List of works - Pietro Liò

A Fine-Grained IoT Data Access Control Scheme Combining Attribute-Based Encryption and Blockchain

scientific article published in 2021

A Hybrid of Metabolic Flux Analysis and Bayesian Factor Modeling for Multiomic Temporal Pathway Activation.

scientific article published on 9 April 2015

A Multi-modal Convolutional Neural Network Framework for the Prediction of Alzheimer's Disease

scientific article published on 01 July 2018

A class-contrastive human-interpretable machine learning approach to predict mortality in severe mental illness

scientific article published on 8 December 2021

A design automation framework for computational bioenergetics in biological networks.

scientific article published in October 2013

A study on multi-omic oscillations in Escherichia coli metabolic networks

scientific article published on 09 July 2018

Advances in Artificial Life: Synthesis and Simulation of Living Systems: Editorial

scientific article published on 06 November 2015

Advances in translational biomedicine from systems approaches

scientific article published on 14 August 2014

An LTE Authentication and Key Agreement Protocol Based on the ECC Self-Certified Public Key

scientific article published on 26 September 2022

Analyzing seasonality of tuberculosis across Indian states and union territories.

scientific article published on 18 March 2015

Animal inference on human mitochondrial diseases.

scientific article

Bayesian Melding Approach to Estimate the Reproduction Number for Tuberculosis Transmission in Indian States and Union Territories.

scientific article published on 16 July 2015

Bioremediation in marine ecosystems: a computational study combining ecological modeling and flux balance analysis.

scientific article published on 12 September 2014

Cancer Markers Selection Using Network-Based Cox Regression: A Methodological and Computational Practice.

scientific article published on 17 June 2016

Cell graph neural networks enable the precise prediction of patient survival in gastric cancer

scientific article published in 2022

CiliateGEM: an open-project and a tool for predictions of ciliate metabolic variations and experimental condition design

scientific article published on 30 November 2018

Collective human mobility pattern from taxi trips in urban area.

scientific article

Combining Pathway Identification and Breast Cancer Survival Prediction via Screening-Network Methods.

scientific article

Community structure in social networks: applications for epidemiological modelling.

scientific article

Computational Modeling, Formal Analysis, and Tools for Systems Biology

scientific article

CytoCom: a Cytoscape app to visualize, query and analyse disease comorbidity networks

scientific article published on 7 November 2014

Distance-Based Opportunistic Mobile Data Offloading.

scientific article

Distinct epigenomic features in end-stage failing human hearts

scientific article

Draft genomes of three Antarctic Psychrobacter strains producing antimicrobial compounds against Burkholderia cepacia complex, opportunistic human pathogens.

scientific article published on 5 January 2014

DrugClust: A machine learning approach for drugs side effects prediction.

scientific article published on 30 March 2017

Efficient behavior of photosynthetic organelles via Pareto optimality, identifiability, and sensitivity analysis

scientific article

Erratum: Predictive analytics of environmental adaptability in multi-omic network models

scientific article published on 20 May 2016

Exploring the complexity of pathway-drug relationships using latent Dirichlet allocation.

scientific article published on 24 August 2014

FisHiCal: an R package for iterative FISH-based calibration of Hi-C data.

scientific article

Forecasting ultra-early intensive care strain from COVID-19 in England

scientific article (preprint)

Genetic effects of welding fumes on the progression of neurodegenerative diseases

scientific article published on 17 December 2018

Genome-Scale Metabolic Network Reconstruction

scientific article published on 01 January 2015

Genome-scale metabolic reconstruction and constraint-based modelling of the Antarctic bacterium Pseudoalteromonas haloplanktis TAC125.

scientific article published on 30 June 2014

Global gene expression profiling and senescence biomarker analysis of hESC exposed to H2O2 induced non-cytotoxic oxidative stress.

scientific article published on 05 July 2017

Graph Attention Networks

scholarly article

Identification of sensitive enzymes in the photosynthetic carbon metabolism.

