RRE: a tool for the extraction of non-coding regions surrounding annotated genes from genomic datasets. - Fulvio Lazzarato; Giuliana Franceschinis; Marco Botta; Francesca Cordero; Raffaele A. Calogero (Bioinform., 2004)

An integrated approach of immunogenomics and bioinformatics to identify new Tumor Associated Antigens (TAA) for mammary cancer immunological prevention. - Federica Cavallo; Annalisa Astolfi; Manuela Iezzi; Francesca Cordero; Pierluigi Lollini; Guido Forni; Raffaele A. Calogero (BMC Bioinform., 2005)

oneChannelGUI: a graphical interface to Bioconductor tools, designed for life scientists who are not familiar with R language. - Remo Sanges; Francesca Cordero; Raffaele A. Calogero (Bioinform., 2007)

Ontology-Driven Co-clustering of Gene Expression Data. - Francesca Cordero; Ruggero G. Pensa; Alessia Visconti; Dino Ienco; Marco Botta (AI*IA, 2009)

Genome-Wide Search for Splicing Defects Associated with Amyotrophic Lateral Sclerosis (ALS). - Silvia C. Lenzken; Silvia Vivarelli; Francesca Zolezzi; Francesca Cordero; Cristina Della Beffa; Raffaele A. Calogero; Silvia Barabino (CISIS, 2009)

On the Use of Stochastic Petri Nets in the Analysis of Signal Transduction Pathways for Angiogenesis Process. - Lucia Napione; Daniele Manini; Francesca Cordero; András Horváth; Andrea Picco; Massimiliano De Pierro; Simona Pavan; Matteo Sereno; Andrea Veglio; Federico Bussolino; Gianfranco Balbo (CMSB, 2009)

A new protein motif extraction framework based on constrained co-clustering. - Francesca Cordero; Alessia Visconti; Marco Botta (SAC, 2009)

Comparison of Approximate Kinetics for Unireactant Enzymes: Michaelis-Menten against the Equivalent Server. - Alessio Angius; Gianfranco Balbo; Francesca Cordero; András Horváth; Daniele Manini (ACSD/Petri Nets Workshops, 2010)

Gene Ontology Rewritten for Computing Gene Functional Similarity. - Alessia Visconti; Francesca Cordero; Marco Botta; Raffaele A. Calogero (CISIS, 2010)

Co-clustering numerical data under user-defined constraints. - Ruggero G. Pensa; Jean-François Boulicaut; Francesca Cordero; Maurizio Atzori (Stat. Anal. Data Min., 2010)

Tackling the DREAM Challenge for Gene Regulatory Networks Reverse Engineering. - Alessia Visconti; Roberto Esposito; Francesca Cordero (AI*IA, 2011)

Cancer stem cell based adjuvant for oncoantingen-driven vaccination. - Francesca Cordero; Stefania Lanzardo; Maddalena Arigoni; Chiara Fornari; Laura Conti; Gianfranco Balbo; Federica Cavallo; Daniele Manini; Raffaele A. Calogero (BCB, 2011)

Barcoding-free BAC Pooling Enables Combinatorial Selective Sequencing of the Barley Gene Space - Stefano Lonardi; Denisa Duma; Matthew Alpert; Francesca Cordero; Marco Beccuti; Prasanna Bhat; Yonghui Wu; Gianfranco Ciardo; Burair Alsaihati; Yaqin Ma; Steve Wanamaker; Josh Resnik; et al. (CoRR, 2011)

Mathematical Approach to Predict the Drug Effects on Cancer Stem Cell Models. - Chiara Fornari; Francesca Cordero; Daniele Manini; Gianfranco Balbo; Raffaele A. Calogero (CS2Bio@DisCoTec, 2011)

Restructuring the Gene Ontology to emphasise regulative pathways and to improve gene similarity queries. - Alessia Visconti; Roberto Esposito; Francesca Cordero (Int. J. Comput. Biol. Drug Des., 2011)

Simplification of a complex signal transduction model using invariants and flow equivalent servers. - Francesca Cordero; András Horváth; Daniele Manini; Lucia Napione; Massimiliano De Pierro; Simona Pavan; Andrea Picco; Andrea Veglio; Matteo Sereno; Federico Bussolino; Gianfranco Balbo (Theor. Comput. Sci., 2011)

A Modular Database Architecture Enabled to Comparative Sequence Analysis. - Paola Bonfante; Francesca Cordero; Stefano Ghignone; Dino Ienco; Luisa Lanfranco; Giorgio Leonardi; Rosa Meo; Stefania Montani; Luca Roversi; Alessia Visconti (Trans. Large Scale Data Knowl. Centered Syst., 2011)

