Works by Di Bernardo, Diego

Results: 72

Investigation of dynamic regulation of TFEB nuclear shuttling by microfluidics and quantitative modelling.

Published in:

Communications Biology, 2025, v. 8, n. 1, p. 1, doi. 10.1038/s42003-025-07870-x

By:

Ruolo, Iacopo;
Napolitano, Sara;
Postiglione, Lorena;
Napolitano, Gennaro;
Ballabio, Andrea;
di Bernardo, Diego

Publication type:

Article

Computer Model for Study of Cardiac Repolarization.

Published in:

Journal of Cardiovascular Electrophysiology, 2000, v. 11, n. 8, p. 895, doi. 10.1111/j.1540-8167.2000.tb00069.x

By:

di Bernardo, Diego;
Murray, Alan

Publication type:

Article

Chemogenomic profiling on a genome-wide scale using reverse-engineered gene networks.

Published in:

Nature Biotechnology, 2005, v. 23, n. 3, p. 377, doi. 10.1038/nbt1075

By:

di Bernardo, Diego;
Thompson, Michael J;
Gardner, Timothy S;
Chobot, Sarah E;
Eastwood, Erin L;
Wojtovich, Andrew P;
Elliott, Sean J;
Schaus, Scott E;
Collins, James J

Publication type:

Article

A Siamese neural network model for the prioritization of metabolic disorders by integrating real and simulated data.

Published in:

Bioinformatics, 2020, v. 36, p. i787, doi. 10.1093/bioinformatics/btaa841

By:

Messa, Gian Marco;
Napolitano, Francesco;
Elsea, Sarah H.;
Bernardo, Diego di;
Gao, Xin

Publication type:

Article

Intrinsic Abnormalities of Cystic Fibrosis Airway Connective Tissue Revealed by an In Vitro 3D Stromal Model.

Published in:

Cells (2073-4409), 2020, v. 9, n. 6, p. 1371, doi. 10.3390/cells9061371

By:

Mazio, Claudia;
Scognamiglio, Laura S.;
De Cegli, Rossella;
Galietta, Luis J. V.;
Di Bernardo, Diego;
Casale, Costantino;
Urciuolo, Francesco;
Imparato, Giorgia;
Netti, Paolo A.

Publication type:

Article

Reverse engineering a mouse embryonic stem cell-specific transcriptional network reveals a new modulator of neuronal differentiation.

Published in:

Nucleic Acids Research, 2013, v. 41, n. 2, p. 711, doi. 10.1093/nar/gks1136

By:

De Cegli, Rossella;
Iacobacci, Simona;
Flore, Gemma;
Gambardella, Gennaro;
Mao, Lei;
Cutillo, Luisa;
Lauria, Mario;
Klose, Joachim;
Illingworth, Elizabeth;
Banfi, Sandro;
di Bernardo, Diego

Publication type:

Article

Transcriptional gene network inference from a massive dataset elucidates transcriptome organization and gene function.

Published in:

Nucleic Acids Research, 2011, v. 39, n. 20, p. 8677, doi. 10.1093/nar/gkr593

By:

Belcastro, Vincenzo;
Siciliano, Velia;
Gregoretti, Francesco;
Mithbaokar, Pratibha;
Dharmalingam, Gopuraja;
Berlingieri, Stefania;
Iorio, Francesco;
Oliva, Gennaro;
Polishchuck, Roman;
Brunetti-Pierri, Nicola;
di Bernardo, Diego

Publication type:

Article

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

Published in:

Nucleic Acids Research, 2005, v. 33, n. suppl 1, p. d505

By:

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

Publication type:

Article

Comprehensive kinome NGS targeted expression profiling by KING-REX.

