相关参考文献
注意:仅列出部分参考文献,下载原文获取全部文献信息。Developing symbiotic consortia for lignocellulosic biofuel production
Trevor R. Zuroff et al.
APPLIED MICROBIOLOGY AND BIOTECHNOLOGY (2012)
The single-cell chemostat: an agarose-based, microfluidic device for high-throughput, single-cell studies of bacteria and bacterial communities
Jeffrey R. Moffitt et al.
LAB ON A CHIP (2012)
A sensing array of radically coupled genetic 'biopixels'
Arthur Prindle et al.
NATURE (2012)
Signaling-mediated bacterial persister formation
Nicole M. Vega et al.
NATURE CHEMICAL BIOLOGY (2012)
Genome-scale promoter engineering by coselection MAGE
Harris H. Wang et al.
NATURE METHODS (2012)
Computational tools for the synthetic design of biochemical pathways
Marnix H. Medema et al.
NATURE REVIEWS MICROBIOLOGY (2012)
InterPro in 2011: new developments in the family and domain prediction database
Sarah Hunter et al.
NUCLEIC ACIDS RESEARCH (2012)
IMG: the integrated microbial genomes database and comparative analysis system
Victor M. Markowitz et al.
NUCLEIC ACIDS RESEARCH (2012)
The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases
Ron Caspi et al.
NUCLEIC ACIDS RESEARCH (2012)
KEGG for integration and interpretation of large-scale molecular data sets
Minoru Kanehisa et al.
NUCLEIC ACIDS RESEARCH (2012)
The Pfam protein families database
Marco Punta et al.
NUCLEIC ACIDS RESEARCH (2012)
Division of labour and the evolution of multicellularity
Iaroslav Ispolatov et al.
PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES (2012)
The Robustness and Restoration of a Network of Ecological Networks
Michael J. O. Pocock et al.
SCIENCE (2012)
The Molecular Diversity of Adaptive Convergence
Olivier Tenaillon et al.
SCIENCE (2012)
OptCom: A Multi-Level Optimization Framework for the Metabolic Modeling and Analysis of Microbial Communities
Ali R. Zomorrodi et al.
PLOS COMPUTATIONAL BIOLOGY (2012)
Intercellular Nanotubes Mediate Bacterial Communication
Gyanendra P. Dubey et al.
CELL (2011)
An Interdependent Metabolic Patchwork in the Nested Symbiosis of Mealybugs
John P. McCutcheon et al.
CURRENT BIOLOGY (2011)
Ecosystems biology of microbial metabolism
Niels Klitgord et al.
CURRENT OPINION IN BIOTECHNOLOGY (2011)
Extracellular signaling and multicellularity in Bacillus subtilis
Elizabeth Anne Shank et al.
CURRENT OPINION IN MICROBIOLOGY (2011)
Colonic mucosal DNA methylation, immune response, and microbiome patterns in Toll-like receptor 2-knockout mice
Richard Kellermayer et al.
FASEB JOURNAL (2011)
Genome-scale dynamic modeling of the competition between Rhodoferax and Geobacter in anoxic subsurface environments
Kai Zhuang et al.
ISME JOURNAL (2011)
Toward defining the autoimmune microbiome for type 1 diabetes
Adriana Giongo et al.
ISME JOURNAL (2011)
Microbial laboratory evolution in the era of genome-scale science
Tom M. Conrad et al.
MOLECULAR SYSTEMS BIOLOGY (2011)
Engineering microbes to sense and eradicate Pseudomonas aeruginosa, a human pathogen
Nazanin Saeidi et al.
MOLECULAR SYSTEMS BIOLOGY (2011)
Distributed biological computation with multicellular engineered networks
Sergi Regot et al.
NATURE (2011)
Robust multicellular computing using genetically encoded NOR gates and chemical 'wires'
Alvin Tamsir et al.
NATURE (2011)
Metagenomic analysis of a permafrost microbial community reveals a rapid response to thaw
Rachel Mackelprang et al.
NATURE (2011)
Ecology drives a global network of gene exchange connecting the human microbiome
Chris S. Smillie et al.
