DynamicME: dynamic simulation and refinement of integrated models of metabolism and protein expression

Modeling the multi-scale mechanisms of macromolecular resource allocation

(2018) Laurence Yang et al.   CURRENT OPINION IN MICROBIOLOGY

COBRAme: A computational framework for genome-scale models of metabolism and gene expression

(2018) Colton J. Lloyd et al.   PLoS Computational Biology

Optimal resource allocation enables mathematical exploration of microbial metabolic configurations

(2017) Laurent Tournier et al.   JOURNAL OF MATHEMATICAL BIOLOGY

Thermosensitivity of growth is determined by chaperone-mediated proteome reallocation

(2017) Ke Chen et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Reliable and efficient solution of genome-scale models of Metabolism and macromolecular Expression

(2017) Ding Ma et al.   Scientific Reports

solveME: fast and reliable solution of nonlinear ME models

(2016) Laurence Yang et al.   BMC BIOINFORMATICS

Bacterial persistence is an active σSstress response to metabolic flux limitation

(2016) Jakub Leszek Radzikowski et al.   Molecular Systems Biology

The EcoCyc database: reflecting new knowledge aboutEscherichia coliK-12

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

A Geometric Approach to Archetypal Analysis and Nonnegative Matrix Factorization

(2016) Anil Damle et al.   TECHNOMETRICS

Multi-omic data integration enables discovery of hidden biological regularities

(2016) Ali Ebrahim et al.   Nature Communications

Quantification and Classification of E. coli Proteome Utilization and Unused Protein Costs across Environments

(2016) Edward J. O’Brien et al.   PLoS Computational Biology

Principles of proteome allocation are revealed using proteomic data and genome-scale models

(2016) Laurence Yang et al.   Scientific Reports

Using Genome-scale Models to Predict Biological Capabilities

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

Next-generation genome-scale models for metabolic engineering

(2015) Zachary A King et al.   CURRENT OPINION IN BIOTECHNOLOGY

Computing the functional proteome: recent progress and future prospects for genome-scale models

(2015) Edward J O’Brien et al.   CURRENT OPINION IN BIOTECHNOLOGY

Dynamic optimization of metabolic networks coupled with gene expression

(2015) Steffen Waldherr et al.   JOURNAL OF THEORETICAL BIOLOGY

Quantitative prediction of genome-wide resource allocation in bacteria

(2015) Anne Goelzer et al.   METABOLIC ENGINEERING

Characterizing metabolic pathway diversification in the context of perturbation size

(2015) Laurence Yang et al.   METABOLIC ENGINEERING

Overflow metabolism in Escherichia coli results from efficient proteome allocation

(2015) Markus Basan et al.   NATURE

Inferring biological tasks using Pareto analysis of high-dimensional data

(2015) Yuval Hart et al.   NATURE METHODS

Systems biology definition of the core proteome of metabolism and expression is consistent with high-throughput data

(2015) Laurence Yang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Elucidating temporal resource allocation and diurnal dynamics in phototrophic metabolism using conditional FBA

(2015) Marco Rügen et al.   Scientific Reports

Use of Adaptive Laboratory Evolution To Discover Key Mutations Enabling Rapid Growth of Escherichia coli K-12 MG1655 on Glucose Minimal Medium

(2014) Ryan A. LaCroix et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Reconstruction and modeling protein translocation and compartmentalization in Escherichia coli at the genome-scale

(2014) Joanne K Liu et al.   BMC Systems Biology

Evolution of Escherichia coli to 42 °C and Subsequent Genetic Engineering Reveals Adaptive Mechanisms and Novel Mutations

(2014) Troy E. Sandberg et al.   MOLECULAR BIOLOGY AND EVOLUTION

Constraint-based models predict metabolic and associated cellular functions

(2014) Aarash Bordbar et al.   NATURE REVIEWS GENETICS

Robust flux balance analysis of multiscale biochemical reaction networks

(2013) Yuekai Sun et al.   BMC BIOINFORMATICS

Dynamic strain scanning optimization: an efficient strain design strategy for balanced yield, titer, and productivity. DySScO strategy for strain design

(2013) Kai Zhuang et al.   BMC BIOTECHNOLOGY

Optimal control of gene expression for fast proteome adaptation to environmental change

(2013) M. Y. Pavlov et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Insights into the regulation of protein abundance from proteomic and transcriptomic analyses

(2012) Christine Vogel et al.   NATURE REVIEWS GENETICS

Constraining the metabolic genotype–phenotype relationship using a phylogeny of in silico methods

(2012) Nathan E. Lewis et al.   NATURE REVIEWS MICROBIOLOGY

Multiscale Modeling of Metabolism and Macromolecular Synthesis in E. coli and Its Application to the Evolution of Codon Usage

(2012) Ines Thiele et al.   PLoS One

In silico method for modelling metabolism and gene product expression at genome scale

(2012) Joshua A. Lerman et al.   Nature Communications

Parallel distributed computing using Python

(2011) Lisandro D. Dalcin et al.   ADVANCES IN WATER RESOURCES

Bacterial growth rate reflects a bottleneck in resource allocation

(2011) A. Goelzer et al.   BIOCHIMICA ET BIOPHYSICA ACTA-GENERAL SUBJECTS

Functional and Metabolic Effects of Adaptive Glycerol Kinase (GLPK) Mutants inEscherichia coli

(2011) M. Kenyon Applebee et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Systematizing the generation of missing metabolic knowledge

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

What is flux balance analysis?

(2010) Jeffrey D Orth et al.   NATURE BIOTECHNOLOGY

Genome-Scale Reconstruction of Escherichia coli's Transcriptional and Translational Machinery: A Knowledge Base, Its Mathematical Formulation, and Its Functional Characterization

(2009) Ines Thiele et al.   PLoS Computational Biology

Whole-genome resequencing of Escherichia coli K-12 MG1655 undergoing short-term laboratory evolution in lactate minimal media reveals flexible selection of adaptive mutations

(2009) Tom M Conrad et al.   GENOME BIOLOGY

Dynamic metabolic engineering for increasing bioprocess productivity

(2008) Nikolaos Anesiadis et al.   METABOLIC ENGINEERING

Regulatory activity revealed by dynamic correlations in gene expression noise

(2008) Mary J Dunlop et al.   NATURE GENETICS