Francesca Cordero
Editorial activities
R.G. Pensa, F. Cordero, C. Rouveirol. R. Kanawati, J.A. Troyano, P. Rosso. Dynamic Networks and Knowledge Discovery. Proceedings of the 1st Workshop on Dynamic Networks and Knowledge Discovery (DyNaK 2010) , Barcelona, Spain, 24 september 2010. CEUR-WS.org, Vol-655. CEUR-WS
In Refereed International Journal
Cordero F, Beccuti M, Arigoni M, Donatelli S, Calogero RA Dissecting a massive parallel sequencing workflow for quantitative miRNA expression analysis International Journal PLoS ONE (In press)
Cordero F, Horvath A, Manini D, Napione L., De Pierro M, Pavan S, Picco A, Veglio A, Sereno M., Bussolino F. and Balbo G. Simplification of a complex signal transduction model by the application of invariants and flow equivalent server Theoretical Computer Science Elsevier 2011 Oct; vol:412, pp 6036-6057, ISSN: 0304-3975.
Baldi A, Piccolo MT, Boccellino MR, Donizetti A, Cardillo I, La Porta R, Quagliuolo L, Spugnini EP, Cordero F., Citro G, Menegozzo M, Calogero RA, Crispi S. Apoptosis Induced by Piroxicam plus Cisplatin Combined Treatment Is Triggered by p21 in Mesothelioma. PLOS ONE, (2011) vol. 6(8); ISSN: 1932-6203.
Bonfante P., Cordero F., Ghignone S., Ienco D., Lanfranco L., Leonardi G., Meo R., Montani S., Roversi L., and Visconti A., A Modular Database Architecture Enabled to Comparative Sequence Analysis LNCS Transactions on Large-Scale Data- and Knowledge-Centered Systems, Springer,2011, vol:6934, pp 372-382, ISSN: 1869-1994.
Visconti A., Esposito R., and Cordero F. Restructuring the Gene Ontology to Emphasize Regulative Pathways and to Improve Gene Similarity Queries International Journal Computational Biology and Drug Design Inderscience Publishers, vol:4, pp 220-238. ISSN 1756-0764.
Cordero F, Beccuti M, Donatelli S, Calogero RA. Disclosing the nature of computational tools for the analysis of Next Generation Sequencing data. Current Pharmaceutical Biotechnology Ed. Bentham Science. To be publish
Lenzken SC, Romeo V, Zolezzi F, Cordero F, Lamorte G, Bonanno D, Biancolini D, Cozzolino M, Pesaresi MG, Maracchioni A, Sanges R, Achsel T, Carrí MT, Calogero RA, Barabino SM. Mutant SOD1 and mitochondrial damage alter expression and splicing of genes controlling neuritogenesis in models of neurodegeneration. Human Mutation 2011 Feb;32(2) pp 168-82. ISSN: 1098-1004.
Pensa RG, Boulicaut J-F, Cordero F, Atzori M. Co-clustering Numerical Data under User-defined Constraints Statistical Analysis and Data Mining Wiley-Blackwell. Vol. 3(1) 2010. pp 38-55. ISSN: 1932-1864. [pdf]
Della Beffa C, Cordero F, Calogero RA. Dissecting an alternative splicing analysis workflow for GeneChip Exon 1.0 ST Affymetrix arrays BMC Genomics 2008 Nov 28;9:571. ISSN: 1471-2164.[pdf]
Cordero F, Botta M, Calogero RA. Microarray data analysis and mining approaches Functional Genomics and Proteomics 2007 Dec;6(4):265-81. Epub 2008 Jan 22. ISSN: 1473-9550.[pdf]
Calogero RA, Cordero F, Forni G, Cavallo F Inflammation and breast cancer. Inflammatory component of mammary carcinogenesis in ErbB2 transgenic mice Breast Cancer Research 2007 Aug 10;9(4):211 ISSN: 1465-542X.[pdf]
Sanges R, Cordero F, Calogero RA oneChannelGUI: a graphical interface to Bioconductor tools, designed for life scientists who are not familiar with R language Bioinformatics 2007 Sep 17. ISSN: 1367-4803.[pdf]
Saviozzi S, Cordero F, Lo Iacono M, Novello S, Scagliotti G, Calogero AR Selection of suitable reference genes for accurate normalization of gene expression profile studies in non-small cell lung cancer BMC Cancer 2006 6:2006. ISSN: 1471-2407.[pdf]
Cavallo F, Astolfi A, Iezzi M, Cordero F, Lollini PL, Forni G, Calogero RA An integrated approach of immunogenomics and bioinformatics to identify new Tumor Associated Antigens (TAA) for mammary cancer immunological prevention BMC Bioinformatics 2005 Dic 1. ISSN: 1471-2105.[pdf]
Lazzarato F, Franceschinis G, Botta M, Cordero F, Calogero RA RRE: a tool for the extraction of non-coding regions surrounding annotated genes from genomic datasets Bioinformatics 2004 Nov 1;20(16):2848-50. 2004 Apr 29. ISSN 1367-4803.[pdf]
Proceeding of Refereed International Conferences
Visconti A., Esposito R., and Cordero F., Tackling the DREAM Challenge for Gene Regulatory Networks Reverse Engineering In Proceedings of AI*IA 2011, XII International Conferences of the Italian Association for Artificial Intelligence 2011, Palermo, Italy.