NATURE (2011)
SignalP 4.0: discriminating signal peptides from transmembrane regions
Thomas Nordahl Petersen et al.
NATURE METHODS (2011)
The sociobiology of molecular systems
Kevin R. Foster
NATURE REVIEWS GENETICS (2011)
Cooperative Adaptation to Establishment of a Synthetic Bacterial Mutualism
Kazufumi Hosoda et al.
PLOS ONE (2011)
Self-Organization, Layered Structure, and Aggregation Enhance Persistence of a Synthetic Biofilm Consortium
Katie Brenner et al.
PLOS ONE (2011)
Microdroplet-Enabled Highly Parallel Co-Cultivation of Microbial Communities
Jihyang Park et al.
PLOS ONE (2011)
Aphid genome expression reveals host-symbiont cooperation in the production of amino acids
Allison K. Hansen et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2011)
Bacterial community assembly based on functional genes rather than species
Catherine Burke et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2011)
Negative Epistasis Between Beneficial Mutations in an Evolving Bacterial Population
Aisha I. Khan et al.
SCIENCE (2011)
Predicting a Human Gut Microbiota's Response to Diet in Gnotobiotic Mice
Jeremiah J. Faith et al.
SCIENCE (2011)
Diminishing Returns Epistasis Among Beneficial Mutations Decelerates Adaptation
Hsin-Hung Chou et al.
SCIENCE (2011)
Acceleration of Emergence of Bacterial Antibiotic Resistance in Connected Microenvironments
Qiucen Zhang et al.
SCIENCE (2011)
Reciprocal Rewards Stabilize Cooperation in the Mycorrhizal Symbiosis
E. Toby Kiers et al.
SCIENCE (2011)
Rescuing ecosystems from extinction cascades through compensatory perturbations
Sagar Sahasrabudhe et al.
NATURE COMMUNICATIONS (2011)
Bacterial Contact-Dependent Delivery Systems
Christopher S. Hayes et al.
ANNUAL REVIEW OF GENETICS, VOL 44 (2010)
Recombineering Using RecTE from Pseudomonas syringae
Bryan Swingle et al.
APPLIED AND ENVIRONMENTAL MICROBIOLOGY (2010)
Classic and contemporary approaches to modeling biochemical reactions
William W. Chen et al.
GENES & DEVELOPMENT (2010)
Creating and characterizing communities of human gut microbes in gnotobiotic mice
Jeremiah J. Faith et al.
ISME JOURNAL (2010)
Oligonucleotide recombination in Gram-negative bacteria
Bryan Swingle et al.
MOLECULAR MICROBIOLOGY (2010)
Emergent cooperation in microbial metabolism
Edwin H. Wintermute et al.
MOLECULAR SYSTEMS BIOLOGY (2010)
Bacterial charity work leads to population-wide resistance
Henry H. Lee et al.
NATURE (2010)
A synchronized quorum of genetic clocks
Tal Danino et al.
NATURE (2010)
Synthetic biology: applications come of age
Ahmad S. Khalil et al.
NATURE REVIEWS GENETICS (2010)
Bacterial competition: surviving and thriving in the microbial jungle
Michael E. Hibbing et al.
NATURE REVIEWS MICROBIOLOGY (2010)
The impact of the microbiota on the pathogenesis of IBD: lessons from mouse infection models
Sandra Nell et al.
NATURE REVIEWS MICROBIOLOGY (2010)
Engineered bacterial communication prevents Vibrio cholerae virulence in an infant mouse model
Faping Duan et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2010)
Organismal, genetic, and transcriptional variation in the deeply sequenced gut microbiomes of identical twins
Peter J. Turnbaugh et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2010)
Emergence of Spatial Structure in Cell Groups and the Evolution of Cooperation
Carey D. Nadell et al.
PLOS COMPUTATIONAL BIOLOGY (2010)
Actobiotics (TM) as a Novel Method for Cytokine Delivery The Interleukin-10 Case
Lothar Steidler et al.
CYTOKINE THERAPIES: NOVEL APPROACHES FOR CLINICAL INDICATIONS (2009)
Interspecies Chemical Communication in Bacterial Development
Paul D. Straight et al.
