Uncovering and resolving challenges of quantitative modeling in a simplified community of interacting cells

Designing microbial consortia with defined social interactions

(2018) Wentao Kong et al.   Nature Chemical Biology

Tuning Transcriptional Regulation through Signaling: A Predictive Theory of Allosteric Induction

(2018) Manuel Razo-Mejia et al.   Cell Systems

A review of control strategies for manipulating the feed rate in fed-batch fermentation processes

(2017) Lisa Mears et al.   JOURNAL OF BIOTECHNOLOGY

Perspectives on theory at the interface of physics and biology

(2017) William Bialek   REPORTS ON PROGRESS IN PHYSICS

Lotka-Volterra pairwise modeling fails to capture diverse pairwise microbial interactions

(2017) Babak Momeni et al.   eLife

Modeling Microbial Communities: A Call for Collaboration between Experimentalists and Theorists

(2017) et al.   Processes

Inferring human microbial dynamics from temporal metagenomics data: Pitfalls and lessons

(2016) Hong-Tai Cao et al.   BIOESSAYS

Engineering microbial consortia for controllable outputs

(2016) Stephen R Lindemann et al.   ISME Journal

Physical and Mathematical Modeling in Experimental Papers

(2015) Wolfram Möbius et al.   CELL

Better together: engineering and application of microbial symbioses

(2015) Stephanie G Hays et al.   CURRENT OPINION IN BIOTECHNOLOGY

A growth-rate composition formula for the growth of E. coli on co-utilized carbon substrates

(2015) R. Hermsen et al.   Molecular Systems Biology

Overflow metabolism in Escherichia coli results from efficient proteome allocation

(2015) Markus Basan et al.   NATURE

Acknowledging selection at sub-organismal levels resolves controversy on pro-cooperation mechanisms

(2015) Wenying Shou   eLife

Synthetic microbial communities

(2014) Tobias Großkopf et al.   CURRENT OPINION IN MICROBIOLOGY

Inference of interactions in cyanobacterial–heterotrophic co-cultures via transcriptome sequencing

(2014) Alexander S Beliaev et al.   ISME Journal

Discovery of a SAR11 growth requirement for thiamin’s pyrimidine precursor and its distribution in the Sargasso Sea

(2014) Paul Carini et al.   ISME Journal

Models overestimate Ebola cases

(2014) Declan Butler   NATURE

Genetic drift opposes mutualism during spatial population expansion

(2014) M. J. I. Muller et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Global epistasis makes adaptation predictable despite sequence-level stochasticity

(2014) S. Kryazhimskiy et al.   SCIENCE

Genomic distribution of B-vitamin auxotrophy and uptake transporters in environmental bacteria from theChloroflexiphylum

(2014) Irina A. Rodionova et al.   Environmental Microbiology Reports

A Low Cost, Customizable Turbidostat for Use in Synthetic Circuit Characterization

(2014) Chris N. Takahashi 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

An Ecological Network of Polysaccharide Utilization among Human Intestinal Symbionts

(2013) Seth Rakoff-Nahoum et al.   CURRENT BIOLOGY

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

Mathematical modeling of primary succession of murine intestinal microbiota

(2013) S. Marino et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Reliable Prediction of Complex Phenotypes from a Modular Design in Free Energy Space: An Extensive Exploration of the lac Operon

(2013) Jose M. G. Vilar et al.   ACS Synthetic Biology

Ecological Modeling from Time-Series Inference: Insight into Dynamics and Stability of Intestinal Microbiota

(2013) Richard R. Stein et al.   PLoS Computational Biology

Spatial self-organization favors heterotypic cooperation over cheating

(2013) Babak Momeni et al.   eLife

Strong inter-population cooperation leads to partner intermixing in microbial communities

(2013) Babak Momeni et al.   eLife

Structure, mechanism and regulation of an artificial microbial ecosystem for vitamin C production

