Using PROTEUS for Modeling Data Mining Analysis of Proteomics Experiments on the Grid. - Mario Cannataro; Pietro Hiram Guzzi; Tommaso Mazza; Pierangelo Veltri (OTM Workshops, 2004)

Mass Spectrometry Data Analysis for Early Detection of Inherited Breast Cancer. - Francesco Baudi; Mario Cannataro; Rita Casadonte; Francesco Costanzo; Giovanni Cuda; Maria Concetta Faniello; Marco Gaspari; Pietro Hiram Guzzi; Tommaso Mazza; Barbara Quaresima; Pierosandro Tagliaferri; Giuseppe Tradigo; et al. (WIRN, 2004)

Preprocessing of Mass Spectrometry Proteomics Data on the Grid. - Mario Cannataro; Pietro Hiram Guzzi; Tommaso Mazza; Giuseppe Tradigo; Pierangelo Veltri (CBMS, 2005)

Using Ontologies in PROTEUS for Modeling Proteomics Data Mining Applications. - Mario Cannataro; Pietro Hiram Guzzi; Tommaso Mazza; Giuseppe Tradigo; Pierangelo Veltri (HealthGrid, 2005)

Algorithms and Databases in Bioinformatics: Towards a Proteomic Ontology. - Mario Cannataro; Pietro Hiram Guzzi; Tommaso Mazza; Giuseppe Tradigo; Pierangelo Veltri (ITCC (1), 2005)

MS-Analyzer: Intelligent Preprocessing, Management, and Data Mining Analysis of Mass Spectrometry Data on the Grid. - Mario Cannataro; Pietro Hiram Guzzi; Tommaso Mazza; Pierangelo Veltri (SKG, 2005)

Distributed Management of Ontologies on the Grid. - Mario Cannataro; Pietro Hiram Guzzi; Tommaso Mazza; Pierangelo Veltri (WETICE, 2005)

On the Preprocessing of Mass Spectrometry Proteomics Data. - Mario Cannataro; Pietro Hiram Guzzi; Tommaso Mazza; Giuseppe Tradigo; Pierangelo Veltri (WIRN/NAIS, 2005)

Analysis and Classification of Proteomics Data, a Case Study. - Pietro Hiram Guzzi; Mario Cannataro; Marco Gaspari; Tommaso Mazza; Barbara Quaresima; Pierangelo Veltri; Francesco Saverio Costanzo (CBMS, 2006)

Mitotic Oscillators as MP Graphs. - Giuditta Franco; Pietro Hiram Guzzi; Vincenzo Manca; Tommaso Mazza (Workshop on Membrane Computing, 2006)

Managing ontologies for Grid computing. - Mario Cannataro; Pietro Hiram Guzzi; Tommaso Mazza; Giuseppe Tradigo; Pierangelo Veltri (Multiagent Grid Syst., 2006)

Towards a Complete Covering of SBML Functionalities. - Tommaso Mazza (Workshop on Membrane Computing, 2007)

Cyto-Sim: a formal language model and stochastic simulator of membrane-enclosed biochemical processes. - Sean Sedwards; Tommaso Mazza (Bioinform., 2007)

Using ontologies for preprocessing and mining spectra data on the Grid. - Mario Cannataro; Pietro Hiram Guzzi; Tommaso Mazza; Giuseppe Tradigo; Pierangelo Veltri (Future Gener. Comput. Syst., 2007)

On Parallel Stochastic Simulation of Diffusive Systems. - Lorenzo Dematté; Tommaso Mazza (CMSB, 2008)

Studying Irreversible Transitions in a Model of Cell Cycle Regulation. - Paolo Ballarini; Tommaso Mazza; Alida Palmisano; Attila Csikász-Nagy (PASM@EPEW, 2008)

Cell Cycle and Tumor Growth in Membrane Systems with Peripheral Proteins. - Tommaso Mazza; Matteo Cavaliere (MeCBIC, 2008)

Analyzing various models of Circadian Clock and Cell Cycle coupling. - Attila Csikász-Nagy; Adrien Fauré; Roberto Larcher; Paola Lecca; Ivan Mura; Ferenc Jordán; Alida Palmisano; Alessandro Romanel; Sean Sedwards; Heike Siebert; Sylvain Soliman; Denis Thieffry; et al. (Formal Methods in Molecular Biology, 2009)

Fastest parallel molecular algorithms for the elliptic curve discrete logarithm problem over GF(2n). - Gennaro Iaccarino; Tommaso Mazza (BADS@ICAC, 2009)

Taming the complexity of biological pathways through parallel computing. - Paolo Ballarini; Rosita Guido; Tommaso Mazza; Davide Prandi (Briefings Bioinform., 2009)

Efficient Parallel Statistical Model Checking of Biochemical Networks - Paolo Ballarini; Michele Forlin; Tommaso Mazza; Davide Prandi (PDMC, 2009)

Editorial: Accelerating systems biology. - Tommaso Mazza (Briefings Bioinform., 2010)

Estimating the divisibility of complex biological networks by sparseness indices. - Tommaso Mazza; Alessandro Romanel; Ferenc Jordán (Briefings Bioinform., 2010)

Snazer: the simulations and networks analyzer. - Tommaso Mazza; Gennaro Iaccarino; Corrado Priami (BMC Syst. Biol., 2010)

Stability analysis of biological network topologies during stochastic simulation. - Tommaso Mazza; Davide Prandi (SimuTools, 2011)

