Research graph
References from Mitigating biomass composition uncertainties in flux balance analysis using ensemble representations. Local targets link to admitted publications; unresolved targets remain external evidence.
10.1016/j.cell.2015.05.019
10.1016/j.cell.2015.05.019 · External reference
10.1038/nrmicro2737
10.1038/nrmicro2737 · External reference
10.1093/bib/bbp011
10.1093/bib/bbp011 · External reference
10.1186/s13059-019-1730-3
10.1186/s13059-019-1730-3 · External reference
10.1038/s41579-020-00440-4
10.1038/s41579-020-00440-4 · External reference
What is flux balance analysis
10.1038/nbt.1614 · 2010 · External reference
The biomass objective function
10.1016/j.mib.2010.03.003 · 2011 · External reference
Systematic evaluation of objective functions for predicting intracellular fluxes in Escherichia coli
10.1038/msb4100162 · 2007 · External reference
Measuring cellular biomass composition for computational biology applications
2018 · External reference
10.1371/journal.pone.0023126
10.1371/journal.pone.0023126 · External reference
What CHO is made of: variations in the biomass composition of Chinese hamster ovary cell lines
10.1016/j.ymben.2020.06.002 · 2020 · External reference
10.1126/science.1192588
10.1126/science.1192588 · External reference
Predicting dynamic metabolic demands in the photosynthetic eukaryote chlorella vulgaris
10.1104/pp.17.00605 · 2018 · External reference
A genome-scale metabolic reconstruction for Escherichia coli K-12 MG1655 that accounts for 1260 ORFs and thermodynamic information
10.1038/msb4100155 · 2007 · External reference
10.1007/s11306-015-0819-2
10.1007/s11306-015-0819-2 · External reference
Genome-scale modeling and transcriptome analysis of Leuconostoc mesenteroides unravel the redox governed metabolic states in obligate heterofermentative lactic acid bacteria
10.1038/s41598-017-16026-9 · 2017 · External reference
10.1016/j.ymben.2021.03.013
10.1016/j.ymben.2021.03.013 · External reference
Quantifying the propagation of parametric uncertainty on flux balance analysis
10.1016/j.ymben.2021.10.012 · 2022 · External reference
Effect of Escherichia coli biomass composition on central metabolic fluxes predicted by a stoichiometric model
10.1002/(sici)1097-0290(19981020)60:2<230::aid-bit10>3.0.co;2-q · 1998 · External reference
10.1016/j.ymben.2016.12.002
10.1016/j.ymben.2016.12.002 · External reference
BOFdat: generating biomass objective function stoichiometric coefficients from experimental data
10.1371/journal.pcbi.1006971 · 2019 · External reference
10.1371/journal.pcbi.1008528
10.1371/journal.pcbi.1008528 · External reference
In silico method for modelling metabolism and gene product expression at genome scale
10.1038/ncomms1928 · 2012 · External reference
Multiscale modeling of metabolism and macromolecular synthesis in E. coli and its application to the evolution of codon usage
10.1371/journal.pone.0045635 · 2012 · External reference
Genome-scale models of metabolism and gene expression extend and refine growth phenotype prediction
10.1038/msb.2013.52 · 2013 · External reference
10.1093/nar/gkv1189
10.1093/nar/gkv1189 · External reference
The international nucleotide sequence database collaboration
2021 · External reference
Gene expression omnibus: NCBI gene expression and hybridization array data repository
2002 · External reference
Version 4.0 of PaxDb: protein abundance data, integrated across model organisms, tissues, and cell-lines
2015 · External reference
10.1038/msb.2010.47
10.1038/msb.2010.47 · External reference
Quantitative prediction of cellular metabolism with constraint-based models: the COBRA Toolbox v2.0
10.1038/nprot.2011.308 · 2011 · External reference
iML1515, a knowledgebase that computes Escherichia coli traits
2017 · External reference
A consensus S. cerevisiae metabolic model Yeast8 and its ecosystem for comprehensively probing cellular metabolism
2019 · External reference
Enzyme capacity-based genome scale modelling of CHO cells
10.1016/j.ymben.2020.04.005 · 2020 · External reference
Major characteristics of the prokaryotic world
2000 · External reference
Alteration in cellular fatty acid composition as a response to salt, acid, oxidative and thermal stresses in Lactobacillus helveticus
10.1099/00221287-147-8-2255 · 2001 · External reference
Response of cellular fatty acids to environmental stresses in endophytic Micrococcus spp
10.1007/s13213-015-1061-x · 2015 · External reference
Lipidomic and biophysical homeostasis of mammalian membranes counteracts dietary lipid perturbations to maintain cellular fitness
10.1038/s41467-020-15203-1 · 2020 · External reference
10.1038/nprot.2009.203
10.1038/nprot.2009.203 · External reference
A computation tool for the estimation of biomass composition from genomic and transcriptomic information
2016 · External reference
iOD907, the first genome-scale metabolic model for the milk yeast Kluyveromyces lactis
10.1002/biot.201300242 · 2014 · External reference
Genome-scale metabolic modeling and in silico analysis of lipid accumulating yeast Candida tropicalis for dicarboxylic acid production
10.1002/bit.25955 · 2016 · External reference
Reconstruction and analysis of the genome-scale metabolic model of Lactobacillus casei LC2W
10.1016/j.gene.2014.10.034 · 2015 · External reference
10.1002/biot.201000078
10.1002/biot.201000078 · External reference
Improving the phenotype predictions of a yeast genome‐scale metabolic model by incorporating enzymatic constraints
10.15252/msb.20167411 · 2017 · External reference
10.1128/jb.187.9.3171-3179.2005
10.1128/jb.187.9.3171-3179.2005 · External reference
10.1128/aem.72.2.1164-1172.2006
10.1128/aem.72.2.1164-1172.2006 · External reference
Metabolic flux responses to pyruvate kinase knockout in Escherichia coli
10.1128/jb.184.1.152-164.2002 · 2002 · External reference
Large-scale 13C-flux analysis reveals distinct transcriptional control of respiratory and fermentative metabolism in Escherichia coli
10.1038/msb.2011.9 · 2011 · External reference
Synergy between (13)C-metabolic flux analysis and flux balance analysis for understanding metabolic adaptation to anaerobiosis in E. coli
10.1016/j.ymben.2010.11.004 · 2011 · External reference
The amazing complexity of the human transcriptome
2005 · External reference
Analysis of intra-genomic GC content homogeneity within prokaryotes
2010 · External reference
Metabolic efficiency and amino acid composition in the proteomes of Escherichia coli and Bacillus subtilis
2002 · External reference