Diego di Bernardo

Diego di Bernardo

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Diego di Bernardo

Diego di Bernardo

Publications by authors named "Diego di Bernardo"

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A tunable dual-input system for on-demand dynamic gene expression regulation.

Nat Commun 2019 Oct 2;10(1):4481. Epub 2019 Oct 2.

Department of Engineering Mathematics, University of Bristol, Bristol, BS8 1UB, UK.

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http://dx.doi.org/10.1038/s41467-019-12329-9DOI Listing
October 2019

A Tool for Visualization and Analysis of Single-Cell RNA-Seq Data Based on Text Mining.

Front Genet 2019 9;10:734. Epub 2019 Aug 9.

University of Naples Federico II, Department of Chemical Materials and Industrial Engineering, Naples, Italy.

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http://dx.doi.org/10.3389/fgene.2019.00734DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6696874PMC
August 2019

Quantitative Characterization of α-Synuclein Aggregation in Living Cells through Automated Microfluidics Feedback Control.

Cell Rep 2019 Apr;27(3):916-927.e5

Telethon Institute of Genetics and Medicine (TIGEM), Via Campi Flegrei 34, 80078 Pozzuoli (NA), Italy; Department of Chemical, Materials and Industrial Production Engineering, University of Naples Federico II, Piazzale Tecchio 80, 80125 Naples, Italy. Electronic address:

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http://dx.doi.org/10.1016/j.celrep.2019.03.081DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6484782PMC
April 2019

Regulation of Gene Expression and Signaling Pathway Activity in Mammalian Cells by Automated Microfluidics Feedback Control.

ACS Synth Biol 2018 11 22;7(11):2558-2565. Epub 2018 Oct 22.

Telethon Institute of Genetics and Medicine , Via Campi Flegrei 34 , 80078 Pozzuoli (NA), Italy.

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http://pubs.acs.org/doi/10.1021/acssynbio.8b00235
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http://dx.doi.org/10.1021/acssynbio.8b00235DOI Listing
November 2018

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

Bioinformatics 2018 05;34(9):1498-1505

Systems and Synthetic Biology Lab, Telethon Institute of Genetics and Medicine (TIGEM), Pozzuoli (NA) 80078, Italy.

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https://academic.oup.com/bioinformatics/article/34/9/1498/47
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http://dx.doi.org/10.1093/bioinformatics/btx800DOI Listing
May 2018

Reconstitution of an Ultradian Oscillator in Mammalian Cells by a Synthetic Biology Approach.

ACS Synth Biol 2018 05 10;7(5):1447-1455. Epub 2018 May 10.

Telethon Institute of Genetics and Medicine (TIGEM) , 80078 Pozzuoli , Italy.

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http://dx.doi.org/10.1021/acssynbio.8b00083DOI Listing
May 2018

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

NPJ Syst Biol Appl 2017 25;3:23. Epub 2017 Aug 25.

Telethon Institute of Genetics and Medicine (TIGEM), System Biology and Bioinformatics lab. and High Content Screening facility, Via Campi Flegrei 34, 80078 Pozzuoli (NA), Italy.

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http://www.nature.com/articles/s41540-017-0022-3
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http://dx.doi.org/10.1038/s41540-017-0022-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5572457PMC
August 2017

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

Nat Commun 2017 01 19;8:14126. Epub 2017 Jan 19.

The Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, Center for Reproductive Sciences, University of California, San Francisco, San Francisco, California 94143, USA.

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http://dx.doi.org/10.1038/ncomms14126DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5253645PMC
January 2017

Guest Editorial.

IET Syst Biol 2016 Oct;10(5):167

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http://dx.doi.org/10.1049/iet-syb.2016.0038DOI Listing
October 2016

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

Nucleic Acids Res 2016 07 27;44(12):5773-84. Epub 2016 May 27.

Telethon Institute of Genetics and Medicine (TIGEM), Via Campi Flegrei 34, 80078 Pozzuoli, Italy Dept. Of Chemical, Materials and Industrial Production Engineering, University of Naples 'Federico II', Piazzale Tecchio 80, 80125 Naples, Italy

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http://dx.doi.org/10.1093/nar/gkw486DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4937338PMC
July 2016

Linking network topology to function: Comment on "Drivers of structural features in gene regulatory networks: From biophysical constraints to biological function" by O.C. Martin, A. Krzywicki and M. Zagorski.

Phys Life Rev 2016 Jul 21;17:159-60. Epub 2016 Jun 21.

