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2020 – today
- 2023
[j27]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:
CONNECTOR, fitting and clustering of longitudinal data to reveal a new risk stratification system. Bioinform. 39(5) (2023)- [j26]Simone Pernice, Alessandro Maglione, Dora Tortarolo, Roberta Sirovich, Marinella Clerico, Simona Rolla, Marco Beccuti, Francesca Cordero:
A new computational workflow to guide personalized drug therapy. J. Biomed. Informatics 148: 104546 (2023) - [c17]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:
OmniReprodubileCellAnalysis: a comprehensive toolbox for the analysis of cellular biology data. BIBM 2023: 3748-3755 - [c16]Carlo Alberto Barbano, Marco Beccuti, Francesca Cordero, Desislav Nikolaev Ivanov, Nicola Licheri, Simone Pernice, Alberto Presta, Riccardo Renzulli, Marco Grangetto:
Artificial intelligence methods for biomedical imaging and omics data. Ital-IA 2023: 154-159 - 2021
- [c15]Carmelo Pino, Simone Palazzo, Francesca Trenta, Francesca Cordero, Ulas Bagci, Francesco Rundo, Sebastiano Battiato, Daniela Giordano, Marco Aldinucci, Concetto Spampinato:
Interpretable Deep Model For Predicting Gene-Addicted Non-Small-Cell Lung Cancer In Ct Scans. ISBI 2021: 891-894 - 2020
- [j25]Simone Pernice, Laura Follia, Alessandro Maglione, Marzio Pennisi, Francesco Pappalardo, Francesco Novelli, Marinella Clerico, Marco Beccuti, Francesca Cordero, Simona Rolla:
Computational modeling of the immune response in multiple sclerosis using epimod framework. BMC Bioinform. 21-S(17): 550 (2020) - [j24]Simone Pernice, Laura Follia, Gianfranco Balbo, Luciano Milanesi, Giulia Sartini, Niccoló Totis, Pietro Lió, Ivan Merelli, Francesca Cordero, Marco Beccuti:
Integrating Petri Nets and Flux Balance Methods in Computational Biology Models: a Methodological and Computational Practice. Fundam. Informaticae 171(1-4): 367-392 (2020) - [i2]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:
Multiple Sclerosis disease: a computational approach for investigating its drug interactions. CoRR abs/2006.00813 (2020)
2010 – 2019
- 2019
- [j23]Simone Pernice, Marzio Pennisi, Greta Romano, Alessandro Maglione, Santina Cutrupi, Francesco Pappalardo, Gianfranco Balbo, Marco Beccuti, Francesca Cordero, Raffaele A. Calogero:
A computational approach based on the colored Petri net formalism for studying multiple sclerosis. BMC Bioinform. 20-S(6): 623 (2019) - [j22]Francesca Cordero, Raffaele A. Calogero, Michele Caselle:
BITS2018: the fifteenth annual meeting of the Italian Society of Bioinformatics. BMC Bioinform. 20-S(9): 562:1-562:4 (2019) - [c14]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:
Multiple Sclerosis Disease: A Computational Approach for Investigating Its Drug Interactions. CIBB 2019: 299-308 - 2018
- [j21]Marco Beccuti, Francesca Cordero, Maddalena Arigoni, Riccardo Panero, Elvio Gilberto Amparore, Susanna Donatelli, Raffaele A. Calogero:
SeqBox: RNAseq/ChIPseq reproducible analysis on a consumer game computer. Bioinform. 34(5): 871-872 (2018) - [j20]Neha Kulkarni, Luca Alessandrì, Riccardo Panero, Maddalena Arigoni, Martina Olivero, Giulio Ferrero, Francesca Cordero, Marco Beccuti, Raffaele A. Calogero:
Reproducible bioinformatics project: a community for reproducible bioinformatics analysis pipelines. BMC Bioinform. 19-S(10): 211-219 (2018) - 2017
- [j19]Marco Beccuti, Elisa Genuardi, Greta Romano, Luigia Monitillo, Daniela Barbero, Mario Boccadoro, Marco Ladetto, Raffaele A. Calogero, Simone Ferrero, Francesca Cordero:
HashClone: a new tool to quantify the minimal residual disease in B-cell lymphoma from deep sequencing data. BMC Bioinform. 18(1): 516 (2017) - [j18]Niccoló Totis, Laura Follia, Chiara Riganti, Francesco Novelli, Francesca Cordero, Marco Beccuti:
Overcoming the lack of kinetic information in biochemical reactions networks. SIGMETRICS Perform. Evaluation Rev. 44(4): 91-102 (2017) - [c13]Giorgia Chivassa, Chiara Fornari, Roberta Sirovich, Marzio Pennisi, Marco Beccuti, Francesca Cordero:
A mathematical model to study breast cancer growth. BIBM 2017: 1438-1445 - 2016
- [j17]Paolo Romano, Francesca Cordero:
NETTAB 2014: From high-throughput structural bioinformatics to integrative systems biology. BMC Bioinform. 17(S-4): 62 (2016) - [j16]Paolo Romano, Francesca Cordero:
Erratum to: 'NETTAB 2014: From high-throughput structural bioinformatics to integrative systems biology'. BMC Bioinform. 17: 293 (2016) - [c12]Niccoló Totis, Marco Beccuti, Francesca Cordero, Laura Follia, Chiara Riganti, Francesco Novelli:
Dealing with indetermination in biochemical networks. VALUETOOLS 2016 - 2015
- [j15]Matteo Carrara, Josephine Lum, Francesca Cordero, Marco Beccuti, Michael Poidinger, Susanna Donatelli, Raffaele A. Calogero, Francesca Zolezzi:
Alternative splicing detection workflow needs a careful combination of sample prep and bioinformatics analysis. BMC Bioinform. 16(S-9): S2 (2015) - [j14]Chiara Fornari, Gianfranco Balbo, Sami M. Halawani, Omar M. Ba-Rukab, Ab Rahman Ahmad, Raffaele A. Calogero, Francesca Cordero, Marco Beccuti:
A versatile mathematical work-flow to explore how Cancer Stem Cell fate influences tumor progression. BMC Syst. Biol. 9(S-3): S1 (2015) - [c11]Denise Duma, Francesca Cordero, Marco Beccuti, Gianfranco Ciardo, Timothy J. Close, Stefano Lonardi:
Scrible: Ultra-Accurate Error-Correction of Pooled Sequenced Reads. WABI 2015: 162-174 - 2014
- [j13]Marco Beccuti, Matteo Carrara, Francesca Cordero, Fulvio Lazzarato, Susanna Donatelli, Francesca Nadalin, Alberto Policriti, Raffaele A. Calogero:
Chimera: a Bioconductor package for secondary analysis of fusion products. Bioinform. 30(24): 3556-3557 (2014) - [j12]Alessia Visconti, Francesca Cordero, Ruggero G. Pensa:
Leveraging additional knowledge to support coherent bicluster discovery in gene expression data. Intell. Data Anal. 18(5): 837-855 (2014) - [c10]Francesca Cordero, Chiara Fornari, Marco Gribaudo, Daniele Manini:
Markovian Agents Population Models to Study Cancer Evolution. ASMTA 2014: 16-32 - 2013
- [j11]Francesca Cordero, Marco Beccuti, Chiara Fornari, Stefania Lanzardo, Laura Conti, Federica Cavallo, Gianfranco Balbo, Raffaele A. Calogero:
Multi-level model for the investigation of oncoantigen-driven vaccination effect. BMC Bioinform. 14(S-6): S11 (2013) - [j10]Matteo Carrara, Marco Beccuti, Federica Cavallo, Susanna Donatelli, Fulvio Lazzarato, Francesca Cordero, Raffaele A. Calogero:
State of art fusion-finder algorithms are suitable to detect transcription-induced chimeras in normal tissues? BMC Bioinform. 14(S-7): S2 (2013) - [j9]Ruggero G. Pensa, Francesca Cordero, Céline Rouveirol, Rushed Kanawati:
Guest Editorial. Intell. Data Anal. 17(1): 1-3 (2013) - [j8]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:
Combinatorial Pooling Enables Selective Sequencing of the Barley Gene Space. PLoS Comput. Biol. 9(4) (2013) - 2011
- [j7]Alessia Visconti, Roberto Esposito, Francesca Cordero:
Restructuring the Gene Ontology to emphasise regulative pathways and to improve gene similarity queries. Int. J. Comput. Biol. Drug Des. 4(3): 220-238 (2011) - [j6]Francesca Cordero, András Horváth, Daniele Manini, Lucia Napione, Massimiliano De Pierro, Simona Pavan, Andrea Picco, Andrea Veglio, Matteo Sereno, Federico Bussolino, Gianfranco Balbo:
Simplification of a complex signal transduction model using invariants and flow equivalent servers. Theor. Comput. Sci. 412(43): 6036-6057 (2011) - [j5]Paola Bonfante, Francesca Cordero, Stefano Ghignone, Dino Ienco, Luisa Lanfranco, Giorgio Leonardi, Rosa Meo, Stefania Montani, Luca Roversi, Alessia Visconti:
A Modular Database Architecture Enabled to Comparative Sequence Analysis. Trans. Large Scale Data Knowl. Centered Syst. 4: 124-147 (2011) - [c9]Alessia Visconti, Roberto Esposito, Francesca Cordero:
Tackling the DREAM Challenge for Gene Regulatory Networks Reverse Engineering. AI*IA 2011: 372-382 - [c8]Francesca Cordero, Stefania Lanzardo, Maddalena Arigoni, Chiara Fornari, Laura Conti, Gianfranco Balbo, Federica Cavallo, Daniele Manini, Raffaele A. Calogero:
Cancer stem cell based adjuvant for oncoantingen-driven vaccination. BCB 2011: 564-568 - [c7]Chiara Fornari, Francesca Cordero, Daniele Manini, Gianfranco Balbo, Raffaele A. Calogero:
Mathematical Approach to Predict the Drug Effects on Cancer Stem Cell Models. CS2Bio@DisCoTec 2011: 29-39 - [i1]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:
Barcoding-free BAC Pooling Enables Combinatorial Selective Sequencing of the Barley Gene Space. CoRR abs/1112.4438 (2011) - 2010
- [j4]Ruggero G. Pensa, Jean-François Boulicaut, Francesca Cordero, Maurizio Atzori:
Co-clustering numerical data under user-defined constraints. Stat. Anal. Data Min. 3(1): 38-55 (2010) - [c6]Alessio Angius, Gianfranco Balbo, Francesca Cordero, András Horváth, Daniele Manini:
Comparison of Approximate Kinetics for Unireactant Enzymes: Michaelis-Menten against the Equivalent Server. ACSD/Petri Nets Workshops 2010: 55-69 - [c5]Alessia Visconti, Francesca Cordero, Marco Botta, Raffaele A. Calogero:
Gene Ontology Rewritten for Computing Gene Functional Similarity. CISIS 2010: 694-699 - [e1]Ruggero G. Pensa, Francesca Cordero, Céline Rouveirol, Rushed Kanawati, José A. Troyano, Paolo Rosso:
Proceedings of the 1st Workshop on Dynamic Networks and Knowledge Discovery, Barcelona, Spain, September 24, 2010. CEUR Workshop Proceedings 655, CEUR-WS.org 2010 [contents]
2000 – 2009
- 2009
- [c4]Francesca Cordero, Ruggero G. Pensa, Alessia Visconti, Dino Ienco, Marco Botta:
Ontology-Driven Co-clustering of Gene Expression Data. AI*IA 2009: 426-435 - [c3]Silvia C. Lenzken, Silvia Vivarelli, Francesca Zolezzi, Francesca Cordero, Cristina Della Beffa, Raffaele A. Calogero, Silvia Barabino:
Genome-Wide Search for Splicing Defects Associated with Amyotrophic Lateral Sclerosis (ALS). CISIS 2009: 795-799 - [c2]Lucia Napione, Daniele Manini, Francesca Cordero, András Horváth, Andrea Picco, Massimiliano De Pierro, Simona Pavan, Matteo Sereno, Andrea Veglio, Federico Bussolino, Gianfranco Balbo:
On the Use of Stochastic Petri Nets in the Analysis of Signal Transduction Pathways for Angiogenesis Process. CMSB 2009: 281-295 - [c1]Francesca Cordero, Alessia Visconti, Marco Botta:
A new protein motif extraction framework based on constrained co-clustering. SAC 2009: 776-781 - 2007
- [j3]Remo Sanges, Francesca Cordero, Raffaele A. Calogero:
oneChannelGUI: a graphical interface to Bioconductor tools, designed for life scientists who are not familiar with R language. Bioinform. 23(24): 3406-3408 (2007) - 2005
- [j2]Federica Cavallo, Annalisa Astolfi, Manuela Iezzi, Francesca Cordero, Pierluigi Lollini, Guido Forni, Raffaele A. Calogero:
An integrated approach of immunogenomics and bioinformatics to identify new Tumor Associated Antigens (TAA) for mammary cancer immunological prevention. BMC Bioinform. 6(S-4) (2005) - 2004
- [j1]Fulvio Lazzarato, Giuliana Franceschinis, Marco Botta, Francesca Cordero, Raffaele A. Calogero:
RRE: a tool for the extraction of non-coding regions surrounding annotated genes from genomic datasets. Bioinform. 20(16): 2848-2850 (2004)
Coauthor Index
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