ANNUAL REVIEW OF MICROBIOLOGY (2009)
Prokaryotic Genomes and Diversity in Surface Ocean Waters: Interrogating the Global Ocean Sampling Metagenome
Erin J. Biers et al.
APPLIED AND ENVIRONMENTAL MICROBIOLOGY (2009)
Use of the λ Red-recombineering method for genetic engineering of Pantoea ananatis
Joanna I. Katashkina et al.
BMC MOLECULAR BIOLOGY (2009)
In silico approaches to study mass and energy flows in microbial consortia: a syntrophic case study
Reed Taffs et al.
BMC SYSTEMS BIOLOGY (2009)
A Synthetic Genetic Edge Detection Program
Jeffrey J. Tabor et al.
CELL (2009)
Identifying Genetic Determinants Needed to Establish a Human Gut Symbiont in Its Habitat
Andrew L. Goodman et al.
CELL HOST & MICROBE (2009)
Efflux-Mediated Drug Resistance in Bacteria An Update
Xian-Zhi Li et al.
DRUGS (2009)
Microbial community profiling for human microbiome projects: Tools, techniques, and challenges
Micah Hamady et al.
GENOME RESEARCH (2009)
Simultaneous assay of every Salmonella Typhi gene using one million transposon mutants
Gemma C. Langridge et al.
GENOME RESEARCH (2009)
The NIH Human Microbiome Project
Jane Peterson et al.
GENOME RESEARCH (2009)
Low Counts of Faecalibacterium prausnitzii in Colitis Microbiota
H. Sokol et al.
INFLAMMATORY BOWEL DISEASES (2009)
Synthesis of Methyl Halides from Biomass Using Engineered Microbes
Travis S. Bayer et al.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2009)
Competitive activation of the Escherichia coli argO gene coding for an arginine exporter by the transcriptional regulators Lrp and ArgP
Eveline Peeters et al.
MOLECULAR MICROBIOLOGY (2009)
A core gut microbiome in obese and lean twins
Peter J. Turnbaugh et al.
NATURE (2009)
Snowdrift game dynamics and facultative cheating in yeast
Jeff Gore et al.
NATURE (2009)
Programming cells by multiplex genome engineering and accelerated evolution
Harris H. Wang et al.
NATURE (2009)
Genome engineering
Peter A. Carr et al.
NATURE BIOTECHNOLOGY (2009)
Next-generation synthetic gene networks
Timothy K. Lu et al.
NATURE BIOTECHNOLOGY (2009)
Global discovery of adaptive mutations
Hani Goodarzi et al.
NATURE METHODS (2009)
Tn-seq: high-throughput parallel sequencing for fitness and genetic interaction studies in microorganisms
Tim van Opijnen et al.
NATURE METHODS (2009)
Reconstruction of biochemical networks in microorganisms
Adam M. Feist et al.
NATURE REVIEWS MICROBIOLOGY (2009)
Engineering for biofuels: exploiting innate microbial capacity or importing biosynthetic potential?
Hal Alper et al.
NATURE REVIEWS MICROBIOLOGY (2009)
Convergent evolution of metabolic roles in bacterial co-symbionts of insects
John P. McCutcheon et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2009)
Tracking insertion mutants within libraries by deep sequencing and a genome-wide screen for Haemophilus genes required in the lung
Jeffrey D. Gawronski et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2009)
The Bacterial Species Challenge: Making Sense of Genetic and Ecological Diversity
Christophe Fraser et al.
SCIENCE (2009)
The role of colonic metabolism in lactose intolerance
T. He et al.
EUROPEAN JOURNAL OF CLINICAL INVESTIGATION (2008)
Historical and contingent factors affect re-evolution of a complex feature lost during mass extinction in communities of digital organisms
G. Yedid et al.
JOURNAL OF EVOLUTIONARY BIOLOGY (2008)
A synthetic Escherichia coli predator-prey ecosystem
Frederick K. Balagadde et al.
MOLECULAR SYSTEMS BIOLOGY (2008)
Refinement and standardization of synthetic biological parts and devices
Barry Canton et al.
