C. Angione

发表

Human Systems Biology and Metabolic Modelling: A Review—From Disease Metabolism to Precision Medicine

C. Angione, 2019, BioMed research international.

A Hybrid Flux Balance Analysis and Machine Learning Pipeline Elucidates Metabolic Adaptation in Cyanobacteria

C. Angione, S. Vijayakumar, P. Rahman, 2020, iScience.

Maxwell-Boltzmann and Bose-Einstein Distributions for the SAT Problem

Giuseppe Nicosia, C. Angione, A. Occhipinti, 2013 .

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

Naruemon Pratanwanich, P. Lio’, C. Angione, 2015, ACS synthetic biology.

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

P. Lio’, C. Angione, A. Occhipinti, 2018, BMC Bioinformatics.

Discrete Optimization Bose – Einstein condensation in satisfiability problems

Giuseppe Nicosia, C. Angione, G. Stracquadanio, 2013 .

Modelling pyruvate dehydrogenase under hypoxia and its role in cancer metabolism

C. Angione, F. Eyassu, Filmon Eyassu, 2017, Royal Society Open Science.

Pareto Optimality in Organelle Energy Metabolism Analysis

Pietro Liò, Giuseppe Nicosia, Jole Costanza, 2013, IEEE/ACM Transactions on Computational Biology and Bioinformatics.

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

P. Lio’, M. Marini, C. Angione, 2014, Front. Genet..

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

Pietro Liò, Claudio Angione, Sara Saheb Kashaf, 2017, BMC Systems Biology.

Bioinformatics Challenges and Potentialities in Studying Extreme Environments

Pietro Liò, Andrea Telatin, Ugur Sezerman, 2015, CIBB.

Design and strain selection criteria for bacterial communication networks

Pietro Liò, Giuseppe Nicosia, Jole Costanza, 2013, bioRxiv.

Social dynamics modeling of chrono-nutrition

Pietro Liò, Alessandro Di Stefano, Aurelio La Corte, 2019, PLoS Comput. Biol..

How to Compute with Metabolism in Bacteria?

Pietro Liò, Giuseppe Nicosia, Claudio Angione, 2012, ERCIM News.

A design automation framework for computational bioenergetics in biological networks.

Giuseppe Nicosia, Jole Costanza, Claudio Angione, 2013, Molecular bioSystems.

Rational design of organelle compartments in cells

P. Lio’, Giuseppe Nicosia, C. Angione, 2012 .

The Role of the Genome in the Evolution of the Complexity of Metabolic Machines

P. Lio’, Giuseppe Nicosia, C. Angione, 2013 .

Genome Sequencing Variations in the Octodon degus, an Unconventional Natural Model of Aging and Alzheimer's Disease

T. Holmes, B. Wilkinson, M. Coba, 2022, Frontiers in Aging Neuroscience.

A hybrid of multi-omics FBA and Bayesian factor modeling to identify pathway crosstalks

Naruemon Pratanwanich, P. Lio’, C. Angione, 2014 .

List of Algorithms Introduction

C. Angione, 2010 .

In silico engineering of Pseudomonas metabolism reveals new biomarkers for increased biosurfactant production

C. Angione, A. Occhipinti, F. Eyassu, 2018, PeerJ.

Loss of full-length dystrophin expression results in major cell-autonomous abnormalities in proliferating myoblasts

S. Robson, M. Korostyński, C. Angione, 2021, bioRxiv.

Clinical stratification improves the diagnostic accuracy of small omics datasets within machine learning and genome-scale metabolic modelling methods

C. Angione, G. Magazzù, Guido Zampieri, 2022, Comput. Biol. Medicine.

Whole‐genome sequencing and genome‐scale metabolic modeling of Chromohalobacter canadensis 85B to explore its salt tolerance and biotechnological use

C. Angione, M. Mutlu, Pınar Aytar Çelik, 2022, MicrobiologyOpen.

Mechanistic effects of influenza in bronchial cells through poly-omic genome-scale modelling

C. Angione, E. Yaneske, 2018 .

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

Claudio Angione, Pietro Lió, P. Lio’, 2016, Scientific Reports.

Computational methods for multi-omic models of cell metabolism and their importance for theoretical computer science

Claudio Angione, C. Angione, 2015 .

Predictive analytics of environmental adaptability in multi-omic network models

Claudio Angione, Pietro Lió, P. Lio’, 2015, Scientific Reports.