Dept. of Chemical, Materials and Industrial Production Engineering, University of Naples "Federico II", Piazzale Tecchio, 80, 80125 Naples, Italy; Telethon Institute of Genetics and Medicine, Via Dei Campi Flegrei 34, 80038 Pozzuoli (Naples), Italy. Electronic address:

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http://dx.doi.org/10.1016/j.plrev.2016.06.009DOI Listing
July 2016

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

Cell Rep 2016 06 26;15(10):2292-2300. Epub 2016 May 26.

Telethon Institute of Genetics and Medicine, 80078 Pozzuoli, Italy; Department of Chemical, Materials and Industrial Engineering, Federico II University, 80125 Naples, Italy. Electronic address:

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http://dx.doi.org/10.1016/j.celrep.2016.05.014DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4906368PMC
June 2016

Automatic Control of Gene Expression in Mammalian Cells.

ACS Synth Biol 2016 Apr 6;5(4):296-302. Epub 2015 Oct 6.

TeleThon Institute of Genetics and Medicine (TIGEM) , 80078 Pozzuoli, Italy.

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http://dx.doi.org/10.1021/acssynbio.5b00141DOI Listing
April 2016

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

ACS Synth Biol 2016 Feb 4;5(2):154-62. Epub 2015 Dec 4.

TeleThon Institute of Genetics and Medicine (TIGEM), 80078 Pozzuoli, Italy.

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http://dx.doi.org/10.1021/acssynbio.5b00135DOI Listing
February 2016

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

Nucleic Acids Res 2016 Feb 26;44(4):1525-40. Epub 2016 Jan 26.

Telethon Institute of Genetics and Medicine, via Campi Flegrei 34, 80078 Pozzuoli (NA), Italy Department of Biochemistry, Biophysics and General Pathology, Second University of Naples, via Luigi De Crecchio 7, 80138 Naples (NA), Italy

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http://dx.doi.org/10.1093/nar/gkw039DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4770244PMC
February 2016

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

Bioinformatics 2016 Jan 28;32(2):235-41. Epub 2015 Sep 28.

Systems and Synthetic Biology Lab, Telethon Institute of Genetics and Medicine (TIGEM), 80078 Pozzuoli (NA), Italy and Department of Electrical Engineering and Information Technology, University of Naples Federico II, 80125 Naples, Italy.

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http://dx.doi.org/10.1093/bioinformatics/btv536DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4795590PMC
January 2016

Metabolic regulation of the ultradian oscillator Hes1 by reactive oxygen species.

J Mol Biol 2015 May 18;427(10):1887-902. Epub 2015 Mar 18.

Telethon Institute of Genetics and Medicine, Via Campi Flegrei 34, Pozzuoli, 80078 Naples, Italy; Department of Electrical Engineering and Information Technology, University of Naples Federico II, 80138 Napoli, Italy. Electronic address:

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http://dx.doi.org/10.1016/j.jmb.2015.03.007DOI Listing
May 2015

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

BMC Genomics 2014 Aug 7;15:658. Epub 2014 Aug 7.

Telethon Institute of Genetics and Medicine (TIGEM), Naples, Italy.

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http://dx.doi.org/10.1186/1471-2164-15-658DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4137083PMC
August 2014

Reverse engineering transcriptional gene networks.

Methods Mol Biol 2014 ;1101:179-96

Faculty of Engineering, University of Naples "Federico II", Naples, Italy.

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http://dx.doi.org/10.1007/978-1-62703-721-1_10DOI Listing
June 2014

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

Bioinformatics 2014 Jun 20;30(12):1787-8. Epub 2014 Feb 20.

Telethon Institute of Genetics and Medicine, Via P. Castellino 111, 80131 Naples, Interactive SRL, Via Fratelli Bisogno 5, 83100 Avellino, Dip. di Studi Aziendali e Quantitativi Università degli studi di Napoli 'Parthenope', Via Generale Parisi 13, 80132 Naples, Institute for High-Performance Computing - ICAR - CNR, Via P. Castellino 111, 80131 Naples and Department of Electrical Engineering and Information Technology, University of Naples 'Federico II', Via Claudio 21, 80125 Naples, ItalyTelethon Institute of Genetics and Medicine, Via P. Castellino 111, 80131 Naples, Interactive SRL, Via Fratelli Bisogno 5, 83100 Avellino, Dip. di Studi Aziendali e Quantitativi Università degli studi di Napoli 'Parthenope', Via Generale Parisi 13, 80132 Naples, Institute for High-Performance Computing - ICAR - CNR, Via P. Castellino 111, 80131 Naples and Department of Electrical Engineering and Information Technology, University of Naples 'Federico II', Via Claudio 21, 80125 Naples, Italy.

