Francesca Cordero

52 papers C 1Misc 3Journal 31Unranked 16

Year	Rank	Type	Title / Venue / Authors
2026	J	`jnl`	Long-read microbial genome assembly, gene prediction and functional annotation: a service of the MIRRI ERIC Italian node. Frontiers Bioinform. Sandro Gepiro Contaldo, Antonio d'Acierno, Lorenzo Bosio, Francesco Venice, Elisa Li Perottino, Janneth Estefania Hoyos Rea, Giovanna Cristina Varese, Francesca Cordero, Marco Beccuti
2025	J	`jnl`	UnifiedGreatMod: a new holistic modelling paradigm for studying biological systems on a complete and harmonious scale. Bioinform. Riccardo Aucello, Simone Pernice, Dora Tortarolo, Raffaele A. Calogero, Celia Herrera-Rincon, Giulia Ronchi, Stefano Geuna, Francesca Cordero, Pietro Lió, Marco Beccuti
2024	—	`conf`	Functional Data Analysis and Clustering of Haematological Parameters in SARS-CoV-2 Patients. CIBB Daniela Volpatto, Marco Frattarola, Simone Pernice, Francesca Cordero, Marco Beccuti, Giulio Mengozzi, Stefano De Angelis, Roberta Sirovich
2023	J	`jnl`	A new computational workflow to guide personalized drug therapy. J. Biomed. Informatics Simone Pernice, Alessandro Maglione, Dora Tortarolo, Roberta Sirovich, Marinella Clerico, Simona Rolla, Marco Beccuti, Francesca Cordero
2023	—	`conf`	Artificial intelligence methods for biomedical imaging and omics data. Ital-IA Carlo Alberto Barbano, Marco Beccuti, Francesca Cordero, Desislav Nikolaev Ivanov, Nicola Licheri, Simone Pernice, Alberto Presta, Riccardo Renzulli, Marco Grangetto
2023	J	`jnl`	CONNECTOR, fitting and clustering of longitudinal data to reveal a new risk stratification system. Bioinform. Simone Pernice, Roberta Sirovich, Elena Grassi, Marco Viviani, Martina Ferri, Francesco Sassi, Luca Alessandrì, Dora Tortarolo, Raffaele A. Calogero, Livio Trusolino, Andrea Bertotti, Marco Beccuti, Martina Olivero, Francesca Cordero
2023	—	`conf`	Extension of the GreatMod Modeling Framework to Simulate Non-Markovian Processes with General-Distributed Events. CIBB Irene Terrone, Daniela Volpatto, Simone Pernice, Elvio G. Amparore, Roberta Sirovich, Francesca Cordero, Marco Beccuti
2023	—	`conf`	OmniReprodubileCellAnalysis: a comprehensive toolbox for the analysis of cellular biology data. BIBM 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, Francesca Cordero
2023	—	`conf`	Synergy Between Mechanistic Modelling and Ensemble Feature Selection Approaches to Explore Multiscale Biological Heterogeneity. CIBB Riccardo Aucello, Nicola Licheri, Elena Rosso, Giulio Ferrero, Sandro Gepiro Contaldo, Simone Pernice, Pietro Lió, Francesca Cordero, Marco Beccuti
2021	—	`conf`	Interpretable Deep Model For Predicting Gene-Addicted Non-Small-Cell Lung Cancer In Ct Scans. ISBI Carmelo Pino, Simone Palazzo, Francesca Trenta, Francesca Cordero, Ulas Bagci, Francesco Rundo, Sebastiano Battiato, Daniela Giordano, Marco Aldinucci, Concetto Spampinato
2020	J	`jnl`	Computational modeling of the immune response in multiple sclerosis using epimod framework. BMC Bioinform. Simone Pernice, Laura Follia, Alessandro Maglione, Marzio Pennisi, Francesco Pappalardo, Francesco Novelli, Marinella Clerico, Marco Beccuti, Francesca Cordero, Simona Rolla