Fornari C, Cordero F, Manini D, Calogero RA, Balbo G Mathematical approach to predict the drug effects on cancer stem cell models. Proceedings of the CS2Bio 2nd International Workshop on Interactions between Computer Science and Biology 2011, Reykjavik, Iceland.
Cordero F, Fornari C, Cavallo F, Lanzardo S, Conti L, Manini D, Arigoni M, Balbo G, Calogero RA, Cancer Stem Cell based adjuvant for oncoantingen-driven vaccination. Proceedings of the BCB' 11: ACM International Conference on Bioinformatics, Computational Biology and Biomedicine Proceedings 2011, Chicago, USA.
Angius A, Balbo G, Cordero F, Horvath A, Manini D, Comparison of approximate kinetics for unireactant enzymes: Michaelis-Menten against the equivalent server Proceedings of the International Workshop on Biological Processes and Petri Nets (BioPPN) 2010, Braga, Portugal. ISBN: 978-972-8692-53-7 [pdf]
Visconti A., Cordero F., Botta M. and Calogero R.A., Gene Ontology rewritten for computing gene functional similarity In Proceedings of the Fourth International Conferences on Complex, Intelligent and Software Intensive Systems , February 15-18 2010, IEEE Computer Society Press, pag 694-699 ISBN 978-0-7695-3967-6 [pdf]
Cordero F, Manini D, Gribaudo M, Balbo G An intuitive object-oriented methodology to model biological pathways In Proceeding of the fourth Sysbiohealth Symposium Loncomia Innovazione Press. pp 62-64 November 25-27, 2009, Milano, Italy. ISBN 978-88-903154-6-6
Cordero F, Pensa RG, Visconti A, Ienco D, Botta M Ontology-driven Co-clustering of Gene Expression Data In Proceedings of the 11th Conference of the Italian Association for Artificial Intelligence (AI*IA) LNAI 5883 Springer pp 426-435. December 9-12, 2009, Reggio Emilia, Italy. ISSN: 0302-9743.[pdf]
Cordero F, Manini D, Gribaudo M. Modeling Biological Pathways: an Object-oriented like Methodology Based on Mean Field Analysis In Proceedings of the Third International Conference on Advanced Engineering Computing and Applications in Sciences (ADVCOM) IEEE Computer Society Press. October 2009, Sliema,Malta.[pdf]
Napione L, Manini D, Cordero F, Horvath A, Picco A, De Pierro M, Pavan S, Sereno M, Veglio A, Bussolino F and Balbo G On the use of Stochastic Petri Nets in the analysis of a signal transduction pathways for angiogenesis process In Proceedings Lectures Notes in Bioinformatics of the Computational Methods of System Biology LNBI 5688 Springer-Verlag, pp. 281-295, 2009 Bologna Italy. ISSN: 0302-9743.[pdf]
Lenzken SC, Vivarelli S, Zolezzi F, Cordero F, Della Beffa C, Calogero RA and Barabino S Genome-wide Search For Splicing Defects Associated with Amyotrophic Lateral Sclerosis (ALS) In Proceeding of CISIS (International Conference on Complex, Intelligent and Software Intensive Systems) IEEE. Fukuoka, Japan, March 16-19 2009, p. 20-27[pdf]
Cordero F, Visconti A, and Botta M A new protein motif extraction framework based on constrained co-clustering In Proceedings of the 24th Annual ACM Symposium on Applied Computing ACM Press, March 2009, Hololulu, Hawaii USA.[pdf]
Books
Visconti A., Cordero F., Ienco D., and Pensa R.G. Coclustering under Gene Ontology Derived Constraints for Pathway Identification, Biological Knowledge Discovery Handbook: Preprocessing, Mining and Postprocessing of Biological Data, Mourad Elloumi and Albert Y. Zomaya (Eds.), Wiley, USA .
