Diego di Bernardo

According to our database, Diego di Bernardo authored at least 39 papers between 2003 and 2021.

Collaborative distances:

• Dijkstra number of four.
• Erdős number of four.

2021

Automatic synchronisation of the cell cycle in budding yeast through closed-loop feedback control.

Giansimone Perrino, Sara Napolitano, Francesca Galdi, Antonella La Regina, Davide Fiore, Teresa Giuliano, Mario di Bernardo, Diego di Bernardo

Dataset, March, 2021

2020

Cyber-yeast: Automatic synchronisation of the cell cycle in budding yeast through closed-loop feedback control.

Giansimone Perrino, Sara Napolitano, Francesca Galdi, Antonella La Regina, Davide Fiore, Teresa Giuliano, Mario di Bernardo, Diego di Bernardo

Dataset, November, 2020

gep2pep: a bioconductor package for the creation and analysis of pathway-based expression profiles.

Francesco Napolitano, Diego Carrella, Xin Gao, Diego di Bernardo

Bioinform., 2020

2019

A GPU algorithm for tracking yeast cells in phase-contrast microscopy images.

Domenico Rea, Giansimone Perrino, Diego di Bernardo, Livia Marcellino, Diego Romano

Int. J. High Perform. Comput. Appl., 2019

Towards feedback control of the cell-cycle across a population of yeast cells.

Giansimone Perrino, Davide Fiore, Sara Napolitano, Mario di Bernardo, Diego di Bernardo

Proceedings of the 17th European Control Conference, 2019

Feedback control promotes synchronisation of the cell-cycle across a population of yeast cells.

Giansimone Perrino, Davide Fiore, Sara Napolitano, Francesca Galdi, Antonella La Regina, Mario di Bernardo, Diego di Bernardo

Proceedings of the 58th IEEE Conference on Decision and Control, 2019

Cybergenetics: Theory and Methods for Genetic Control System.

Mustafa Khammash, Mario di Bernardo, Diego di Bernardo

Proceedings of the 58th IEEE Conference on Decision and Control, 2019

2018

gene2drug: a computational tool for pathway-based rational drug repositioning.

Francesco Napolitano, Diego Carrella, Barbara Mandriani, Sandra Pisonero-Vaquero, Francesco Sirci, Diego L. Medina, Nicola Brunetti-Pierri, Diego di Bernardo

Bioinform., 2018

2016

Drug-set enrichment analysis: a novel tool to investigate drug mode of action.

Francesco Napolitano, Francesco Sirci, Diego Carrella, Diego di Bernardo

Bioinform., 2016

Modelling, simulation and control of single cell expression dynamics of the galactose-inducible promoter in yeast.

Giansimone Perrino, Diego di Bernardo

Proceedings of the 55th IEEE Conference on Decision and Control, 2016

2015

Combining flux balance analysis and model checking for metabolic network validation and analysis.

Roberto Pagliarini, Mara Sangiovanni, Adriano Peron, Diego di Bernardo

Nat. Comput., 2015

A reverse-engineering approach to dissect post-translational modulators of transcription factor's activity from transcriptional data.

Gennaro Gambardella, Ivana Peluso, Sandro Montefusco, Mukesh Bansal, Diego L. Medina, Neil D. Lawrence, Diego di Bernardo

BMC Bioinform., 2015

2014

<i>In-Vivo</i> Real-Time Control of Protein Expression from Endogenous and Synthetic Gene Networks.

Filippo Menolascina, Gianfranco Fiore, Emanuele Orabona, Luca De Stefano, Mike Ferry, Jeff Hasty, Mario di Bernardo, Diego di Bernardo

PLoS Comput. Biol., 2014

Mantra 2.0: an online collaborative resource for drug mode of action and repurposing by network analysis.

Diego Carrella, Francesco Napolitano, Rossella Rispoli, Mario Miglietta, Annamaria Carissimo, Luisa Cutillo, Francesco Sirci, Francesco Gregoretti, Diego di Bernardo

Bioinform., 2014

2013

Colocalization of Coregulated Genes: A Steered Molecular Dynamics Study of Human Chromosome 19.

Marco Di Stefano, Angelo Rosa, Vincenzo Belcastro, Diego di Bernardo, Cristian Micheletti

PLoS Comput. Biol., 2013

A Genome-Scale Modeling Approach to Study Inborn Errors of Liver Metabolism: Toward an In Silico Patient.

Roberto Pagliarini, Diego di Bernardo

J. Comput. Biol., 2013

Network based elucidation of drug response: from modulators to targets.

Francesco Iorio, Julio Saez-Rodriguez, Diego di Bernardo

BMC Syst. Biol., 2013

Differential network analysis for the identification of condition-specific pathway activity and regulation.

Gennaro Gambardella, Maria Nicoletta Moretti, Rossella de Cegli, Luca Cardone, Adriano Peron, Diego di Bernardo

Bioinform., 2013

2012

Reverse Engineering and Analysis of Genome-Wide Gene Regulatory Networks from Gene Expression Profiles Using High-Performance Computing.

