Metabolic function|based normalization improves transcriptome data ...

Metabolic function-based normalization improves transcriptome data ...

Genome-scale metabolic models (GEMs) are extensively used to simulate cell metabolism and predict cell phenotypes. GEMs can also be tailored ...

mahjalili/ssGSEAGEM - GitHub

Metabolic function-based normalization improves transcriptome data-driven reduction of genome-scale metabolic models. - mahjalili/ssGSEAGEM.

A benchmark of RNA-seq data normalization methods for ... - Nature

Since there is no consensus in the literature on defining a biological objective function for human metabolism, mapping algorithms that do not ...

Shamim Sarhadi on LinkedIn: Metabolic function-based ...

Metabolic function-based normalization improves transcriptome data-driven reduction of genome-scale metabolic models - npj Systems Biology and Applications.

A benchmark of RNA-seq data normalization methods for ...

... better predictions about disease mechanisms and improve our knowledge of metabolic changes that occur in various health conditions. Lüleci HB, Uzuner D ...

Genome-Scale Metabolic Modeling Enables In-Depth ...

Pathway tools have 12 different biomass reactions based on experimental data from the literature for different taxonomic linkages. CoReCo contains a function to ...

Guidelines for extracting biologically relevant context-specific ...

Metabolic function-based normalization improves transcriptome data-driven reduction of genome-scale metabolic models. 2023, npj Systems Biology and ...

Integrating Omics Data in Genome-Scale Metabolic Modeling

... improve the reproducibility and ... normalization methods for high density oligonucleotide array data based on variance and bias.

Transcriptome and Metabolic Modeling - ResearchGate

Metabolic function-based normalization improves transcriptome data-driven reduction of genome-scale metabolic models. Article. Full-text available. May 2023.

[PDF] Applications of genome-scale metabolic models to investigate ...

Metabolic function-based normalization improves transcriptome data-driven reduction of genome-scale metabolic models ... data is with a particular metabolic ...

Applications of genome-scale metabolic models to investigate ...

, et al. Metabolic function-based normalization improves transcriptome data-driven reduction of genome-scale metabolic models . NPJ Syst ...

Toward modeling metabolic state from single-cell transcriptomics

We review and compare approaches for computational single-cell modeling of cellular metabolism based predominantly on transcriptomic data. ... function based on ...

[PDF] Assessing key decisions for transcriptomic data integration in ...

Metabolic function-based normalization improves transcriptome data-driven reduction of genome-scale metabolic models · M. JaliliMartin ScharmO. WolkenhauerAli ...

Exploring the associations between transcript levels and fluxes in ...

... transcriptomics data with genome-scale metabolic reconstructions to increase accuracy of inferences of intracellular metabolic flux ...

Transcriptome-guided parsimonious flux analysis improves ... - PLOS

... metabolic function that organism is able to employ. ... Systematic evaluation of methods for integration of transcriptomic data into constraint-based models of ...

FLUXestimator: a webserver for predicting metabolic flux and ...

... metabolic reaction based on gene expression data. In addition, scFEA ... metabolic flux estimation analysis using transcriptomics data, we ...

A benchmark of RNA-seq data normalization methods for ... - CoLab

A benchmark of RNA-seq data normalization methods for transcriptome mapping on human genome-scale metabolic networks. Hatice Büşra Lüleci. ,. Dilara Uzuner.

Protocol for hybrid flux balance, statistical, and machine learning ...

... transcriptomic data into constraint-based models of metabolism. PLoS ... Normalization of rna-seq data using factor analysis of control ...

Integration of transcriptomic data in a genome-scale metabolic ...

It is based on the assumption that an organism aims to maximise a specific cellular metabolic process, recognised as an objective function [17– ...

Systematic Evaluation of Methods for Integration of Transcriptomic ...

... Transcriptomic Data into Constraint-Based Models of Metabolism. PLoS Comput ... Hence, the formulation of an objective function based on gene or protein ...