scholarly article | Q13442814 |
P50 | author | Eytan Ruppin | Q83763065 |
P2093 | author name string | Tomer Shlomi | |
Omer Berkman | |||
P2860 | cites work | An expanded genome-scale model of Escherichia coli K-12 (iJR904 GSM/GPR) | Q21194867 |
Genome-scale reconstruction of the Saccharomyces cerevisiae metabolic network | Q24561581 | ||
The Escherichia coli MG1655 in silico metabolic genotype: its definition, characteristics, and capabilities | Q24655269 | ||
Genomic expression programs in the response of yeast cells to environmental changes | Q27860823 | ||
Analysis of optimality in natural and perturbed metabolic networks | Q28213254 | ||
Metabolic network structure determines key aspects of functionality and regulation | Q28214885 | ||
Escherichia coli K-12 undergoes adaptive evolution to achieve in silico predicted optimal growth | Q29397612 | ||
The effects of alternate optimal solutions in constraint-based genome-scale metabolic models | Q29616019 | ||
Integrated genomic and proteomic analyses of a systematically perturbed metabolic network | Q29616021 | ||
In silico predictions of Escherichia coli metabolic capabilities are consistent with experimental data | Q29618471 | ||
Fat synthesis in adipose tissue. An examination of stoichiometric constraints | Q30051073 | ||
Just-in-time transcription program in metabolic pathways | Q33202257 | ||
Advances in flux balance analysis | Q33973453 | ||
Metabolic efficiency and amino acid composition in the proteomes of Escherichia coli and Bacillus subtilis | Q34019786 | ||
Metabolic flux responses to pyruvate kinase knockout in Escherichia coli | Q34104879 | ||
Selection for short introns in highly expressed genes | Q34140547 | ||
Gene expression and molecular evolution | Q34420781 | ||
Genome-scale microbial in silico models: the constraints-based approach. | Q35101082 | ||
Thirteen years of building constraint-based in silico models of Escherichia coli | Q35109629 | ||
Metabolic pathways in the post-genome era. | Q35135595 | ||
Saccharomyces cerevisiae phenotypes can be predicted by using constraint-based analysis of a genome-scale reconstructed metabolic network | Q37087145 | ||
Genome-scale in silico models of E. coli have multiple equivalent phenotypic states: assessment of correlated reaction subsets that comprise network states. | Q39968205 | ||
Responses of the central metabolism in Escherichia coli to phosphoglucose isomerase and glucose-6-phosphate dehydrogenase knockouts | Q40345478 | ||
Analysis of metabolic and physiological responses to gnd knockout in Escherichia coli by using C-13 tracer experiment and enzyme activity measurement | Q44387160 | ||
Metabolic flux analysis for a ppc mutant Escherichia coli based on 13C-labelling experiments together with enzyme activity assays and intracellular metabolite measurements. | Q44906592 | ||
Transient responses and adaptation to steady state in a eukaryotic gene regulation system | Q46735883 | ||
Metabolic gene-deletion strains of Escherichia coli evolve to computationally predicted growth phenotypes | Q46791266 | ||
Principles of transcriptional control in the metabolic network of Saccharomyces cerevisiae | Q47359603 | ||
The regulatory software of cellular metabolism | Q47442512 | ||
Large-scale evaluation of in silico gene deletions in Saccharomyces cerevisiae | Q47609184 | ||
Optimization-based framework for inferring and testing hypothesized metabolic objective functions | Q47995846 | ||
Prediction of temporal gene expression. Metabolic opimization by re-distribution of enzyme activities | Q52954618 | ||
A discrete model of bacterial metabolism | Q68705409 | ||
Use of mathematical models for predicting the metabolic effect of large-scale enzyme activity alterations. Application to enzyme deficiencies of red blood cells | Q72221379 | ||
P433 | issue | 21 | |
P407 | language of work or name | English | Q1860 |
P921 | main subject | flux | Q5463013 |
P304 | page(s) | 7695-700 | |
P577 | publication date | 2005-05-24 | |
P1433 | published in | Proceedings of the National Academy of Sciences of the United States of America | Q1146531 |
P1476 | title | Regulatory on/off minimization of metabolic flux changes after genetic perturbations | |
P478 | volume | 102 |
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