User profiles for Nathan E. Lewis
Nathan E LewisProfessor, University of California, San Diego Verified email at ucsd.edu Cited by 19178 |
Quantitative prediction of cellular metabolism with constraint-based models: the COBRA Toolbox v2. 0
Over the past decade, a growing community of researchers has emerged around the use of
constraint-based reconstruction and analysis (COBRA) methods to simulate, analyze and …
constraint-based reconstruction and analysis (COBRA) methods to simulate, analyze and …
[HTML][HTML] The genomic sequence of the Chinese hamster ovary (CHO)-K1 cell line
Chinese hamster ovary (CHO)–derived cell lines are the preferred host cells for the
production of therapeutic proteins. Here we present a draft genomic sequence of the CHO-K1 …
production of therapeutic proteins. Here we present a draft genomic sequence of the CHO-K1 …
[HTML][HTML] Deciphering cell–cell interactions and communication from gene expression
…, A Officer, O Harismendy, NE Lewis - Nature Reviews …, 2021 - nature.com
Cell–cell interactions orchestrate organismal development, homeostasis and single-cell
functions. When cells do not properly interact or improperly decode molecular messages, …
functions. When cells do not properly interact or improperly decode molecular messages, …
BiGG Models: A platform for integrating, standardizing and sharing genome-scale models
Genome-scale metabolic models are mathematically-structured knowledge bases that can
be used to predict metabolic pathway usage and growth phenotypes. Furthermore, they can …
be used to predict metabolic pathway usage and growth phenotypes. Furthermore, they can …
[HTML][HTML] Escher: a web application for building, sharing, and embedding data-rich visualizations of biological pathways
Escher is a web application for visualizing data on biological pathways. Three key features
make Escher a uniquely effective tool for pathway visualization. First, users can rapidly …
make Escher a uniquely effective tool for pathway visualization. First, users can rapidly …
Creation and analysis of biochemical constraint-based models using the COBRA Toolbox v. 3.0
Constraint-based reconstruction and analysis (COBRA) provides a molecular mechanistic
framework for integrative analysis of experimental molecular systems biology data and …
framework for integrative analysis of experimental molecular systems biology data and …
Constraining the metabolic genotype–phenotype relationship using a phylogeny of in silico methods
NE Lewis, H Nagarajan, BO Palsson - Nature Reviews Microbiology, 2012 - nature.com
Reconstructed microbial metabolic networks facilitate a mechanistic description of the
genotype–phenotype relationship through the deployment of constraint-based reconstruction and …
genotype–phenotype relationship through the deployment of constraint-based reconstruction and …
Design and analysis of synthetic carbon fixation pathways
Carbon fixation is the process by which CO 2 is incorporated into organic compounds. In
modern agriculture in which water, light, and nutrients can be abundant, carbon fixation could …
modern agriculture in which water, light, and nutrients can be abundant, carbon fixation could …
Omic data from evolved E. coli are consistent with computed optimal growth from genome‐scale models
After hundreds of generations of adaptive evolution at exponential growth, Escherichia coli
grows as predicted using flux balance analysis (FBA) on genome‐scale metabolic models (…
grows as predicted using flux balance analysis (FBA) on genome‐scale metabolic models (…
[HTML][HTML] Genomic landscapes of Chinese hamster ovary cell lines as revealed by the Cricetulus griseus draft genome
Chinese hamster ovary (CHO) cells, first isolated in 1957, are the preferred production host
for many therapeutic proteins. Although genetic heterogeneity among CHO cell lines has …
for many therapeutic proteins. Although genetic heterogeneity among CHO cell lines has …