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2019
290 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
34 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