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https://academic.oup.com/bioinformatics/article-lookup/doi/1
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http://dx.doi.org/10.1093/bioinformatics/btu058DOI Listing
June 2014

The phytoestrogen genistein modulates lysosomal metabolism and transcription factor EB (TFEB) activation.

J Biol Chem 2014 Jun 25;289(24):17054-69. Epub 2014 Apr 25.

From the Laboratory of Molecular Biology (affiliated with the University of Gdańsk), Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Wita Stwosza 59, 80-308 Gdańsk, Poland,

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http://dx.doi.org/10.1074/jbc.M114.555300DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4059147PMC
June 2014

In-vivo real-time control of protein expression from endogenous and synthetic gene networks.

PLoS Comput Biol 2014 May 15;10(5):e1003625. Epub 2014 May 15.

TeleThon Institute of Genetics and Medicine (TIGEM), Naples, Italy; Department of Electrical Engineering and Information Technology, University of Naples Federico II, Naples, Italy.

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http://dx.doi.org/10.1371/journal.pcbi.1003625DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4022480PMC
May 2014

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

Nat Commun 2013 ;4:2364

1] Telethon Institute of Genetics and Medicine (TIGEM), Via P. Castellino 111, 80131 Naples, Italy [2] Department of Biological Engineering, Massachusetts Institute of Technology. 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, USA [3].

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http://dx.doi.org/10.1038/ncomms3364DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3836244PMC
April 2014

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

BMC Syst Biol 2013 Dec 13;7:139. Epub 2013 Dec 13.

Telethon Institute of Genetics and Medicine, Naples, Italy.

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http://dx.doi.org/10.1186/1752-0509-7-139DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3878740PMC
December 2013

Colocalization of coregulated genes: a steered molecular dynamics study of human chromosome 19.

PLoS Comput Biol 2013 28;9(3):e1003019. Epub 2013 Mar 28.

International School for Advanced Studies, SISSA, Trieste, Italy.

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http://dx.doi.org/10.1371/journal.pcbi.1003019DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3610629PMC
November 2013

A genome-scale modeling approach to study inborn errors of liver metabolism: toward an in silico patient.

J Comput Biol 2013 May 6;20(5):383-97. Epub 2013 Mar 6.

Telethon Institute of Genetics and Medicine, Naples, Italy.

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http://dx.doi.org/10.1089/cmb.2012.0276DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3646339PMC
May 2013

Discovering drug mode of action using reverse-engineered gene networks.

Conf Proc IEEE Eng Med Biol Soc 2005 ;5:4739-42

Mukesh Bansal is PhD Student at Telethon Institute of Genetics and Medicine (TIGEM), Via P.Castellino 111, Naples 80131, Italy.

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http://dx.doi.org/10.1109/IEMBS.2005.1615530DOI Listing
October 2012

Reverse engineering and analysis of genome-wide gene regulatory networks from gene expression profiles using high-performance computing.

IEEE/ACM Trans Comput Biol Bioinform 2012 May-Jun;9(3):668-78

Telethon Institute of Genetics and Medicine-TIGEM, Via P. Castellino 111, Naples 80131, Italy.

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http://ieeexplore.ieee.org/document/5740843/
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http://dx.doi.org/10.1109/TCBB.2011.60DOI Listing
September 2012

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

FEBS Lett 2012 Jul 10;586(15):2122-8. Epub 2012 May 10.

Telethon Institute of Genetics and Medicine, Via P. Castellino 111, 80131 Naples, Italy.

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http://dx.doi.org/10.1016/j.febslet.2012.04.050DOI Listing
July 2012

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

Nat Cell Biol 2012 Apr 22;14(5):477-87. Epub 2012 Apr 22.

Institute for Cancer Genetics, Columbia University Medical Center, New York, New York 10032, USA.

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http://dx.doi.org/10.1038/ncb2490DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3635493PMC
April 2012

Predicting synthetic gene networks.

Methods Mol Biol 2012 ;813:57-81

Faculty of Engineering, University of Naples "Fecerico II", Naples, Italy.

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http://dx.doi.org/10.1007/978-1-61779-412-4_4DOI Listing
March 2012

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

J Math Biol 2011 May 12;62(5):685-706. Epub 2010 Jun 12.

Telethon Institute of Genetics and Medicine (TIGEM), 80131 Naples, Italy.

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http://dx.doi.org/10.1007/s00285-010-0350-zDOI Listing
May 2011

Reverse engineering gene network identifies new dysferlin-interacting proteins.

J Biol Chem 2011 Feb 30;286(7):5404-13. Epub 2010 Nov 30.

TIGEM-Telethon Institute of Genetics and Medicine, 80131 Naples, Italy.

