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    di Bernardo Lab - Systems and Synthetic Biology Lab
    You are here: Home Publications Peer Reviewed Journals

    Peer Reviewed Journals

    Selected Peer reviewed publications (for a full list please use PubMed)










            • De Cegli R, Iacobacci S, Flore G, Gambardella G, Mao L, Cutillo L, Lauria M, Klose J, Illingworth E, Banfi S and di Bernardo D. Reverse engineering a mouse embryonic stem cell-specific transcriptional network reveals a new modulator of neuronal differentiation. Nucleic Acids Research Abstract and Full text
            • Menolascina F, Siciliano V, di Bernardo D. Engineering and control of biological systems: A new way to tackle complex diseases FEBS Letters. 586(15):2122-8. Review.Abstract and Full text
            • di Bernardo D, Marucci L, Menolascina F, Siciliano V. Predicting synthetic gene networks. Methods Mol Biol. 2012;813:57-81. Review. Abstract



            • Vincenzo Belcastro, Velia Siciliano, Francesco Gregoretti, Pratibha Mithbaokar, Gopuraja Dharmalingam, Stefania Berlingieri, Francesco Iorio, Gennaro Oliva, Roman Polishchuck, Nicola Brunetti-Pierri and Diego di Bernardo. Transcriptional gene network inference from a massive dataset elucidates transcriptome organization and gene function. Nucleic Acids Research 2011 Full Text - PDF.
            • Velia Siciliano, Filippo Menolascina*, Lucia Marucci*, Chiara Fracassi, Immacolata Garzilli, Maria Nicoletta Moretti, Diego di Bernardo. Construction and modelling of an inducible positive feedback loop stably integrated in a mammalian cell-line. PLoS Computational Biology, 2011. *These authors contributed equally. PDF - Full Text
            • Menolascina F, di Bernardo M, di Bernardo D. Analysis, design and implementation of a novel scheme for in-vivo control of synthetic gene regulatory network. Automatica 47 1265-1270, 2011. Abstract - PDF
            • Belcastro V*, Gregoretti F*, Siciliano V, Santoro M, D’Angelo G, Oliva G+ and di Bernardo D+ Reverse-engineering and analysis of genome-wide gene regulatory networks from gene expression profiles using high-performance computing. IEEE Trans. in Computational Biology and Bioinformatics. 2011, in press. *Equal contributors; +corresponding authors abstract
            • Cuccato G, Polynikis A, Siciliano V, Graziano M, di Bernardo M, di Bernardo D. Modeling RNA interference in mammalian cells. BMC Syst Biol. 2011 Jan 27;5(1):19. PDF - Abstract
            • Polynikis A, Cuccato G, Criscuolo S, Hogan SJ, di Bernardo M, di Bernardo D. Design and construction of a versatile synthetic network for bistable gene expression in Mammalian systems. J Comput Biol. 2011 Feb;18(2):195-203. abstract



            • 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
            • Iorio F, Isacchi A, di Bernardo D, Brunetti-Pierri N. Identification of small molecules enhancing autophagic function from drug network analysis. Autophagy 2010 Nov 16;6(8):1204-5. Epub 2010 Nov 16. PMID: 20930556 [News & Views]
            • Cacciottolo M, Belcastro V, Laval S, Bushby K, Di Bernardo D, Nigro V. Reverse-engineering gene network identifies new dysferlin interacting proteins. J Biol Chem. 2010 Nov 30. 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 [Link]



            • 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 authors Asbtract - PDF - Data in XLS format - Supplementary Material [News and Views]
            • 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 Abstract - PDF
            • Francesco Iorio, Roberto Tagliaferri and Diego di Bernardo. Identifying Network of Drug Mode of Action by Gene Expression Profiling. Journal of Computational Biology, 2009; Feb;16(2):241-51. Abstract - PDF




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







            • Ambesi-Impiombato A, Bansal M, Lio P, di Bernardo D. Computational framework for the prediction of transcription factor binding sites by multiple data integration. BMC Neurosci., 2006 Oct 30;7 Suppl 1:S8 Full Text - PDF
            • M. Bansal, G. Della Gatta, D. di Bernardo. Inference of gene regulatory networks and compound mode of action from time course gene expression profiles. Bioinformatics, 2006 abstract - Supplemental Info - PDF
            • A. Ambesi-Impiombato, D. di Bernardo. Computational Biology and Drug Discovery: From Single-Target to Network Drugs. Current Bioinformatics, 2006 PDF - Abstract




            • 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
            • 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. Chemogenomic profiling on a genome-wide scale using reverse-engineered gene networks. Nature Biotechnology; 23,377 - 383, 2005. * These authors contributed equally to this work. abstract - PDF



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




            • Gardner TS*, di Bernardo D*, Lorenz D, Collins JJ. . Inferring genetic networks and identifying compound mode of action via expression profiling. Science; 301:102-105,2003. * These authors contributed equally to this work. abstract - PDF - Supplementary Material - PDF
            • di Bernardo D, Down T, Hubbard T. ddbRNA: Detection of conserved secondary structures in multiple alignments. Bioinformatics, 19:1606-1611, 2003 abstractPDF