DISSEMINATION

Publications

Sales G, Coppe A, Bicciato S, Bortoluzzi S, Romualdi C. Impact of probe annotation on the integration of miRNA-mRNA expression profiles for miRNA target detection. Nucleic Acids Res. Nucleic Acids Res. 2010 Jan 13.
Biasiolo M, Forcato M, Possamai L, Ferrari F, Agnelli L, Lionetti M, Todoerti K, Neri A, Marchiori M, Bortoluzzi S, Bicciato S. Critical analysis of transcriptional and post-transcriptional regulatory networks in multiple myeloma. Blood. Pac Symp Biocomput. 2010:397-408
Lionetti M*, Biasiolo M*, Agnelli L, Todoerti K, Mosca L, Fabris S, Sales G, Lambertenghi Deliliers G, Bicciato S, Lombardi L, Bortoluzzi S, Neri A. (2009) Identification of microRNA expression patterns and definition of a microRNA/mRNA regulatory network in distinct molecular groups of multiple myeloma. Blood. Epub ahead of print. *Equally contributing first author.
Bisognin A, Coppe A, Ferrari F, Risso D, Romualdi C, Bicciato S and Bortoluzzi S. (2009) A-MADMAN: Annotation-based MicroArray Data Meta-ANalysis tool. BMC Bioinformatics. 10:201
Nie H, Neerincx PB, Poel J, Ferrari F, Bicciato S, Leunissen JA, Groenen MA. (2009) Microarray data mining using Bioconductor packages. BMC Proceedings. 3 Suppl 4:S9
Adorno M, Cordenonsi M, Montagner M, Dupont S, Wong C, Hann B, Solari A, Bobisse S, Rondina MB, Guzzardo V, Parenti AR, Rosato A, Bicciato S, Balmain A, Piccolo S. (2009) A Mutant-p53/Smad complex opposes p63 to empower TGFbeta-induced metastasis. Cell. 137(1):28
Romualdi C, Giuliani A, Millino C, Celegato B, Benigni R, Lanfranchi G. (2009) Correlation between gene expression and clinical data through linear and nonlinear principal components analyses: muscular dystrophies as case studies. OMICS. 13(3):173
Carraro L, Ferraresso S, Cardazzo B, Romualdi C, Montesissa C, Gottardo F, Patarnello T, Castagnaro M, Bargelloni L. (2009) Expression profiling of skeletal muscle in young bulls treated with steroidal growth promoters. Physiol Genomics. 38(2):138
Coppe A, Ferrari F, Bisognin A, Danieli GA, Ferrari S, Bicciato S and Bortoluzzi S. (2009) Motif discovery in promoters of genes co-localized and co-expressed during myeloid cells differentiation. NAR. 37(2):533
Chiogna M, Massa MS, Risso D, Romualdi C. (2009) A comparison on effects of normalizations in the detection of differentially expressed genes. BMC Bioinformatics 10:61
Risso D., Massa S, Chiogna M. and Romualdi C. (2009) A modified LOESS normalization applied to microRNA arrays: a comparative evaluation. Bioinformatics 25(20):2685
Bicciato S, Spinelli R, Zampieri M, Mangano E, Ferrari F, Beltrame L, Cifola I, Peano C, Battaglia C. (2009) A computational procedure to identify significant overlap of differentially expressed and genomic imbalanced regions in cancers datasets. Nucleic Acids Research 37(15):5057
Calura E, Cagnin S, Raffaello A, Laveder P., Lanfranchi G, Romualdi C. (2008) Meta-analysis of expression signatures of muscle atrophy: gene interaction networks in early and late stages. BMC Genomics 9:630.
Ferrari F, Bortoluzzi S, Coppe A, Sirota A, Safran M, Shmoish M, Ferrari S, Lancet D, Danieli GA and Bicciato S. (2007) Novel definition files for human GeneChips based on GeneAnnot. BMC BIOINFORMATICS. 8:446.

