Parameter Estimation for Cell Cycle Ordinary Differential Equation (ODE) Models using a Grid Approach. - Roberta Alfieri; Ettore Mosca; Ivan Merelli; Luciano Milanesi (HealthGrid, 2007)

A data integration approach for cell cycle analysis oriented to model simulation in systems biology. - Roberta Alfieri; Ivan Merelli; Ettore Mosca; Luciano Milanesi (BMC Syst. Biol., 2007)

The cell cycle DB: a systems biology approach to cell cycle analysis. - Roberta Alfieri; Ivan Merelli; Ettore Mosca; Luciano Milanesi (Nucleic Acids Res., 2008)

Sys-Bio Gateway: a Framework of Bioinformatics Database Resources Oriented to Systems Biology. - Luciano Milanesi; Roberta Alfieri; Ettore Mosca; Federica Viti; Pasqualina D'Ursi; Ivan Merelli (IWPLS, 2009)

A Novel Variant of P Systems for the Modelling and Simulation of Biochemical Systems. - Paolo Cazzaniga; Giancarlo Mauri; Luciano Milanesi; Ettore Mosca; Dario Pescini (Workshop on Membrane Computing, 2009)

Ontological Enrichment of the Genes-to-Systems Breast Cancer Database. - Federica Viti; Ettore Mosca; Ivan Merelli; Andrea Calabria; Roberta Alfieri; Luciano Milanesi (MTSR, 2009)

Identification of functionally related genes using data mining and data integration: a breast cancer case study. - Ettore Mosca; Gloria Bertoli; Eleonora Piscitelli; Laura Vilardo; Rolland A. Reinbold; Ileana Zucchi; Luciano Milanesi (BMC Bioinform., 2009)

Modelling Spatial Heterogeneity and Macromolecular Crowding with Membrane Systems. - Ettore Mosca; Paolo Cazzaniga; Dario Pescini; Giancarlo Mauri; Luciano Milanesi (Int. Conf. on Membrane Computing, 2010)

A multilevel data integration resource for breast cancer study. - Ettore Mosca; Roberta Alfieri; Ivan Merelli; Federica Viti; Andrea Calabria; Luciano Milanesi (BMC Syst. Biol., 2010)

Overlapping Genes May Control Reprogramming of Mouse Somatic Cells into Induced Pluripotent Stem Cells (iPSCs) and Breast Cancer Stem Cells. - Ettore Mosca; Cinzia Cocola; Davood Sabour; Paride Pelucchi; Giovanni Bertalot; Orazio Palumbo; Massimo Carella; Martin Götte; Hans R. Schöler; Rolland A. Reinbold; Ileana Zucchi; Luciano Milanesi (Silico Biol., 2010)

SNPRanker: a tool for identification and scoring of SNPs associated to target genes. - Andrea Calabria; Ettore Mosca; Federica Viti; Ivan Merelli; Luciano Milanesi (J. Integr. Bioinform., 2010)

Modeling Biochemical Pathways. - Ettore Mosca; Luciano Milanesi (Mathematical Approaches to Polymer Sequence Analysis and Related Problems, 2011)

Grid Computing for Sensitivity Analysis of Stochastic Biological Models. - Ivan Merelli; Dario Pescini; Ettore Mosca; Paolo Cazzaniga; Carlo Maj; Giancarlo Mauri; Luciano Milanesi (PaCT, 2011)

Ontology-based resources for bioinformatics analysis. - Federica Viti; Ivan Merelli; Andrea Calabria; Paolo Cozzi; Ettore Mosca; Roberta Alfieri; Luciano Milanesi (Int. J. Metadata Semant. Ontologies, 2011)

A Parallel Implementation of the Stau-DPP Stochastic Simulator for the Modelling of Biological Systems. - Ettore Mosca; Ivan Merelli; Luciano Milanesi; Andrea Clematis; Daniele D'Agostino (PDP, 2013)

SNPranker 2.0: a gene-centric data mining tool for diseases associated SNP prioritization in GWAS. - Ivan Merelli; Andrea Calabria; Paolo Cozzi; Federica Viti; Ettore Mosca; Luciano Milanesi (BMC Bioinform., 2013)

