scholarly journals The Edinburgh human metabolic network reconstruction and its functional analysis

2007 ◽  
Vol 3 (1) ◽  
pp. 135 ◽  
Author(s):  
Hongwu Ma ◽  
Anatoly Sorokin ◽  
Alexander Mazein ◽  
Alex Selkov ◽  
Evgeni Selkov ◽  
...  
Keyword(s):  
Functional Analysis ◽  
Metabolic Network ◽  
Network Reconstruction ◽  
Metabolic Network Reconstruction

scholarly journals A genome‐scale metabolic network reconstruction of tomato ( Solanum lycopersicum L.) and its application to photorespiratory metabolism

2016 ◽  
Vol 85 (2) ◽  
pp. 289-304 ◽  
Author(s):  
Huili Yuan ◽  
C.Y. Maurice Cheung ◽  
Mark G. Poolman ◽  
Peter A. J. Hilbers ◽  
Natal A. W. Riel
Keyword(s):  
Metabolic Network ◽  
Solanum Lycopersicum ◽  
Network Reconstruction ◽  
Metabolic Network Reconstruction ◽  
Solanum Lycopersicum L ◽  
A Genome ◽  
Genome Scale

scholarly journals RAVEN 2.0: A versatile toolbox for metabolic network reconstruction and a case study on Streptomyces coelicolor

2018 ◽  
Vol 14 (10) ◽  
pp. e1006541 ◽  
Author(s):  
Hao Wang ◽  
Simonas Marcišauskas ◽  
Benjamín J. Sánchez ◽  
Iván Domenzain ◽  
Daniel Hermansson ◽  
...  
Keyword(s):  
Metabolic Network ◽  
Streptomyces Coelicolor ◽  
Network Reconstruction ◽  
Metabolic Network Reconstruction

scholarly journals mmnet: An R Package for Metagenomics Systems Biology Analysis

2015 ◽  
Vol 2015 ◽  
pp. 1-5 ◽  
Author(s):  
Yang Cao ◽  
Xiaofei Zheng ◽  
Fei Li ◽  
Xiaochen Bo
Keyword(s):  
Metabolic Network ◽  
Human Microbiome ◽  
R Package ◽  
Network Reconstruction ◽  
Community Level ◽  
System Level ◽  
Metagenomic Data ◽  
Pure Species ◽  
Integrated Network ◽  
Metabolic Network Reconstruction

The human microbiome plays important roles in human health and disease. Previous microbiome studies focused mainly on single pure species function and overlooked the interactions in the complex communities on system-level. A metagenomic approach introduced recently integrates metagenomic data with community-level metabolic network modeling, but no comprehensive tool was available for such kind of approaches. To facilitate these kinds of studies, we developed an R package,mmnet, to implement community-level metabolic network reconstruction. The package also implements a set of functions for automatic analysis pipeline construction including functional annotation of metagenomic reads, abundance estimation of enzymatic genes, community-level metabolic network reconstruction, and integrated network analysis. The result can be represented in an intuitive way and sent to Cytoscape for further exploration. The package has substantial potentials in metagenomic studies that focus on identifying system-level variations of human microbiome associated with disease.

scholarly journals A simplified metabolic network reconstruction to promote understanding and development of flux balance analysis tools

2019 ◽  
Vol 105 ◽  
pp. 64-71 ◽  
Author(s):  
Kristopher D. Rawls ◽  
Bonnie V. Dougherty ◽  
Edik M. Blais ◽  
Ethan Stancliffe ◽  
Glynis L. Kolling ◽  
...  
Keyword(s):  
Metabolic Network ◽  
Flux Balance Analysis ◽  
Network Reconstruction ◽  
Metabolic Network Reconstruction ◽  
Flux Balance ◽  
Analysis Tools ◽  
Balance Analysis

scholarly journals A consensus yeast metabolic network reconstruction obtained from a community approach to systems biology

2008 ◽  
Vol 26 (10) ◽  
pp. 1155-1160 ◽  
Author(s):  
Markus J Herrgård ◽  
Neil Swainston ◽  
Paul Dobson ◽  
Warwick B Dunn ◽  
K Yalçin Arga ◽  
...  
Keyword(s):  
Systems Biology ◽  
Metabolic Network ◽  
Network Reconstruction ◽  
Metabolic Network Reconstruction ◽  
Community Approach

scholarly journals Metabolic network reconstruction of Chlamydomonas offers insight into light‐driven algal metabolism

2011 ◽  
Vol 7 (1) ◽  
pp. 518 ◽  
Author(s):  
Roger L Chang ◽  
Lila Ghamsari ◽  
Ani Manichaikul ◽  
Erik F Y Hom ◽  
Santhanam Balaji ◽  
...  
Keyword(s):  
Metabolic Network ◽  
Network Reconstruction ◽  
Metabolic Network Reconstruction ◽  
Algal Metabolism ◽  
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