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1

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

di Bernardo, Diego, Signorini, Maria G.

Journal:

International Journal of Bifurcation and Chaos

Year:

1998

Language:

english

File:

PDF, 446 KB

english, 1998

2

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

Journal:

Year:

2011

Language:

english

File:

PDF, 795 KB

english, 2011

3

Medical physics: Explaining the T-wave shape in the ECG

di Bernardo, Diego, Murray, Alan

Journal:

Year:

2000

Language:

english

File:

PDF, 54 KB

english, 2000

4

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

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

Journal:

Nature Biotechnology

Year:

2005

Language:

english

File:

PDF, 570 KB

english, 2005

5

Id proteins synchronize stemness and anchorage to the niche of neural stem cells

Niola, Francesco, Zhao, Xudong, Singh, Devendra, Castano, Angelica, Sullivan, Ryan, Lauria, Mario, Nam, Hyung-song, Zhuang, Yuan, Benezra, Robert, Di Bernardo, Diego

Journal:

Nature Cell Biology

Year:

2012

Language:

english

File:

PDF, 3.48 MB

english, 2012

6

miRNAs confer phenotypic robustness to gene networks by suppressing biological noise

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

Journal:

Nature Communications

Year:

2013

Language:

english

File:

PDF, 456 KB

english, 2013

7

[IEEE Distributed Methods in Verification and 2nd Intl Wkshp on High Performance Computational Systems Biology (PDMC-HiBi) - Enschede, TBD, Netherlands (2010.09.30-2010.10.1)] 2010 Ninth International Workshop on Parallel and Distributed Methods in Verification, and Second International Workshop on High Performance Computational Systems Biology - Parallel Computing Algorithms for Reverse-Engineering and Analysis of Genome-Wide Gene Regulatory Networks from Gene Expression Profiles

Belcastro, Vincenzo, Bernardo, Diego di, Gregoretti, Francesco, Oliva, Gennaro

Year:

2010

Language:

english

File:

PDF, 1011 KB

english, 2010

8

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

Polynikis, Athanasios, Cuccato, Giulia, Criscuolo, Stefania, Hogan, Stephen J., Bernardo, Mario Di, Bernardo, Diego Di

Journal:

Journal of Computational Biology

Year:

2011

Language:

english

File:

PDF, 512 KB

english, 2011

9

How to infer gene networks from expression profiles

Bansal, Mukesh, Belcastro, Vincenzo, Ambesi-Impiombato, Alberto, di Bernardo, Diego

Journal:

Molecular Systems Biology

Year:

2007

Language:

english

File:

PDF, 59 KB

english, 2007

10

Modelling cardiac repolarisation for the study of the T wave: effect of repolarisation sequence

Diego di Bernardo, Alan Murray

Journal:

Chaos, Solitons & Fractals

Year:

2002

Language:

english

File:

PDF, 277 KB

english, 2002

11

Effect of Lead Exclusion for the Manual Measurement of QT Dispersion

PHILIP LANGLEY, DIEGO DI BERNARDO, ALAN MURRAY

Journal:

Pacing and Clinical Electrophysiology

Year:

2001

Language:

english

File:

PDF, 248 KB

english, 2001

12

Quantification of T Wave Shape Changes Following Exercise

PHILIP LANGLEY, DIEGO DI BERNARDO, ALAN MURRAY

Journal:

Pacing and Clinical Electrophysiology

Year:

2002

Language:

english

File:

PDF, 217 KB

english, 2002

13

Modeling RNA interference in mammalian cells

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

Journal:

BMC Systems Biology

Year:

2011

Language:

english

File:

PDF, 1.64 MB

english, 2011

14

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

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

Journal:

Journal of Mathematical Biology

Year:

2011

Language:

english

File:

PDF, 750 KB

english, 2011

15

Dispersion of QT Intervals: A Measure of Dispersion of Repolarization or Simply a Projection Effect?

DIEGO DI BERNARDO, PHILIP LANGLEY, ALAN MURRAY

Journal:

Pacing and Clinical Electrophysiology

Year:

2000

Language:

english

File:

PDF, 2.58 MB

english, 2000

16

Computer Model for Study of Cardiac Repolarization

DIEGO di BERNARDO, ALAN MURRAY

Journal:

Journal of Cardiovascular Electrophysiology

Year:

2000

Language:

english

File:

PDF, 2.18 MB

english, 2000

17

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

Mario Lauria, Francesco Iorio, Diego Di Bernardo

Journal:

Annals of the New York Academy of Sciences

Year:

2009

Language:

english

File:

PDF, 217 KB

english, 2009

18

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

Filippo Menolascina, Velia Siciliano, Diego di Bernardo

Journal:

