icona publicationsPublications

Francesca Cordero's publications:



    2019

    Pernice S, Pennisi M, Romano G, Maglione A, Cutrupi S, Pappalardo F, Balbo G, Beccuti M, Cordero F, Calogero RA. A computational approach based on the Colored Petri Net formalism for studying Multiple Sclerosis BMC Bioinformatics 20(623)

    Tarallo S, Ferrero G, Gallo G, Francavilla A, Clerico G, Realis Luc A, Manghi P, Thomas AM, Vineis P, Segata N, Pardini B, Naccarati A, Cordero F. Altered Fecal Small RNA Profiles in Colorectal Cancer Reflect Gut Microbiome Composition in Stool Samples. mSystems ;4(5). doi: 10.1128/mSystems.00289-19.

    Alessandrì L, Cordero F, Beccuti M, Arigoni M, Olivero M, Romano G, Rabellino S, Licheri N, De Libero G, Pace L, Calogero RA. rCASC: reproducible classification analysis of single-cell sequencing data. GigaScience ;8(9).doi: 10.1093/gigascience/giz105.

    Thomas AM, Manghi P, Asnicar F, Pasolli E, Armanini F, Zolfo M, Beghini F, Manara S, Karcher N, Pozzi C, Gandini S, Serrano D, Tarallo S, Francavilla A, Gallo G, Trompetto M, Ferrero G, Mizutani S, Shiroma H, Shiba S, Shibata T, Yachida S, Yamada T, Wirbel J, Schrotz-King P, Ulrich CM, Brenner H, Arumugam M, Bork P, Zeller G, Cordero F, Dias-Neto E, Setubal JC, Tett A, Pardini B, Rescigno M, Waldron L, Naccarati A, Segata N. Metagenomic analysis of colorectal cancer datasets identifies cross-cohort microbial diagnostic signatures and a link with choline degradation. NATURE MEDICE ; 25(4):667-678. doi: 10.1038/s41591-019-0405-7. Epub 2019 Apr 1.

    Follia L, Ferrero G, Mandili G, Beccuti M, Giordano D, Spadi R, Satolli MA, Evangelista A, Katayama H, Hong W, Momin AA, Capello M, Hanash SM, Novelli F, Cordero F. Integrative Analysis of Novel Metabolic Subtypes in Pancreatic Cancer Fosters New Prognostic Biomarkers. FRONTIERS IN ONCOLOGY ;9:115. doi: 10.3389/fonc.2019.00115. eCollection 2019.

    Iannello A, Rolla S, Maglione A, Ferrero G, Bardina V, Inaudi I, De Mercanti S, Novelli F, D'Antuono L, Cardaropoli S, Todros T, Turrini MV, Cordioli C, Puorro G, Marsili A, Lanzillo R, Brescia Morra V, Cordero F, De Bortoli M, Durelli L, Visconti A, Cutrupi S, Clerico M. Pregnancy Epigenetic Signature in T Helper 17 and T Regulatory Cells in Multiple Sclerosis. FRONTIERS IN IMMUNOLOGY ; 9:3075. doi: 10.3389/fimmu.2018.03075. eCollection 2018.



    2018

    Kulkarni N, Alessandrì L, Panero R, Arigoni M, Olivero M, Ferrero G, Cordero F, Beccuti M, Calogero RA. Reproducible bioinformatics project: a community for reproducible bioinformatics analysis pipelines. BMC Bioinformatics ;19(Suppl 10):349. doi: 10.1186/s12859-018-2296-x.

    Ferrero G, Cordero F, Tarallo S, Arigoni M, Riccardo F, Gallo G, Ronco G, Allasia M, Kulkarni N, Matullo G, Vineis P, Calogero RA, Pardini B, Naccarati A. Small non-coding RNA profiling in human biofluids and surrogate tissues from healthy individuals: description of the diverse and most represented species. Oncotarget ;9(3):3097-3111. doi: 10.18632/oncotarget.23203. eCollection 2018 Jan 9.