AURA: Atlas of UTR Regulatory Activity. - Erik Dassi; A. Malossini; Angela Re; Tommaso Mazza; Toma Tebaldi; Luigi Caputi; Alessandro Quattrone (Bioinform., 2012)

Modeling and Simulation of Smart and Green Computing Systems. - Kaushik R. Chowdhury; Dave Cavalcanti 001; Mostafa El-Said; Tommaso Mazza; Chittabrata Ghosh (Computer, 2012)

High Performance Computational Systems Biology. - Tommaso Mazza (IEEE ACM Trans. Comput. Biol. Bioinform., 2012)

The Relevance of Topology in Parallel Simulation of Biological Networks. - Tommaso Mazza; Paolo Ballarini; Rosita Guido; Davide Prandi (IEEE ACM Trans. Comput. Biol. Bioinform., 2012)

Multi-Sided Compression Performance Assessment of ABI SOLiD WES Data. - Tommaso Mazza; Stefano Castellana (Algorithms, 2013)

Estimating the global density of graphs by a sparseness index. - Salvatore Menniti; Emanuele Castagna; Tommaso Mazza (Appl. Math. Comput., 2013)

Congruency in the prediction of pathogenic missense mutations: state-of-the-art web-based tools. - Stefano Castellana; Tommaso Mazza (Briefings Bioinform., 2013)

A solid quality-control analysis of AB SOLiD short-read sequencing data. - Stefano Castellana; Marta Romani; Enza Maria Valente; Tommaso Mazza (Briefings Bioinform., 2013)

Affinity analysis of differentially expressed genes in hepatocytes expressing HCV core genotype 1b or 3a. - Tommaso Mazza; Stefano Castellana; Angelo Andriulli; Charles Auffray; Manlio Vinciguerra; Valerio Pazienza (Biosyst., 2013)

Functional Impact of Autophagy-Related Genes on the Homeostasis and Dynamics of Pancreatic Cancer Cell Lines. - Tommaso Mazza; Caterina Fusilli; Chiara Saracino; Gianluigi Mazzoccoli; Francesca Tavano; Manlio Vinciguerra; Valerio Pazienza (IEEE ACM Trans. Comput. Biol. Bioinform., 2015)

High-confidence assessment of functional impact of human mitochondrial non-synonymous genome variations by APOGEE. - Stefano Castellana; Caterina Fusilli; Gianluigi Mazzoccoli; Tommaso Biagini; Daniele Capocefalo; Massimo Carella; Angelo L. Vescovi; Tommaso Mazza (PLoS Comput. Biol., 2017)

Molecular dynamics recipes for genome research. - Tommaso Biagini; Giovanni Chillemi; Gianluigi Mazzoccoli; Alessandro Grottesi; Caterina Fusilli; Daniele Capocefalo; Stefano Castellana; Angelo L. Vescovi; Tommaso Mazza (Briefings Bioinform., 2018)

Food Web Topology and Nested Keystone Species Complexes. - Daniele Capocefalo; Juliana O. Pereira; Tommaso Mazza; Ferenc Jordán (Complex., 2018)

A comparative benchmark of classic DNA motif discovery tools on synthetic data. - Stefano Castellana; Tommaso Biagini; Luca Parca; Francesco Petrizzelli; Salvatore Daniele Bianco; Angelo Luigi Vescovi; Massimo Carella; Tommaso Mazza (Briefings Bioinform., 2021)

MitImpact 3: modeling the residue interaction network of the Respiratory Chain subunits. - Stefano Castellana; Tommaso Biagini; Francesco Petrizzelli; Luca Parca; Noemi Panzironi; Viviana Caputo; Angelo L. Vescovi; Massimo Carella; Tommaso Mazza (Nucleic Acids Res., 2021)

A novel framework based on network embedding for the simulation and analysis of disease progression. - Francesco Chiodo; Mario Torchia; Enza Messina; Elisabetta Fersini; Tommaso Mazza; Pietro Hiram Guzzi (BIBM, 2022)

Disease spreading modeling and analysis: a survey. - Pietro Hiram Guzzi; Francesco Petrizzelli; Tommaso Mazza (Briefings Bioinform., 2022)

TMBleR: a bioinformatic tool to optimize TMB estimation and predictive power. - Laura Fancello; Alessandro Guida; Gianmaria Frige; Arnaud Céol; Gabriele Babini; Giovanni Luca Scaglione; Mario Zanfardino; Tommaso Mazza; Lorenzo Ferrando; Pier Giuseppe Pelicci; Luca Mazzarella (Bioinform., 2022)

Beyond COVID-19 Pandemic: Topology-aware optimisation of vaccination strategy for minimising virus spreading. - Francesco Petrizzelli; Pietro Hiram Guzzi; Tommaso Mazza (CoRR, 2022)

Connecting the dots: A practical evaluation of web-tools for describing protein dynamics as networks. - Francesco Petrizzelli; Tommaso Biagini; Salvatore Daniele Bianco; Niccolò Liorni; Alessandro Napoli 003; Stefano Castellana; Tommaso Mazza (Frontiers Bioinform., 2022)

Anomaly Detection in Individual Specific Networks through Explainable Generative Adversarial Attributed Networks. - Pietro Hiram Guzzi; Ugo Lomoio; Tommaso Mazza; Pierangelo Veltri (BIBM, 2024)

E-ABIN: an Explainable module for Anomaly detection in BIological Networks. - Ugo Lomoio; Tommaso Mazza; Pierangelo Veltri; Pietro Hiram Guzzi (CoRR, 2025)