Year:

2012

Language:

english

File:

PDF, 375 KB

english, 2012

19

CoGemiR: A comparative genomics microRNA database

Vincenza Maselli, Diego Di Bernardo, Sandro Banfi

Journal:

Year:

2008

Language:

english

File:

PDF, 1.28 MB

english, 2008

20

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

Alberto Ambesi-Impiombato, Mukesh Bansal, Pietro Liò, Diego di Bernardo

Journal:

BMC Neuroscience

Year:

2006

Language:

english

File:

PDF, 662 KB

english, 2006

21

A Yeast Synthetic Network for In Vivo Assessment of Reverse-Engineering and Modeling Approaches

Irene Cantone, Lucia Marucci, Francesco Iorio, Maria Aurelia Ricci, Vincenzo Belcastro, Mukesh Bansal, Stefania Santini, Mario di Bernardo, Diego di Bernardo, Maria Pia Cosma

Journal:

Year:

2009

Language:

english

File:

PDF, 999 KB

english, 2009

22

Transcriptional network dynamics in macrophage activation

Roland Nilsson, Vladimir B. Bajic, Harukazu Suzuki, Diego di Bernardo, Johan Björkegren, Shintaro Katayama, James F. Reid, Matthew J. Sweet, Manuela Gariboldi, Piero Carninci, Yosihide Hayashizaki, Da

Journal:

Year:

2006

Language:

english

File:

PDF, 787 KB

english, 2006

23

How to infer gene networks from expression profiles

Bansal, Mukesh, Belcastro, Vincenzo, Ambesi-Impiombato, Alberto, di Bernardo, Diego

Journal:

Molecular Systems Biology

Year:

2007

Language:

english

File:

PDF, 173 KB

english, 2007

24

Network based elucidation of drug response: from modulators to targets

Iorio, Francesco, Saez-Rodriguez, Julio, Bernardo, Diego di

Journal:

BMC Systems Biology

Year:

2013

Language:

english

File:

PDF, 218 KB

english, 2013

25

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

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

Journal:

Natural Computing

Year:

2015

Language:

english

File:

PDF, 2.12 MB

english, 2015

26

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

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

Journal:

Year:

2014

Language:

english

File:

PDF, 799 KB

english, 2014

27

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

Roberto Amato,Manuela Morleo,Laura Giaquinto,Diego di Bernardo…

Journal:

Year:

2014

Language:

english

File:

PDF, 1.63 MB

english, 2014

28

Identifying Network of Drug Mode of Action by Gene Expression Profiling

Iorio, Francesco, Tagliaferri, Roberto, Bernardo, Diego di

Journal:

Journal of Computational Biology

Year:

2009

Language:

english

File:

PDF, 5.44 MB

english, 2009

29

[IEEE 2010 International Joint Conference on Neural Networks (IJCNN) - Barcelona, Spain (2010.07.18-2010.07.23)] The 2010 International Joint Conference on Neural Networks (IJCNN) - Gene ontology fuzzy-enrichment analysis to investigate drug mode-of-action

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

Year:

2010

Language:

english

File:

PDF, 1.06 MB

english, 2010

30

[IEEE 2010 49th IEEE Conference on Decision and Control (CDC) - Atlanta, GA, USA (2010.12.15-2010.12.17)] 49th IEEE Conference on Decision and Control (CDC) - Design and implementation of a feedback control strategy for IRMA, a novel synthetic gene regulatory network

Menolascina, Filippo, di Bernardo, Mario, di Bernardo, Diego

Year:

2010

Language:

english

File:

PDF, 202 KB

english, 2010

31

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

Pagliarini, Roberto, di Bernardo, Diego

Journal:

Journal of Computational Biology

Year:

2013

Language:

english

File:

PDF, 558 KB

english, 2013

32

Simulation of Heartbeat Dynamics: A Nonlinear Model

Signorini, Maria G., di Bernardo, Diego

Journal:

International Journal of Bifurcation and Chaos

Year:

1998

Language:

english

File:

PDF, 370 KB

english, 1998

33

Reverse Engineering Gene Network Identifies New Dysferlin-interacting Proteins

Cacciottolo, Mafalda, Belcastro, Vincenzo, Laval, Steve, Bushby, Kate, di Bernardo, Diego, Nigro, Vincenzo

Journal:

Journal of Biological Chemistry

Year:

2011

Language:

english

File:

PDF, 2.31 MB

english, 2011

34

Nanog Variability and Pluripotency Regulation of Embryonic Stem Cells - Insights from a Mathematical Model Analysis

Glauche, Ingmar, Herberg, Maria, Roeder, Ingo, Di Bernardo, Diego

Journal:

Year:

2010

Language:

english

File:

PDF, 661 KB

english, 2010

35

In-Vivo Real-Time Control of Protein Expression from Endogenous and Synthetic Gene Networks

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

Journal:

PLoS Computational Biology

Year:

2014

Language:

english

File:

PDF, 2.32 MB

english, 2014

36

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

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

Journal:

PLoS Computational Biology

Year:

2011

Language:

english

File:

PDF, 1.24 MB

english, 2011

37

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

Di Stefano, Marco, Rosa, Angelo, Belcastro, Vincenzo, di Bernardo, Diego, Micheletti, Cristian, Wasserman, Wyeth W.

