Diego di Bernardo

Publication Activity (10 Years)

Years Active: 2003-2020
Publications (10 Years): 10

Top Topics

High Throughput

Reverse Engineering

Regulatory Networks

Top Venues

PLoS Comput. Biol.

IEEE ACM Trans. Comput. Biol. Bioinform.

Publications

Francesco Napolitano, Diego Carrella, Xin Gao, Diego di Bernardo
gep2pep: a bioconductor package for the creation and analysis of pathway-based expression profiles. Bioinform. 36 (6) (2020)
Giansimone Perrino, Davide Fiore, Sara Napolitano, Mario di Bernardo, Diego di Bernardo
Towards feedback control of the cell-cycle across a population of yeast cells. ECC (2019)
Giansimone Perrino, Davide Fiore, Sara Napolitano, Francesca Galdi, Antonella La Regina, Mario di Bernardo, Diego di Bernardo
Feedback control promotes synchronisation of the cell-cycle across a population of yeast cells. CDC (2019)
Domenico Rea, Giansimone Perrino, Diego di Bernardo, Livia Marcellino, Diego Romano
A GPU algorithm for tracking yeast cells in phase-contrast microscopy images. Int. J. High Perform. Comput. Appl. 33 (4) (2019)
Mustafa H. Khammash, Mario di Bernardo, Diego di Bernardo
Cybergenetics: Theory and Methods for Genetic Control System. CDC (2019)
Francesco Napolitano, Diego Carrella, Barbara Mandriani, Sandra Pisonero-Vaquero, Francesco Sirci, Diego L. Medina, Nicola Brunetti-Pierri, Diego di Bernardo
gene2drug: a computational tool for pathway-based rational drug repositioning. Bioinform. 34 (9) (2018)
Giansimone Perrino, Diego di Bernardo
Modelling, simulation and control of single cell expression dynamics of the galactose-inducible promoter in yeast. CDC (2016)
Francesco Napolitano, Francesco Sirci, Diego Carrella, Diego di Bernardo
Drug-set enrichment analysis: a novel tool to investigate drug mode of action. Bioinform. 32 (2) (2016)
Roberto Pagliarini, Mara Sangiovanni, Adriano Peron, Diego di Bernardo
Combining flux balance analysis and model checking for metabolic network validation and analysis. Nat. Comput. 14 (3) (2015)
Gennaro Gambardella, Ivana Peluso, Sandro Montefusco, Mukesh Bansal, Diego L. Medina, Neil D. Lawrence, Diego di Bernardo
A reverse-engineering approach to dissect post-translational modulators of transcription factor's activity from transcriptional data. BMC Bioinform. 16 (2015)
Diego Carrella, Francesco Napolitano, Rossella Rispoli, Mario Miglietta, Annamaria Carissimo, Luisa Cutillo, Francesco Sirci, Francesco Gregoretti, Diego di Bernardo
Mantra 2.0: an online collaborative resource for drug mode of action and repurposing by network analysis. Bioinform. 30 (12) (2014)
Filippo Menolascina, Gianfranco Fiore, Emanuele Orabona, Luca De Stefano, Mike Ferry, Jeff Hasty, Mario di Bernardo, Diego di Bernardo
Real-Time Control of Protein Expression from Endogenous and Synthetic Gene Networks. PLoS Comput. Biol. 10 (5) (2014)
Roberto Pagliarini, Diego di Bernardo
A Genome-Scale Modeling Approach to Study Inborn Errors of Liver Metabolism: Toward an In Silico Patient. J. Comput. Biol. 20 (5) (2013)
Francesco Iorio, Julio Saez-Rodriguez, Diego di Bernardo
Network based elucidation of drug response: from modulators to targets. BMC Syst. Biol. 7 (2013)
Gennaro Gambardella, Maria Nicoletta Moretti, Rossella de Cegli, Luca Cardone, Adriano Peron, Diego di Bernardo
Differential network analysis for the identification of condition-specific pathway activity and regulation. Bioinform. 29 (14) (2013)
Marco Di Stefano, Angelo Rosa, Vincenzo Belcastro, Diego di Bernardo, Cristian Micheletti
Colocalization of Coregulated Genes: A Steered Molecular Dynamics Study of Human Chromosome 19. PLoS Comput. Biol. 9 (3) (2013)
Vincenzo Belcastro, Francesco Gregoretti, Velia Siciliano, Michele Santoro, Giovanni D'Angelo, Gennaro Oliva, Diego di Bernardo
Reverse Engineering and Analysis of Genome-Wide Gene Regulatory Networks from Gene Expression Profiles Using High-Performance Computing. IEEE ACM Trans. Comput. Biol. Bioinform. 9 (3) (2012)
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 Comput. Biol. 7 (6) (2011)
Giulia Cuccato, Athanasios Polynikis, Velia Siciliano, Mafalda Graziano, Mario di Bernardo, Diego di Bernardo
Modeling RNA interference in mammalian cells. BMC Syst. Biol. 5 (2011)