Presentation to Congresses

Bortoluzzi S. From integration of miRNAs and genes expression profiles to reconstruction and analysis of regulatory networks. MACS Symposia 2009, MicroRNAs in physiology and disease, Bologna, Italy, December 1, 2009.
Sales G, Biasiolo M, Bicciato S, Bortoluzzi S, Romualdi C. A systematic analysis of alternative 3' UTR of human transcripts: improvment of detection of microRNA targets. MACS Symposia 2009, MicroRNAs in physiology and disease, Bologna, Italy, December 1, 2009.
Biasiolo M, Forcato M, Possamai L, Ferrari F, Agnelli L, Lionetti M, Todoerti K, Neri A, Marchiori M, Bortoluzzi S, Bicciato S. Critical analysis of transcriptional and post-transcriptional regulatory networks in multiple myeloma. Pacific Symposium on Biocomputing, Big Island of Hawaii, HI, USA, January 4-8, 2010.
Forcato M, Possamai L, Ferrari F, Agnelli L, Neri A, Marchiori M, Bicciato S. Critical component Analysis of transcriptional regulatory networks. EMBO Practical Course on Networks in Biology analysis, modeling and reverse engineering, Bologna, Italy, September 22-25, 2009.
Forcato M, Possamai L, Ferrari F, Agnelli L, Todoerti K, Lambertenghi Deliliers G, Bortoluzzi S, Marchiori M, Neri A, Bicciato S. Reverse engineering and critical analysis of gene regulatory networks in multiple myeloma. Machine learning in integrative genomics (MLIG'09) special session, 4th IAPR International Conference in Pattern Recognition or Bioinformatics (PRIB 2009), City Hall, Sheffield, United Kingdom September 7-9, 2009.
Ferrari F, Bortoluzzi S, Bicciato S. A computational biology frameworkfor the integrative analysis of functional genomics data in relation to chromosomal positions. EMBO conference series on “Nuclear structure & dynamics”, Isle sur la Sorgue, France, 30 September - 4 October 2009.
Ferrari F, Coppe A, Spinelli R, Battaglia C, Bortoluzzi S, Bicciato S. PREDA: Position RElated Data Analysis tool for functional genomics applications. BioC2009 conference and Bioconductor developers meeting, Seattle, WA, USA, July 27-29, 2009.
Sales G, Biasiolo M, Bicciato S, Bortoluzzi S, Romualdi C. A systematic analysis of alternative 3' UTR of human transcripts: improvment of detection of microRNA targets. 17th annual meeting of the International Society for Computational Biology (ISCB) and the 8th annual meeting of the European Conference on Computational Biology (ECCB), June 27 - July 2, 2009, Stockholm, Sweden.
Risso D, Massa MS, Romualdi C. A modified LOESS normalization applied to miRNA arrays: a comparative evaluation. 17th annual meeting of the International Society for Computational Biology (ISCB) and the 8th annual meeting of the European Conference on Computational Biology (ECCB), June 27 - July 2, 2009, Stockholm, Sweden.
Biasiolo M, Forcato M, Sales G, Coppe A, Bortoluzzi S, Bicciato S. Integrated Analysis of microRNA and Gene Expression Data to Reconstruct Regulatory Networks. BITS '09 Sixth Annual Meeting of the Bioinformatics Italian Society, March 18-20, 2009, Genoa, Italy.
Bisognin A, Coppe A, Ferrari F, Davide R, Bicciato S, Bortoluzzi S. A-MADMAN: Annotation-based MicroArray Data Meta-ANalysis tool. BITS '09 Sixth Annual Meeting of the Bioinformatics Italian Society, March 18-20, 2009, Genoa, Italy.
Sales G, Biasiolo M, Romualdi C. A systematic analysis of alternative 3' UTR of human transcripts: improvment of detection of microRNA targets. BITS '09 Sixth Annual Meeting of the Bioinformatics Italian Society, March 18-20, 2009, Genoa, Italy.
Risso D, Bisognin A, Romualdi C. Integration methods for microarray data. BITS '09 Sixth Annual Meeting of the Bioinformatics Italian Society, March 18-20, 2009, Genoa, Italy.
