List of works - Diego di Bernardo

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

article

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

scientific article

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

scientific article published on 6 March 2013

A mouse embryonic stem cell bank for inducible overexpression of human chromosome 21 genes

scientific article

A multi-step approach to time series analysis and gene expression clustering.

scientific article

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

scientific article

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

A parallel implementation of the network identification by multiple regression (NIR) algorithm to reverse-engineer regulatory gene networks

scientific article

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

scientific article

A single-cell analysis of breast cancer cell lines to study tumour heterogeneity and drug response

scientific article published on 31 March 2022

A transcriptomic study of Williams-Beuren syndrome associated genes in mouse embryonic stem cells

scientific article published on 06 November 2019

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

scientific article published on 02 October 2019

A yeast synthetic network for in vivo assessment of reverse-engineering and modeling approaches

scientific article

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

scientific article published on 27 May 2016

Analysis, design and implementation of a novel scheme for in-vivo control of synthetic gene regulatory networks

article

Author Correction: Impaired mitophagy links mitochondrial disease to epithelial stress in methylmalonyl-CoA mutase deficiency

scientific article published on 01 April 2020

Automatic Control of Gene Expression in Mammalian Cells

scientific article

Autophagosome-lysosome fusion triggers a lysosomal response mediated by TLR9 and controlled by OCRL

scientific article published on 11 July 2016

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

scientific article published on 28 October 2015

Building Maps of Drugs Mode-of-Action from Gene Expression Data

article

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

scientific article (publication date: March 2005)

CoGemiR: a comparative genomics microRNA database

scientific article

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

scientific article

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

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

scientific article published on 25 August 2017

Computational Drug Networks: a computational approach to elucidate drug mode of action and to facilitate drug repositioning for neurodegenerative diseases

scholarly article by Francesco Sirci et al published 2016 in Drug discovery today. Disease models

Computational drugs repositioning identifies inhibitors of oncogenic PI3K/AKT/P70S6K-dependent pathways among FDA-approved compounds

scientific article published on 16 August 2016

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

scientific article

Computer Model for Study of Cardiac Repolarization

article

Construction and modelling of an inducible positive feedback loop stably integrated in a mammalian cell-line

scientific article

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

article

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

scientific article

Deficiency of multidrug resistance 2 contributes to cell transformation through oxidative stress

scientific article

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

scientific article published on 12 June 2010

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

scientific article published in February 2011

Design and implementation of a feedback control strategy for IRMA, a novel synthetic gene regulatory network

article

Differential Equation Based Reverse-Engineering Algorithms: Pros and Cons

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

scientific article published on 6 June 2013

Direct targets of the TRP63 transcription factor revealed by a combination of gene expression profiling and reverse engineering

scientific article published on 25 April 2008

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

scientific article published on 28 September 2015

Effect of Lead Exclusion for the Manual Measurement of QT Dispersion

scientific article published on 01 January 2001

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

scientific article published on 01 May 2002

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

scientific article published on 10 May 2012

Erratum: TFEB controls cellular lipid metabolism through a starvation-induced autoregulatory loop

scholarly article published in Nature Cell Biology

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

scientific article published on 10 March 2016

Explaining the T-wave shape in the ECG

scientific article published in Nature

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

scientific article published on 5 September 2014

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

article

GADD34 is a modulator of autophagy during starvation

scientific article published on 25 September 2020

Gene ontology fuzzy-enrichment analysis to investigate drug mode-of-action

article

Glatiramer Acetate modulates ion channels expression and calcium homeostasis in B cell of patients with relapsing-remitting multiple sclerosis

scientific article published on 12 March 2019

Goblet Cell Hyperplasia Requires High Bicarbonate Transport To Support Mucin Release

scientific article published on 27 October 2016

Guest Editorial.

scientific article

High-Throughput Analysis of the Drug Mode of Action of PB28, MC18 and MC70, Three Cyclohexylpiperazine Derivative New Molecules

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

scientific article published on 26 January 2016

How to infer gene networks from expression profiles

scientific article published on 13 February 2007

How to turn a genetic circuit into a synthetic tunable oscillator, or a bistable switch

scientific article

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

scientific article published on 22 April 2012

Identification of small molecules enhancing autophagic function from drug network analysis

scientific article

Identification of small molecules enhancing autophagic function from drug network analysis

article

Identifying network of drug mode of action by gene expression profiling

scientific article

Impaired mitophagy links mitochondrial disease to epithelial stress in methylmalonyl-CoA mutase deficiency

scientific article published on 20 February 2020

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

scientific article published on 26 May 2016

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

scientific article published on 10 November 2015

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

scientific article

Inference of gene networks from temporal gene expression profiles.

scientific article published in September 2007

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

scientific article

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

scientific article (publication date: 4 July 2003)

Linear matrix inequalities approach to reconstruction of biological networks.

scientific article published in May 2007

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

scientific article published on 21 June 2016

MANIA: A Gene Network Reverse Algorithm for Compounds Mode-of-Action and Genes Interactions Inference

article

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

scientific article published on 20 February 2014

Metabolic regulation of the ultradian oscillator Hes1 by reactive oxygen species

scientific article

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

scientific article published on January 2013

Modeling RNA interference in mammalian cells

scientific article

Modeling the Cell Cycle of Fission Yeast by Means of Piecewise Linear Systems

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

Modelling, simulation and control of single cell expression dynamics of the galactose-inducible promoter in yeast

