Genome-scale Modeling of Metabolism and Macromolecular Expression and Their Applications

2020 ◽  
Vol 25 (6) ◽  
pp. 931-943
Author(s):  
Sanjeev Dahal ◽  
Jiao Zhao ◽  
Laurence Yang
Keyword(s):  
Scale Modeling ◽  
Genome Scale

A Genome-Scale Modeling Approach to Investigate the Antibiotics-Triggered Perturbation in the Metabolism of Pseudomonas aeruginosa

2016 ◽  
Vol 2 (3) ◽  
pp. 39-42 ◽  
Author(s):  
Zhaobin Xu ◽  
Nicholas Ribaudo ◽  
Xianhua Li ◽  
Thomas K. Wood ◽  
Zuyi Huang
Keyword(s):  
Pseudomonas Aeruginosa ◽  
Modeling Approach ◽  
Scale Modeling ◽  
A Genome ◽  
Genome Scale

scholarly journals Rhodosporidium toruloides - A potential red yeast chassis for lipids and beyond

2020 ◽  
Vol 20 (5) ◽  
Author(s):  
Zhiqiang Wen ◽  
Sufang Zhang ◽  
Chuks Kenneth Odoh ◽  
Mingjie Jin ◽  
Zongbao K Zhao
Keyword(s):  
Lipid Production ◽  
Rhodosporidium Toruloides ◽  
Biotechnological Applications ◽  
Future Directions ◽  
The Past ◽  
Enhanced Production ◽  
Scale Modeling ◽  
Red Yeast ◽  
Genome Scale ◽  
Made In

ABSTRACT The red yeast Rhodosporidium toruloides naturally produces microbial lipids and carotenoids. In the past decade or so, many studies demonstrated R. toruloides as a promising platform for lipid production owing to its diverse substrate appetites, robust stress resistance and other favorable features. Also, significant progresses have been made in genome sequencing, multi-omic analysis and genome-scale modeling, thus illuminating the molecular basis behind its physiology, metabolism and response to environmental stresses. At the same time, genetic parts and tools are continuously being developed to manipulate this distinctive organism. Engineered R. toruloides strains are emerging for enhanced production of conventional lipids, functional lipids as well as other interesting metabolites. This review updates those progresses and highlights future directions for advanced biotechnological applications.

scholarly journals Integrating Extracellular Flux Measurements and Genome-Scale Modeling Reveals Differences between Brown and White Adipocytes

Cell Reports ◽  
2017 ◽  
Vol 21 (11) ◽  
pp. 3040-3048 ◽  
Author(s):  
Alfred K. Ramirez ◽  
Matthew D. Lynes ◽  
Farnaz Shamsi ◽  
Ruidan Xue ◽  
Yu-Hua Tseng ◽  
...  
Keyword(s):  
Extracellular Flux ◽  
Scale Modeling ◽  
White Adipocytes ◽  
Flux Measurements ◽  
Genome Scale

scholarly journals Diagnostics for Stochastic Genome-Scale Modeling via Model Slicing and Debugging

PLoS ONE ◽  
2014 ◽  
Vol 9 (11) ◽  
pp. e110380
Author(s):  
Kevin J. Tsai ◽  
Chuan-Hsiung Chang
Keyword(s):  
Scale Modeling ◽  
Genome Scale

scholarly journals Genome-Scale Modeling of Light-Driven Reductant Partitioning and Carbon Fluxes in Diazotrophic Unicellular Cyanobacterium Cyanothece sp. ATCC 51142

2012 ◽  
Vol 8 (4) ◽  
pp. e1002460 ◽  
Author(s):  
Trang T. Vu ◽  
Sergey M. Stolyar ◽  
Grigoriy E. Pinchuk ◽  
Eric A. Hill ◽  
Leo A. Kucek ◽  
...  
Keyword(s):  
Carbon Fluxes ◽  
Unicellular Cyanobacterium ◽  
Scale Modeling ◽  
Genome Scale

scholarly journals Genome-scale modeling using flux ratio constraints to enable metabolic engineering of clostridial metabolism in silico

2012 ◽  
Vol 6 (1) ◽  
pp. 42 ◽  
Author(s):  
Michael J McAnulty ◽  
Jiun Y Yen ◽  
Benjamin G Freedman ◽  
Ryan S Senger
Keyword(s):  
Metabolic Engineering ◽  
In Silico ◽  
Flux Ratio ◽  
Scale Modeling ◽  
Genome Scale

scholarly journals Genome Scale Modeling in Systems Biology: Algorithms and Resources

2014 ◽  
Vol 15 (2) ◽  
pp. 130-159 ◽  
Author(s):  
Ali Najafi ◽  
Gholamreza Bidkhori ◽  
Joseph Bozorgmehr ◽  
Ina Koch ◽  
Ali Masoudi-Nejad
Keyword(s):  
Systems Biology ◽  
Scale Modeling ◽  
Genome Scale
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