Engineering ecosystems and synthetic ecologies

Developing symbiotic consortia for lignocellulosic biofuel production

(2012) Trevor R. Zuroff et al.   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

The single-cell chemostat: an agarose-based, microfluidic device for high-throughput, single-cell studies of bacteria and bacterial communities

(2012) Jeffrey R. Moffitt et al.   LAB ON A CHIP

Signaling-mediated bacterial persister formation

(2012) Nicole M Vega et al.   Nature Chemical Biology

Genome-scale promoter engineering by coselection MAGE

(2012) Harris H Wang et al.   NATURE METHODS

Computational tools for the synthetic design of biochemical pathways

(2012) Marnix H. Medema et al.   NATURE REVIEWS MICROBIOLOGY

The Robustness and Restoration of a Network of Ecological Networks

(2012) M. J. O. Pocock et al.   SCIENCE

The Molecular Diversity of Adaptive Convergence

(2012) O. Tenaillon et al.   SCIENCE

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

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

Intercellular Nanotubes Mediate Bacterial Communication

(2011) Gyanendra P. Dubey et al.   CELL

An Interdependent Metabolic Patchwork in the Nested Symbiosis of Mealybugs

(2011) John P. McCutcheon et al.   CURRENT BIOLOGY

Ecosystems biology of microbial metabolism

(2011) Niels Klitgord et al.   CURRENT OPINION IN BIOTECHNOLOGY

Extracellular signaling and multicellularity in Bacillus subtilis

(2011) Elizabeth Anne Shank et al.   CURRENT OPINION IN MICROBIOLOGY

Colonic mucosal DNA methylation, immune response, and microbiome patterns in Toll-like receptor 2-knockout mice

(2011) Richard Kellermayer et al.   FASEB JOURNAL

Microbial laboratory evolution in the era of genome-scale science

(2011) T. M. Conrad et al.   Molecular Systems Biology

Engineering microbes to sense and eradicate Pseudomonas aeruginosa, a human pathogen

(2011) N. Saeidi et al.   Molecular Systems Biology

Metagenomic analysis of a permafrost microbial community reveals a rapid response to thaw

(2011) Rachel Mackelprang et al.   NATURE

A sensing array of radically coupled genetic ‘biopixels’

(2011) Arthur Prindle et al.   NATURE

Ecology drives a global network of gene exchange connecting the human microbiome

(2011) Chris S. Smillie et al.   NATURE

SignalP 4.0: discriminating signal peptides from transmembrane regions

(2011) Thomas Nordahl Petersen et al.   NATURE METHODS

The sociobiology of molecular systems

(2011) Kevin R. Foster   NATURE REVIEWS GENETICS

InterPro in 2011: new developments in the family and domain prediction database

(2011) S. Hunter et al.   NUCLEIC ACIDS RESEARCH

IMG: the integrated microbial genomes database and comparative analysis system

(2011) V. M. Markowitz et al.   NUCLEIC ACIDS RESEARCH

The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases

(2011) R. Caspi et al.   NUCLEIC ACIDS RESEARCH

KEGG for integration and interpretation of large-scale molecular data sets

(2011) M. Kanehisa et al.   NUCLEIC ACIDS RESEARCH

The Pfam protein families database

(2011) M. Punta et al.   NUCLEIC ACIDS RESEARCH

Cooperative Adaptation to Establishment of a Synthetic Bacterial Mutualism

(2011) Kazufumi Hosoda et al.   PLoS One

Self-Organization, Layered Structure, and Aggregation Enhance Persistence of a Synthetic Biofilm Consortium

(2011) Katie Brenner et al.   PLoS One

Microdroplet-Enabled Highly Parallel Co-Cultivation of Microbial Communities

(2011) Jihyang Park et al.   PLoS One

Aphid genome expression reveals host-symbiont cooperation in the production of amino acids

(2011) A. K. Hansen et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Bacterial community assembly based on functional genes rather than species

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

Division of labour and the evolution of multicellularity

(2011) I. Ispolatov et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Negative Epistasis Between Beneficial Mutations in an Evolving Bacterial Population