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

Giuseppe Nicosia, Alessio Papini, Jole Costanza, 2013, ACS synthetic biology.

Metatranscriptomics-guided genome-scale metabolic modeling of microbial communities

S. Campanaro, C. Angione, L. Treu, 2023, Cell reports methods.

Integrating genome-scale metabolic modelling and transfer learning for human gene regulatory network reconstruction

Michelangelo Ceci, C. Angione, P. Mignone, 2021, Bioinform..

Modeling Customer Experience in a Contact Center through Process Log Mining

Claudio Angione, Guido Zampieri, Yifeng Zeng, 2021, ACM Trans. Intell. Syst. Technol..

The poly-omics of ageing through individual-based metabolic modelling

Claudio Angione, Elisabeth Yaneske, C. Angione, 2018, BMC Bioinformatics.

Using machine learning as a surrogate model for agent-based simulations

C. Angione, E. Silverman, E. Yaneske, 2022, PloS one.

Situating agent-based modelling in population health research pdf

Eric Silverman, Claudio Angione, Jonatan Almagor, 2020, Emerging Themes in Epidemiology.

Using Machine Learning to Emulate Agent-Based Simulations

C. Angione, E. Silverman, E. Yaneske, 2020, ArXiv.

Dissecting the transcriptome in cardiovascular disease

G. Condorelli, Y. Devaux, F. Martelli, 2021, Cardiovascular research.

Integrated multi-omics analysis of ovarian cancer using variational autoencoders

Muta Tah Hira, C. Angione, J. Scrivens, 2021, Scientific Reports.

Machine and deep learning meet genome-scale metabolic modeling

Claudio Angione, Supreeta Vijayakumar, Elisabeth Yaneske, 2019, PLoS Comput. Biol..

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

Pietro Liò, Claudio Angione, Maxwell Conway, 2016, BMC Bioinformatics.

A mechanism-aware and multiomic machine-learning pipeline characterizes yeast cell growth

Claudio Angione, Supreeta Vijayakumar, Christopher Culley, 2020, Proceedings of the National Academy of Sciences.

Multi-dimensional experimental and computational exploration of metabolism pinpoints complex probiotic interactions.

C. Angione, Guido Zampieri, G. Efthimiou, 2023, Metabolic engineering.

Integrating splice‐isoform expression into genome‐scale models characterizes breast cancer metabolism

Claudio Angione, C. Angione, 2018, Bioinform..

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

Pietro Lió, Claudio Angione, Supreeta Vijayakumar, 2017, Briefings Bioinform..

Multi-Target Analysis and Design of Mitochondrial Metabolism

Giuseppe Nicosia, Jole Costanza, Claudio Angione, 2015, PloS one.

Discovering Essential Multiple Gene Effects Through Large Scale Optimization: An Application to Human Cancer Metabolism

Hillel Kugler, Youssef Hamadi, Claudio Angione, 2020, IEEE/ACM Transactions on Computational Biology and Bioinformatics.

The diagnostic and prognostic potential of the EGFR/MUC4/MMP9 axis in glioma patients

A. Khundakar, Meez Islam, C. Angione, 2022, Scientific Reports.

A pipeline and comparative study of 12 machine learning models for text classification

C. Angione, A. Occhipinti, Louis Rogers, 2022, Expert Syst. Appl..

Iterative Multi Level Calibration of Metabolic Networks

Pietro Liò, Claudio Angione, Max Conway, 2016 .

Pareto epsilon-dominance and identifiable solutions for BioCAD modeling

Pietro Liò, Giuseppe Nicosia, Jole Costanza, 2013, 2013 50th ACM/EDAC/IEEE Design Automation Conference (DAC).

Multi objective design for bacterial communication networks

Pietro Liò, Giuseppe Nicosia, Jole Costanza, 2013, 2013 IEEE International Conference on Communications Workshops (ICC).

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

Claudio Angione, Supreeta Vijayakumar, Max Conway, 2018, Methods in molecular biology.

Robust design of microbial strains

Pietro Liò, Giuseppe Nicosia, Jole Costanza, 2012, Bioinform..

Computing with Metabolic Machines

Pietro Liò, Giuseppe Nicosia, Jole Costanza, 2012, Turing-100.