    Beccuti M, Cordero F, Arigoni M, Panero R, Amparore EG, Donatelli S, Calogero RA. SeqBox: RNAseq/ChIPseq reproducible analysis on a consumer game computer. Bioinformatics ;34(5):871-872. doi: 10.1093/bioinformatics/btx674.

    Coscujuela Tarrero L, Ferrero G, Miano V, De Intinis C, Ricci L, Arigoni M, Riccardo F, Annaratone L, Castellano I, Calogero RA, Beccuti M, Cordero F, De Bortoli M. Luminal breast cancer-specific circular RNAs uncovered by a novel tool for data analysis. Oncotarget. 2018 Feb 19;9(18):14580-14596. doi: 10.18632/oncotarget.24522.

    Pardini B, Cordero F, Naccarati A, Viberti C, Birolo G, Oderda M, Di Gaetano C, Arigoni M, Martina F, Calogero RA, Sacerdote C, Gontero P, Vineis P, Matullo G. microRNA profiles in urine by next-generation sequencing can stratify bladder cancer subtypes. Oncotarget. 2018 Apr 17;9(29):20658-20669. doi: 10.18632/oncotarget.25057. eCollection 2018 Apr 17.

    Allione A, Pardini B, Viberti C, Giribaldi G, Turini S, Di Gaetano C, Guarrera S, Cordero F, Oderda M, Allasia M, Gontero P, Sacerdote C, Vineis P, Matullo G. MMP23B expression and protein levels in blood and urine are associated with bladder cancer. Carcinogenesis. 2018 Jul 20. doi: 10.1093/carcin/bgy098.



    2017

    Ferrero G, Cordero F, Tarallo S, Arigoni M, Riccardo F, Gallo G, Ronco G, Allasia M, Kulkarni N, Matullo G, Vineis P , Calogero R, Pardini B and Naccarati A Small non-coding RNA profiling in human biofluids and surrogate tissues from healthy individuals: description of the diverse and most represented species Oncotarget Dec 14;9(3):3097-3111

    Beccuti M, Genuardi E, Romano G, Monitillo L, Barbero D, Boccadoro M, Ladetto M, Calogero R, Ferrero S and Cordero F. HashClone: a new tool to quantify the minimal residual disease in B-cell lymphoma from deep sequencing data BMC Bioinformatics Nov 23;18(1):516.

    Beccuti M, Cordero F, Arigoni M, Panero R, Amparore EG, Donatelli S, Calogero RA. SeqBox: RNAseq/ChIPseq reproducible analysis on a consumer game computer. Bioinformatics 2017 Oct 23

    Ferrero G, Miano V, Beccuti M, Balbo G, De Bortoli M and Cordero F. Dissecting the genomic activity of a transcriptional regulator by the integrative analysis of omics data. Scientific Reports. 2017 Aug 17; 7(1)

    Martina F, Beccuti M, Balbo G, Cordero F A New Features Selection Method to Improve Classification Performances in Imbalanced Data Sets. PLoS ONE 2017 Aug 14; 12(8)

    Totis N, Follia L, Cordero F, Riganti C, Novelli F, Balbo G and Beccuti M. Overcoming the lack of kinetic information in biochemical reactions networks. ACM SIGMETRICS Performance Evaluation Review. Volume 44 Issue 4, March 2017, Pages 91-102. ACM New York, NY, USA



    2016

    Rosso MC, Badino P, Ferrero G, Costa R, Cordero F, Steidler S. Biologic Data of Cynomolgus Monkeys Maintained under Laboratory Conditions. PLoS ONE 2016 Jun 9; 11(6)

    Romano P, Cordero F. NETTAB 2014: From high-throughput structural bioinformatics to integrative systems biology. BMC Bioinformatics, 2016 Mar 2; 17 Suppl 4:62. Editorial

    Miano V, Ferrero G, Reineri S, Caizzi L, Annaratone L, Ricci L, Cutrupi S, Castellano I, Cordero F, De Bortoli M. Luminal long non-coding RNAs regulated by estrogen receptor alpha in a ligand-independent manner show functional roles in breast cancer. Oncotarget, 2016 Jan 19;7(3):3201-16.

