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2019
291 Downloads (Pure)

Combining metabolic modelling with machine learning accurately predicts yeast growth rate

Culley, C., Vijayakumar, S., Zampieri, G. & Angione, C., Jun 2019, (Accepted/In press).

Research output: Contribution to conferencePaper

Open Access
File
Metabolic engineering
Gene expression
Yeast
Industrial applications
Learning systems
143 Downloads (Pure)
Open Access
File
Precision Medicine
Systems Biology
Metabolism
Medicine
Genes
74 Downloads (Pure)

Machine and deep learning meet genome-scale metabolic modeling

Zampieri, G., Vijayakumar, S., Yaneske, E. & Angione, C., 11 Jul 2019, In : PLoS Computational Biology. 15, 7, 29 p., e1007084.

Research output: Contribution to journalArticle

Open Access
File
artificial intelligence
Learning systems
Machine Learning
Genome
learning
110 Downloads (Pure)

Social Dynamics Modeling of Chrono-nutrition

Di Stefano, A., Scata, M., Vijayakumar, S., Angione, C., La Corte, A. & Lio, P., 30 Jan 2019, In : PLoS Computational Biology. 15, 1, p. e1006714 e1006714.

Research output: Contribution to journalArticle

Open Access
File
Social Dynamics
human behavior
Nutrition
Human Behavior
Dynamic Modeling
2018
156 Downloads (Pure)

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

Mancini, A., Eyassu, F., Conway, M., Occhipinti, A., Lió, P., Angione, C. & Pucciarelli, S., 30 Nov 2018, In : BMC Bioinformatics. 19, (Suppl 15), p. 442-442 1 p.

Research output: Contribution to journalArticle

Open Access
File
Metabolism
Research Design
Glucose
Metabolic Network
Prediction
212 Downloads (Pure)

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

Occhipinti, A., Eyassu, F., Rahman, T., Rahman, P. & Angione, C., 17 Dec 2018, In : PeerJ. 6, p. e6046 25 p.

Research output: Contribution to journalArticle

Open Access
File
biosurfactants
Pseudomonas putida
Biomarkers
Pseudomonas
Metabolism
35 Downloads (Pure)

Integrated computational extraction of cross-cancer poly-omic signatures

Zampieri, G. & Angione, C., 19 May 2018, (Accepted/In press).

Research output: Contribution to conferencePaper

File
Neoplasms
Genome
125 Downloads (Pure)

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

Angione, C., 1 Feb 2018, In : Bioinformatics. 34, 3, p. 494–501 8 p.

Research output: Contribution to journalArticle

Open Access
File
Breast Cancer
Metabolism
Protein Isoforms
Genome
Genes
17 Downloads (Pure)

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

Yaneske, E. & Angione, C., 16 May 2018, (Accepted/In press).

Research output: Contribution to conferencePaper

File
Biomarkers
Viruses
Genes
Fluxes
50 Downloads (Pure)

Optimisation of multi-omic genome-scale models: methodologies, hands-on tutorial and perspectives

Vijayakumar, S., Conway, M., Lió, P. & Angione, C., 1 Jan 2018, Metabolic Network Reconstruction and Modeling. Springer, p. 389-408

Research output: Chapter in Book/Report/Conference proceedingChapter

Open Access
File
Genome
Systems Biology
Metabolic Networks and Pathways
Codon
Shock
1 Citation (Scopus)

Optimization of multi-omic genome-scale models: Methodologies, hands-on tutorial, and perspectives

Vijayakumar, S., Conway, M., Lió, P. & Angione, C., 1 Jan 2018, Methods in Molecular Biology. Humana Press Inc., p. 389-408 20 p. (Methods in Molecular Biology; vol. 1716).

Research output: Chapter in Book/Report/Conference proceedingChapter

Genome
Systems Biology
Metabolic Networks and Pathways
Codon
Shock
101 Downloads (Pure)

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

Yaneske, E. & Angione, C., 20 Nov 2018, In : BMC Bioinformatics. 19 , (Suppl 14), 415.

Research output: Contribution to journalArticle

Open Access
File
Aging of materials
Gene Expression
Modeling
Gene expression
Genes
2017
113 Downloads (Pure)

A data- and model-driven analysis reveals the multi-omic landscape of ageing

Yaneske, E. & Angione, C., Apr 2017.