Genome‐scale metabolic modelling of SARS‐CoV‐2 in cancer cells reveals an increased shift to glycolytic energy production

C. Angione, Guido Zampieri, L. Bertoldi, 2021, FEBS letters.

A poly-omics machine-learning method to predict metabolite production in CHO cells

Giorgio Valle, Claudio Angione, Guido Zampieri, 2017 .

An Integrated Approach to Adaptive Control and Supervisory Optimisation of HVAC Control Systems for Demand Response Applications

Michael Short, Claudio Angione, Akinkunmi Adegbenro, 2021, Energies.

Computational profiling of natural compounds as promising inhibitors against the spike proteins of SARS‐CoV‐2 wild‐type and the variants of concern, viral cell‐entry process, and cytokine storm in COVID‐19

C. Angione, A. Roy, A. Anandraj, 2022, Journal of cellular biochemistry.

Editorial: Artificial intelligence for data discovery and reuse in endocrinology and metabolism

N. Burtt, C. Angione, Huajin Wang, 2023, Frontiers in Endocrinology.

A hybrid flux balance analysis and machine learning pipeline elucidates the metabolic response of cyanobacteria to different growth conditions

Claudio Angione, Supreeta Vijayakumar, Pattanathu Kaja-Mohideen Sheikh Mujibur Rahman, 2020 .

Status of Omics Research Capacity on Oral Cancer in Africa: A Systematic Scoping Review Protocol

C. Ibingira, C. Angione, R. Jayasinghe, 2023, BioMedInformatics.

Developments in AI and Machine Learning for Neuroimaging

Andreas Holzinger, Fleur Jeanquartier, Claire Jean-Quartier, 2020, AI and ML for Digital Pathology.

Protocol for hybrid flux balance, statistical, and machine learning analysis of multi-omic data from the cyanobacterium Synechococcus sp. PCC 7002

C. Angione, S. Vijayakumar, 2021, STAR protocols.

Multimodal regularized linear models with flux balance analysis for mechanistic integration of omics data

C. Angione, G. Magazzù, Guido Zampieri, 2021, Bioinform..

Glycosylation spectral signatures for glioma grade discrimination using Raman spectroscopy

A. Khundakar, Meez Islam, C. Angione, 2023, BMC Cancer.

Ten quick tips for avoiding pitfalls in multi-omics data integration analyses

D. Chicco, C. Angione, Fabio Cumbo, 2023, PLoS Comput. Biol..

Machine Learning Methods for Survival Analysis with Clinical and Transcriptomics Data of Breast Cancer.

C. Angione, A. Occhipinti, Le Minh Thao Doan, 2023, Methods in molecular biology.

Integration of epigenetic regulatory mechanisms in heart failure

G. Condorelli, Y. Devaux, F. Martelli, 2023, Basic Research in Cardiology.

Analysis and design of molecular machines

Pietro Liò, Giuseppe Nicosia, Jole Costanza, 2015, Theor. Comput. Sci..

Multi-objective Optimisation, Sensitivity and Robustness Analysis in FBA Modelling

Pietro Liò, Giuseppe Nicosia, Jole Costanza, 2012, CMSB.

Robust Design of Microbial Strains - Supplementary Information

Giuseppe Nicosia, Jole Costanza, Claudio Angione, 2012 .

A Data- and Model-Driven Analysis Reveals the Multi-omic Landscape of Ageing

Claudio Angione, Elisabeth Yaneske, C. Angione, 2017, IWBBIO.

Platinum Sponsor Gold Sponsor Sponsor

I. Tagkopoulos, C. Angione, Dr Densmore, 2013 .

Multi-omic Data Integration Elucidates Synechococcus Adaptation Mechanisms to Fluctuations in Light Intensity and Salinity

Claudio Angione, Supreeta Vijayakumar, C. Angione, 2017, IWBBIO.

A Practical Guide to Integrating Multimodal Machine Learning and Metabolic Modeling.

C. Angione, A. Occhipinti, S. Vijayakumar, 2022, Methods in molecular biology.

Satisfiability by Maxwell-Boltzmann and Bose-Einstein Statistical Distributions

Giuseppe Nicosia, Claudio Angione, Annalisa Occhipinti, 2015, ACM J. Exp. Algorithmics.

Journal Pre-proof A hybrid flux balance analysis and machine learning pipeline elucidates the metabolic response of cyanobacteria to different growth conditions

C. Angione, Pattanathu Supreeta Vijayakumar, Kaja-Mohideen Sheikh, 2020 .