2020	J	`jnl`	Integrating Petri Nets and Flux Balance Methods in Computational Biology Models: a Methodological and Computational Practice. Fundam. Informaticae Simone Pernice, Laura Follia, Gianfranco Balbo, Luciano Milanesi, Giulia Sartini, Niccoló Totis, Pietro Lió, Ivan Merelli, Francesca Cordero, Marco Beccuti
2020	J	`jnl`	Multiple Sclerosis disease: a computational approach for investigating its drug interactions. CoRR Simone Pernice, Marco Beccuti, Greta Romano, Marzio Pennisi, Alessandro Maglione, Santina Cutrupi, Francesco Pappalardo, Lorenzo Capra, Giuliana Franceschinis, Massimiliano De Pierro, Gianfranco Balbo, Francesca Cordero, Raffaele A. Calogero
2019	J	`jnl`	A computational approach based on the colored Petri net formalism for studying multiple sclerosis. BMC Bioinform. Simone Pernice, Marzio Pennisi, Greta Romano, Alessandro Maglione, Santina Cutrupi, Francesco Pappalardo, Gianfranco Balbo, Marco Beccuti, Francesca Cordero, Raffaele A. Calogero
2019	J	`jnl`	BITS2018: the fifteenth annual meeting of the Italian Society of Bioinformatics. BMC Bioinform. Francesca Cordero, Raffaele A. Calogero, Michele Caselle
2019	—	`conf`	Multiple Sclerosis Disease: A Computational Approach for Investigating Its Drug Interactions. CIBB Simone Pernice, Marco Beccuti, Greta Romano, Marzio Pennisi, Alessandro Maglione, Santina Cutrupi, Francesco Pappalardo, Lorenzo Capra, Giuliana Franceschinis, Massimiliano De Pierro, Gianfranco Balbo, Francesca Cordero, Raffaele A. Calogero
2018	J	`jnl`	Reproducible bioinformatics project: a community for reproducible bioinformatics analysis pipelines. BMC Bioinform. Neha Kulkarni, Luca Alessandrì, Riccardo Panero, Maddalena Arigoni, Martina Olivero, Giulio Ferrero, Francesca Cordero, Marco Beccuti, Raffaele A. Calogero
2018	J	`jnl`	SeqBox: RNAseq/ChIPseq reproducible analysis on a consumer game computer. Bioinform. Marco Beccuti, Francesca Cordero, Maddalena Arigoni, Riccardo Panero, Elvio Gilberto Amparore, Susanna Donatelli, Raffaele A. Calogero
2017	—	`conf`	A mathematical model to study breast cancer growth. BIBM Giorgia Chivassa, Chiara Fornari, Roberta Sirovich, Marzio Pennisi, Marco Beccuti, Francesca Cordero
2017	J	`jnl`	HashClone: a new tool to quantify the minimal residual disease in B-cell lymphoma from deep sequencing data. BMC Bioinform. Marco Beccuti, Elisa Genuardi, Greta Romano, Luigia Monitillo, Daniela Barbero, Mario Boccadoro, Marco Ladetto, Raffaele A. Calogero, Simone Ferrero, Francesca Cordero
2017	J	`jnl`	Overcoming the lack of kinetic information in biochemical reactions networks. SIGMETRICS Perform. Evaluation Rev. Niccoló Totis, Laura Follia, Chiara Riganti, Francesco Novelli, Francesca Cordero, Marco Beccuti
2016	—	`conf`	Dealing with indetermination in biochemical networks. VALUETOOLS Niccoló Totis, Marco Beccuti, Francesca Cordero, Laura Follia, Chiara Riganti, Francesco Novelli
2016	J	`jnl`	Erratum to: 'NETTAB 2014: From high-throughput structural bioinformatics to integrative systems biology'. BMC Bioinform. Paolo Romano, Francesca Cordero
2016	J	`jnl`	NETTAB 2014: From high-throughput structural bioinformatics to integrative systems biology. BMC Bioinform. Paolo Romano, Francesca Cordero