(2012) Wei Zou et al.   CRITICAL REVIEWS IN MICROBIOLOGY

Towards synthetic microbial consortia for bioprocessing

(2012) Jasmine Shong et al.   CURRENT OPINION IN BIOTECHNOLOGY

cn.MOPS: mixture of Poissons for discovering copy number variations in next-generation sequencing data with a low false discovery rate

(2012) Günter Klambauer et al.   NUCLEIC ACIDS RESEARCH

Mass spectral molecular networking of living microbial colonies

(2012) J. Watrous et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Adaptation to a new environment allows cooperators to purge cheaters stochastically

(2012) A. J. Waite et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Application of Ecological Theory Toward an Understanding of the Human Microbiome

(2012) E. K. Costello et al.   SCIENCE

Targeted Restoration of the Intestinal Microbiota with a Simple, Defined Bacteriotherapy Resolves Relapsing Clostridium difficile Disease in Mice

(2012) Trevor D. Lawley et al.   PLoS Pathogens

Acetate scavenging activity in Escherichia coli: interplay of acetyl–CoA synthetase and the PEP–glyoxylate cycle in chemostat cultures

(2011) Sergio Renilla et al.   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

The variant call format and VCFtools

(2011) P. Danecek et al.   BIOINFORMATICS

Insights into the Evolution of Vitamin B12 Auxotrophy from Sequenced Algal Genomes

(2011) K. E. Helliwell et al.   MOLECULAR BIOLOGY AND EVOLUTION

Integrative genomics viewer

(2011) James T Robinson et al.   NATURE BIOTECHNOLOGY

Integrated Proteomic and Metabolomic Analysis of an Artificial Microbial Community for Two-Step Production of Vitamin C

(2011) Qian Ma et al.   PLoS One

A fitness trade-off between local competition and dispersal in Vibrio cholerae biofilms

(2011) C. D. Nadell et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Regulation of Membrane Protein Degradation by Starvation-Response Pathways

(2011) Charles B. Jones et al.   TRAFFIC

The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data

(2010) A. McKenna et al.   GENOME RESEARCH

Viral and microbial community dynamics in four aquatic environments

(2010) Beltran Rodriguez-Brito et al.   ISME Journal

Environments that Induce Synthetic Microbial Ecosystems

(2010) Niels Klitgord et al.   PLoS Computational Biology

Rapid, low-input, low-bias construction of shotgun fragment libraries by high-density in vitro transposition

(2010) Andrew Adey et al.   GENOME BIOLOGY

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

Polymorphisms in Multiple Genes Contribute to the Spontaneous Mitochondrial Genome Instability of Saccharomyces cerevisiae S288C Strains

(2009) L. N. Dimitrov et al.   GENETICS

One Is Not Enough

(2009) Robert Daber et al.   JOURNAL OF MOLECULAR BIOLOGY

Non-genetic heterogeneity — a mutation-independent driving force for the somatic evolution of tumours

(2009) Amy Brock et al.   NATURE REVIEWS GENETICS

Opportunities for renewable bioenergy using microorganisms

(2008) Bruce E. Rittmann   BIOTECHNOLOGY AND BIOENGINEERING

Arrestin-Related Ubiquitin-Ligase Adaptors Regulate Endocytosis and Protein Turnover at the Cell Surface

(2008) Charles H. Lin et al.   CELL

Estimating the Per-Base-Pair Mutation Rate in the Yeast Saccharomyces cerevisiae

(2008) Gregory I. Lang et al.   GENETICS

A synthetic Escherichia coli predator–prey ecosystem

(2008) Frederick K Balagaddé et al.   Molecular Systems Biology

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

(2008) Markus J Herrgård et al.   NATURE BIOTECHNOLOGY

Virus Population Dynamics and Acquired Virus Resistance in Natural Microbial Communities

(2008) A. F. Andersson et al.   SCIENCE

Engineering microbial consortia: a new frontier in synthetic biology

(2008) Katie Brenner et al.   TRENDS IN BIOTECHNOLOGY