Davide Cora' Institute for Cancer Research and Treatment (IRCC), Department of Oncology, University of Torino Str. Prov. 142 Km. 3.95, I-10060 Candiolo, Torino, Italy Tel. +39 - 011 - 9933241 E-mail: davide.cora[_AT_]ircc.it Office: "-"

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• After a Post-doc at the Department of Theoretical Physics, I moved ... Next stop is the IRCC , Systems Biology Lab (a.k.a. Physical Biology of the Cancer Cell Lab), where I'm currently Research Associate.

  
  

  I'm Adjunct Lecturer of Bioinformatics at the University of Turin.

  I'm member of the Center for Complex Systems in Molecular Biology and Medicine of the University of Turin.

  I obtained my Ph.D degree in the Ph.D Programme in complexity in post-genomic biology .    

  
  

Research ...

My work is mainly related to Systems Biology and Bioinformatics. I'm interested in the application of methods from Computer Science and Physics to understand Biology and Genomics.

• In particular, my current research interests are:

  • Cancer and Plants genomics;

  • Gene regulation, microRNAs, regulatory networks;

  • Software development for Next Generation Sequencing applications;

  • Genomes evolution;

  • Statistical properties of genomes;

Bookmarks ...

• A step back in my old physics ... the CERN home page. LHC is now starting ! First Beam was on 10 September 2008.

  ... and now ... a Biology fan ... http://abstrusegoose.com/156

• Computational Biology Group FB11 / TO61 Torino home page.
  
        Link to the FB11 / TO61 papers Supplementary Info.
  

• BITS Societa' Italiana di Bioinformatica.

Photos ...

• My Yahoo Photo Album

• I have a lot of nice photos of mountains, taken around Valle d'Aosta. If you are interested, send an email to me and I will give you whatever you like.

Teaching ...

• Master in Bioinformatica

• Laboratorio Biomolecolare (modulo Bioinformatica) link diretto al materiale delle lezioni.

• Ensembl Advanced Course - TORINO 2006

• R course

• Statbio

Publications ...

• "Computational identification of transcription factor binding sites by functional analysis of set of genes sharing
    overrepresented uptream motifs"

                 Cora' D., Di Cunto F., Provero P., Silengo L., Caselle M.
                  BMC Bioinformatics. 2004 May 11;5(1):57.

• "Ab initio identification of putative human transcription factor binding sites by comparative genomics"

                  Cora' D.,  Herrmann C., Dieterich C., Di Cunto F., Provero P., Caselle M.
                  BMC Bioinformatics. 2005 May 2;6(1):110.

                 Supplemetary material available at: http://www.to.infn.it/ftbio/tf_human/supplementary.html
                                                                              or FB11 / TO61 papers Supplementary Info.

• "Multifactorial regulation in yeast: looking for correlated binding sequences"

                  I. Pesando, M. Caselle, D. Cora'
                  Proceedings of the ECCB 2004 Conference.

• " Identifying Networks of Estrogen-Responsive Genes in Breast Cancer Cells"

                  G. Altobelli, D. Cora', F. Cordero, M. Caselle, M. De Bortoli
                  The 3rd EMBL Biennial Symposium: From Functional Genomics to Systems Biology EMBL 2006.

• "Correlated fragile site expression allows the identification of candidate fragile genes involved in immunity and associated with carcinogenesis"

                  Re A., Cora' D., Puliti AM., Caselle M., Sbrana I.

                  BMC Bioinformatics. 2006 Sep 18;7(1):413

• "Identification of candidate regulatory sequences in mammalian 3' UTRs by statistical analysis of oligonucleotide frequencies."

                  Cora' D.,  Di Cunto F., Caselle M., Provero P.
                  BMC Bioinformatics. 2007, 8:174.

                 Supplemetary material available at: http://www.to.infn.it/ftbio/mirna_human/supplementary.html
                                                                              or FB11 / TO61 papers Supplementary Info.

• "VRG database: a database of Vascular dysfunctions Related Genes."

                  Zanivan S., Cora' D., Caselle M., Bussolino F.
                  Computers and Mathematics with Applications, 2008, 55(5) ,

                 Supplemetary material available at: http://www.to.infn.it/ftbio/VRG-database/main.html
                                                                              or FB11 / TO61 papers Supplementary Info.

• "Genome-wide survey of microRNA-transcription factor feed-forward regulatory circuits in human."

                  Re A., Cora' D. Taverna D., Caselle M.
                  Mol Biosyst. 2009 Aug;5(8):854-67.

                 Supplemetary material available at: http://personalpages.to.infn.it/~cora/circuits/index.html/
                                                                              or FB11 / TO61 papers Supplementary Info.

• "Molecular models for intrastrand DNA G-quadruplexes."

                 Fogolari F, Haridas H, Corazza A, Viglino P, Cora' D, Caselle M, Esposito G, Xodo LE.
                  BMC Structural Biology 2009, 9:64.

• "Nucleation dynamics in two-dimensional cylindrical Ising models and chemotaxis."

                 Bosia C., Caselle M. and Cora' D.
                  Phys. Rev. E 81, 021907 (2010).

• "Identification of functional TFAP2A and SP1 binding sites in new TFAP2A-modulated genes."

                 Orso F, Cora' D, Ubezio B, Provero P, Caselle M, Taverna D.
                  BMC Genomics 2010, 11:35.

• "CircuitsDB: a database of mixed microRNA / transcription factor feed-forward regulatory circuits in human and mouse."

                 Olivier Friard, Angela Re, Daniela Taverna, Michele De Bortoli and Davide Cora'.
                  BMC Bioinformatics 2010, 11:435.