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

scientific article published in March 2009

Network based elucidation of drug response: from modulators to targets

scientific article

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

scientific article published on 01 January 2002

PML-RARA-associated cooperating mutations belong to a transcriptional network that is deregulated in myeloid leukemias.

scientific article published on 27 December 2016

Parallel Computing Algorithms for Reverse-Engineering and Analysis of Genome-Wide Gene Regulatory Networks from Gene Expression Profiles

article

Predicting synthetic gene networks.

scientific article published in January 2012

Predictive Signatures Inform the Effective Repurposing of Decitabine to Treat KRAS-Dependent Pancreatic Ductal Adenocarcinoma

scientific article published on 05 September 2019

Quantification of T Wave Shape Changes Following Exercise

scientific article published on 01 August 2002

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

scientific article published on 01 April 2019

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

scientific article published on 10 May 2018

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

article

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

scientific journal article

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

scientific article published in May 2012

Reverse engineering gene network identifies new dysferlin-interacting proteins

scientific article published on 30 November 2010

Reverse engineering transcriptional gene networks

scientific article published on January 2014

Simulation of Heartbeat Dynamics: A Nonlinear Model

article

Systems and Synthetic biology: tackling genetic networks and complex diseases.

scientific article published on 04 March 2009

TFEB controls cellular lipid metabolism through a starvation-induced autoregulatory loop

scientific article published on 21 April 2013

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

scientific article published on 19 January 2017

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

scientific article

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

scientific article published on 23 July 2011

Transcriptional network dynamics in macrophage activation

scientific article published on 12 May 2006

Unravelling druggable signalling networks that control F508del-CFTR proteostasis

scientific article published on 23 December 2015

ddbRNA: detection of conserved secondary structures in multiple alignments

scientific article published in September 2003

List of works by Diego di Bernardo

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

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

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

A mouse embryonic stem cell bank for inducible overexpression of human chromosome 21 genes

A multi-step approach to time series analysis and gene expression clustering.

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

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

A parallel implementation of the network identification by multiple regression (NIR) algorithm to reverse-engineer regulatory gene networks

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

A single-cell analysis of breast cancer cell lines to study tumour heterogeneity and drug response

A transcriptomic study of Williams-Beuren syndrome associated genes in mouse embryonic stem cells

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

A yeast synthetic network for in vivo assessment of reverse-engineering and modeling approaches

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

Analysis, design and implementation of a novel scheme for in-vivo control of synthetic gene regulatory networks

Author Correction: Impaired mitophagy links mitochondrial disease to epithelial stress in methylmalonyl-CoA mutase deficiency

Automatic Control of Gene Expression in Mammalian Cells

Autophagosome-lysosome fusion triggers a lysosomal response mediated by TLR9 and controlled by OCRL

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

Building Maps of Drugs Mode-of-Action from Gene Expression Data

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

CoGemiR: a comparative genomics microRNA database

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

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

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

Computational Drug Networks: a computational approach to elucidate drug mode of action and to facilitate drug repositioning for neurodegenerative diseases

Computational drugs repositioning identifies inhibitors of oncogenic PI3K/AKT/P70S6K-dependent pathways among FDA-approved compounds

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

Computer Model for Study of Cardiac Repolarization

Construction and modelling of an inducible positive feedback loop stably integrated in a mammalian cell-line

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

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

Deficiency of multidrug resistance 2 contributes to cell transformation through oxidative stress

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

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

Design and implementation of a feedback control strategy for IRMA, a novel synthetic gene regulatory network

Differential Equation Based Reverse-Engineering Algorithms: Pros and Cons

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

Direct targets of the TRP63 transcription factor revealed by a combination of gene expression profiling and reverse engineering

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

Effect of Lead Exclusion for the Manual Measurement of QT Dispersion

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

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

Erratum: TFEB controls cellular lipid metabolism through a starvation-induced autoregulatory loop

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

Explaining the T-wave shape in the ECG

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

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

GADD34 is a modulator of autophagy during starvation

Gene ontology fuzzy-enrichment analysis to investigate drug mode-of-action

Glatiramer Acetate modulates ion channels expression and calcium homeostasis in B cell of patients with relapsing-remitting multiple sclerosis

Goblet Cell Hyperplasia Requires High Bicarbonate Transport To Support Mucin Release

Guest Editorial.

High-Throughput Analysis of the Drug Mode of Action of PB28, MC18 and MC70, Three Cyclohexylpiperazine Derivative New Molecules

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

How to infer gene networks from expression profiles

How to turn a genetic circuit into a synthetic tunable oscillator, or a bistable switch

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

Identification of small molecules enhancing autophagic function from drug network analysis

Identification of small molecules enhancing autophagic function from drug network analysis

Identifying network of drug mode of action by gene expression profiling

Impaired mitophagy links mitochondrial disease to epithelial stress in methylmalonyl-CoA mutase deficiency

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

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

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

Inference of gene networks from temporal gene expression profiles.

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

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

Linear matrix inequalities approach to reconstruction of biological networks.

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

MANIA: A Gene Network Reverse Algorithm for Compounds Mode-of-Action and Genes Interactions Inference

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

Metabolic regulation of the ultradian oscillator Hes1 by reactive oxygen species

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

Modeling RNA interference in mammalian cells

Modeling the Cell Cycle of Fission Yeast by Means of Piecewise Linear Systems

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

Modelling, simulation and control of single cell expression dynamics of the galactose-inducible promoter in yeast

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