(2011) A. I. Khan et al.   SCIENCE

Predicting a Human Gut Microbiota's Response to Diet in Gnotobiotic Mice

(2011) J. J. Faith et al.   SCIENCE

Diminishing Returns Epistasis Among Beneficial Mutations Decelerates Adaptation

(2011) H.-H. Chou et al.   SCIENCE

Acceleration of Emergence of Bacterial Antibiotic Resistance in Connected Microenvironments

(2011) Q. Zhang et al.   SCIENCE

Reciprocal Rewards Stabilize Cooperation in the Mycorrhizal Symbiosis

(2011) E. T. Kiers et al.   SCIENCE

Rescuing ecosystems from extinction cascades through compensatory perturbations

(2011) Sagar Sahasrabudhe et al.   Nature Communications

Bacterial Contact-Dependent Delivery Systems

(2010) Christopher S. Hayes et al.   Annual Review of Genetics

Recombineering Using RecTE from Pseudomonas syringae

(2010) B. Swingle et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Classic and contemporary approaches to modeling biochemical reactions

(2010) W. W. Chen et al.   GENES & DEVELOPMENT

Genome-scale dynamic modeling of the competition between Rhodoferax and Geobacter in anoxic subsurface environments

(2010) Kai Zhuang et al.   ISME Journal

Creating and characterizing communities of human gut microbes in gnotobiotic mice

(2010) Jeremiah J Faith et al.   ISME Journal

Toward defining the autoimmune microbiome for type 1 diabetes

(2010) Adriana Giongo et al.   ISME Journal

Emergent cooperation in microbial metabolism

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

Bacterial charity work leads to population-wide resistance

(2010) Henry H. Lee et al.   NATURE

Distributed biological computation with multicellular engineered networks

(2010) Sergi Regot et al.   NATURE

Robust multicellular computing using genetically encoded NOR gates and chemical ‘wires’

(2010) Alvin Tamsir et al.   NATURE

A synchronized quorum of genetic clocks

(2010) Tal Danino et al.   NATURE

Synthetic biology: applications come of age

(2010) Ahmad S. Khalil et al.   NATURE REVIEWS GENETICS

The impact of the microbiota on the pathogenesis of IBD: lessons from mouse infection models

(2010) Sandra Nell et al.   NATURE REVIEWS MICROBIOLOGY

Engineered bacterial communication prevents Vibrio cholerae virulence in an infant mouse model

(2010) F. Duan et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Organismal, genetic, and transcriptional variation in the deeply sequenced gut microbiomes of identical twins

(2010) P. J. Turnbaugh et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Emergence of Spatial Structure in Cell Groups and the Evolution of Cooperation

(2010) Carey D. Nadell et al.   PLoS Computational Biology

Actobiotics™ as a Novel Method for Cytokine Delivery

(2009) Lothar Steidler et al.   Annals of the New York Academy of Sciences

Interspecies Chemical Communication in Bacterial Development

(2009) Paul D. Straight et al.   Annual Review of Microbiology

Prokaryotic Genomes and Diversity in Surface Ocean Waters: Interrogating the Global Ocean Sampling Metagenome

(2009) E. J. Biers et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Use of the λ Red-recombineering method for genetic engineering of Pantoea ananatis

(2009) Joanna I Katashkina et al.   BMC MOLECULAR BIOLOGY

In silico approaches to study mass and energy flows in microbial consortia: a syntrophic case study

(2009) Reed Taffs et al.   BMC Systems Biology

A Synthetic Genetic Edge Detection Program

(2009) Jeffrey J. Tabor et al.   CELL

Identifying Genetic Determinants Needed to Establish a Human Gut Symbiont in Its Habitat

(2009) Andrew L. Goodman et al.   Cell Host & Microbe

Efflux-Mediated Drug Resistance in Bacteria

(2009) Xian-Zhi Li et al.   DRUGS

Microbial community profiling for human microbiome projects: Tools, techniques, and challenges