scientific article published in January 2012

Identification of targeted analyte clusters for studies of schizophrenia

scientific article

Integrating multi-omic features exploiting Chromosome Conformation Capture data.

scientific article

Intra- and inter-chromosomal interactions correlate with CTCF binding genome wide.

scientific article published on November 2010

Investigating meta-approaches for reconstructing gene networks in a mammalian cellular context.

scientific article

Making life difficult for Clostridium difficile: augmenting the pathogen's metabolic model with transcriptomic and codon usage data for better therapeutic target characterization

scientific article

MeDuSa: a multi-draft based scaffolder.

scientific article published on 25 March 2015

Metabolic disorders: how can systems modelling help?

scientific article published on 12 February 2016

Modeling Social Groups, Policies and Cognitive Behavior in COVID-19 Epidemic Phases. Basic Scenarios

scholarly article published on Substantia in 2020

Modeling TGF-β in early stages of cancer tissue dynamics.

scientific article

Modelling circulating tumour cells for personalised survival prediction in metastatic breast cancer

scientific article published on 15 May 2015

Modelling osteomyelitis

scientific article

MtPAN(3): site-class specific amino acid replacement matrices for mitochondrial proteins of Pancrustacea and Collembola.

scientific article published on 10 February 2014

Multi -omics and metabolic modelling pipelines: challenges and tools for systems microbiology

scientific article

Multi-Target Analysis and Design of Mitochondrial Metabolism.

scientific article published on 16 September 2015

Multilevel Computational Modeling and Quantitative Analysis of Bone Remodeling ⬇️

scientific article published on September 1, 2012

Multiplex methods provide effective integration of multi-omic data in genome-scale models

scientific article

Muxstep: an open-source C ++ multiplex HMM library for making inferences on multiple data types.

scientific article

Network regularised Cox regression and multiplex network models to predict disease comorbidities and survival of cancer

scientific article published on 19 October 2015

Network-based analysis of comorbidities risk during an infection: SARS and HIV case studies

scientific article

Neural network fusion: a novel CT-MR Aortic Aneurysm image segmentation method

scientific article published on 01 March 2018

NuChart: an R package to study gene spatial neighbourhoods with multi-omics annotations.

scientific article

On synergy between ultrahigh throughput screening and machine learning in biocatalyst engineering

scientific article published in 2024

Opportunities for community awareness platforms in personal genomics and bioinformatics education.

scientific article published on 30 August 2016

Optimization of Multi-Omic Genome-Scale Models: Methodologies, Hands-on Tutorial, and Perspectives.

scientific article published in January 2018

Parapred: antibody paratope prediction using convolutional and recurrent neural networks

scientific article published on 01 September 2018

Pareto optimality in organelle energy metabolism analysis

scientific article published in July 2013

Pathway-based Bayesian inference of drug-disease interactions

scientific article

Physio-environmental sensing and live modeling.

scientific article published on 30 January 2013

Predictive analytics of environmental adaptability in multi-omic network models.

scientific article

Quantifying the Role of Homophily in Human Cooperation Using Multiplex Evolutionary Game Theory

scientific article published on 23 October 2015

Quantifying the propagation of distress and mental disorders in social networks

scientific article published on 22 March 2018

Robust design of microbial strains.

scientific article published on 7 October 2012

STAble: a novel approach to de novo assembly of RNA-seq data and its application in a metabolic model network based metatranscriptomic workflow

scientific article published on 09 July 2018

Seeing the wood for the trees: a forest of methods for optimization and omic-network integration in metabolic modelling.

