The genetic basis for adaptation of model-designed syntrophic co-cultures

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

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

Machine learning applied to enzyme turnover numbers reveals protein structural correlates and improves metabolic models

(2018) David Heckmann et al.   Nature Communications

iML1515, a knowledgebase that computes Escherichia coli traits

(2017) Jonathan M Monk et al.   NATURE BIOTECHNOLOGY

Paradoxes in leaky microbial trade

(2017) Yoav Kallus et al.   Nature Communications

Genome-driven evolutionary game theory helps understand the rise of metabolic interdependencies in microbial communities

(2017) Ali R. Zomorrodi et al.   Nature Communications

SteadyCom: Predicting microbial abundances while ensuring community stability

(2017) Siu Hung Joshua Chan et al.   PLoS Computational Biology

Metabolic Models of Protein Allocation Call for the Kinetome

(2017) Avlant Nilsson et al.   Cell Systems

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

Synthetic Ecology of Microbes: Mathematical Models and Applications

(2016) Ali R. Zomorrodi et al.   JOURNAL OF MOLECULAR BIOLOGY

Generation of genome-scale metabolic reconstructions for 773 members of the human gut microbiota

(2016) Stefanía Magnúsdóttir et al.   NATURE BIOTECHNOLOGY

Global characterization of in vivo enzyme catalytic rates and their correspondence to in vitrokcatmeasurements

(2016) Dan Davidi et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Multi-omic data integration enables discovery of hidden biological regularities

(2016) Ali Ebrahim et al.   Nature Communications

Pervasive Selection for Cooperative Cross-Feeding in Bacterial Communities

(2016) Sebastian Germerodt et al.   PLoS Computational Biology

Metabolic Network Modeling of Microbial Interactions in Natural and Engineered Environmental Systems

(2016) Octavio Perez-Garcia et al.   Frontiers in Microbiology

Bacterial evolution: Genomics of metabolic trade-offs

(2016) Martin F. Polz et al.   Nature Microbiology

Potential production platform of n-butanol in Escherichia coli

(2015) Mukesh Saini et al.   METABOLIC ENGINEERING

Overflow metabolism in Escherichia coli results from efficient proteome allocation

(2015) Markus Basan et al.   NATURE

Distributing a metabolic pathway among a microbial consortium enhances production of natural products

(2015) Kang Zhou et al.   NATURE BIOTECHNOLOGY

The Pfam protein families database: towards a more sustainable future

(2015) Robert D. Finn et al.   NUCLEIC ACIDS RESEARCH

EngineeringEscherichia colicoculture systems for the production of biochemical products

(2015) Haoran Zhang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Synthetic communities, the sum of parts

(2015) B. P. Teague et al.   SCIENCE

Membrane transporter engineering in industrial biotechnology and whole cell biocatalysis

(2015) Douglas B. Kell et al.   TRENDS IN BIOTECHNOLOGY

Adaptive Evolution of Synthetic Cooperating Communities Improves Growth Performance

(2014) Xiaolin Zhang et al.   PLoS One

Erosion of functional independence early in the evolution of a microbial mutualism

(2014) K. L. Hillesland et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Syntrophic exchange in synthetic microbial communities

(2014) M. T. Mee et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Evolutionary limits to cooperation in microbial communities

(2014) Nuno M. Oliveira et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

d-OptCom: Dynamic Multi-level and Multi-objective Metabolic Modeling of Microbial Communities

(2014) Ali R. Zomorrodi et al.   ACS Synthetic Biology

Metabolic Resource Allocation in Individual Microbes Determines Ecosystem Interactions and Spatial Dynamics

(2014) William R. Harcombe et al.   Cell Reports

Emergent Biosynthetic Capacity in Simple Microbial Communities

(2014) Hsuan-Chao Chiu et al.   PLoS Computational Biology

Consortia-mediated bioprocessing of cellulose to ethanol with a symbiotic Clostridium phytofermentans/yeast co-culture

(2013) Trevor R Zuroff et al.   Biotechnology for Biofuels

COBRApy: COnstraints-Based Reconstruction and Analysis for Python

(2013) Ali Ebrahim et al.   BMC Systems Biology

Nitrogen Assimilation in Escherichia coli: Putting Molecular Data into a Systems Perspective

(2013) W. C. van Heeswijk et al.   MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS

Genome-scale models of metabolism and gene expression extend and refine growth phenotype prediction

(2013) E. J. O{middle dot}Brien et al.   Molecular Systems Biology

Community Flux Balance Analysis for Microbial Consortia at Balanced Growth

(2013) Ruchir A. Khandelwal et al.   PLoS One

Design and characterization of synthetic fungal-bacterial consortia for direct production of isobutanol from cellulosic biomass

(2013) Jeremy J. Minty et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Stochastic simulations of a synthetic bacteria-yeast ecosystem

(2012) Konstantinos Biliouris et al.   BMC Systems Biology

Gap-filling analysis of the iJO1366 Escherichia coli metabolic network reconstruction for discovery of metabolic functions

(2012) Jeffrey D Orth et al.   BMC Systems Biology

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

The impact of nutrition on the human microbiome

(2012) Harry J Flint   NUTRITION REVIEWS

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

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

OptCom: A Multi-Level Optimization Framework for the Metabolic Modeling and Analysis of Microbial Communities

(2012) Ali R. Zomorrodi et al.   PLoS Computational Biology

MICROBIAL CONSORTIA ENGINEERING FOR CELLULAR FACTORIES: IN VITRO TO IN SILICO SYSTEMS

(2012) Hans C Bernstein et al.   Computational and Structural Biotechnology Journal

A comprehensive genome-scale reconstruction of Escherichia coli metabolism--2011

(2011) J. D. Orth et al.   Molecular Systems Biology

Cooperative Adaptation to Establishment of a Synthetic Bacterial Mutualism

(2011) Kazufumi Hosoda et al.   PLoS One

Cumulative Number of Cell Divisions as a Meaningful Timescale for Adaptive Laboratory Evolution of Escherichia coli

(2011) Dae-Hee Lee et al.   PLoS One

Competitive and cooperative metabolic interactions in bacterial communities

(2011) Shiri Freilich et al.   Nature Communications

The biomass objective function

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

Emergent cooperation in microbial metabolism

(2010) Edwin H Wintermute et al.   Molecular Systems Biology

Direct Exchange of Electrons Within Aggregates of an Evolved Syntrophic Coculture of Anaerobic Bacteria

(2010) Z. M. Summers et al.   SCIENCE

Environments that Induce Synthetic Microbial Ecosystems

(2010) Niels Klitgord et al.   PLoS Computational Biology

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Predicting metabolic engineering knockout strategies for chemical production: accounting for competing pathways

(2009) N. Tepper et al.   BIOINFORMATICS

Evolution by leaps: gene duplication in bacteria

(2009) Margrethe H Serres et al.   Biology Direct

Model-driven evaluation of the production potential for growth-coupled products of Escherichia coli

(2009) Adam M. Feist et al.   METABOLIC ENGINEERING

Reconstruction of biochemical networks in microorganisms

(2008) Adam M. Feist et al.   NATURE REVIEWS MICROBIOLOGY