Sensitivity Analysis for Studying the Relation between biochemical reactions and metabolic phenotypes. - Carlo Maj; Ettore Mosca; Ivan Merelli; Giancarlo Mauri; Luciano Milanesi (J. Bioinform. Comput. Biol., 2013)

Evaluating mixed HTC/cloud approaches for parameter sweep applications in systems biology. - Ivan Merelli; Ettore Mosca; Daniele Cesini; Elisabetta Ronchieri; Luciano Milanesi (IWBBIO, 2014)

A CUDA Implementation of the Spatial TAU-Leaping in Crowded Compartments (STAUCC) Simulator. - Giulia Pasquale; Carlo Maj; Andrea Clematis; Ettore Mosca; Luciano Milanesi; Ivan Merelli; Daniele D'Agostino (PDP, 2014)

Systems medicine of inflammaging. - Gastone C. Castellani; Giulia Menichetti; Paolo Garagnani; Maria Giulia Bacalini; Chiara Pirazzini; Claudio Franceschi; Sebastiano Collino; Claudia Sala; Daniel Remondini; Enrico Giampieri; Ettore Mosca; Matteo Bersanelli; et al. (Briefings Bioinform., 2016)

Methods for the integration of multi-omics data: mathematical aspects. - Matteo Bersanelli; Ettore Mosca; Daniel Remondini; Enrico Giampieri; Claudia Sala; Gastone C. Castellani; Luciano Milanesi (BMC Bioinform., 2016)

Stochastic neutral modelling of the Gut Microbiota's relative species abundance from next generation sequencing data. - Claudia Sala; Silvia Vitali; Enrico Giampieri; Ìtalo Faria do Valle; Daniel Remondini; Paolo Garagnani; Matteo Bersanelli; Ettore Mosca; Luciano Milanesi; Gastone C. Castellani (BMC Bioinform., 2016)

isma: an R package for the integrative analysis of mutations detected by multiple pipelines. - Noemi Di Nanni; Marco Moscatelli; Matteo Gnocchi; Luciano Milanesi; Ettore Mosca (BMC Bioinform., 2019)

Gene relevance based on multiple evidences in complex networks. - Noemi Di Nanni; Matteo Gnocchi; Marco Moscatelli; Luciano Milanesi; Ettore Mosca (Bioinform., 2020)

Characterization and comparison of gene-centered human interactomes. - Ettore Mosca; Matteo Bersanelli; Tommaso Matteuzzi; Noemi Di Nanni; Gastone C. Castellani; Luciano Milanesi; Daniel Remondini (Briefings Bioinform., 2021)

Intrinsic-Dimension Analysis for Guiding Dimensionality Reduction in Multi-Omics Data. - Valentina Guarino; Jessica Gliozzo; Ferdinando Clarelli; Béatrice Pignolet; Kaalindi Misra; Elisabetta Mascia; Giordano Antonino; Silvia Santoro; Laura Ferré; Miryam Cannizzaro; Melissa Sorosina; Roland Liblau; et al. (BIOINFORMATICS, 2023)

scMuffin: an R package to disentangle solid tumor heterogeneity by single-cell gene expression analysis. - Valentina Nale; Alice Chiodi; Noemi Di Nanni; Ingrid Cifola; Marco Moscatelli; Cinzia Cocola; Matteo Gnocchi; Eleonora Piscitelli; Ada Sula; Ileana Zucchi; Rolland A. Reinbold; Luciano Milanesi; et al. (BMC Bioinform., 2023)

Advances and challenges in cell-cell communication inference: a comprehensive review of tools, resources, and future directions. - Giulia Cesaro; James Shiniti Nagai; Nicolò Gnoato; Alice Chiodi; Gaia Tussardi; Vanessa Klöker; Carmelo Vittorio Musumarra; Ettore Mosca; Ivan G. Costa; Barbara Di Camillo; Enrica Calura; Giacomo Baruzzo (Briefings Bioinform., 2025)