    Miglio G, Sabatino AD, Veglia E, Giraudo MT, Beccuti M, Cordero F. A computational analysis of S-(2-succino)cysteine sites in proteins. Biochim Biophys Acta, 2016, Feb;1864(2):211-8.



    2015

    Munoz-Amatriain M., Lonardi S., Luo M., ..., Cordero F., et al. Sequencing of 15,622 gene-bearing BACs clarifies the gene-dense regions of the barley genome. The Plant Journal, 2015, doi: 10.1111/tpj.12959

    Cordero F, Ferrero G, Polidoro S, Fiorito G, Campanella G, Sacerdote C, Mattiello A, Masala G, Agnoli C, Frasca G, Panico S, Palli D, Krogh V, Tumino R, Vineis P, Naccarati A. Differentially methylated microRNAs in prediagnostic samples of subjects who developed breast cancer in the European Prospective Investigation into Nutrition and Cancer (EPIC-Italy) cohort. Carcinogenesis, 2015

    Fornari C., Balbo G., Halawani S.M., a-Rukab O., Ahmad A.R., Calogero R.A., Cordero F. and Beccuti M. A versatile mathematical work-flow to explore how Cancer Stem Cell fate influences tumor progression. BMC Systems Biology, 2015, 9(3:S1)

    Carrara M., Lum J., Cordero F., Beccuti M., Donatelli S., Calogero R.A. and Zolezzi F. Alternative splicing detection workflow needs a careful combination of sample prep and bioinformatics analysis. BMC Bioinformatics, 2015, 16(9:S2)

    Medico E., Russo M., Picco G., Cancelliere C., Valtorta E., Corti G., Buscarino M., Isella C., Lamba S., Martinoglio B., Veronese S., Siena S., Sarote-Bianchi A., Beccuti M., Mottolese M., Linnebacher M., Cordero F., Di Nicolantonio F. and Bardelli A. The molecular landscape of colorectal cancer cell lines unveils clinically actionable targets. Nature Communications, 2015, 6, Article number 7002



    2014

    Beccuti M, Carrara M, Cordero F, Lazzarato F, Donatelli S, Nadalin F, Policriti A, Calogero RA. Chimera: a Bioconductor package for secondary analysis of fusion products. Bioinformatics, 2014, 30(24) Pag: 3556-3557

    Fornari C, Beccuti M, Lanzardo S, Conti L, Balbo G, Cavallo F, Calogero RA, Cordero F A mathematical-biological joint effort to investigate the tumor-initiating ability of Cancer Stem Cells. PLoS One, 2014; 9(9):e106193

    Caizzi L, Ferrero G, Cutrupi S, Cordero F, Ballare C, Miano V, Reineri S, Ricci L, Friard O, Testori A, Cora D, Caselle M, Di Croce L and De Bortoli M. Genome-wide activity of unliganded Estrogen Receptor alfa in breast cancer cells. PNAS, 2014; 111(13) pag:4892-7

    Slyskova J, Cordero F, Pardini B, Korenkova V, Vymetalkova V, Ludovit Bielik L, Vodickova L, Pitule P, Matejka VM, Levy M, Buchler T, Kubista M, Naccarati A, Vodicka P. Post-treatment recovery of suboptimal DNA repair activity and gene expression levels in colorectal cancer patients, Molecular Carcinogenesis. doi: 10.1002/mc.22141, 2014

    Visconti A., Cordero F., Pensa R.G. Leveraging additional knowledge to support coherent bicluster discovery in gene expression data. Intelligent Data Analysis, Vol. 18(5) 2014

    Cutrupi S., Ferrero G., Reineri S., Cordero F., De Bortoli M. Genomic lens on neuroglobin transcription. IUBMB Life , 2014; 66(1) pag:46-51



    2013

    Beccuti M., Carrara M., Cordero F., Donatelli S., Calogero R.A.. The structure of state of art gene fusion-finder algorithms. Journal of of OA Bioinformatics , Volume 1(1), 2013.