Published in:

BMC Genomics, 2019, v. 20, n. 1, p. N.PAG, doi. 10.1186/s12864-019-5676-3

By:

Carapezza, Giovanni;
Cusi, Carlo;
Raddrizzani, Laura;
Di Bella, Sebastiano;
Somaschini, Alessio;
Leone, Antonella;
Lupi, Rosita;
Isacchi, Antonella;
Bosotti, Roberta;
Magni, Paolo;
Rizzo, Ettore;
Mutarelli, Margherita;
Nigro, Vincenzo;
di Bernardo, Diego

Publication type:

Article

Derivation, identification and validation of a computational model of a novel synthetic regulatory network in yeast.

Published in:

Journal of Mathematical Biology, 2011, v. 62, n. 5, p. 685, doi. 10.1007/s00285-010-0350-z

By:

Marucci, Lucia;
Santini, Stefania;
Bernardo, Mario;
di Bernardo, Diego

Publication type:

Article

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

Published in:

Bioinformatics, 2006, v. 22, n. 7, p. 815, doi. 10.1093/bioinformatics/btl003

By:

Mukesh Bansal;
Giusy Della Gatta;
Diego di Bernardo

Publication type:

Article

ddbRNA: detection of conserved secondary structures in multiple alignments.

Published in:

Bioinformatics, 2003, v. 19, n. 13, p. 1606, doi. 10.1093/bioinformatics/btg229

By:

Diego di Bernardo;
Thomas Down;
Tim Hubbard

Publication type:

Article

Dissection of metabolic reprogramming in polycystic kidney disease reveals coordinated rewiring of bioenergetic pathways.

Published in:

Communications Biology, 2018, v. 1, n. 1, p. N.PAG, doi. 10.1038/s42003-018-0200-x

By:

Podrini, Christine;
Rowe, Isaline;
Pagliarini, Roberto;
Costa, Ana S. H.;
Chiaravalli, Marco;
Di Meo, Ivano;
Kim, Hyunho;
Distefano, Gianfranco;
Tiranti, Valeria;
Qian, Feng;
di Bernardo, Diego;
Frezza, Christian;
Boletta, Alessandra

Publication type:

Article

Comparing structural and transcriptional drug networks reveals signatures of drug activity and toxicity in transcriptional responses.

Published in:

NPJ Systems Biology & Applications, 2017, v. 3, n. 1, p. N.PAG, doi. 10.1038/s41540-017-0022-3

By:

Sirci, Francesco;
Napolitano, Francesco;
Pisonero-Vaquero, Sandra;
Carrella, Diego;
Medina, Diego L.;
di Bernardo, Diego

Publication type:

Article

Drug Repurposing in Rare Diseases: An Integrative Study of Drug Screening and Transcriptomic Analysis in Nephropathic Cystinosis.

Published in:

International Journal of Molecular Sciences, 2021, v. 22, n. 23, p. 12829, doi. 10.3390/ijms222312829

By:

Bellomo, Francesco;
De Leo, Ester;
Taranta, Anna;
Giaquinto, Laura;
Di Giovamberardino, Gianna;
Montefusco, Sandro;
Rega, Laura Rita;
Pastore, Anna;
Medina, Diego Luis;
Di Bernardo, Diego;
De Matteis, Maria Antonietta;
Emma, Francesco

Publication type:

Article

Author Correction: The VersaLive platform enables microfluidic mammalian cell culture for versatile applications.

Published in:

2022

By:

Nocera, Giovanni Marco;
Viscido, Gaetano;
Criscuolo, Stefania;
Brillante, Simona;
Carbone, Fabrizia;
Staiano, Leopoldo;
Carrella, Sabrina;
di Bernardo, Diego

Publication type:

Correction Notice

The VersaLive platform enables microfluidic mammalian cell culture for versatile applications.

Published in:

Communications Biology, 2022, v. 5, n. 1, p. 1, doi. 10.1038/s42003-022-03976-8

By:

Nocera, Giovanni Marco;
Viscido, Gaetano;
Criscuolo, Stefania;
Brillante, Simona;
Carbone, Fabrizia;
Staiano, Leopoldo;
Carrella, Sabrina;
di Bernardo, Diego

Publication type:

Article

Analysis of inhibitors of the anoctamin‐1 chloride channel (transmembrane member 16A, TMEM16A) reveals indirect mechanisms involving alterations in calcium signalling.

