Diego di Bernardo

39 papers A* 1B 1C 1Misc 1Journal 24Unranked 11

Year	Rank	Type	Title / Venue / Authors
2024	—	`conf`	Designing high performance whole-cell biosensors by integrating Synthetic Biology with Control Engineering. CDC Virginia Fusco, Davide Fiore, Mario di Bernardo, Diego di Bernardo
2020	J	`jnl`	A Siamese neural network model for the prioritization of metabolic disorders by integrating real and simulated data. Bioinform. Gian Marco Messa, Francesco Napolitano, Sarah H. Elsea, Diego di Bernardo, Xin Gao
2020	J	`jnl`	gep2pep: a bioconductor package for the creation and analysis of pathway-based expression profiles. Bioinform. Francesco Napolitano, Diego Carrella, Xin Gao, Diego di Bernardo
2019	J	`jnl`	A GPU algorithm for tracking yeast cells in phase-contrast microscopy images. Int. J. High Perform. Comput. Appl. Domenico Rea, Giansimone Perrino, Diego di Bernardo, Livia Marcellino, Diego Romano
2019	—	`conf`	Cybergenetics: Theory and Methods for Genetic Control System. CDC Mustafa Khammash, Mario di Bernardo, Diego di Bernardo
2019	—	`conf`	Feedback control promotes synchronisation of the cell-cycle across a population of yeast cells. CDC Giansimone Perrino, Davide Fiore, Sara Napolitano, Francesca Galdi, Antonella La Regina, Mario di Bernardo, Diego di Bernardo
2019	—	`conf`	Towards feedback control of the cell-cycle across a population of yeast cells. ECC Giansimone Perrino, Davide Fiore, Sara Napolitano, Mario di Bernardo, Diego di Bernardo
2018	J	`jnl`	gene2drug: a computational tool for pathway-based rational drug repositioning. Bioinform. Francesco Napolitano, Diego Carrella, Barbara Mandriani, Sandra Pisonero-Vaquero, Francesco Sirci, Diego L. Medina, Nicola Brunetti-Pierri, Diego di Bernardo
2016	J	`jnl`	Drug-set enrichment analysis: a novel tool to investigate drug mode of action. Bioinform. Francesco Napolitano, Francesco Sirci, Diego Carrella, Diego di Bernardo
2016	—	`conf`	Modelling, simulation and control of single cell expression dynamics of the galactose-inducible promoter in yeast. CDC Giansimone Perrino, Diego di Bernardo
2015	J	`jnl`	A reverse-engineering approach to dissect post-translational modulators of transcription factor's activity from transcriptional data. BMC Bioinform. Gennaro Gambardella, Ivana Peluso, Sandro Montefusco, Mukesh Bansal, Diego L. Medina, Neil D. Lawrence, Diego di Bernardo
2015	J	`jnl`	Combining flux balance analysis and model checking for metabolic network validation and analysis. Nat. Comput. Roberto Pagliarini, Mara Sangiovanni, Adriano Peron, Diego di Bernardo
2014	J	`jnl`	Mantra 2.0: an online collaborative resource for drug mode of action and repurposing by network analysis. Bioinform. Diego Carrella, Francesco Napolitano, Rossella Rispoli, Mario Miglietta, Annamaria Carissimo, Luisa Cutillo, Francesco Sirci, Francesco Gregoretti, Diego di Bernardo
2013	J	`jnl`	A Genome-Scale Modeling Approach to Study Inborn Errors of Liver Metabolism: Toward an In Silico Patient. J. Comput. Biol. Roberto Pagliarini, Diego di Bernardo
2013	J	`jnl`	Colocalization of Coregulated Genes: A Steered Molecular Dynamics Study of Human Chromosome 19. PLoS Comput. Biol. Marco Di Stefano, Angelo Rosa, Vincenzo Belcastro, Diego di Bernardo, Cristian Micheletti
2013	J	`jnl`	Differential network analysis for the identification of condition-specific pathway activity and regulation. Bioinform. Gennaro Gambardella, Maria Nicoletta Moretti, Rossella de Cegli, Luca Cardone, Adriano Peron, Diego di Bernardo
2013	J	`jnl`	Network based elucidation of drug response: from modulators to targets. BMC Syst. Biol. Francesco Iorio, Julio Saez-Rodriguez, Diego di Bernardo
2012	J	`jnl`	Reverse Engineering and Analysis of Genome-Wide Gene Regulatory Networks from Gene Expression Profiles Using High-Performance Computing. IEEE ACM Trans. Comput. Biol. Bioinform. Vincenzo Belcastro, Francesco Gregoretti, Velia Siciliano, Michele Santoro, Giovanni D'Angelo, Gennaro Oliva, Diego di Bernardo