    Lonardi S., Duma D., Alpert M., Cordero F., Beccuti M., Bhat P. R., Wu Y., Ciardo G., Alsaihati B., Y. Ma Y., Wanamaker S., Resnik J., Luo M., Close T. J. Combinatorial Pooling Enables Selective Sequencing of the Barley Gene Space. PLOS Computational Biology. . 2013 Apr;9(4)

    Carrara M., Beccuti M., Lazzarato F., Cordero F., Calogero R. A., Donatelli S. and Cavallo F. State of art fusion-finder algorithms sensitivity and specificity. BioMed Research International. 2013, February 2013

    Carrara M., Beccuti M., Cavallo F., Donatelli S., Lazzarato F., Cordero F., and Calogero R. A. State of art fusion-finder algorithms are suitable to detect Transcription-Induced Chimeras in normal tissues? BMC Bioinformatics.. 2013;14 Suppl 7:S2.

    Cordero F., Beccuti M., Fornari C., Lanzardo S., Conti L., Cavallo F., Balbo G. and Calogero RA. Multi-level model for the investigation of oncoantigen-driven vaccination effect. BMC Bioinformatics . 2013;14 Suppl 6:S11.



    2012

    Mayer KF, ..., Cordero F, Beccuti M, et al. A physical, genetic and functional sequence assembly of the barley genome Nature 491, 711:716, November 2012

    Marbach D., Costello J.C., Kuffner R., Vega N., Prill R.J., Camacho D., Allison K.R., the DREAM5 Consortium, Kellis M., Collins J.J., and Stolovitzky G., Wisdom of crowds for robust gene network inference Nature Methods vol. 9, p. 796-804, 2012, Francesca Cordero co-authored the paper as member of a consortium.

    Cordero F., Beccuti M, Donatelli S, Calogero RA. Large Disclosing the Nature of Computational Tools for the Analysis of Next Generation Sequencing Data. Current Topics in Medicinal Chemistry vol. 12, p. 1320-1330, 2012

    Cordero F, Beccuti M, Arigoni M, Donatelli S, Calogero RA Dissecting a massive parallel sequencing workflow for quantitative miRNA expression analysis PLoS ONE 2012; 7(2).



    2011

    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.

    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.



    From 2004 to 2010

    Pensa RG, Boulicaut J-F, Cordero F, Atzori M. Co-clustering Numerical Data under User-defined Constraints Statistical Analysis and Data Mining, 2010 Wiley-Blackwell. Vol. 3(1) 2010. pp 38-55. ISSN: 1932-1864.

    Della Beffa C, Cordero F, Calogero RA. Dissecting an alternative splicing analysis workflow for GeneChip Exon 1.0 ST Affymetrix arrays BMC Genomics, 2008 2008 Nov 28;9:571. ISSN: 1471-2164.

    Cordero F, Botta M, Calogero RA. Microarray data analysis and mining approaches Functional Genomics and Proteomics 2008 Dec;6(4):265-81.

    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.

    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 2077 Sep 17. ISSN: 1367-4803.

    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 Jul 26;6:200.

    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 Dic 1. ISSN: 1471-2105.

    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.

    Duma D., Cordero F., Beccuti M., Ciardo G., Close T.J. and Lonardi S. Scrible: Ultra-Accurate Error-Correction of Pooled Sequenced Reads. Proceedings of 15th Workshop on Algorithms in Bioinformatics (WABI'15), Spring LNCS, September 10-12, 2015, USA, Atlanta.
    (To be published)

    F. Cordero, C. Fornari, M. Gribaudo e D. Manini, Markovian Agents Population Models to study Cancer Evolution., in Proceedings of 21st International Conference on Analytical and Stochastic Modelling Techniques and Applications (ASMTA ’14), Budapest, Hungary. Springer Verlag Lecture Notes in Computer Science (LNCS) series., 2014.

    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'09) LNAI 5883 Springer pp 426-435. December 9-12, 2009, Reggio Emilia, Italy. ISSN: 0302-9743.

