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An analytical theory of balanced cellular growth

https://doi.org/10.1101/607374
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What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

inferredcites →https://doi.org/10.1002/9780470253489openalex-snapshot
Analysis of Biological Networks
inferredcites →https://doi.org/10.1007/s002030050248openalex-snapshot
Buoyant density of Escherichia coli is determined solely by the osmolarity of the culture medium
inferredcites →https://doi.org/10.1016/0022-2836(91)90212-oopenalex-snapshot
Characterization of the cytoplasm of Escherichia coli K-12 as a function of external osmolarity
inferredcites →https://doi.org/10.1016/b978-0-12-152801-0.50007-9openalex-snapshot
Limitation of Metabolite Concentrations and the Conservation of Solvent Capacity in the Living Cell
inferredcites →https://doi.org/10.1016/j.cell.2009.12.001openalex-snapshot
Growth Rate-Dependent Global Effects on Gene Expression in Bacteria
inferredcites →https://doi.org/10.1016/j.celrep.2015.12.015openalex-snapshot
The Cost of Protein Production
inferredcites →https://doi.org/10.1016/j.jtbi.2013.11.015openalex-snapshot
Enzyme allocation problems in kinetic metabolic networks: Optimal solutions are elementary flux modes
inferredcites →https://doi.org/10.1016/j.ymben.2015.10.003openalex-snapshot
Quantitative prediction of genome-wide resource allocation in bacteria
inferredcites →https://doi.org/10.1016/s0006-3495(00)76726-9openalex-snapshot
Biophysical Characterization of Changes in Amounts and Activity of Escherichia coli Cell and Compartment Water and Turgor Pressure in Response to Osmotic Stress
inferredcites →https://doi.org/10.1016/s0022-5193(88)80073-0openalex-snapshot
Metabolic control theory: A structural approach
inferredcites →https://doi.org/10.1038/msb.2009.82openalex-snapshot
Shifts in growth strategies reflect tradeoffs in cellular economics
inferredcites →https://doi.org/10.1038/msb.2011.34openalex-snapshot
Economics of membrane occupancy and respiro‐fermentation
inferredcites →https://doi.org/10.1038/msb.2013.52openalex-snapshot
Genome‐scale models of metabolism and gene expression extend and refine growth phenotype prediction
inferredcites →https://doi.org/10.1038/nature01149openalex-snapshot
Escherichia coli K-12 undergoes adaptive evolution to achieve in silico predicted optimal growth
inferredcites →https://doi.org/10.1038/nature03842openalex-snapshot
Optimality and evolutionary tuning of the expression level of a protein
inferredcites →https://doi.org/10.1038/nature15765openalex-snapshot
Overflow metabolism in Escherichia coli results from efficient proteome allocation
inferredcites →https://doi.org/10.1038/nbt.3418openalex-snapshot
The quantitative and condition-dependent Escherichia coli proteome
inferredcites →https://doi.org/10.1038/ncomms14123openalex-snapshot
Optimality and sub-optimality in a bacterial growth law
inferredcites →https://doi.org/10.1038/nmicrobiol.2016.231openalex-snapshot
Reduction of translating ribosomes enables Escherichia coli to maintain elongation rates during slow growth
inferredcites →https://doi.org/10.1038/nrg2603openalex-snapshot
Fitness and its role in evolutionary genetics
inferredcites →https://doi.org/10.1038/nrmicro2737openalex-snapshot
Constraining the metabolic genotype–phenotype relationship using a phylogeny of in silico methods
inferredcites →https://doi.org/10.1038/s41467-018-07652-6openalex-snapshot
Machine learning applied to enzyme turnover numbers reveals protein structural correlates and improves metabolic models
inferredcites →https://doi.org/10.1042/bst0121093openalex-snapshot
Metabolic maps for the Apple II
inferredcites →https://doi.org/10.1073/pnas.0609845104openalex-snapshot
Intracellular crowding defines the mode and sequence of substrate uptake by Escherichia coli and constrains its metabolic activity
inferredcites →https://doi.org/10.1073/pnas.1310377110openalex-snapshot
Molecular crowding limits translation and cell growth
inferredcites →https://doi.org/10.1073/pnas.1416533112openalex-snapshot
Mechanistic links between cellular trade-offs, gene expression, and growth
inferredcites →https://doi.org/10.1073/pnas.1421138111openalex-snapshot
Bacterial growth laws reflect the evolutionary importance of energy efficiency
