzzi; Stefano Izzo; Fabio Giampaolo; Salvatore Cuomo; Marco Vanoni; Lilia Alberghina; Chiara Damiani; Francesco Piccialli (PDP, 2023)

Exponential growth conditions for a coarse-grain model of ribosome synthesis. - Pasquale Palumbo; Federico Papa; Stefano Busti; Marco Vanoni (CDC, 2024)