Published in:

British Journal of Pharmacology, 2023, v. 180, n. 6, p. 775, doi. 10.1111/bph.15995

By:

Genovese, Michele;
Buccirossi, Martina;
Guidone, Daniela;
De Cegli, Rossella;
Sarnataro, Sergio;
di Bernardo, Diego;
Galietta, Luis J. V.

Publication type:

Article

Origin on the electrocardiogram of U-waves and abnormal U-wave inversion.

Published in:

Cardiovascular Research, 2002, v. 53, n. 1, p. 202, doi. 10.1016/S0008-6363(01)00439-4

By:

di Bernardo, Diego;
Murray, Alan

Publication type:

Article

Definition of the transcriptional units of inherited retinal disease genes by meta-analysis of human retinal transcriptome data.

Published in:

BMC Genomics, 2023, v. 24, n. 1, p. 1, doi. 10.1186/s12864-023-09300-w

By:

Ruiz-Ceja, Karla Alejandra;
Capasso, Dalila;
Pinelli, Michele;
Del Prete, Eugenio;
Carrella, Diego;
di Bernardo, Diego;
Banfi, Sandro

Publication type:

Article

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

Published in:

Bioinformatics, 2020, v. 36, n. 6, p. 1944, doi. 10.1093/bioinformatics/btz803

By:

Napolitano, Farancesco;
Carrella, Diego;
Gao, Xin;
Bernardo, Diego di

Publication type:

Article

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

Published in:

Bioinformatics, 2018, v. 34, n. 9, p. 1498, doi. 10.1093/bioinformatics/btx800

By:

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

Publication type:

Article

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

Published in:

Bioinformatics, 2016, v. 32, n. 2, p. 235, doi. 10.1093/bioinformatics/btv536

By:

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

Publication type:

Article

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

Published in:

Bioinformatics, 2014, v. 30, n. 12, p. 1787, doi. 10.1093/bioinformatics/btu058

By:

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

Publication type:

Article

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

Published in:

Bioinformatics, 2013, v. 29, n. 14, p. 1776, doi. 10.1093/bioinformatics/btt290

By:

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

Publication type:

Article

Engineering a synthetic gene circuit for high-performance inducible expression in mammalian systems.

Published in:

Nature Communications, 2024, v. 15, n. 1, p. 1, doi. 10.1038/s41467-024-47592-y

By:

De Carluccio, Giuliano;
Fusco, Virginia;
di Bernardo, Diego

Publication type:

Article

Engineering and control of biological systems: A new way to tackle complex diseases.

Published in:

FEBS Letters, 2012, v. 586, n. 15, p. 2122, doi. 10.1016/j.febslet.2012.04.050

By:

Menolascina, Filippo;
Siciliano, Velia;
di Bernardo, Diego

Publication type:

Article

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

Published in:

BMC Systems Biology, 2013, v. 7, n. 1, p. 2, doi. 10.1186/1752-0509-7-139

By:

Iorio, Francesco;
Saez-Rodriguez, Julio;
Di Bernardo, Diego

Publication type:

Article

Modeling RNA interference in mammalian cells.

Published in:

BMC Systems Biology, 2011, v. 5, n. 1, p. 19, doi. 10.1186/1752-0509-5-19

By:

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

Publication type:

Article

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

Published in:

International Journal of High Performance Computing Applications, 2019, v. 33, n. 4, p. 651, doi. 10.1177/1094342018801482

By:

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

Publication type:

Article

Blood transcriptomics of drug-naïve sporadic Parkinson's disease patients.