Journal:

PLoS Computational Biology

Year:

2013

Language:

english

File:

PDF, 4.79 MB

english, 2013

38

Metabolic Regulation of the Ultradian Oscillator Hes1 by Reactive Oxygen Species

Ventre, Simona, Indrieri, Alessia, Fracassi, Chiara, Franco, Brunella, Conte, Ivan, Cardone, Luca, di Bernardo, Diego

Journal:

Journal of Molecular Biology

Year:

2015

Language:

english

File:

PDF, 1.49 MB

english, 2015

39

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

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

Journal:

Nature Communications

Year:

2014

Language:

english

File:

PDF, 3.81 MB

english, 2014

40

In Vivo Real-Time Control of Gene Expression: A Comparative Analysis of Feedback Control Strategies in Yeast

Fiore, Gianfranco, Perrino, Giansimone, di Bernardo, Mario, di Bernardo, Diego

Journal:

ACS Synthetic Biology

Year:

2015

Language:

english

File:

PDF, 2.80 MB

english, 2015

41

Identification of small molecules enhancing autophagic function from drug network analysis

Iorio, Francesco, Isacchi, Antonella, di Bernardo, Diego, Brunetti-Pierri, Nicola

Journal:

Year:

2010

Language:

english

File:

PDF, 388 KB

english, 2010

42

Evaluation of a systems biology approach to identify pharmacological correctors of the mutant CFTR chloride channel

Pesce, Emanuela, Gorrieri, Giulia, Sirci, Francesco, Napolitano, Francesco, Carrella, Diego, Caci, Emanuela, Tomati, Valeria, Zegarra-Moran, Olga, di Bernardo, Diego, Galietta, Luis J.V.

Journal:

Journal of Cystic Fibrosis

Year:

2016

Language:

english

File:

PDF, 1.88 MB

english, 2016

43

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

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

Journal:

Year:

2015

Language:

english

File:

PDF, 444 KB

english, 2015

44

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

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

Journal:

BMC Bioinformatics

Year:

2015

Language:

english

File:

PDF, 888 KB

english, 2015

45

In Silico Modeling of Liver Metabolism in a Human Disease Reveals a Key Enzyme for Histidine and Histamine Homeostasis

Pagliarini, Roberto, Castello, Raffaele, Napolitano, Francesco, Borzone, Roberta, Annunziata, Patrizia, Mandrile, Giorgia, De Marchi, Mario, Brunetti-Pierri, Nicola, di Bernardo, Diego

Journal:

Year:

2016

Language:

english

File:

PDF, 1.45 MB

english, 2016

46

Linking network topology to function

di Bernardo, Diego

Journal:

Physics of Life Reviews

Year:

2016

Language:

english

File:

PDF, 141 KB

english, 2016

47

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

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

Journal:

Nature Communications

Year:

2017

Language:

english

File:

PDF, 1.13 MB

english, 2017

48

[IEEE 2016 IEEE 55th Conference on Decision and Control (CDC) - Las Vegas, NV, USA (2016.12.12-2016.12.14)] 2016 IEEE 55th Conference on Decision and Control (CDC) - Modelling, simulation and control of single cell expression dynamics of the galactose-inducible promoter in yeast

Perrino, Giansimone, di Bernardo, Diego

Year:

2016

Language:

english

File:

PDF, 1.94 MB

english, 2016

49

Control of gene expression for the study of neurodegenerative disorders: a proof-of-principle experimental study

Perrino, Giansimone, Wilson, Cathal, Santorelli, Marco, di Bernardo, Diego

Journal:

IFAC-PapersOnLine

Year:

2016

Language:

english

File:

PDF, 586 KB

english, 2016

50

From a discrete to continuous actuation for improved real-time control of gene expression in mammalian cells

Postiglione, Lorena, Santorelli, Marco, Tumaini, Barbara, di Bernardo, Diego

Journal:

IFAC-PapersOnLine

Year:

2016

Language:

english

File:

PDF, 683 KB

english, 2016