2015	J	`jnl`	A versatile mathematical work-flow to explore how Cancer Stem Cell fate influences tumor progression. BMC Syst. Biol. Chiara Fornari, Gianfranco Balbo, Sami M. Halawani, Omar M. Ba-Rukab, Ab Rahman Ahmad, Raffaele A. Calogero, Francesca Cordero, Marco Beccuti
2015	J	`jnl`	Alternative splicing detection workflow needs a careful combination of sample prep and bioinformatics analysis. BMC Bioinform. Matteo Carrara, Josephine Lum, Francesca Cordero, Marco Beccuti, Michael Poidinger, Susanna Donatelli, Raffaele A. Calogero, Francesca Zolezzi
2015	C	`conf`	Scrible: Ultra-Accurate Error-Correction of Pooled Sequenced Reads. WABI Denise Duma, Francesca Cordero, Marco Beccuti, Gianfranco Ciardo, Timothy J. Close, Stefano Lonardi
2014	J	`jnl`	Chimera: a Bioconductor package for secondary analysis of fusion products. Bioinform. Marco Beccuti, Matteo Carrara, Francesca Cordero, Fulvio Lazzarato, Susanna Donatelli, Francesca Nadalin, Alberto Policriti, Raffaele A. Calogero
2014	J	`jnl`	Leveraging additional knowledge to support coherent bicluster discovery in gene expression data. Intell. Data Anal. Alessia Visconti, Francesca Cordero, Ruggero G. Pensa
2014	—	`conf`	Markovian Agents Population Models to Study Cancer Evolution. ASMTA Francesca Cordero, Chiara Fornari, Marco Gribaudo, Daniele Manini
2013	J	`jnl`	Combinatorial Pooling Enables Selective Sequencing of the Barley Gene Space. PLoS Comput. Biol. 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, Serdar Bozdag, Ming-Cheng Luo, Timothy J. Close
2013	J	`jnl`	Guest Editorial. Intell. Data Anal. Ruggero G. Pensa, Francesca Cordero, Céline Rouveirol, Rushed Kanawati
2013	J	`jnl`	Multi-level model for the investigation of oncoantigen-driven vaccination effect. BMC Bioinform. Francesca Cordero, Marco Beccuti, Chiara Fornari, Stefania Lanzardo, Laura Conti, Federica Cavallo, Gianfranco Balbo, Raffaele A. Calogero
2013	J	`jnl`	State of art fusion-finder algorithms are suitable to detect transcription-induced chimeras in normal tissues? BMC Bioinform. Matteo Carrara, Marco Beccuti, Federica Cavallo, Susanna Donatelli, Fulvio Lazzarato, Francesca Cordero, Raffaele A. Calogero
2011	J	`jnl`	A Modular Database Architecture Enabled to Comparative Sequence Analysis. Trans. Large Scale Data Knowl. Centered Syst. Paola Bonfante, Francesca Cordero, Stefano Ghignone, Dino Ienco, Luisa Lanfranco, Giorgio Leonardi, Rosa Meo, Stefania Montani, Luca Roversi, Alessia Visconti
2011	J	`jnl`	Barcoding-free BAC Pooling Enables Combinatorial Selective Sequencing of the Barley Gene Space CoRR Stefano Lonardi, Denisa Duma, Matthew Alpert, Francesca Cordero, Marco Beccuti, Prasanna Bhat, Yonghui Wu, Gianfranco Ciardo, Burair Alsaihati, Yaqin Ma, Steve Wanamaker, Josh Resnik, Timothy J. Close
2011	—	`conf`	Cancer stem cell based adjuvant for oncoantingen-driven vaccination. BCB Francesca Cordero, Stefania Lanzardo, Maddalena Arigoni, Chiara Fornari, Laura Conti, Gianfranco Balbo, Federica Cavallo, Daniele Manini, Raffaele A. Calogero
2011	—	`conf`	Mathematical Approach to Predict the Drug Effects on Cancer Stem Cell Models. CS2Bio@DisCoTec Chiara Fornari, Francesca Cordero, Daniele Manini, Gianfranco Balbo, Raffaele A. Calogero