(2009) M. Hamady et al.   GENOME RESEARCH

Simultaneous assay of every Salmonella Typhi gene using one million transposon mutants

(2009) G. C. Langridge et al.   GENOME RESEARCH

The NIH Human Microbiome Project

(2009) et al.   GENOME RESEARCH

Low counts of Faecalibacterium prausnitzii in colitis microbiota

(2009) H. Sokol et al.   INFLAMMATORY BOWEL DISEASES

Synthesis of Methyl Halides from Biomass Using Engineered Microbes

(2009) Travis S. Bayer et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Competitive activation of the Escherichia coli argO gene coding for an arginine exporter by the transcriptional regulators Lrp and ArgP

(2009) Eveline Peeters et al.   MOLECULAR MICROBIOLOGY

Oligonucleotide recombination in Gram-negative bacteria

(2009) Bryan Swingle et al.   MOLECULAR MICROBIOLOGY

Snowdrift game dynamics and facultative cheating in yeast

(2009) Jeff Gore et al.   NATURE

Programming cells by multiplex genome engineering and accelerated evolution

(2009) Harris H. Wang et al.   NATURE

Genome engineering

(2009) Peter A Carr et al.   NATURE BIOTECHNOLOGY

Next-generation synthetic gene networks

(2009) Timothy K Lu et al.   NATURE BIOTECHNOLOGY

Global discovery of adaptive mutations

(2009) Hani Goodarzi et al.   NATURE METHODS

Tn-seq: high-throughput parallel sequencing for fitness and genetic interaction studies in microorganisms

(2009) Tim van Opijnen et al.   NATURE METHODS

Engineering for biofuels: exploiting innate microbial capacity or importing biosynthetic potential?

(2009) Hal Alper et al.   NATURE REVIEWS MICROBIOLOGY

Bacterial competition: surviving and thriving in the microbial jungle

(2009) Michael E. Hibbing et al.   NATURE REVIEWS MICROBIOLOGY

Convergent evolution of metabolic roles in bacterial co-symbionts of insects

(2009) J. P. McCutcheon et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Tracking insertion mutants within libraries by deep sequencing and a genome-wide screen for Haemophilus genes required in the lung

(2009) J. D. Gawronski et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Bacterial Species Challenge: Making Sense of Genetic and Ecological Diversity

(2009) C. Fraser et al.   SCIENCE

The role of colonic metabolism in lactose intolerance

(2008) T. He et al.   EUROPEAN JOURNAL OF CLINICAL INVESTIGATION

Historical and contingent factors affect re-evolution of a complex feature lost during mass extinction in communities of digital organisms

(2008) G. YEDID et al.   JOURNAL OF EVOLUTIONARY BIOLOGY

A synthetic Escherichia coli predator–prey ecosystem

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

A core gut microbiome in obese and lean twins

(2008) Peter J. Turnbaugh et al.   NATURE

Refinement and standardization of synthetic biological parts and devices

(2008) Barry Canton et al.   NATURE BIOTECHNOLOGY

Symbiotic conversations are revealed under genetic interrogation

(2008) Edward G. Ruby   NATURE REVIEWS MICROBIOLOGY

Molecular eco-systems biology: towards an understanding of community function

(2008) Jeroen Raes et al.   NATURE REVIEWS MICROBIOLOGY

Reconstruction of biochemical networks in microorganisms

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

Defined spatial structure stabilizes a synthetic multispecies bacterial community

(2008) H. J. Kim et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Identification and analysis of recombineering functions from Gram-negative and Gram-positive bacteria and their phages

(2008) S. Datta et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Microbial Engines That Drive Earth's Biogeochemical Cycles

(2008) P. G. Falkowski et al.   SCIENCE

Population Genomic Analysis of Strain Variation in Leptospirillum Group II Bacteria Involved in Acid Mine Drainage Formation

(2008) Sheri L Simmons et al.   PLOS BIOLOGY

The Emergence and Fate of Horizontally Acquired Genes in Escherichia coli

(2008) Mark W. J. van Passel et al.   PLoS Computational Biology