NATURE BIOTECHNOLOGY (2008)
Symbiotic conversations are revealed under genetic interrogation
Edward G. Ruby
NATURE REVIEWS MICROBIOLOGY (2008)
Systems microbiology - Timeline - Molecular eco-systems biology: towards an understanding of community function
Jeroen Raes et al.
NATURE REVIEWS MICROBIOLOGY (2008)
Defined spatial structure stabilizes a synthetic multispecies bacterial community
Hyun Jung Kim et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2008)
Identification and analysis of recombineering functions from Gram-negative and Gram-positive bacteria and their phages
Simanti Datta et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2008)
The microbial engines that drive Earth's biogeochemical cycles
Paul G. Falkowski et al.
SCIENCE (2008)
Population genomic analysis of strain variation in Leptospirillum group II bacteria involved in acid mine drainage formation
Sheri L. Simmons et al.
PLOS BIOLOGY (2008)
The emergence and fate of horizontally acquired genes in Escherichia coli
Mark W. J. van Passel et al.
PLOS COMPUTATIONAL BIOLOGY (2008)
Metagenomic and functional analysis of hindgut microbiota of a wood-feeding higher termite
Falk Warnecke et al.
NATURE (2007)
Engineered bidirectional communication mediates a consensus in a microbial biofilm consortium
Katie Brenner et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2007)
An ecological and evolutionary perspective on human-microbe mutualism and disease
Les Dethlefsen et al.
NATURE (2007)
The Human Microbiome Project
Peter J. Turnbaugh et al.
NATURE (2007)
YddG from Escherichia coli promotes export of aromatic amino acids
Vera Doroshenko et al.
FEMS MICROBIOLOGY LETTERS (2007)
Genome-scale reconstruction of metabolic network in Bacillus subtilis based on high-throughput phenotyping and gene essentiality data
You-Kwan Oh et al.
JOURNAL OF BIOLOGICAL CHEMISTRY (2007)
Oligonucleotide transformation of yeast reveals mismatch repair complexed to be differentially active on DNA replication strands
Yoke W. Kow et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2007)
Metabolic modeling of a mutualistic microbial community
Sergey Stolyar et al.
MOLECULAR SYSTEMS BIOLOGY (2007)
Global reconstruction of the human metabolic network based on genomic and bibliomic data
Natalie C. Duarte et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2007)
Synthetic cooperation in engineered yeast populations
Wenying Shou et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2007)
Recombineering in Mycobacterium tuberculosis
Julia C. van Kessel et al.
NATURE METHODS (2007)
Beyond toothpicks: new methods for isolating mutant bacteria
A. James Link et al.
NATURE REVIEWS MICROBIOLOGY (2007)
Five rules for the evolution of cooperation
Martin A. Nowak
SCIENCE (2006)
Integration of curated databases to identify genotype-phenotype associations
Chern-Sing Goh et al.
BMC GENOMICS (2006)
Social evolution theory for microorganisms
Stuart A. West et al.
NATURE REVIEWS MICROBIOLOGY (2006)
Synergy and discounting of cooperation in social dilemmas
C Hauert et al.
JOURNAL OF THEORETICAL BIOLOGY (2006)
Reduced diversity of faecal microbiota in Crohn's disease revealed by a metagenomic approach
C Manichanh et al.
GUT (2006)
In vitro functional characterization of BtuCD-F, the Escherichia coli ABC transporter for vitamin B12 uptake
EL Borths et al.
BIOCHEMISTRY (2005)
Stable coexistence of five bacterial strains as a cellulose-degrading community
S Kato et al.
APPLIED AND ENVIRONMENTAL MICROBIOLOGY (2005)
The yeaS (leuE) gene of Escherichia coli encodes an exporter of leucine, and the Lrp protein regulates its expression
EA Kutukova et al.
FEBS LETTERS (2005)
Obesity alters gut microbial ecology
RE Ley et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2005)
Long-term monitoring of bacteria undergoing programmed population control in a microchemostat
FK Balagaddé et al.