Research output: Contribution to conferencePaper

Open Access
File
Gene Expression
Metabolic Networks and Pathways
Parturition
Genome
T-Lymphocytes
172 Downloads (Pure)

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

Zampieri, G., Coggins, M., Valle, G. & Angione, C., 20 Nov 2017.

Research output: Contribution to conferencePaper

Open Access
File
87 Downloads (Pure)
Open Access
File
Clostridium
Clostridium difficile
Pathogens
Codon
Bacteria
94 Downloads (Pure)

Modelling pyruvate dehydrogenase under hypoxia 1 and its role in cancer metabolism

Angione, C. & Eyassu, F., 25 Oct 2017, In : Royal Society Open Science. p. -

Research output: Contribution to journalArticle

Open Access
File
Pyruvic Acid
Oxidoreductases
Neoplasms
Citric Acid Cycle
Glycolysis
95 Downloads (Pure)
Open Access
File
12 Downloads (Pure)
Open Access
File
Statistical methods
Fluxes
Principal component analysis
Genes
48 Downloads (Pure)

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

Vijayakumar, S., Conway, M., Lió, P. & Angione, C., 30 May 2017, In : Briefings in Bioinformatics. 19, 6, p. 1218–1235

Research output: Contribution to journalArticle

Open Access
File
Learning systems
Data integration
Multiobjective optimization
Wood
Systems Biology
2016
87 Downloads (Pure)

Bioinformatics challenges and potentialities in studying extreme environments

Angione, C., Lió, P., Pucciarelli, S., Can, B., Conway, M., Lotti, M., Bukhari, H., Mancini, A., Sezerman, U. & Telatin, A., 31 Jul 2016, In : Lecture Notes in Bioinformatics. 9874

Research output: Contribution to journalConference article

Open Access
File
83 Downloads (Pure)

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

Angione, C., Conway, M. & Lió, P., 2 Mar 2016, In : BMC Bioinformatics. p. -

Research output: Contribution to journalArticle

Open Access
File
Genome
Genes
Fusion reactions
Information Services
Electric fuses
2015
91 Downloads (Pure)

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

Angione, C., Pratanwanich, N. & Lió, P., 21 Aug 2015, In : ACS Synthetic Biology. p. -

Research output: Contribution to journalArticle

Open Access
File
Metabolic Flux Analysis
Chemical activation
Fluxes
Cross Reactions
Physiology
83 Downloads (Pure)

Analysis and design of molecular machines

Angione, C., Costanza, J., Carapezza, G., Lió, P. & Nicosia, G., 22 Jan 2015, In : Theoretical Computer Science. p. -

Research output: Contribution to journalArticle

Open Access
File
Bacteria
Codomain
Turing machines
Pareto Optimality
Pareto Optimal Solution
94 Downloads (Pure)

Iterative Multi Level Calibration of Metabolic Networks

Conway, M., Angione, C. & Lió, P., 3 Dec 2015, In : Current Bioinformatics. p. -

Research output: Contribution to journalArticle

Open Access
File
Electricity
Metabolic Network
Metabolic Networks and Pathways
Biomass
Calibration

Measuring adaptation to extreme environments with a multi-omic approach

Angione, C., Pucciarelli, S., Can, B., Lotti, M., Mancini, A. & Telatin, A., 10 Sep 2015, Computational Intelligence Methods for Bioinformatics and Biostatistics . Naples, Italy: Department of Informatics, University of Salerno and Istituto pe r le Applicazioni del Calcolo CNR

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Open Access
Systems Biology
Information Storage and Retrieval
Cellular Structures
Ecology
Computational Biology

Measuring adaptation to extreme environments with a multi-omic approach

Angione, C., Pucciarelli, S., Simionati, B. & Lió, P., 10 Sep 2015.

Research output: Contribution to conferencePaper

91 Downloads (Pure)

Multi-Target Analysis and Design of Mitochondrial Metabolism

Angione, C., Costanza, J., Carapezza, G., Lió, P. & Nicosia, G., 16 Sep 2015, In : PLoS ONE. p. -

Research output: Contribution to journalArticle

Open Access
File
Metabolism
NAD
Fluxes
metabolism
Biomedical Engineering
97 Downloads (Pure)

Predictive analytics of environmental adaptability in multi-omic network models

Angione, C. & Lió, P., 20 Oct 2015, In : Scientific Reports. p. -

Research output: Contribution to journalArticle

Open Access
File
Codon
Life Style
Theoretical Models
Escherichia coli
Phenotype
102 Downloads (Pure)
Open Access
File
statistical distributions
entropy
Boltzmann distribution
condensation
methodology
2014
81 Downloads (Pure)