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http://dx.doi.org/10.1074/jbc.M110.173559DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3037653PMC
February 2011

Design and construction of a versatile synthetic network for bistable gene expression in mammalian systems.

J Comput Biol 2011 Feb;18(2):195-203

Department of Engineering Mathematics, University of Bristol, Bristol, United Kingdom.

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http://dx.doi.org/10.1089/cmb.2010.0208DOI Listing
February 2011

Modeling RNA interference in mammalian cells.

BMC Syst Biol 2011 Jan 27;5:19. Epub 2011 Jan 27.

Telethon Institute of Genetics and Medicine (TIGEM), Naples, Italy.

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http://dx.doi.org/10.1186/1752-0509-5-19DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3040133PMC
January 2011

Identification of small molecules enhancing autophagic function from drug network analysis.

Autophagy 2010 Nov 16;6(8):1204-5. Epub 2010 Nov 16.

Telethon Institute of Genetics and Medicine, Naples, Italy.

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http://dx.doi.org/10.1073/pnas.1000138107DOI Listing
November 2010

NIRest: a tool for gene network and mode of action inference.

Ann N Y Acad Sci 2009 Mar;1158:257-64

Systems Biology Lab, Telethon Institute of Genetics and Medicine, Naples, Italy.

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http://dx.doi.org/10.1111/j.1749-6632.2008.03761.xDOI Listing
March 2009

Identifying network of drug mode of action by gene expression profiling.

J Comput Biol 2009 Feb;16(2):241-51

Systems and Synthetic Biology Lab, TeleThon Institute of Genetics and Medicine (TIGEM), Naples, Italy.

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http://dx.doi.org/10.1089/cmb.2008.10TTDOI Listing
February 2009

CoGemiR: a comparative genomics microRNA database.

BMC Genomics 2008 Oct 6;9:457. Epub 2008 Oct 6.

TIGEM Telethon Institute of Genetics and Medicine, Via Pietro Castellino 111, 80131 Naples Italy.

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http://dx.doi.org/10.1186/1471-2164-9-457DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2567348PMC
October 2008

How to infer gene networks from expression profiles.

Mol Syst Biol 2007 13;3:78. Epub 2007 Feb 13.

Telethon Institute of Genetics and Medicine, Via P Castellino, Naples, Italy.

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http://dx.doi.org/10.1038/msb4100120DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1828749PMC
March 2007

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

BMC Neurosci 2006 Oct 30;7 Suppl 1:S8. Epub 2006 Oct 30.

TIGEM, Telethon Institute of Genetics and Medicine, Naples, Italy.

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http://dx.doi.org/10.1186/1471-2202-7-S1-S8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1775048PMC
October 2006

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

Bioinformatics 2006 Apr 17;22(7):815-22. Epub 2006 Jan 17.

Telethon Institute of Genetics and Medicine, Via P. Castellino 111, 80131 Naples, Italy.

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http://dx.doi.org/10.1093/bioinformatics/btl003DOI Listing
April 2006

ddbRNA: detection of conserved secondary structures in multiple alignments.

Bioinformatics 2003 Sep;19(13):1606-11

Telethon Institute of Genetics and Medicine, Via P Castellino 111, 80133 Naples, Italy.

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http://dx.doi.org/10.1093/bioinformatics/btg229DOI Listing
September 2003

Inferring genetic networks and identifying compound mode of action via expression profiling.

Science 2003 Jul;301(5629):102-5

Center for BioDynamics and Department of Biomedical Engineering, Boston University, 44 Cummington Street, Boston, MA 02215, USA.

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http://dibernardo.tigem.it/files/papers/2003/1081900revisedt
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http://dx.doi.org/10.1126/science.1081900DOI Listing
July 2003

Quantification of T wave shape changes following exercise.

Pacing Clin Electrophysiol 2002 Aug;25(8):1230-4

Regional Medical Physics Department, Freeman Hospital, Newcastle upon Tyne, United Kingdom.

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http://doi.wiley.com/10.1046/j.1460-9592.2002.01230.x
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http://dx.doi.org/10.1046/j.1460-9592.2002.01230.xDOI Listing
August 2002

Effect of changes in heart rate and in action potential duration on the electrocardiogram T wave shape.

Physiol Meas 2002 May;23(2):355-64

Regional Medical Physics Department, Freeman Hospital, Newcastle upon Tyne, UK.

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May 2002

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

Cardiovasc Res 2002 Jan;53(1):202-8

Regional Medical Physics Department, Freeman Hospital, Newcastle-upon-Tyne NE7 7DN, UK.

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http://dx.doi.org/10.1016/s0008-6363(01)00439-4DOI Listing
January 2002