Article (Scientific journals)
scFASTCORMICS: A Contextualization Algorithm to Reconstruct Metabolic Multi-Cell Population Models from Single-Cell RNAseq Data
Pires Pacheco, Maria Irene; Ji, Jimmy; Prohaska, Tessy et al.
2022In Metabolites
Peer reviewed
 

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Keywords :
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.
Research center :
ULHPC - University of Luxembourg: High Performance Computing
Disciplines :
Biochemistry, biophysics & molecular biology
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)
External co-authors :
no
Language :
English
Title :
scFASTCORMICS: A Contextualization Algorithm to Reconstruct Metabolic Multi-Cell Population Models from Single-Cell RNAseq Data
Publication date :
December 2022
Journal title :
Metabolites
ISSN :
2218-1989
Publisher :
MDPI AG
Peer reviewed :
Peer reviewed
Available on ORBilu :
since 12 January 2023

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