BOFdat: Generating biomass objective functions for genome-scale metabolic models from experimental data

Measuring Cellular Biomass Composition for Computational Biology Applications

(2018) Ashley Beck et al.   Processes

Mutant phenotypes for thousands of bacterial genes of unknown function

(2018) Morgan N. Price et al.   NATURE

Integration of Biomass Formulations of Genome-Scale Metabolic Models with Experimental Data Reveals Universally Essential Cofactors in Prokaryotes

(2017) Joana C. Xavier et al.   METABOLIC ENGINEERING

iML1515, a knowledgebase that computes Escherichia coli traits

(2017) Jonathan M Monk et al.   NATURE BIOTECHNOLOGY

Optimal classifier for imbalanced data using Matthews Correlation Coefficient metric

(2017) Sabri Boughorbel et al.   PLoS One

A Comprehensive, CRISPR-based Functional Analysis of Essential Genes in Bacteria

(2016) Jason M. Peters et al.   CELL

The EcoCyc database: reflecting new knowledge aboutEscherichia coliK-12

(2016) Ingrid M. Keseler et al.   NUCLEIC ACIDS RESEARCH

An Unexpected Route to an Essential Cofactor: Escherichia coli Relies on Threonine for Thiamine Biosynthesis

(2016) Jannell V. Bazurto et al.   mBio

Using Genome-scale Models to Predict Biological Capabilities

(2015) Edward J. O’Brien et al.   CELL

Biomass composition: the “elephant in the room” of metabolic modelling

(2015) Duygu Dikicioglu et al.   Metabolomics

The quantitative and condition-dependent Escherichia coli proteome

(2015) Alexander Schmidt et al.   NATURE BIOTECHNOLOGY

MetaNetX/MNXref – reconciliation of metabolites and biochemical reactions to bring together genome-scale metabolic networks

(2015) Sébastien Moretti et al.   NUCLEIC ACIDS RESEARCH

BiGG Models: A platform for integrating, standardizing and sharing genome-scale models

(2015) Zachary A. King et al.   NUCLEIC ACIDS RESEARCH

Optimizing genome-scale network reconstructions

(2014) Jonathan Monk et al.   NATURE BIOTECHNOLOGY

Large-scale 13C-flux analysis reveals distinct transcriptional control of respiratory and fermentative metabolism in Escherichia coli

(2011) B. R. B. Haverkorn van Rijsewijk et al.   Molecular Systems Biology

Condition-Dependent Cell Volume and Concentration of Escherichia coli to Facilitate Data Conversion for Systems Biology Modeling

(2011) Benjamin Volkmer et al.   PLoS One

Systematizing the generation of missing metabolic knowledge

(2010) Jeffrey D. Orth et al.   BIOTECHNOLOGY AND BIOENGINEERING

The biomass objective function

(2010) Adam M Feist et al.   CURRENT OPINION IN MICROBIOLOGY

What is flux balance analysis?

(2010) Jeffrey D Orth et al.   NATURE BIOTECHNOLOGY

A protocol for generating a high-quality genome-scale metabolic reconstruction

(2010) Ines Thiele et al.   Nature Protocols

Interdependence of Cell Growth and Gene Expression: Origins and Consequences

(2010) M. Scott et al.   SCIENCE

Pathway identification by network pruning in the metabolic network of Escherichia coli

(2009) P. Gerlee et al.   BIOINFORMATICS

GrowMatch: An Automated Method for Reconciling In Silico/In Vivo Growth Predictions

(2009) Vinay Satish Kumar et al.   PLoS Computational Biology

Predicting biological system objectives de novo from internal state measurements

(2008) Erwin P Gianchandani et al.   BMC BIOINFORMATICS

A consensus yeast metabolic network reconstruction obtained from a community approach to systems biology

(2008) Markus J Herrgård et al.   NATURE BIOTECHNOLOGY