Filippo Menolascina, Mario di Bernardo, Diego di Bernardo
Analysis, design and implementation of a novel scheme for in-vivo control of synthetic gene regulatory networks. Autom. 47 (6) (2011)
Athanasios Polynikis, Giulia Cuccato, Stefania Criscuolo, Stephen John Hogan, Mario di Bernardo, Diego di Bernardo
Design and Construction of a Versatile Synthetic Network for Bistable Gene Expression in Mammalian Systems. J. Comput. Biol. 18 (2) (2011)
Darong Lai, Hongtao Lu, Mario Lauria, Diego di Bernardo, Christine Nardini
Mania: a Gene Network Reverse Algorithm for Compounds Mode-of-Action and genes Interactions Inference. Adv. Complex Syst. 13 (1) (2010)
Francesco Iorio, Loredana Murino, Diego di Bernardo, Giancarlo Raiconi, Roberto Tagliaferri
Gene ontology fuzzy-enrichment analysis to investigate drug mode-of-action. IJCNN (2010)
Filippo Menolascina, Mario di Bernardo, Diego di Bernardo
Design and implementation of a feedback control strategy for IRMA, a novel synthetic gene regulatory network. CDC (2010)
Francesco Iorio, Roberto Tagliaferri, Diego di Bernardo
Identifying Network of Drug Mode of Action by Gene Expression Profiling. J. Comput. Biol. 16 (2) (2009)
Darong Lai, Hongtao Lu, Mario Lauria, Diego di Bernardo, Christine Nardini
MANIA: A Gene Network Reverse Algorithm for Compounds Mode-of-Action and Genes Interactions Inference. Complex (1) (2009)
Francesco Iorio, Roberto Tagliaferri, Diego di Bernardo
Building Maps of Drugs Mode-of-Action from Gene Expression Data. CIBB (2008)
Vitoantonio Bevilacqua, Paolo Pannarale, Giuseppe Mastronardi, Amalia Azzariti, Stefania Tommasi, Filippo Menolascina, Francesco Iorio, Diego di Bernardo, Angelo Paradiso, Nicola A. Colabufo, Francesco Berardi, Roberto Perrone, Roberto Tagliaferri
High-Throughput Analysis of the Drug Mode of Action of PB28, MC18 and MC70, Three Cyclohexylpiperazine Derivative New Molecules. ICIC (2) (2008)
Carlo Cosentino, Walter Curatola, Mukesh Bansal, Diego di Bernardo, Francesco Amato
Piecewise affine approach to inferring cell cycle regulatory network in fission yeast. Biomed. Signal Process. Control. 2 (3) (2007)
Francesco Amato, Carlo Cosentino, Walter Curatola, Diego di Bernardo
LMI-based Algorithm for the Reconstruction of Biological Networks. ACC (2007)
Mukesh Bansal, Giusy Della Gatta, Diego di Bernardo
Inference of gene regulatory networks and compound mode of action from time course gene expression profiles. Bioinform. 22 (7) (2006)
Roberto Amato, Angelo Ciaramella, Natalia Deniskina, Carmine Del Mondo, Diego di Bernardo, Ciro Donalek, Giuseppe Longo, Giuseppe Mangano, Gennaro Miele, Giancarlo Raiconi, Antonino Staiano, Roberto Tagliaferri
A multi-step approach to time series analysis and gene expression clustering. Bioinform. 22 (5) (2006)
Roberto Amato, Angelo Ciaramella, Natalia Deniskina, Carmine Del Mondo, Diego di Bernardo, Ciro Donalek, Giuseppe Longo, Giuseppe Mangano, Gennaro Miele, Giancarlo Raiconi, Antonino Staiano, Roberto Tagliaferri
NEC for Gene Expression Analysis. WILF (2005)
Angelo Boccia, Mauro Petrillo, Diego di Bernardo, Alessandro Guffanti, Flavio Mignone, Stefano Confalonieri, Lucilla Luzi, Graziano Pesole, Giovanni Paolella, Andrea Ballabio, Sandro Banfi
DG-CST (Disease Gene Conserved Sequence Tags), a database of human-mouse conserved elements associated to disease genes. Nucleic Acids Res. 33 (Database-Issue) (2005)
Antonino Staiano, Roberto Tagliaferri, Lara De Vinco, Angelo Ciaramella, Giancarlo Raiconi, Giuseppe Longo, Gennaro Miele, Roberto Amato, Carmine Del Mondo, Ciro Donalek, Giuseppe Mangano, Diego di Bernardo
Mining Yeast Gene Microarray Data with Latent Variable Models. WIRN (2004)
Antonino Staiano, Lara De Vinco, Angelo Ciaramella, Giancarlo Raiconi, Roberto Tagliaferri, Roberto Amato, Giuseppe Longo, Ciro Donalek, Gennaro Miele, Diego di Bernardo
Probabilistic Principal Surfaces for Yeast Gene Microarray Data Mining. ICDM (2004)
Diego di Bernardo, Timothy S. Gardner, James J. Collins
Robust Identification of Large Genetic Networks. Pacific Symposium on Biocomputing (2004)
Diego di Bernardo, Thomas A. Down, Tim J. P. Hubbard
ddbRNA: detection of conserved secondary structures in multiple alignments. Bioinform. 19 (13) (2003)