2011	J	`jnl`	Analysis, design and implementation of a novel scheme for in-vivo control of synthetic gene regulatory networks. Autom. Filippo Menolascina, Mario di Bernardo, Diego di Bernardo
2011	J	`jnl`	Construction and Modelling of an Inducible Positive Feedback Loop Stably Integrated in a Mammalian Cell-Line. PLoS Comput. Biol. Velia Siciliano, Filippo Menolascina, Lucia Marucci, Chiara Fracassi, Immacolata Garzilli, Maria Nicoletta Moretti, Diego di Bernardo
2011	J	`jnl`	Design and Construction of a Versatile Synthetic Network for Bistable Gene Expression in Mammalian Systems. J. Comput. Biol. Athanasios Polynikis, Giulia Cuccato, Stefania Criscuolo, Stephen John Hogan, Mario di Bernardo, Diego di Bernardo
2011	J	`jnl`	Modeling RNA interference in mammalian cells. BMC Syst. Biol. Giulia Cuccato, Athanasios Polynikis, Velia Siciliano, Mafalda Graziano, Mario di Bernardo, Diego di Bernardo
2010	—	`conf`	Design and implementation of a feedback control strategy for IRMA, a novel synthetic gene regulatory network. CDC Filippo Menolascina, Mario di Bernardo, Diego di Bernardo
2010	B	`conf`	Gene ontology fuzzy-enrichment analysis to investigate drug mode-of-action. IJCNN Francesco Iorio, Loredana Murino, Diego di Bernardo, Giancarlo Raiconi, Roberto Tagliaferri
2010	J	`jnl`	Mania: a Gene Network Reverse Algorithm for Compounds Mode-of-Action and genes Interactions Inference. Adv. Complex Syst. Darong Lai, Hongtao Lu, Mario Lauria, Diego di Bernardo, Christine Nardini
2009	J	`jnl`	Identifying Network of Drug Mode of Action by Gene Expression Profiling. J. Comput. Biol. Francesco Iorio, Roberto Tagliaferri, Diego di Bernardo
2009	—	`conf`	MANIA: A Gene Network Reverse Algorithm for Compounds Mode-of-Action and Genes Interactions Inference. Complex (1) Darong Lai, Hongtao Lu, Mario Lauria, Diego di Bernardo, Christine Nardini
2008	—	`conf`	Building Maps of Drugs Mode-of-Action from Gene Expression Data. CIBB Francesco Iorio, Roberto Tagliaferri, Diego di Bernardo
2008	—	`conf`	High-Throughput Analysis of the Drug Mode of Action of PB28, MC18 and MC70, Three Cyclohexylpiperazine Derivative New Molecules. ICIC (2) 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
2007	C	`conf`	LMI-based Algorithm for the Reconstruction of Biological Networks. ACC Francesco Amato, Carlo Cosentino, Walter Curatola, Diego di Bernardo
2007	J	`jnl`	Piecewise affine approach to inferring cell cycle regulatory network in fission yeast. Biomed. Signal Process. Control. Carlo Cosentino, Walter Curatola, Mukesh Bansal, Diego di Bernardo, Francesco Amato
2006	J	`jnl`	A multi-step approach to time series analysis and gene expression clustering. Bioinform. 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
2006	J	`jnl`	Inference of gene regulatory networks and compound mode of action from time course gene expression profiles. Bioinform. Mukesh Bansal, Giusy Della Gatta, Diego di Bernardo
2005	J	`jnl`	DG-CST (Disease Gene Conserved Sequence Tags), a database of human-mouse conserved elements associated to disease genes. Nucleic Acids Res. Angelo Boccia, Mauro Petrillo, Diego di Bernardo, Alessandro Guffanti, Flavio Mignone, Stefano Confalonieri, Lucilla Luzi, Graziano Pesole, Giovanni Paolella, Andrea Ballabio, Sandro Banfi
2005	—	`conf`	NEC for Gene Expression Analysis. WILF 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
2004	—	`conf`	Mining Yeast Gene Microarray Data with Latent Variable Models. WIRN 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
2004	A*	`conf`	Probabilistic Principal Surfaces for Yeast Gene Microarray Data Mining. ICDM Antonino Staiano, Lara De Vinco, Angelo Ciaramella, Giancarlo Raiconi, Roberto Tagliaferri, Roberto Amato, Giuseppe Longo, Ciro Donalek, Gennaro Miele, Diego di Bernardo
2004	Misc	`conf`	Robust Identification of Large Genetic Networks. Pacific Symposium on Biocomputing Diego di Bernardo, Timothy S. Gardner, James J. Collins
2003	J	`jnl`	ddbRNA: detection of conserved secondary structures in multiple alignments. Bioinform. Diego di Bernardo, Thomas A. Down, Tim J. P. Hubbard