    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 (CMSB'09) LNBI 5688 Springer-Verlag, pp. 281-295, 2009 Bologna Italy. ISSN: 0302-9743.

    Alessio Naccarati, Daniela De Maria, Francesca Cordero, Barbara Pardini, Stavrula Gouzounis, Maddalena Arigoni, Raffaella Rizzolo, Laura De Marco, Anna Gillio-Tos, Paolo Vineis, Guglielmo Ronco. miRNA as markers of CIN risk and persistence for optimization of HPV-based cervical cancer screening In Proceedings of American Association for Cancer Research (AACR) 2016, New Orleans.

    Alessio Naccarati, Daniela De Maria, Francesca Cordero, Barbara Pardini, Stavrula Gouzounis, Maddalena Arigoni, Raffaella Rizzolo, Laura De Marco, Anna Gillio-Tos, Paolo Vineis, Guglielmo Ronco. miRNA as markers of CIN risk and persistence for optimization of HPV-based cervical cancer screening In Proceedings of Global Cancer: Occurrence, Causes and Avenues to Prevention (IARC50) 2016, Lyon.

    Barbara Pardini, Francesca Cordero, Alessandra Allione, Clara Viberti, Maddalena Arigoni, Raffaele Calogero, Marco Oderda, Paolo Gontero, Carlotta Sacerdote, Giuseppe Matullo. MicroRNA profiling by a Next Generation Sequencing approach in urine and plasma samples: from genomics to diagnostics and prognostics of bladder cancer. In Proceedings of XIX SIGU societa italiana genetica Umana , 2016 Torino

    Barbara Pardini Francesca Cordero, Alessandra Allione, Clara Viberti, Alessio Naccarati, Marco Oderda, Mirko Preto, Marco Allasia, Maddalena Arigoni, Federica Riccardo, Raffaele Calogero, Carlotta Sacerdote, Giuseppe Matullo. MicroRNA profiling by a Next Generation Sequencing approach in urine and plasma samples: from genomics to diagnostics and prognostics of bladder cancer. In Proceedings of American Association for Cancer research (AACR) Annual meeting 2016, New Orleans (USA)

    Barbara Pardini, Francesca Cordero, Alessandra Allione, Alessio Naccarati, Simonetta Guarrera, Giovanni Fiorito, Clara Viberti, Alessia Russo, Elisabetta Casalone, Rossana Critelli, Cornelia Di Gaetano, Maddalena Arigoni, Raffaele Calogero, Paolo Vineis, Carlotta Sacerdote6, Giuseppe Matullo A Next Generation Sequencing approach for microRNA profiling in plasma for bladder cancer characterization. In Proceedings of SIBBM, Società Italiana di Biofisica e Biologia Molecolare 2015, Torino

    Francesca Cordero, Marco Beccuti, Maddalena Arigoni and Raffaele A. Calogero Enhancing the detec,on of genomic rearrangements to better understand cancer pathology In Proceedings of RECOMB/ISCB Conference on Regulatory and Systems Genomics with DREAM Challenges 2015, Philadelphia (USA)

    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 ELSEVIER Electronic Notes in Theoretical Computer Science (ENTCS) 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

    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

    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, 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.

    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

    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.

    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.

    C. Fornari, M. Beccuti, S. Lanzardo, L. Conti, F. Cavallo, G. Balbo, R. Calogero e F. Cordero, A mathematical perspective on cancer stem cell dynamics. , In Roma, BITS Bioinformatics Italian Society Annual Meeting, 2014.

    C. Fornari, M. Beccuti, S. Lanzardo, L. Conti, G. Balbo, F. Cavallo, F. Cordero e R. Calogero, Cancer stem cell theory and tumor heterogeneity: a mathematical perspective , In Heidelberg, EMBO Conference Series From functional genomics to systems biology, 2014.

    G. Ferrero, L. Caizzi, V. Miano, G. Balbo, M. D. Bortoli, M. Beccuti e F. Cordero., Exploration of hormone-independent Estrogen Receptor activity by integrative and comparative approaches. , In Roma, BITS Bioinformatics Italian Society Annual Meeting, 2014.