Published in:

BMC Genomics, 2015, v. 16, p. 1, doi. 10.1186/s12864-015-2058-3

By:

Calligaris, Raffaella;
Banica, Mihaela;
Roncaglia, Paola;
Robotti, Elisa;
Finaurini, Sara;
Vlachouli, Christina;
Antonutti, Lucia;
Iorio, Francesco;
Carissimo, Annamaria;
Cattaruzza, Tatiana;
Ceiner, Andrea;
Lazarevic, Dejan;
Cucca, Alberto;
Pangher, Nicola;
Marengo, Emilio;
di Bernardo, Diego;
Pizzolato, Gilberto;
Gustincich, Stefano

Publication type:

Article

A network-based approach to dissect the cilia/centrosome complex interactome.

Published in:

BMC Genomics, 2014, v. 15, n. 1, p. 658, doi. 10.1186/1471-2164-15-658

By:

Amato, Roberto;
Morleo, Manuela;
Giaquinto, Laura;
di Bernardo, Diego;
Franco, Brunella

Publication type:

Article

A community-based resource for automatic exome variant-calling and annotation in Mendelian disorders.

Published in:

BMC Genomics, 2014, v. 15, p. 1, doi. 10.1186/1471-2164-15-S3-S5

By:

Mutarelli, Margherita;
Marwah, Veer Singh;
Rispoli, Rossella;
Carrella, Diego;
Dharmalingam, Gopuraja;
Oliva, Gennaro;
di Bernardo, Diego

Publication type:

Article

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

Published in:

BMC Bioinformatics, 2015, v. 16, n. 1, p. 1, doi. 10.1186/s12859-015-0700-3

By:

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

Publication type:

Article

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

Published in:

BMC Bioinformatics, 2015, v. 16, n. 1, p. 279, doi. 10.1186/s12859-015-0700-3

By:

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

Publication type:

Article

TRPV4 and purinergic receptor signalling pathways are separately linked in airway epithelia to CFTR and TMEM16A chloride channels.

Published in:

Journal of Physiology, 2019, v. 597, n. 24, p. 5859, doi. 10.1113/JP278784

By:

Genovese, Michele;
Borrelli, Anna;
Venturini, Arianna;
Guidone, Daniela;
Caci, Emanuela;
Viscido, Gaetano;
Gambardella, Gennaro;
di Bernardo, Diego;
Scudieri, Paolo;
Galietta, Luis J.V.

Publication type:

Article

The impact of microRNAs on transcriptional heterogeneity and gene co-expression across single embryonic stem cells.

Published in:

Nature Communications, 2017, v. 8, n. 1, p. 14126, doi. 10.1038/ncomms14126

By:

Gambardella, Gennaro;
Carissimo, Annamaria;
Chen, Amy;
Cutillo, Luisa;
Nowakowski, Tomasz J.;
di Bernardo, Diego;
Blelloch, Robert

Publication type:

Article

Fibroblast growth factor signalling controls nervous system patterning and pigment cell formation in Ciona intestinalis.

Published in:

Nature Communications, 2014, v. 5, n. 9, p. 4830, doi. 10.1038/ncomms5830

By:

Racioppi, Claudia;
Kamal, Ashwani K.;
Razy-Krajka, Florian;
Gambardella, Gennaro;
Zanetti, Laura;
di Bernardo, Diego;
Sanges, Remo;
Christiaen, Lionel A.;
Ristoratore, Filomena

Publication type:

Article

miRNAs confer phenotypic robustness to gene networks by suppressing biological noise.

Published in:

Nature Communications, 2013, v. 4, n. 9, p. 2364, doi. 10.1038/ncomms3364

By:

Siciliano, Velia;
Garzilli, Immacolata;
Fracassi, Chiara;
Criscuolo, Stefania;
Ventre, Simona;
di Bernardo, Diego

Publication type:

Article

Computational framework for the prediction of transcription factor binding sites by multiple data integration.