Cordero F, Ghignone S, Lanfranco L, Leonardi G, Meo R, Montani S, Roversi L. BIOBITS: A Study on Candidatus Glomeribacter Gigasporarum with a Data Warehouse Database Technology for Life Sciences and Medicine Claudia Plant, Christian Bohm (ed.), Chapter 10, pp. 203 - 220. World Scientific Publishing, Singapore, Summer 2011 (pubblication scheduled date). ISBN: 978-981-4307-70-3.
Refereed International Conferences and Posters
Beccuti M, Donatelli S, Calogero R.A. and Cordero F. DS-gen: a tool to generate SOLiD and ILLUMINA synthetic NGS datasets to test mapping tools behavior 7th Annual General Meeting of the Italian Bioinformatics Society 14-16 April 2010, Bari (IT)
Cordero F, Beccuti M, Donatelli S and Calogero RA. SeqMDD: efficient and exhaustive sequence mapping in color and nucleotide space exploiting symbolic data structures. Conference of System Biology and New Sequencing Tecnhologies Center for Genomics Regulation (CRG) June 16-18 2010, Barcelona, Spain.
Cordero F, Beccuti M, Donatelli S and Calogero R SeqMDD: efficient and exhaustive sequence mapping in color and nucleotide space through the use of symbolic data structures System Biology and New Sequencing Tecnhologies Center for Genomics Regulation (CRG) June 16-18 2010, Barcelona, Spain.
Cordero F, Visconti A and Botta M A web interface to extract protein motifs by constrained co-clustering RECOMB Satellite on Regulatory Genomics 2008 Boston MIT Broad Oct 28 Nov 2 2008, Boston.
Cordero F., Visconti A. and Botta M. A motif extraction framework applied on RNA secondary structure Alternative Splicing Workshop}, October 3, 2008, Milano
Cordero F. and Gary D Stormo. Crystal structure and phylogenetic data to infer the binding motif for new protein The 4th Annual RECOMB Satellite on Regulatory Genomics 2007 Boston MIT Broad Oct. 11-13 2007, Boston.
G. Altobelli, D. Cora; , F. Cordero, M. Caselle and M. De Bortoli Identifying Networks of Estrogen-Responsive Genes in Breast Cancer Cells The 3rd EMBL Biennial Symposium: From Functional Genomics to Systems Biology Oct. 14-17 2006, Heidelberg
Cordero F., Saviozzi S, Di Renzo MF, Oliveiro M, Cirenei N, Calogero RA Microarray cross-platforms differential expression validation Bioinformatics Italian Society-BITS 2006 Bologna 28-29 April 2006.
Cavallo F, Astolfi A, Iezzi M, Cordero F, Lollini PL, Forni G, Calogero RA An integrated approach of immunogenomics and bioinformatics to identify new Tumor Associates Antigen (TAA) for mammary cancer immuno-prevention. Models and Methods for Human Genomics FIMA International Conference, Ayas-Champoluc, Aosta Valley, January 23-27, 2006
Cardamone M, Cordero F, Lazzarato F, Cicatiello D, Scafoglio C, Cimino D, Basile A, Weisz A, Calogero RA, De Bortoli M. Bioinformatic and functional analysis of ERE-contain Genes EMBO Conference, Nuclear receptors from chromatin to disease Riva del Garda, 29 Sept - 1Oct 2005
Important Copyright Notice: This material is presented to ensure timely dissemination of scholarly and technical work. Copyright and all rights therein are retained by authors or by other copyright holders. All persons copying this information are expected to adhere to the terms and constraints invoked by each author's copyright. In most cases, these works may not be reposted without explicit permission of the copyright holder.