inferredcites →https://doi.org/10.1073/pnas.1514240113openalex-snapshot
Global characterization of in vivo enzyme catalytic rates and their correspondence to in vitro k cat measurements
inferredcites →https://doi.org/10.1073/pnas.80.2.622openalex-snapshot
Calculation of volume fluctuation for globular protein models.
inferredcites →https://doi.org/10.1093/nar/gks1027openalex-snapshot
EcoCyc: fusing model organism databases with systems biology
inferredcites →https://doi.org/10.1093/oso/9780198504405.001.0001openalex-snapshot
Natural selection
inferredcites →https://doi.org/10.1098/rsbl.2010.0580openalex-snapshot
On measuring selection in experimental evolution
inferredcites →https://doi.org/10.1098/rsif.2017.0502openalex-snapshot
Mathematical modelling of microbes: metabolism, gene expression and growth
inferredcites →https://doi.org/10.1101/128009openalex-snapshot
Enzymes and Substrates Are Balanced at Minimal Combined Mass Concentration in vivo
inferredcites →https://doi.org/10.1101/483867openalex-snapshot
Optimal metabolic states in cells
inferredcites →https://doi.org/10.1101/483891openalex-snapshot
The value structure of metabolic states
inferredcites →https://doi.org/10.1111/febs.12722openalex-snapshot
Metabolic states with maximal specific rate carry flux through an elementary flux mode
inferredcites →https://doi.org/10.1126/science.1192588openalex-snapshot
Interdependence of Cell Growth and Gene Expression: Origins and Consequences
inferredcites →https://doi.org/10.1128/br.21.4.263-272.1957openalex-snapshot
SYNCHRONIZATION OF CELL DIVISION
inferredcites →https://doi.org/10.1128/ecosal.5.2.3openalex-snapshot
Modulation of Chemical Composition and Other Parameters of the Cell at Different Exponential Growth Rates
inferredcites →https://doi.org/10.1137/0120037openalex-snapshot
Theory of Maxima and the Method of Lagrange
inferredcites →https://doi.org/10.1142/s0218339094000131openalex-snapshot
ON ELEMENTARY FLUX MODES IN BIOCHEMICAL REACTION SYSTEMS AT STEADY STATE
inferredcites →https://doi.org/10.1186/1471-2105-5-175openalex-snapshot
Computation of elementary modes: a unifying framework and the new binary approach
inferredcites →https://doi.org/10.1186/gb-2010-11-4-r43openalex-snapshot
Flux balance analysis accounting for metabolite dilution
inferredcites →https://doi.org/10.1371/journal.pcbi.1001120openalex-snapshot
The Morphology of the Rat Vibrissal Array: A Model for Quantifying Spatiotemporal Patterns of Whisker-Object Contact
inferredcites →https://doi.org/10.1371/journal.pcbi.1004721openalex-snapshot
Investigating the Consequences of Interference between Multiple CD8+ T Cell Escape Mutations in Early HIV Infection
inferredcites →https://doi.org/10.1371/journal.pcbi.1004802openalex-snapshot
Dynamical Allocation of Cellular Resources as an Optimal Control Problem: Novel Insights into Microbial Growth Strategies
inferredcites →https://doi.org/10.1371/journal.pcbi.1006223openalex-snapshot
OpenSim: Simulating musculoskeletal dynamics and neuromuscular control to study human and animal movement
inferredcites →https://doi.org/10.1371/journal.pcbi.1006858openalex-snapshot
The number of active metabolic pathways is bounded by the number of cellular constraints at maximal metabolic rates
inferredcites →https://doi.org/10.1371/journal.pcbi.1007559openalex-snapshot
Elementary Growth Modes provide a molecular description of cellular self-fabrication
inferredcites →https://doi.org/10.15252/msb.20145697openalex-snapshot
Quantitative proteomic analysis reveals a simple strategy of global resource allocation in bacteria
inferredcites →https://doi.org/10.15252/msb.20156178openalex-snapshot
Inflating bacterial cells by increased protein synthesis
inferredcites →https://doi.org/10.15252/msb.20166998openalex-snapshot
Bacterial persistence is an active σS stress response to metabolic flux limitation

What points at this work

Incoming claims: where this work appears in other papers’ reference lists and arguments.

inferred← citeshttps://doi.org/10.1007/s00018-019-03380-2openalex-snapshot
The common message of constraint-based optimization approaches: overflow metabolism is caused by two growth-limiting constraints
inferred← citeshttps://doi.org/10.1371/journal.pcbi.1007559openalex-snapshot
Elementary Growth Modes provide a molecular description of cellular self-fabrication
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