Published in:

BMC Neuroscience, 2006, v. 7, p. S8, doi. 10.1186/1471-2202-7-S1-S8

By:

Ambesi-Impiombato, Alberto;
Bansal, Mukesh;
Liò, Pietro;
Di Bernardo, Diego

Publication type:

Article

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

Published in:

PLoS Computational Biology, 2014, v. 10, n. 5, p. 1, doi. 10.1371/journal.pcbi.1003625

By:

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

Publication type:

Article

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

Published in:

PLoS Computational Biology, 2013, v. 9, n. 3, p. 1, doi. 10.1371/journal.pcbi.1003019

By:

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

Publication type:

Article

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

Published in:

PLoS Computational Biology, 2011, v. 7, n. 6, p. 1, doi. 10.1371/journal.pcbi.1002074

By:

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

Publication type:

Article

NIRest: A Tool for Gene Network and Mode of Action Inference.

Published in:

Annals of the New York Academy of Sciences, 2009, v. 1158, p. 257, doi. 10.1111/j.1749-6632.2008.03761.x

By:

Lauria, Mario;
Iorio, Francesco;
Di Bernardo, Diego

Publication type:

Article

An atlas of gene expression and gene co-regulation in the human retina.

Published in:

Nucleic Acids Research, 2016, v. 44, n. 12, p. 5773, doi. 10.1093/nar/gkw486

By:

Pinelli, Michele;
Carissimo, Annamaria;
Cutillo, Luisa;
Ching-Hung Lai;
Mutarelli, Margherita;
Moretti, Maria Nicoletta;
Singh, Marwah Veer;
Karali, Marianthi;
Carrella, Diego;
Pizzo, Mariateresa;
Russo, Francesco;
Ferrari, Stefano;
Ponzin, Diego;
Angelini, Claudia;
Banfi, Sandro;
di Bernardo, Diego

Publication type:

Article

High-resolution analysis of the human retina miRNome reveals isomiR variations and novel microRNAs.

Published in:

Nucleic Acids Research, 2016, v. 44, n. 4, p. 1525, doi. 10.1093/nar/gkw039

By:

Karali, Marianthi;
Persico, Maria;
Mutarelli, Margherita;
Carissimo, Annamaria;
Pizzo, Mariateresa;
Marwah, Veer Singh;
Ambrosio, Concetta;
Pinelli, Michele;
Carrella, Diego;
Ferrari, Stefano;
Ponzin, Diego;
Nigro, Vincenzo;
di Bernardo, Diego;
Banfi, Sandro

Publication type:

Article

A Model of Two Nonlinear Coupled Oscillators for the Study of Heartbeat Dynamics.

Published in:

International Journal of Bifurcation & Chaos in Applied Sciences & Engineering, 1998, v. 8, n. 10, p. 1975, doi. 10.1142/S0218127498001637

By:

di Bernardo, Diego;
Signorini, Maria G.

Publication type:

Article

Simulation of Heartbeat Dynamics: A Nonlinear Model.

Published in:

International Journal of Bifurcation & Chaos in Applied Sciences & Engineering, 1998, v. 8, n. 8, p. 1725, doi. 10.1142/S0218127498001418

By:

Signorini, Maria G.;
di Bernardo, Diego

Publication type:

Article

Quantification of T Wave Shape Changes Following Exercise.

Published in:

Pacing & Clinical Electrophysiology, 2002, v. 25, n. 8, p. 1230, doi. 10.1046/j.1460-9592.2002.01230.x

By:

Langley, Philip;
Di Bernardo, Diego;
Murray, Alan

Publication type:

Article

Effect of Lead Exclusion for the Manual Measurement of QT Dispersion.

Published in:

Pacing & Clinical Electrophysiology, 2001, v. 24, n. 1, p. 75, doi. 10.1046/j.1460-9592.2001.00075.x

By:

Langley, Philip;
Di Bernardo, Diego;
Murray, Alan

Publication type:

Article