R.G. Pensa, F. Cordero, C. Rouveirol. R. Kanawati, J.A. Troyano, P. Rosso. Dynamic Networks and Knowledge Discovery. Proceedings of the 1st Workshop on Dynamic Networks and Knowledge Discovery (DyNaK 2010) , Barcelona, Spain, 24 september 2010. CEUR-WS.org, Vol-655. CEUR-WS
In Refereed International Journal
Cordero F, Beccuti M, Arigoni M, Donatelli S, Calogero RA Dissecting a massive parallel sequencing workflow for quantitative miRNA expression analysis International Journal PLoS ONE (In press)
Cordero F, Horvath A, Manini D, Napione L., De Pierro M, Pavan S, Picco A, Veglio A, Sereno M., Bussolino F. and Balbo G. Simplification of a complex signal transduction model by the application of invariants and flow equivalent server Theoretical Computer Science Elsevier 2011 Oct; vol:412, pp 6036-6057, ISSN: 0304-3975.
Baldi A, Piccolo MT, Boccellino MR, Donizetti A, Cardillo I, La Porta R, Quagliuolo L, Spugnini EP, Cordero F., Citro G, Menegozzo M, Calogero RA, Crispi S. Apoptosis Induced by Piroxicam plus Cisplatin Combined Treatment Is Triggered by p21 in Mesothelioma. PLOS ONE, (2011) vol. 6(8); ISSN: 1932-6203.
Bonfante P., Cordero F., Ghignone S., Ienco D., Lanfranco L., Leonardi G., Meo R., Montani S., Roversi L., and Visconti A., A Modular Database Architecture Enabled to Comparative Sequence Analysis LNCS Transactions on Large-Scale Data- and Knowledge-Centered Systems, Springer,2011, vol:6934, pp 372-382, ISSN: 1869-1994.
Visconti A., Esposito R., and Cordero F. Restructuring the Gene Ontology to Emphasize Regulative Pathways and to Improve Gene Similarity Queries International Journal Computational Biology and Drug Design Inderscience Publishers, vol:4, pp 220-238. ISSN 1756-0764.
Cordero F, Beccuti M, Donatelli S, Calogero RA. Disclosing the nature of computational tools for the analysis of Next Generation Sequencing data. Current Pharmaceutical Biotechnology Ed. Bentham Science. To be publish
Lenzken SC, Romeo V, Zolezzi F, Cordero F, Lamorte G, Bonanno D, Biancolini D, Cozzolino M, Pesaresi MG, Maracchioni A, Sanges R, Achsel T, Carrí MT, Calogero RA, Barabino SM. Mutant SOD1 and mitochondrial damage alter expression and splicing of genes controlling neuritogenesis in models of neurodegeneration. Human Mutation 2011 Feb;32(2) pp 168-82. ISSN: 1098-1004.
Pensa RG, Boulicaut J-F, Cordero F, Atzori M. Co-clustering Numerical Data under User-defined Constraints Statistical Analysis and Data Mining Wiley-Blackwell. Vol. 3(1) 2010. pp 38-55. ISSN: 1932-1864. [pdf]
Della Beffa C, Cordero F, Calogero RA. Dissecting an alternative splicing analysis workflow for GeneChip Exon 1.0 ST Affymetrix arrays BMC Genomics 2008 Nov 28;9:571. ISSN: 1471-2164.[pdf]
Cordero F, Botta M, Calogero RA. Microarray data analysis and mining approaches Functional Genomics and Proteomics 2007 Dec;6(4):265-81. Epub 2008 Jan 22. ISSN: 1473-9550.[pdf]
Calogero RA, Cordero F, Forni G, Cavallo F Inflammation and breast cancer. Inflammatory component of mammary carcinogenesis in ErbB2 transgenic mice Breast Cancer Research 2007 Aug 10;9(4):211 ISSN: 1465-542X.[pdf]
Sanges R, Cordero F, Calogero RA oneChannelGUI: a graphical interface to Bioconductor tools, designed for life scientists who are not familiar with R language Bioinformatics 2007 Sep 17. ISSN: 1367-4803.[pdf]
Saviozzi S, Cordero F, Lo Iacono M, Novello S, Scagliotti G, Calogero AR Selection of suitable reference genes for accurate normalization of gene expression profile studies in non-small cell lung cancer BMC Cancer 2006 6:2006. ISSN: 1471-2407.[pdf]
Cavallo F, Astolfi A, Iezzi M, Cordero F, Lollini PL, Forni G, Calogero RA An integrated approach of immunogenomics and bioinformatics to identify new Tumor Associated Antigens (TAA) for mammary cancer immunological prevention BMC Bioinformatics 2005 Dic 1. ISSN: 1471-2105.[pdf]
Lazzarato F, Franceschinis G, Botta M, Cordero F, Calogero RA RRE: a tool for the extraction of non-coding regions surrounding annotated genes from genomic datasets Bioinformatics 2004 Nov 1;20(16):2848-50. 2004 Apr 29. ISSN 1367-4803.[pdf]
Proceeding of Refereed International Conferences
Visconti A., Esposito R., and Cordero F., Tackling the DREAM Challenge for Gene Regulatory Networks Reverse Engineering In Proceedings of AI*IA 2011, XII International Conferences of the Italian Association for Artificial Intelligence 2011, Palermo, Italy.