scientific article published on 30 May 2017

Simultaneous Transients of Intracranial Pressure and Heart Rate in Traumatic Brain Injury: Methods of Analysis

scientific article published on 01 January 2018

Single-cell RNA-sequencing uncovers transcriptional states and fate decisions in haematopoiesis

scientific article

Social dynamics modeling of chrono-nutrition

scientific article published on 30 January 2019

State of the Art and Potentialities of Graph-level Learning

scientific article published on 13 September 2024

Statistical approaches to use a model organism for regulatory sequences annotation of newly sequenced species

scientific article

Statistical mechanics of rumour spreading in network communities

Stochastic analysis of a miRNA-protein toggle switch.

scientific article published on 30 June 2011

System Neural Network: Evolution and Change Based Structure Learning

scientific article published in 2022

Systems medicine of inflammaging.

scientific article published on 24 August 2015

The BioMart community portal: an innovative alternative to large, centralized data repositories

scientific article (publication date: July 2015)

The Genome Conformation As an Integrator of Multi-Omic Data: The Example of Damage Spreading in Cancer

scientific article

The Impact of Heterogeneity and Awareness in Modeling Epidemic Spreading on Multiplex Networks

scientific article (publication date: 16 November 2016)

The onset of type 2 diabetes: proposal for a multi-scale model.

scientific article published on 31 October 2013

The puzzling role of CXCR4 in human immunodeficiency virus infection.

scientific article published on 13 January 2013

TrafficMOT: A Challenging Dataset for Multi-Object Tracking in Complex Traffic Scenarios

scientific article published on 26 October 2024

Transcriptome and proteome analysis of Salmonella enterica serovar Typhimurium systemic infection of wild type and immune-deficient mice.

scientific article

Warped Matrix Factorisation for Multi-view Data Integration

comoR: a software for disease comorbidity risk assessment.

scientific article published on 23 May 2014

List of works by Pietro Liò

A Fine-Grained IoT Data Access Control Scheme Combining Attribute-Based Encryption and Blockchain

A Hybrid of Metabolic Flux Analysis and Bayesian Factor Modeling for Multiomic Temporal Pathway Activation.

A Multi-modal Convolutional Neural Network Framework for the Prediction of Alzheimer's Disease

A class-contrastive human-interpretable machine learning approach to predict mortality in severe mental illness

A design automation framework for computational bioenergetics in biological networks.

A study on multi-omic oscillations in Escherichia coli metabolic networks

Advances in Artificial Life: Synthesis and Simulation of Living Systems: Editorial

Advances in translational biomedicine from systems approaches

An LTE Authentication and Key Agreement Protocol Based on the ECC Self-Certified Public Key

Analyzing seasonality of tuberculosis across Indian states and union territories.

Animal inference on human mitochondrial diseases.

Bayesian Melding Approach to Estimate the Reproduction Number for Tuberculosis Transmission in Indian States and Union Territories.

Bioremediation in marine ecosystems: a computational study combining ecological modeling and flux balance analysis.

Cancer Markers Selection Using Network-Based Cox Regression: A Methodological and Computational Practice.

Cell graph neural networks enable the precise prediction of patient survival in gastric cancer

CiliateGEM: an open-project and a tool for predictions of ciliate metabolic variations and experimental condition design

Collective human mobility pattern from taxi trips in urban area.

Combining Pathway Identification and Breast Cancer Survival Prediction via Screening-Network Methods.

Community structure in social networks: applications for epidemiological modelling.

Computational Modeling, Formal Analysis, and Tools for Systems Biology

CytoCom: a Cytoscape app to visualize, query and analyse disease comorbidity networks

Distance-Based Opportunistic Mobile Data Offloading.

Distinct epigenomic features in end-stage failing human hearts

Draft genomes of three Antarctic Psychrobacter strains producing antimicrobial compounds against Burkholderia cepacia complex, opportunistic human pathogens.

DrugClust: A machine learning approach for drugs side effects prediction.

Efficient behavior of photosynthetic organelles via Pareto optimality, identifiability, and sensitivity analysis

Erratum: Predictive analytics of environmental adaptability in multi-omic network models

Exploring the complexity of pathway-drug relationships using latent Dirichlet allocation.

