A Method for Prediction of Accessible Sites on an mRNA Sequence for Target Selection of Hammerhead Ribozymes. - Alberto Mercatanti; Giuseppe Rainaldi; Laura Mariani; Roberto Marangoni; Lorenzo Citti (J. Comput. Biol., 2002)

On Representing Biological Systems through Multiset Rewriting. - Stefano Bistarelli; Iliano Cervesato; Gabriele Lenzini; Roberto Marangoni; Fabio Martinelli (EUROCAST, 2003)

PaTre: A Method for Paralogy Trees Construction. - Nadia Pisanti; Roberto Marangoni; Paolo Ferragina; Antonio Frangioni; A. Savona; C. Pisanelli; Fabrizio Luccio (J. Comput. Biol., 2003)

VICE: A VIrtual CEll. - Davide Chiarugi; Michele Curti; Pierpaolo Degano; Roberto Marangoni (CMSB, 2004)

Feedbacks and Oscillations in the Virtual Cell VICE. - Davide Chiarugi; M. Chinellato; Pierpaolo Degano; G. Lo Brutto; Roberto Marangoni (CMSB, 2006)

A Compression-Based Approach for Coding Sequences Identification. I. Application to Prokaryotic Genomes. - Giulia Menconi; Roberto Marangoni (J. Comput. Biol., 2006)

The BioPrompt-box: an ontology-based clustering tool for searching in biological databases. - Claudio Corsi; Paolo Ferragina; Roberto Marangoni (BMC Bioinform., 2007)

A Computational Approach to the Functional Screening of Genomes. - Davide Chiarugi; Pierpaolo Degano; Roberto Marangoni (PLoS Comput. Biol., 2007)

Cells in Silico: A Holistic Approach. - Davide Chiarugi; Pierpaolo Degano; Jan Bert Van Klinken; Roberto Marangoni (SFM, 2008)

A Semantic Web for bioinformatics: goals, tools, systems, applications. - Nicola Cannata; Michael Schroeder 001; Roberto Marangoni; Paolo Romano 001 (BMC Bioinform., 2008)

Mining Biological Sequences with Masks. - Giovanni Battaglia; Roberto Grossi; Roberto Marangoni; Nadia Pisanti (DEXA Workshops, 2009)

Inferring Mobile Elements in S. Cerevisiae Strains. - Giulia Menconi; Giovanni Battaglia; Roberto Grossi; Nadia Pisanti; Roberto Marangoni (BIOINFORMATICS, 2011)

A Taste of Yeast Mobilomics. - Giulia Menconi; Giovanni Battaglia; Roberto Grossi; Nadia Pisanti; Roberto Marangoni (BIOINFORMATICS, 2012)

Characterization of the emergent properties of a synthetic quasi-cellular system. - Lorenzo Lazzerini-Ospri; Pasquale Stano; Pier Luigi Luisi; Roberto Marangoni (BMC Bioinform., 2012)

BpMatch: An Efficient Algorithm for a Segmental Analysis of Genomic Sequences. - Claudio Felicioli; Roberto Marangoni (IEEE ACM Trans. Comput. Biol. Bioinform., 2012)

Stochastic modelling of non Markovian Dynamics in Biochemical Reactions. - Davide Chiarugi; Moreno Falaschi; Diana Hermith; Roberto Marangoni; Carlos Olarte (IWBBIO, 2013)

Quasi-cellular systems: stochastic simulation analysis at nanoscale range. - Lorenzo Calviello; Pasquale Stano; Fabio Mavelli; Pier Luigi Luisi; Roberto Marangoni (BMC Bioinform., 2013)

Mobilomics in Saccharomyces cerevisiae strains. - Giulia Menconi; Giovanni Battaglia; Roberto Grossi; Nadia Pisanti; Roberto Marangoni (BMC Bioinform., 2013)

From Cells as Computation to Cells as Apps. - Andrea Bracciali; Enrico Cataldo; Luisa Damiano; Claudio Felicioli; Roberto Marangoni; Pasquale Stano (HaPoC, 2015)

On Fine Stochastic Simulations of Liposome-Encapsulated PUREsystem™. - Lorenzo Calviello; Lorenzo Lazzerini-Ospri; Roberto Marangoni (WIVACE, 2015)

Preface: BITS2014, the annual meeting of the Italian Society of Bioinformatics. - Angelo M. Facchiano; Claudia Angelini; Roberta Bosotti; Alessandro Guffanti; Anna Marabotti; Roberto Marangoni; Stefano Pascarella; Paolo Romano 001; Andreas Zanzoni; Manuela Helmer-Citterich (BMC Bioinform., 2015)

Experimental Evidences Suggest High Between-Vesicle Diversity of Artificial Vesicle Populations: Results, Models and Implications. - Pasquale Stano; Roberto Marangoni; Fabio Mavelli (CIBB, 2017)

Wearable Sensors for Assessing the Role of Olfactory Training on the Autonomic Response to Olfactory Stimulation. - Alessandro Tonacci; Lucia Billeci; Irene Di Mambro; Roberto Marangoni; Chiara Sanmartin; Francesca Venturi (Sensors, 2021)

An overview of bioinformatics courses delivered at the academic level in Italy: Reflections and recommendations from BITS. - Roberto Marangoni; Vitoantonio Bevilacqua; Mario Cannataro; Bruno Hay Mele; Giancarlo Mauri; Anna Marabotti (PLoS Comput. Biol., 2023)

DNA Is a Puzzle Enthusiast. - Roberto Marangoni (From Strings to Graphs, and Back Again, 2025)