State of art fusion-finder algorithms are suitable to detect transcription-induced chimeras in normal tissues? - Matteo Carrara; Marco Beccuti; Federica Cavallo; Susanna Donatelli; Fulvio Lazzarato; Francesca Cordero; Raffaele A. Calogero (BMC Bioinform., 2013)

Multi-level model for the investigation of oncoantigen-driven vaccination effect. - Francesca Cordero; Marco Beccuti; Chiara Fornari; Stefania Lanzardo; Laura Conti; Federica Cavallo; Gianfranco Balbo; Raffaele A. Calogero (BMC Bioinform., 2013)

Guest Editorial. - Ruggero G. Pensa; Francesca Cordero; Céline Rouveirol; Rushed Kanawati (Intell. Data Anal., 2013)

Combinatorial Pooling Enables Selective Sequencing of the Barley Gene Space. - Stefano Lonardi; Denisa Duma; Matthew Alpert; Francesca Cordero; Marco Beccuti; Prasanna R. Bhat; Yonghui Wu; Gianfranco Ciardo; Burair Alsaihati; Yaqin Ma; Steve Wanamaker; Josh Resnik; et al. (PLoS Comput. Biol., 2013)

Markovian Agents Population Models to Study Cancer Evolution. - Francesca Cordero; Chiara Fornari; Marco Gribaudo; Daniele Manini (ASMTA, 2014)

Chimera: a Bioconductor package for secondary analysis of fusion products. - Marco Beccuti; Matteo Carrara; Francesca Cordero; Fulvio Lazzarato; Susanna Donatelli; Francesca Nadalin; Alberto Policriti; Raffaele A. Calogero (Bioinform., 2014)

Leveraging additional knowledge to support coherent bicluster discovery in gene expression data. - Alessia Visconti; Francesca Cordero; Ruggero G. Pensa (Intell. Data Anal., 2014)

Scrible: Ultra-Accurate Error-Correction of Pooled Sequenced Reads. - Denise Duma; Francesca Cordero; Marco Beccuti; Gianfranco Ciardo; Timothy J. Close; Stefano Lonardi (WABI, 2015)

Alternative splicing detection workflow needs a careful combination of sample prep and bioinformatics analysis. - Matteo Carrara; Josephine Lum; Francesca Cordero; Marco Beccuti; Michael Poidinger; Susanna Donatelli; Raffaele A. Calogero; Francesca Zolezzi (BMC Bioinform., 2015)

A versatile mathematical work-flow to explore how Cancer Stem Cell fate influences tumor progression. - Chiara Fornari; Gianfranco Balbo; Sami M. Halawani; Omar M. Ba-Rukab; Ab Rahman Ahmad; Raffaele A. Calogero; Francesca Cordero; Marco Beccuti (BMC Syst. Biol., 2015)

Dealing with indetermination in biochemical networks. - Niccoló Totis; Marco Beccuti; Francesca Cordero; Laura Follia; Chiara Riganti; Francesco Novelli (VALUETOOLS, 2016)

Erratum to: 'NETTAB 2014: From high-throughput structural bioinformatics to integrative systems biology'. - Paolo Romano 001; Francesca Cordero (BMC Bioinform., 2016)

NETTAB 2014: From high-throughput structural bioinformatics to integrative systems biology. - Paolo Romano 001; Francesca Cordero (BMC Bioinform., 2016)

A mathematical model to study breast cancer growth. - Giorgia Chivassa; Chiara Fornari; Roberta Sirovich; Marzio Pennisi; Marco Beccuti; Francesca Cordero (BIBM, 2017)

HashClone: a new tool to quantify the minimal residual disease in B-cell lymphoma from deep sequencing data. - Marco Beccuti; Elisa Genuardi; Greta Romano; Luigia Monitillo; Daniela Barbero; Mario Boccadoro; Marco Ladetto; Raffaele A. Calogero; Simone Ferrero; Francesca Cordero (BMC Bioinform., 2017)

Overcoming the lack of kinetic information in biochemical reactions networks. - Niccoló Totis; Laura Follia; Chiara Riganti; Francesco Novelli; Francesca Cordero; Marco Beccuti (SIGMETRICS Perform. Evaluation Rev., 2017)

SeqBox: RNAseq/ChIPseq reproducible analysis on a consumer game computer. - Marco Beccuti; Francesca Cordero; Maddalena Arigoni; Riccardo Panero; Elvio Gilberto Amparore; Susanna Donatelli; Raffaele A. Calogero (Bioinform., 2018)

Reproducible bioinformatics project: a community for reproducible bioinformatics analysis pipelines. - Neha Kulkarni; Luca Alessandrì; Riccardo Panero; Maddalena Arigoni; Martina Olivero; Giulio Ferrero; Francesca Cordero; Marco Beccuti; Raffaele A. Calogero (BMC Bioinform., 2018)