2011	J	`jnl`	Restructuring the Gene Ontology to emphasise regulative pathways and to improve gene similarity queries. Int. J. Comput. Biol. Drug Des. Alessia Visconti, Roberto Esposito, Francesca Cordero
2011	J	`jnl`	Simplification of a complex signal transduction model using invariants and flow equivalent servers. Theor. Comput. Sci. Francesca Cordero, András Horváth, Daniele Manini, Lucia Napione, Massimiliano De Pierro, Simona Pavan, Andrea Picco, Andrea Veglio, Matteo Sereno, Federico Bussolino, Gianfranco Balbo
2011	—	`conf`	Tackling the DREAM Challenge for Gene Regulatory Networks Reverse Engineering. AI*IA Alessia Visconti, Roberto Esposito, Francesca Cordero
2010	J	`jnl`	Co-clustering numerical data under user-defined constraints. Stat. Anal. Data Min. Ruggero G. Pensa, Jean-François Boulicaut, Francesca Cordero, Maurizio Atzori
2010	—	`conf`	Comparison of Approximate Kinetics for Unireactant Enzymes: Michaelis-Menten against the Equivalent Server. ACSD/Petri Nets Workshops Alessio Angius, Gianfranco Balbo, Francesca Cordero, András Horváth, Daniele Manini
2010	Misc	`conf`	Gene Ontology Rewritten for Computing Gene Functional Similarity. CISIS Alessia Visconti, Francesca Cordero, Marco Botta, Raffaele A. Calogero
2010	—	`ed.`	Proceedings of the 1st Workshop on Dynamic Networks and Knowledge Discovery, Barcelona, Spain, September 24, 2010 DyNaK Ruggero G. Pensa, Francesca Cordero, Céline Rouveirol, Rushed Kanawati, José A. Troyano, Paolo Rosso
2009	Misc	`conf`	A new protein motif extraction framework based on constrained co-clustering. SAC Francesca Cordero, Alessia Visconti, Marco Botta
2009	Misc	`conf`	Genome-Wide Search for Splicing Defects Associated with Amyotrophic Lateral Sclerosis (ALS). CISIS Silvia C. Lenzken, Silvia Vivarelli, Francesca Zolezzi, Francesca Cordero, Cristina Della Beffa, Raffaele A. Calogero, Silvia Barabino
2009	—	`conf`	On the Use of Stochastic Petri Nets in the Analysis of Signal Transduction Pathways for Angiogenesis Process. CMSB Lucia Napione, Daniele Manini, Francesca Cordero, András Horváth, Andrea Picco, Massimiliano De Pierro, Simona Pavan, Matteo Sereno, Andrea Veglio, Federico Bussolino, Gianfranco Balbo
2009	—	`conf`	Ontology-Driven Co-clustering of Gene Expression Data. AI*IA Francesca Cordero, Ruggero G. Pensa, Alessia Visconti, Dino Ienco, Marco Botta
2007	J	`jnl`	oneChannelGUI: a graphical interface to Bioconductor tools, designed for life scientists who are not familiar with R language. Bioinform. Remo Sanges, Francesca Cordero, Raffaele A. Calogero
2005	J	`jnl`	An integrated approach of immunogenomics and bioinformatics to identify new Tumor Associated Antigens (TAA) for mammary cancer immunological prevention. BMC Bioinform. Federica Cavallo, Annalisa Astolfi, Manuela Iezzi, Francesca Cordero, Pierluigi Lollini, Guido Forni, Raffaele A. Calogero
2004	J	`jnl`	RRE: a tool for the extraction of non-coding regions surrounding annotated genes from genomic datasets. Bioinform. Fulvio Lazzarato, Giuliana Franceschinis, Marco Botta, Francesca Cordero, Raffaele A. Calogero