SCIENCE (2005)
Gut microorganisms, mammalian metabolism and personalized health care
JK Nicholson et al.
NATURE REVIEWS MICROBIOLOGY (2005)
A synthetic multicellular system for programmed pattern formation
S Basu et al.
NATURE (2005)
Survival strategies of infectious biofilms
CA Fux et al.
TRENDS IN MICROBIOLOGY (2005)
Mobile genetic elements: The agents of open source evolution
LS Frost et al.
NATURE REVIEWS MICROBIOLOGY (2005)
Horizontal gene transfer, genome innovation and evolution
JP Gogarten et al.
NATURE REVIEWS MICROBIOLOGY (2005)
Programmed population control by cell-cell communication and regulated killing
LC You et al.
NATURE (2004)
Ancient invasions: From endosymbionts to organelles
SD Dyall et al.
SCIENCE (2004)
Antibiotic-mediated antagonism leads to a bacterial game of rock-paper-scissors in vivo
BC Kirkup et al.
NATURE (2004)
Bacterial biofilms: From the natural environment to infectious diseases
L Hall-Stoodley et al.
NATURE REVIEWS MICROBIOLOGY (2004)
Membrane topology and mutational analysis of Escherichia coli CydDC, an ABC-type cysteine exporter required for cytochrome assembly
H Cruz-Ramos et al.
MICROBIOLOGY-SGM (2004)
Bacterial persistence as a phenotypic switch
NQ Balaban et al.
SCIENCE (2004)
Adaptive radiation from resource competition in digital organisms
SS Chow et al.
SCIENCE (2004)
Status of the microbial census
PD Schloss et al.
MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS (2004)
Reconstruction and validation of Saccharomyces cerevisiae iND750, a fully compartmentalized genome-scale metabolic model
NC Duarte et al.
GENOME RESEARCH (2004)
Shaping bacterial genomes with integrative and conjugative elements
V Burrus et al.
RESEARCH IN MICROBIOLOGY (2004)
Network-based analysis of metabolic regulation in the human red blood cell
ND Price et al.
JOURNAL OF THEORETICAL BIOLOGY (2003)
The ATP/Substrate stoichiometry of the ATP-binding cassette (ABC) transporter OpuA
JS Patzlaff et al.
JOURNAL OF BIOLOGICAL CHEMISTRY (2003)
The evolutionary origin of complex features
RE Lenski et al.
NATURE (2003)
YfiK from Escherichia coli promotes export of O-acetylserine and cysteine
I Franke et al.
JOURNAL OF BACTERIOLOGY (2003)
New ubiquitous translocators: amino acid export by Corynebacterium glutamicum and Escherichia coli
L Eggeling et al.
ARCHIVES OF MICROBIOLOGY (2003)
Dynamic flux balance analysis of diauxic growth in Escherichia coli
R Mahadevan et al.
BIOPHYSICAL JOURNAL (2002)
Genome-scale metabolic model of Helicobacter pylori 26695
CH Schilling et al.
JOURNAL OF BACTERIOLOGY (2002)
Developmental regulation of microbial biofilms
L Hall-Stoodley et al.
CURRENT OPINION IN BIOTECHNOLOGY (2002)
Metabolic efficiency and amino acid composition in the proteomes of Escherichia coli and Bacillus subtilis
H Akashi et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2002)
Bacterial amino acid transport proteins: occurrence, functions, and significance for biotechnological applications
A Burkovski et al.
APPLIED MICROBIOLOGY AND BIOTECHNOLOGY (2002)
Evolution of digital organisms at high mutation rates leads to survival of the flattest
CO Wilke et al.
NATURE (2001)
Phenotype MicroArrays for high-throughput phenotypic testing and assay of gene function
BR Bochner et al.
GENOME RESEARCH (2001)
High efficiency mutagenesis, repair, and engineering of chromosomal DNA using single-stranded oligonucleotides
HM Ellis et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2001)
Treatment of murine colitis by Lactococcus lactis secreting interleukin-10
L Steidler et al.
SCIENCE (2000)
A functional-phylogenetic classification system for transmembrane solute transporters
MH Saier
MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS (2000)