FisHiCal: an R package for iterative FISH-based calibration of Hi-C data.

Forecasting ultra-early intensive care strain from COVID-19 in England

Genetic effects of welding fumes on the progression of neurodegenerative diseases

Genome-Scale Metabolic Network Reconstruction

Genome-scale metabolic reconstruction and constraint-based modelling of the Antarctic bacterium Pseudoalteromonas haloplanktis TAC125.

Global gene expression profiling and senescence biomarker analysis of hESC exposed to H2O2 induced non-cytotoxic oxidative stress.

Graph Attention Networks

Identification of sensitive enzymes in the photosynthetic carbon metabolism.

Identification of targeted analyte clusters for studies of schizophrenia

Integrating multi-omic features exploiting Chromosome Conformation Capture data.

Intra- and inter-chromosomal interactions correlate with CTCF binding genome wide.

Investigating meta-approaches for reconstructing gene networks in a mammalian cellular context.

Making life difficult for Clostridium difficile: augmenting the pathogen's metabolic model with transcriptomic and codon usage data for better therapeutic target characterization

MeDuSa: a multi-draft based scaffolder.

Metabolic disorders: how can systems modelling help?

Modeling Social Groups, Policies and Cognitive Behavior in COVID-19 Epidemic Phases. Basic Scenarios

Modeling TGF-β in early stages of cancer tissue dynamics.

Modelling circulating tumour cells for personalised survival prediction in metastatic breast cancer

Modelling osteomyelitis

MtPAN(3): site-class specific amino acid replacement matrices for mitochondrial proteins of Pancrustacea and Collembola.

Multi -omics and metabolic modelling pipelines: challenges and tools for systems microbiology

Multi-Target Analysis and Design of Mitochondrial Metabolism.

Multilevel Computational Modeling and Quantitative Analysis of Bone Remodeling ⬇️

Multiplex methods provide effective integration of multi-omic data in genome-scale models

Muxstep: an open-source C ++ multiplex HMM library for making inferences on multiple data types.

Network regularised Cox regression and multiplex network models to predict disease comorbidities and survival of cancer

Network-based analysis of comorbidities risk during an infection: SARS and HIV case studies

Neural network fusion: a novel CT-MR Aortic Aneurysm image segmentation method

NuChart: an R package to study gene spatial neighbourhoods with multi-omics annotations.

On synergy between ultrahigh throughput screening and machine learning in biocatalyst engineering

Opportunities for community awareness platforms in personal genomics and bioinformatics education.

Optimization of Multi-Omic Genome-Scale Models: Methodologies, Hands-on Tutorial, and Perspectives.

Parapred: antibody paratope prediction using convolutional and recurrent neural networks

Pareto optimality in organelle energy metabolism analysis

Pathway-based Bayesian inference of drug-disease interactions

Physio-environmental sensing and live modeling.

Predictive analytics of environmental adaptability in multi-omic network models.

Quantifying the Role of Homophily in Human Cooperation Using Multiplex Evolutionary Game Theory

Quantifying the propagation of distress and mental disorders in social networks

Robust design of microbial strains.

STAble: a novel approach to de novo assembly of RNA-seq data and its application in a metabolic model network based metatranscriptomic workflow

Seeing the wood for the trees: a forest of methods for optimization and omic-network integration in metabolic modelling.

Simultaneous Transients of Intracranial Pressure and Heart Rate in Traumatic Brain Injury: Methods of Analysis

Single-cell RNA-sequencing uncovers transcriptional states and fate decisions in haematopoiesis

Social dynamics modeling of chrono-nutrition

State of the Art and Potentialities of Graph-level Learning

Statistical approaches to use a model organism for regulatory sequences annotation of newly sequenced species

Statistical mechanics of rumour spreading in network communities

Stochastic analysis of a miRNA-protein toggle switch.

System Neural Network: Evolution and Change Based Structure Learning

Systems medicine of inflammaging.