Fornari C, Cordero F, Manini D, Calogero RA, Balbo G Mathematical approach to predict the drug effects on cancer stem cell models. Proceedings of the CS2Bio 2nd International Workshop on Interactions between Computer Science and Biology 2011, Reykjavik, Iceland.
Cordero F, Fornari C, Cavallo F, Lanzardo S, Conti L, Manini D, Arigoni M, Balbo G, Calogero RA, Cancer Stem Cell based adjuvant for oncoantingen-driven vaccination. Proceedings of the BCB' 11: ACM International Conference on Bioinformatics, Computational Biology and Biomedicine Proceedings 2011, Chicago, USA.
Angius A, Balbo G, Cordero F, Horvath A, Manini D, Comparison of approximate kinetics for unireactant enzymes: Michaelis-Menten against the equivalent server Proceedings of the International Workshop on Biological Processes and Petri Nets (BioPPN) 2010, Braga, Portugal. ISBN: 978-972-8692-53-7 [pdf]
Visconti A., Cordero F., Botta M. and Calogero R.A., Gene Ontology rewritten for computing gene functional similarity In Proceedings of the Fourth International Conferences on Complex, Intelligent and Software Intensive Systems , February 15-18 2010, IEEE Computer Society Press, pag 694-699 ISBN 978-0-7695-3967-6 [pdf]
Cordero F, Manini D, Gribaudo M, Balbo G An intuitive object-oriented methodology to model biological pathways In Proceeding of the fourth Sysbiohealth Symposium Loncomia Innovazione Press. pp 62-64 November 25-27, 2009, Milano, Italy. ISBN 978-88-903154-6-6
Cordero F, Pensa RG, Visconti A, Ienco D, Botta M Ontology-driven Co-clustering of Gene Expression Data In Proceedings of the 11th Conference of the Italian Association for Artificial Intelligence (AI*IA) LNAI 5883 Springer pp 426-435. December 9-12, 2009, Reggio Emilia, Italy. ISSN: 0302-9743.[pdf]
Cordero F, Manini D, Gribaudo M. Modeling Biological Pathways: an Object-oriented like Methodology Based on Mean Field Analysis In Proceedings of the Third International Conference on Advanced Engineering Computing and Applications in Sciences (ADVCOM) IEEE Computer Society Press. October 2009, Sliema,Malta.[pdf]
Napione L, Manini D, Cordero F, Horvath A, Picco A, De Pierro M, Pavan S, Sereno M, Veglio A, Bussolino F and Balbo G On the use of Stochastic Petri Nets in the analysis of a signal transduction pathways for angiogenesis process In Proceedings Lectures Notes in Bioinformatics of the Computational Methods of System Biology LNBI 5688 Springer-Verlag, pp. 281-295, 2009 Bologna Italy. ISSN: 0302-9743.[pdf]
Lenzken SC, Vivarelli S, Zolezzi F, Cordero F, Della Beffa C, Calogero RA and Barabino S Genome-wide Search For Splicing Defects Associated with Amyotrophic Lateral Sclerosis (ALS) In Proceeding of CISIS (International Conference on Complex, Intelligent and Software Intensive Systems) IEEE. Fukuoka, Japan, March 16-19 2009, p. 20-27[pdf]
Cordero F, Visconti A, and Botta M A new protein motif extraction framework based on constrained co-clustering In Proceedings of the 24th Annual ACM Symposium on Applied Computing ACM Press, March 2009, Hololulu, Hawaii USA.[pdf]
Books
Visconti A., Cordero F., Ienco D., and Pensa R.G. Coclustering under Gene Ontology Derived Constraints for Pathway Identification, Biological Knowledge Discovery Handbook: Preprocessing, Mining and Postprocessing of Biological Data, Mourad Elloumi and Albert Y. Zomaya (Eds.), Wiley, USA .