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

Taffi, M., Paoletti, N., Angione, C., Pucciarelli, S., Marini, M. & Lió, P., 12 Sep 2014, In : Frontiers in Genetics. p. -

Research output: Contribution to journalArticle

Open Access
File
Environmental Biodegradation
Food Chain
Ecosystem
Polychlorinated Biphenyls
Synthetic Biology
2013
6 Citations (Scopus)

A design automation framework for computational bioenergetics in biological networks

Angione, C., Costanza, J., Carapezza, G., Lió, P. & Nicosia, G., 1 Oct 2013, In : Molecular BioSystems. 9, 10, p. 2554-2564 11 p.

Research output: Contribution to journalArticle

Automation
Energy Metabolism
Mitochondria
Chlamydomonas reinhardtii
Metabolic Networks and Pathways
1 Citation (Scopus)

Bose-Einstein condensation in satisfiability problems

Angione, C., Occhipinti, A., Stracquadanio, G. & Nicosia, G., 16 May 2013, In : European Journal of Operational Research. 227, 1, p. 44-54 11 p.

Research output: Contribution to journalArticle

Bose-Einstein condensation
Bose-Einstein Condensation
Satisfiability Problem
Winner-take-all
Software Verification
1 Citation (Scopus)

Design and strain selection criteria for bacterial communication networks

Angione, C., Carapezza, G., Costanza, J., Lió, P. & Nicosia, G., 1 Dec 2013, In : Nano Communication Networks. 4, 4, p. 155-163 9 p.

Research output: Contribution to journalArticle

Communication Networks
Bacteria
Telecommunication networks
Biomass
Genes
9 Citations (Scopus)

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

Carapezza, G., Umeton, R., Costanza, J., Angione, C., Stracquadanio, G., Papini, A., Lió, P. & Nicosia, G., 17 May 2013, In : ACS Synthetic Biology. 2, 5, p. 274-288 15 p.

Research output: Contribution to journalArticle

Rhodobacter sphaeroides
Chlamydomonas reinhardtii
Metabolites
Metabolic Networks and Pathways
Organelles

Multi objective design for bacterial communication networks

Angione, C., Carapezza, G., Costanza, J., Lio, P. & Nicosia, G., 27 Dec 2013, 2013 IEEE International Conference on Communications Workshops, ICC 2013. p. 813-817 5 p. 6649345

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Telecommunication networks
Bacteria
Biomass
Genes
Gene transfer
2 Citations (Scopus)

Pareto epsilon-dominance and identifiable solutions for BioCAD modeling

Angione, C., Costanza, J., Carapezza, G., Lió, P. & Nicosia, G., 12 Jul 2013, Proceedings of the 50th Annual Design Automation Conference, DAC 2013. 43

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Ground penetrating radar systems
Multiobjective optimization
Metabolism
Metabolic Networks and Pathways
Optimal design
12 Citations (Scopus)

Pareto optimality in organelle energy metabolism analysis

Angione, C., Carapezza, G., Costanza, J., Lio, P. & Nicosia, G., 1 Jul 2013, In : IEEE/ACM Transactions on Computational Biology and Bioinformatics. 10, 4, p. 1032-1044 13 p., 6573957.

Research output: Contribution to journalArticle

Energy Metabolism
Pareto Optimality
Metabolism
Organelles
Pareto Front
2012
1 Citation (Scopus)

Multi-objective optimisation, sensitivity and robustness analysis in FBA modelling

Costanza, J., Carapezza, G., Angione, C., Liò, P. & Nicosia, G., 30 Oct 2012, Computational Methods in Systems Biology - 10th International Conference, CMSB 2012, Proceedings. p. 127-147 21 p. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); vol. 7605 LNBI).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Metabolites
Multiobjective optimization
Sensitivity analysis
Bacteria
Pipelines
34 Citations (Scopus)

Robust design of microbial strains

Costanza, J., Carapezza, G., Angione, C., Lió, P. & Nicosia, G., 1 Dec 2012, In : Bioinformatics. 28, 23, p. 3097-3104 8 p.

Research output: Contribution to journalArticle

Robust Design
Pareto principle
Metabolic engineering
Metabolic Engineering
Biological Phenomena