Multiple Sclerosis Disease: A Computational Approach for Investigating Its Drug Interactions. - Simone Pernice; Marco Beccuti; Greta Romano; Marzio Pennisi; Alessandro Maglione; Santina Cutrupi; Francesco Pappalardo 001; Lorenzo Capra; Giuliana Franceschinis; Massimiliano De Pierro; Gianfranco Balbo; Francesca Cordero; et al. (CIBB, 2019)

BITS2018: the fifteenth annual meeting of the Italian Society of Bioinformatics. - Francesca Cordero; Raffaele A. Calogero; Michele Caselle (BMC Bioinform., 2019)

A computational approach based on the colored Petri net formalism for studying multiple sclerosis. - Simone Pernice; Marzio Pennisi; Greta Romano; Alessandro Maglione; Santina Cutrupi; Francesco Pappalardo 001; Gianfranco Balbo; Marco Beccuti; Francesca Cordero; Raffaele A. Calogero (BMC Bioinform., 2019)

Computational modeling of the immune response in multiple sclerosis using epimod framework. - Simone Pernice; Laura Follia; Alessandro Maglione; Marzio Pennisi; Francesco Pappalardo 001; Francesco Novelli; Marinella Clerico; Marco Beccuti; Francesca Cordero; Simona Rolla (BMC Bioinform., 2020)

Integrating Petri Nets and Flux Balance Methods in Computational Biology Models: a Methodological and Computational Practice. - Simone Pernice; Laura Follia; Gianfranco Balbo; Luciano Milanesi; Giulia Sartini; Niccoló Totis; Pietro Lió; Ivan Merelli; Francesca Cordero; Marco Beccuti (Fundam. Informaticae, 2020)

Interpretable Deep Model For Predicting Gene-Addicted Non-Small-Cell Lung Cancer In Ct Scans. - Carmelo Pino; Simone Palazzo; Francesca Trenta; Francesca Cordero; Ulas Bagci; Francesco Rundo; Sebastiano Battiato; Daniela Giordano; Marco Aldinucci; Concetto Spampinato (ISBI, 2021)

OmniReprodubileCellAnalysis: a comprehensive toolbox for the analysis of cellular biology data. - Dora Tortarolo; Simone Pernice; Fabiana Clapero; Donatella Valdembri; Guido Serini; Federica Riccardo; Lidia Tarone; Chiara Enrico Bena; Carla Bosia; Sandro Gepiro Contaldo; Marco Beccuti; Marzio Pennisi; et al. (BIBM, 2023)

Synergy Between Mechanistic Modelling and Ensemble Feature Selection Approaches to Explore Multiscale Biological Heterogeneity. - Riccardo Aucello; Nicola Licheri; Elena Rosso; Giulio Ferrero; Sandro Gepiro Contaldo; Simone Pernice; Pietro Lió; Francesca Cordero; Marco Beccuti (CIBB, 2023)

Extension of the GreatMod Modeling Framework to Simulate Non-Markovian Processes with General-Distributed Events. - Irene Terrone; Daniela Volpatto; Simone Pernice; Elvio G. Amparore; Roberta Sirovich; Francesca Cordero; Marco Beccuti (CIBB, 2023)

Artificial intelligence methods for biomedical imaging and omics data. - Carlo Alberto Barbano; Marco Beccuti; Francesca Cordero; Desislav Nikolaev Ivanov; Nicola Licheri; Simone Pernice; Alberto Presta; Riccardo Renzulli; Marco Grangetto (Ital-IA, 2023)

CONNECTOR, fitting and clustering of longitudinal data to reveal a new risk stratification system. - Simone Pernice; Roberta Sirovich; Elena Grassi; Marco Viviani 002; Martina Ferri; Francesco Sassi; Luca Alessandrì; Dora Tortarolo; Raffaele A. Calogero; Livio Trusolino; Andrea Bertotti; Marco Beccuti; et al. (Bioinform., 2023)

A new computational workflow to guide personalized drug therapy. - Simone Pernice; Alessandro Maglione; Dora Tortarolo; Roberta Sirovich; Marinella Clerico; Simona Rolla; Marco Beccuti; Francesca Cordero (J. Biomed. Informatics, 2023)

Functional Data Analysis and Clustering of Haematological Parameters in SARS-CoV-2 Patients. - Daniela Volpatto; Marco Frattarola; Simone Pernice; Francesca Cordero; Marco Beccuti; Giulio Mengozzi; Stefano De Angelis; Roberta Sirovich (CIBB, 2024)