Cordero F, Ghignone S, Lanfranco L, Leonardi G, Meo R, Montani S, Roversi L. BIOBITS: A Study on Candidatus Glomeribacter Gigasporarum with a Data Warehouse Database Technology for Life Sciences and Medicine Claudia Plant, Christian Bohm (ed.), Chapter 10, pp. 203 - 220. World Scientific Publishing, Singapore, Summer 2011 (pubblication scheduled date). ISBN: 978-981-4307-70-3.
Refereed International Conferences and Posters
Beccuti M, Donatelli S, Calogero R.A. and Cordero F. DS-gen: a tool to generate SOLiD and ILLUMINA synthetic NGS datasets to test mapping tools behavior 7th Annual General Meeting of the Italian Bioinformatics Society 14-16 April 2010, Bari (IT)
Cordero F, Beccuti M, Donatelli S and Calogero RA. SeqMDD: efficient and exhaustive sequence mapping in color and nucleotide space exploiting symbolic data structures. Conference of System Biology and New Sequencing Tecnhologies Center for Genomics Regulation (CRG) June 16-18 2010, Barcelona, Spain.
Cordero F, Beccuti M, Donatelli S and Calogero R SeqMDD: efficient and exhaustive sequence mapping in color and nucleotide space through the use of symbolic data structures System Biology and New Sequencing Tecnhologies Center for Genomics Regulation (CRG) June 16-18 2010, Barcelona, Spain.
Cordero F, Visconti A and Botta M A web interface to extract protein motifs by constrained co-clustering RECOMB Satellite on Regulatory Genomics 2008 Boston MIT Broad Oct 28 Nov 2 2008, Boston.
Cordero F., Visconti A. and Botta M. A motif extraction framework applied on RNA secondary structure Alternative Splicing Workshop}, October 3, 2008, Milano
Cordero F. and Gary D Stormo. Crystal structure and phylogenetic data to infer the binding motif for new protein The 4th Annual RECOMB Satellite on Regulatory Genomics 2007 Boston MIT Broad Oct. 11-13 2007, Boston.
G. Altobelli, D. Cora; , F. Cordero, M. Caselle and M. De Bortoli Identifying Networks of Estrogen-Responsive Genes in Breast Cancer Cells The 3rd EMBL Biennial Symposium: From Functional Genomics to Systems Biology Oct. 14-17 2006, Heidelberg
Cordero F., Saviozzi S, Di Renzo MF, Oliveiro M, Cirenei N, Calogero RA Microarray cross-platforms differential expression validation Bioinformatics Italian Society-BITS 2006 Bologna 28-29 April 2006.
Cavallo F, Astolfi A, Iezzi M, Cordero F, Lollini PL, Forni G, Calogero RA An integrated approach of immunogenomics and bioinformatics to identify new Tumor Associates Antigen (TAA) for mammary cancer immuno-prevention. Models and Methods for Human Genomics FIMA International Conference, Ayas-Champoluc, Aosta Valley, January 23-27, 2006
Cardamone M, Cordero F, Lazzarato F, Cicatiello D, Scafoglio C, Cimino D, Basile A, Weisz A, Calogero RA, De Bortoli M. Bioinformatic and functional analysis of ERE-contain Genes EMBO Conference, Nuclear receptors from chromatin to disease Riva del Garda, 29 Sept - 1Oct 2005
Important Copyright Notice: This material is presented to ensure timely dissemination of scholarly and technical work. Copyright and all rights therein are retained by authors or by other copyright holders. All persons copying this information are expected to adhere to the terms and constraints invoked by each author's copyright. In most cases, these works may not be reposted without explicit permission of the copyright holder.