    G. Ferrero, V. Miano, G. Balbo, M. D. Bortoli, M. Beccuti e F. Cordero, Integrative strategy for omics data: ER cistrome and epigenome case-study. , In Turin, NETTAB, From structural bioinformatics to integrative systems biology, 2014. G. Ferrero, V. Miano e F. Cordero, Integrative strategy to elucidate the multiple layers of the transcriptional regulation , In Heidelberg, EMBO Conference Series From functional genomics to systems biology, 2014.

    A. Naccarati, B. Pardini, S. Tarallo, G. Mancuso, F. Rosa, S. Landi, E. Barone, F. Cordero, S. Polidoro, P. Vineis, S. Ahern, P. Dowlings, L. Vodickova e P. Vodicka, MicroRNA and colorectal cancer: variations in miRNA binding site, genome-wide miRNA methylation, and the use of miRNAs as cancer biomarkers in different tissues. , In Oxford, 5th International Conference on Biomarkers and Clinical Research, scelto come oral presentation, 2014.

    B. Pardini, F. Cordero, A. Allione, S. Guarrera, G. Fiorito, F. Rosa, A. Russo, C. D. Gaetano, F. Modica, P. Vineis, C. Sacerdote e G. Matullo, A Next Generation Sequencing approach for plasma microRNA profiling in bladder cancer , In Oxford, 5th International Conference on Biomarkers and Clinical Research, scelto come oral presentation, 2014.

    C. Fornari, F. Cordero, M. Beccuti, R. Calogero e G. Balbo, How steady state analysis helps cancer therapies. , In Carmona, II workshop mathways into cancer, 2013.

    C. Fornari, F. Cordero, M. Beccuti, RA. Calogero e G. Balbo, Zoom-in and zoom-out on tumor progression. , In Udine, BITS Bioinformatics Italian Society Annual Meeting, 2013.

    F. Cordero, J. Slyskova, A. Naccarati, B. Pardini, V. Korenkova, M. Levy, P. Pitule, T. Buchler e P. Vodicka, Systems biology strategies to address DNA repair dynamics in colorectal cancer patients. , In Udine, BITS Bioinformatics Italian Society Annual Meeting, scelto come oral presentation, 2013.

    F. Cordero, C. Fornari, M. Beccuti, RA. Calogero e G. Balbo, The multi-level view to investigate the cancer progression. , In Carmona, II workshop mathways into cancer, 2013.

    G. Ferrero, V. Miano, M. Beccuti, G. Balbo, F. Cordero e M. D. Bortoli, Biological and technical variables on lncRNA quantification by RNA-Seq experiments. , In Trento, SIBBM Biophysic and Molecular Biology Society, 2013.

    J. Slyskova, A. Naccarati, B. Pardini, F. Cordero, Z. Smerhovsky, L. Vodickova, M. Levy, V. Liska e P. Vodicka, Involvement of DNA repair in the onset and treatment of sporadic colorectal cancer , In Porto, 10th International Comet Assay Workshop, scelto come oral presentation, 2013.

    C. Fornari, F. Cordero, M. Beccuti, S. Lanzardo, L. Conti, F. Cavallo, G. Balbo e R. Calogero, Multi-level model for the investigation of oncoantigen-driven vaccination effect. , In Barcelona, RECOMB, the 16th Annual International Conference on Research in Computational Molecular Biology, 2012.

    Cordero F., Gribaudo M., and Manini D. An analytical spatially-based approach to study cancer cell population evolutions in proceedings of the Ninth Annual Meeting of the Bioinformatics Italian Society (BITS), 2-4 May 2012, Catania, Italy; published in EMBnet.journal, Supplement A, April 2012, pag 24

    Visconti A., Raffaele R.A., Cordero F., Improving biomarker discovering for chemosensitivity prediction using an integrated approach in proceedings of the Ninth Annual Meeting of the Bioinformatics Italian Society (BITS)}, 2-4 May 2012, Catania, Italy; published in EMBnet.journal, Supplement A, April 2012, pag 24

    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