Coppe A, Ferrari F, Bisognin A, Bicciato S, Ferrari S, Danieli GA, Bortoluzzi S. Motif discovery in promoters of genes co-expressed and co-localized in myelopoiesis, by a novel computational frame work. FEBS-SysBio2009: The 3rd FEBS Advanced Lecture Course on Systems Biology: From Molecular Biology to Biological Function, Alpbach, Austria, March 7-13, 2009.
Biasiolo M, Forcato M, Coppe A, Bisognin A, Bicciato S, Bortoluzzi S. Integrated analysis of miRNA and genes expression data. FEBS-SysBio2009: The 3rd FEBS Advanced Lecture Course on Systems Biology: From Molecular Biology to Biological Function, Alpbach, Austria, March 7-13, 2009.
Solari A, Bicciato S. Pairwise Comparisons for Gene Expression Array Data. XLIV Riunione Scientifica della Società Italiana di Statistica, 24-27 June, Università della Calabria, Campus dio Arcavacata.
Coppe A, Ferrari F, Bisognin A, Bicciato S, Ferrari S, Danieli GA, Bortoluzzi S. A computational framework for the integrated study of the role of promoters similarity and gene clustering in specific regions of the human genome in establishing co-expression of genes: an application to myeloid cells differentiation. I Congresso Nazionale Di Bioingegneria, 3-6 July 2008, Pisa.
Ferrari F, Spinelli R, Mangano E, Beltrame L, Zampieri M, Cifola I, Peano C, Bicciato S, Battaglia C. A computational procedure to identify significant overlap of differentially expressed and genomic imbalanced regions in cancer datasets. I Congresso Nazionale Di Bioingegneria, 3-6 July 2008, Pisa.
Forcato M, Freitas AT, Di Camillo B. Classification of arabidopsis mirna promoter regions using support vector machine. I Congresso Nazionale Di Bioingegneria, 3-6 July 2008, Pisa.
Bicciato S, Spinelli R, Mangano E, Ferrari F, Beltrame L, Zampieri M, Cifola I, Peano C, Battaglia C. A computational procedure to identify significant overlap of differentially expressed and genomic imbalanced regions in cancer datasets. 11th International Meeting of MGED, 1-4 September 2008, Riva del Garda [Selected oral communication].
Coppe A, Ferrari F, Bisognin A, Bicciato S, Ferrari S, Danieli GA, Bortoluzzi S. Motif discovery in promoters of genes co-expressed and co-localized in myelopoiesis by a novel computational frame work. 11th International Meeting of MGED, 1-4 September 2008, Riva del Garda [Selected oral communication].
Coppe A, Ferrari F, Bisognin A, Bicciato S, Ferrari S, Danieli GA, Bortoluzzi S. The role of promoter similarity and gene clustering in establishing co-expression networks in myeloid cells. European Conference on Computational Biology, 22-26 September 2008, Cagliari.
Ferrari F, Spinelli R, Mangano E, Beltrame L, Zampieri M, Cifola I, Peano C, Bicciato S, Battaglia C. A computational procedure to identify significant overlap of differentially expressed and genomic imbalanced regions in cancer datasets. European Conference on Computational Biology, 22-26 September 2008, Cagliari [Embrace congress fellowship assigned to F. Ferrari].
Calura E, Cagnin S, Raffaello A, Lanfranchi G, Romualdi C. Meta-analysis of expression signatures of muscle atrophy: gene interaction networks in early and late stages. European Conference on Computational Biology, 22-26 September 2008, Cagliari.
Risso D, Chiogna M, Massa MS, Romualdi C. A comparison on effects of normalizations in the detection of differentially expressed genes. European Conference on Computational Biology, 22-26 September 2008, Cagliari.

Seminaries

Prof. Rimantas Eidukevicius, University of Vilnius (Lituania), five seminaries on “Graph theory, networks and complex networks in genomics and proteomics”, at the Biology Department, Univ. of Padova.