Peer Reviewed Journals

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Peer reviewed publications

2010:

  • Iorio F, Bosotti R, Scacheri E, Belcastro V, Mithbaokar P, Ferriero R, Murino L, Tagliaferri R, Brunetti-Pierri N, Isacchi A, di Bernardo D. Discovery of drug mode of action and drug repositioning from transcriptional responses. Proc Natl Acad Sci U S A 2010 Aug 17;107(33):14621-6. Epub 2010 Aug 2. Abstract PDF


  • Marucci L, Santini S, di Bernardo M, di Bernardo D. Derivation, identification and validation of a computational model of a novel synthetic regulatory network in yeast. J Math Biol 2010 Abstract PDF.


  • Gregoretti F, Belcastro V, di Bernardo D, Oliva G. A parallel implementation of the network identification by multiple regression (NIR) algorithm to reverse-engineer regulatory gene networks. PLoS One, 2010 [1]


2009:

  • Lucia Marucci, David A. W. Barton, Irene Cantone, Maria Aurelia Ricci, Maria Pia Cosma, Stefania Santini, Diego di Bernardo*, Mario di Bernardo* *Corresponding authors. How to Turn a Genetic Circuit into a Synthetic Tunable Oscillator, or a Bistable Switch. PLoS One, 2009. Full Paper


  • Cantone I, Marucci L, Iorio F, Ricci M, Belcastro V, Bansal M, Santini S, di Bernardo M, di Bernardo D*, Cosma MP*. A Yeast Synthetic Network for In Vivo Assessment of Reverse-Engineering and Modeling Approaches . Cell, Volume 137, Issue 1, 172-181, 26 March 2009 . *Corresponding authorsAsbtract PDF Data in XLS format Supplementary Material [News and Views [2]


  • Mario Lauria*, Francesco Iorio*, Diego di Bernardo NIRest: A Tool for Gene Network and Mode of Action Inference.Annals of the New York Academy of Sciences, (p 257-264), 2009. PDF. *These authors contributed equally to this work.


  • Cuccato G, Della Gatta G, di Bernardo D. Systems and Synthetic biology: tackling genetic networks and complex diseases (Review). Heredity, 2009 AbstractPDF


  • Identifying Network of Drug Mode of Action by Gene Expression Profiling Francesco Iorio, Roberto Tagliaferri and Diego di Bernardo. Journal of Computational Biology, 2009; Feb;16(2):241-51. abstract PDF

2008:

  • Direct targets of the Trp63 transcription factor revealed by a combination of gene expression profiling and reverse engineering. Giusy Della Gatta*, Mukesh Bansal*, Alberto Ambesi-Impiombato, Dario Antonini, Caterina Missero, Diego di Bernardo. Genome Research, 2008 Jun;18(6):939-48. Epub 2008 Apr 25. * These authors contributed equally to this work. abstract PDF.


2007:

  • [3] Inference of gene networks from temporal gene expression profiles. Mukesh Bansal, Diego di Bernardo. IET Systems Biology, 5: 306-312 PDF



2006:


  • Computational framework for the prediction of transcription factor binding sites by multiple data integration. Ambesi-Impiombato A, Bansal M, Lio P, di Bernardo D. BMC Neurosci., 2006 Oct 30;7 Suppl 1:S8 Full Text PDF


  • Inference of gene regulatory networks and compound mode of action from time course gene expression profiles. M. Bansal, G. Della Gatta, D. di Bernardo. Bioinformatics, 2006 abstract Supplemental Info PDF


  • Computational Biology and Drug Discovery: From Single-Target to Network Drugs. A. Ambesi-Impiombato, D. di Bernardo. Current Bioinformatics, 2006 PDF abstract


  • A multi-step approach to time series analysis and gene expression clustering . Amato R., Ciaramella A., Deniskina N., Del Mondo C., di Bernardo D., Donalek C., Longo G., Mangano G., Miele G., Raiconi G., Staiano A., Tagliaferri R. Bioinformatics 2006 Mar 1;22(5):589-96. Epub 2006 Jan 5 abstract


2005:


  • The Transcriptional Landscape of the Mammalian Genome (COLLABORATIVE PROJECT) Fantom Consortium (from our lab: A Ambesi, M Bansal, G Della Gatta,D di Bernardo). Science; 309, 1559-1563, 2005. abstract


  • Chemogenomic profiling on a genome-wide scale using reverse-engineered gene networks Diego di Bernardo*, Michael J Thompson*, Timothy S Gardner*, Sarah E Chobot, Erin L Eastwood, Andrew P Wojtovich, Sean J Elliott, Scott E Schaus, James J Collins. Nature Biotechnology; 23,377 - 383, 2005. * These authors contributed equally to this work. abstract PDF


  • DG-CST (Disease Gene Conserved Sequence Tags), a database of human-mouse conserved elements associated to disease genes.Boccia A, Petrillo M, di Bernardo D, Guffanti A, Mignone F, Confalonieri S, Luzi L, Pesole G, Paolella G, Ballabio A, Banfi S. Nucleic Acids Research. Database issue, 2005. abtract



2004:

Robust identification of large genetic networks.
Di Bernardo D, Gardner TS, Collins JJ. Pac Symp Biocomput; 486-497, 2004.abstract PDF


2003:

Inferring genetic networks and identifying compound mode of action via expression profiling. Gardner TS*, di Bernardo D*, Lorenz D, Collins JJ. Science; 301:102-105,2003. * These authors contributed equally to this work. abstract PDF Supplementary Material - PDF

ddbRNA: Detection of conserved secondary structures in multiple alignments.di Bernardo D, Down T, Hubbard T. Bioinformatics, 19:1606-1611, 2003 abstract PDF

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