                 CircuitsDB Web-site available at: biocluster.di.unito.it/circuits
                                                         

• "Identity and divergence of protein domain architectures after the yeast whole-genome duplication event."

                  Grassi L, Fusco D, Sellerio A, Cora' D, Bassetti B, Caselle M, Lagomarsino MC.
                  Mol Biosyst. 2010, Nov 1;6(11):2305-15.

                

• "A Curated Database of miRNA Mediated Feed-Forward Loops Involving MYC as Master Regulator."

                  Mariama El Baroudi, Davide Cora', Carla Bosia, Matteo Osella, Michele Caselle.
                  PLoS ONE 2011, 6(3): e14742.

                

• "The Role of Incoherent MicroRNA-Mediated Feedforward Loops in Noise Buffering."

                  Matteo Osella, Carla Bosia, Davide Cora' Michele Caselle.
                  PLoS Comput Biol 2011, 7(3): e1001101.

                

• "Genetic and expression analysis of MET, MACC1 and HGF in metastatic colorectal cancer: Response to Met inhibition in patient xenografts and pathological correlations."

                  Galimi F, Torti D, Sassi F, Isella C, Cora' D, Gastaldi S, Ribero D, Muratore A, Massucco P, Siatis D, Paraluppi G, Gonella F, Maione F, Pisacane A, David E, Torchio B, Risio M, Salizzoni M, Capussotti L, Perera T, Medico E, Di Renzo MF, Comoglio PM, Trusolino L, Bertotti A.
                  Clin Cancer Res. 2011 Mar 29.

                

• "Mulcom: a multiple comparison statistical test for microarray data in Bioconductor."

                  Claudio Isella, Tommaso Renzulli, Davide Cora' and Enzo Medico
                  BMC Bioinformatics 2011, 12:382.

                

• "A molecularly annotated platform of patient-derived xenografts ('xenopatients') identifies HER2 as an effective therapeutic target in cetuximab-resistant colorectal cancer."

                  Andrea Bertotti, Giorgia Migliardi, Francesco Galimi, Francesco Sassi, Davide Torti, Claudio Isella, Davide Cora', Federica Di Nicolantonio, Michela Buscarino, Consalvo Petti, Dario Ribero, Nadia Russolillo, Andrea Muratore, Paolo Massucco, Alberto Pisacane, Luca Molinaro, Emanuele Valtorta, Andrea Sartore-Bianchi, Mauro Risio, Lorenzo Capussotti, Marcello Gambacorta, Salvatore Siena, Enzo Medico, Anna Sapino, Silvia Marsoni, Paolo M. Comoglio, Alberto Bardelli and Livio Trusolino
                  Cancer Discovery September 2, 2011 CD-11-0109; Published OnlineFirst September 2, 2011; doi:10.1158/2159-8290.CD-11-0109

                

• "Transcriptional hallmarks of noonan syndrome and noonan-like syndrome with loose anagen hair."

                  Ferrero GB, Picco G, Baldassarre G, Flex E, Isella C, Cantarella D, Cora D, Chiesa N, Crescenzio N, Timeus F, Merla G, Mazzanti L, Zampino G, Rossi C, Silengo M, Tartaglia M, Medico E.
                  Hum Mutat. 2012 Jan 17. doi: 10.1002/humu.22026

                

• "Dynamic Modeling of miRNA-mediated Feed-Forward Loops."

                  Eduati F, di Camillo B, Karbiener M, Scheideler M, Corà D, Caselle M, Toffolo G.
                  J Comput Biol. 2012 Feb;19(2):188-99.

                

• "The role of transposable elements in shaping the combinatorial interaction of transcription factors."

                  Testori A, Caizzi L, Cutrupi S, Friard O, De Bortoli M, Cora' D and Caselle M.
                  BMC Genomics. 2012 Aug 16;13(1):400.

                

• "Gene autoregulation via intronic microRNAs and its functions."

                  Bosia C, Osella M, El Baroudi M, Cora D, Caselle M.
                  BMC Syst Biol. 2012 Oct 10;6(1):131.

                

• "IRF-1 expression is induced by cisplatin in ovarian cancer cells and limits drug effectiveness."

                  Pavan S, Olivero M, Cora D, Di Renzo MF.
                  Eur J Cancer. 2012 Oct 15. pii: S0959-8049(12)00749-6. doi: 10.1016/j.ejca.2012.09.024.

                

• "Molecular and morphologic characterization of superficial- and deep-subcutaneous adipose tissue subdivisions in human obesity."

                  Cancello R, Zulian A, Gentilini D, Maestrini S, Barba AD, Invitti C, Cora' D, Caselle M, Liuzzi A, Di Blasio AM.
                  Obesity (Silver Spring). 2013 Mar 20. doi: 10.1002/oby.20417

                

Some other posters and presentations (last updated December 2008) ...

• Poster yeast at ECCB 2004

• Poster CORG at ECCB 2004

• Poster yeast at Biocomp 2003

• Ph.D  assessment  December 2003

• Ph.D  assessment  June 2004

• Talk at  Milano-Bicocca  September 2004

• Talk at  ECMTB 2005  July 2005

• Poster miRNA at Recomb 2006

• Talk at  BITS 2007  April 2007

• Talk at  ISMB/ECCB 2007  July 2007

• Poster Regulatory Circuits at ICG 2008 and ECCB 2008

• Talk at  BITS 2009  March 2009

• Poster mixed miRNA / TF Feed-Forward Regulatory Circuits at Recomb 2008 - MIT Boston (USA)