Vincenzo Belcastro, Francesco Gregoretti, Velia Siciliano, Michele Santoro, Giovanni D'Angelo, Gennaro Oliva, Diego di Bernardo

IEEE ACM Trans. Comput. Biol. Bioinform., 2012

2011

Construction and Modelling of an Inducible Positive Feedback Loop Stably Integrated in a Mammalian Cell-Line.

Velia Siciliano, Filippo Menolascina, Lucia Marucci, Chiara Fracassi, Immacolata Garzilli, Maria Nicoletta Moretti, Diego di Bernardo

PLoS Comput. Biol., 2011

Design and Construction of a Versatile Synthetic Network for Bistable Gene Expression in Mammalian Systems.

Athanasios Polynikis, Giulia Cuccato, Stefania Criscuolo, Stephen John Hogan, Mario di Bernardo, Diego di Bernardo

J. Comput. Biol., 2011

Modeling RNA interference in mammalian cells.

Giulia Cuccato, Athanasios Polynikis, Velia Siciliano, Mafalda Graziano, Mario di Bernardo, Diego di Bernardo

BMC Syst. Biol., 2011

Analysis, design and implementation of a novel scheme for in-vivo control of synthetic gene regulatory networks.

Filippo Menolascina, Mario di Bernardo, Diego di Bernardo

Autom., 2011

2010

Mania: a Gene Network Reverse Algorithm for Compounds Mode-of-Action and genes Interactions Inference.

Darong Lai, Hongtao Lu, Mario Lauria, Diego di Bernardo, Christine Nardini

Adv. Complex Syst., 2010

Gene ontology fuzzy-enrichment analysis to investigate drug mode-of-action.

Francesco Iorio, Loredana Murino, Diego di Bernardo, Giancarlo Raiconi, Roberto Tagliaferri

Proceedings of the International Joint Conference on Neural Networks, 2010

Design and implementation of a feedback control strategy for IRMA, a novel synthetic gene regulatory network.

Filippo Menolascina, Mario di Bernardo, Diego di Bernardo

Proceedings of the 49th IEEE Conference on Decision and Control, 2010

2009

Identifying Network of Drug Mode of Action by Gene Expression Profiling.

Francesco Iorio, Roberto Tagliaferri, Diego di Bernardo

J. Comput. Biol., 2009

2008

High-Throughput Analysis of the Drug Mode of Action of PB28, MC18 and MC70, Three Cyclohexylpiperazine Derivative New Molecules.

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

Proceedings of the Advanced Intelligent Computing Theories and Applications. With Aspects of Artificial Intelligence, 2008

Building Maps of Drugs Mode-of-Action from Gene Expression Data.

Francesco Iorio, Roberto Tagliaferri, Diego di Bernardo

Proceedings of the Computational Intelligence Methods for Bioinformatics and Biostatistics, 2008

2007

Piecewise affine approach to inferring cell cycle regulatory network in fission yeast.

Carlo Cosentino, Walter Curatola, Mukesh Bansal, Diego di Bernardo, Francesco Amato

Biomed. Signal Process. Control., 2007

LMI-based Algorithm for the Reconstruction of Biological Networks.

Francesco Amato, Carlo Cosentino, Walter Curatola, Diego di Bernardo

Proceedings of the American Control Conference, 2007

2006

Inference of gene regulatory networks and compound mode of action from time course gene expression profiles.

Mukesh Bansal, Giusy Della Gatta, Diego di Bernardo

Bioinform., 2006

A multi-step approach to time series analysis and gene expression clustering.

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

Bioinform., 2006

2005

DG-CST (Disease Gene Conserved Sequence Tags), a database of human-mouse conserved elements associated to disease genes.

Angelo Boccia, Mauro Petrillo, Diego di Bernardo, Alessandro Guffanti, Flavio Mignone, Stefano Confalonieri, Lucilla Luzi, Graziano Pesole, Giovanni Paolella, Andrea Ballabio, Sandro Banfi

Nucleic Acids Res., 2005

NEC for Gene Expression Analysis.

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

Proceedings of the Fuzzy Logic and Applications, 6th International Workshop, 2005

2004

Mining Yeast Gene Microarray Data with Latent Variable Models.

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

Proceedings of the Biological and Artificial Intelligence Environments, 2004

Robust Identification of Large Genetic Networks.

Diego di Bernardo, Timothy S. Gardner, James J. Collins

Proceedings of the Biocomputing 2004, 2004

Probabilistic Principal Surfaces for Yeast Gene Microarray Data Mining.

Antonino Staiano, Lara De Vinco, Angelo Ciaramella, Giancarlo Raiconi, Roberto Tagliaferri, Roberto Amato, Giuseppe Longo, Ciro Donalek, Gennaro Miele, Diego di Bernardo

Proceedings of the 4th IEEE International Conference on Data Mining (ICDM 2004), 2004

2003

ddbRNA: detection of conserved secondary structures in multiple alignments.

Diego di Bernardo, Thomas A. Down, Tim J. P. Hubbard

Bioinform., 2003