Reference : scFASTCORMICS: A Contextualization Algorithm to Reconstruct Metabolic Multi-Cell Popu...

	Document type :	Scientific journals : Article
	Discipline(s) :	Life sciences : Biochemistry, biophysics & molecular biology
	To cite this reference:	http://hdl.handle.net/10993/53621

Title :	scFASTCORMICS: A Contextualization Algorithm to Reconstruct Metabolic Multi-Cell Population Models from Single-Cell RNAseq Data
Language :	English
Author, co-author :	Pires Pacheco, Maria Irene [University of Luxembourg > Faculty of Science, Technology and Medicine (FSTM) > Department of Life Sciences and Medicine (DLSM) >]
	Ji, Jimmy [> >]
	Prohaska, Tessy [> >]
	Moscardo Garcia, Maria [University of Luxembourg > Faculty of Science, Technology and Medicine (FSTM) > Department of Life Sciences and Medicine (DLSM) >]
	Sauter, Thomas [University of Luxembourg > Faculty of Science, Technology and Medicine (FSTM) > Department of Life Sciences and Medicine (DLSM) >]
Publication date :	Dec-2022
Journal title :	Metabolites
Publisher :	MDPI AG
Peer reviewed :	Yes
ISSN :	2218-1989
e-ISSN :	2218-1989
Keywords :	[en] single-cell RNAseq ; metabolism ; modelling ; algorithm
Abstract :	[en] Tumours are composed of various cancer cell populations with different mutation profiles, phenotypes and metabolism that cause them to react to drugs in diverse manners. Increasing the resolution of metabolic models based on single-cell expression data will provide deeper insight into such metabolic differences and improve the predictive power of the models. scFASTCORMICS is a network contextualization algorithm that builds multi-cell population genome-scale models from single-cell RNAseq data. The models contain a subnetwork for each cell population in a tumour, allowing to capture metabolic variations between these clusters. The subnetworks are connected by a union compartment that permits to simulate metabolite exchanges between cell populations in the microenvironment. scFASTCORMICS uses Pareto optimization to simultaneously maximise the compactness, completeness and specificity of the reconstructed metabolic models. scFASTCORMICS is implemented in MATLAB and requires the installation of the COBRA toolbox, rFASTCORMICS and the IBM CPLEX solver.
Permalink :	http://hdl.handle.net/10993/53621

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