ddbRNA: detection of conserved secondary structures in multiple alignments. - Diego di Bernardo; Thomas A. Down; Tim J. P. Hubbard (Bioinform., 2003)

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 (ICDM, 2004)

Robust Identification of Large Genetic Networks. - Diego di Bernardo; Timothy S. Gardner; James J. Collins (Pacific Symposium on Biocomputing, 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 (WIRN, 2004)

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 (WILF, 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)

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)

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)

LMI-based Algorithm for the Reconstruction of Biological Networks. - Francesco Amato 001; Carlo Cosentino; Walter Curatola; Diego di Bernardo (ACC, 2007)

Piecewise affine approach to inferring cell cycle regulatory network in fission yeast. - Carlo Cosentino; Walter Curatola; Mukesh Bansal; Diego di Bernardo; Francesco Amato 001 (Biomed. Signal Process. Control., 2007)

Building Maps of Drugs Mode-of-Action from Gene Expression Data. - Francesco Iorio; Roberto Tagliaferri; Diego di Bernardo (CIBB, 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; et al. (ICIC (2), 2008)

Identifying Network of Drug Mode of Action by Gene Expression Profiling. - Francesco Iorio; Roberto Tagliaferri; Diego di Bernardo (J. Comput. Biol., 2009)

Design and implementation of a feedback control strategy for IRMA, a novel synthetic gene regulatory network. - Filippo Menolascina; Mario di Bernardo; Diego di Bernardo (CDC, 2010)

Gene ontology fuzzy-enrichment analysis to investigate drug mode-of-action. - Francesco Iorio; Loredana Murino; Diego di Bernardo; Giancarlo Raiconi; Roberto Tagliaferri (IJCNN, 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)

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)

Modeling RNA interference in mammalian cells. - Giulia Cuccato; Athanasios Polynikis; Velia Siciliano; Mafalda Graziano; Mario di Bernardo; Diego di Bernardo (BMC Syst. 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)

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)

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)

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)

Network based elucidation of drug response: from modulators to targets. - Francesco Iorio; Julio Saez-Rodriguez; Diego di Bernardo (BMC Syst. 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)

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)

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)

In-Vivo 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)

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)

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)

Modelling, simulation and control of single cell expression dynamics of the galactose-inducible promoter in yeast. - Giansimone Perrino; Diego di Bernardo (CDC, 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)

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)

Cybergenetics: Theory and Methods for Genetic Control System. - Mustafa Khammash; Mario di Bernardo; Diego di Bernardo (CDC, 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 (CDC, 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 (ECC, 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)

A Siamese neural network model for the prioritization of metabolic disorders by integrating real and simulated data. - Gian Marco Messa; Francesco Napolitano; Sarah H. Elsea; Diego di Bernardo; Xin Gao 001 (Bioinform., 2020)

gep2pep: a bioconductor package for the creation and analysis of pathway-based expression profiles. - Francesco Napolitano; Diego Carrella; Xin Gao 001; Diego di Bernardo (Bioinform., 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 (Zenodo, 2020)

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 (Zenodo, 2021)

Designing high performance whole-cell biosensors by integrating Synthetic Biology with Control Engineering. - Virginia Fusco; Davide Fiore; Mario di Bernardo; Diego di Bernardo (CDC, 2024)