Published in J Mol Biol on April 12, 2014
VFDB 2016: hierarchical and refined dataset for big data analysis-10 years on. Nucleic Acids Res (2015) 1.21
Universality of human microbial dynamics. Nature (2016) 1.07
From Hype to Hope: The Gut Microbiota in Enteric Infectious Disease. Cell (2015) 1.01
Community-level cohesion without cooperation. Elife (2016) 0.92
Metabolic network modeling of microbial communities. Wiley Interdiscip Rev Syst Biol Med (2015) 0.83
Which games are growing bacterial populations playing? J R Soc Interface (2015) 0.82
The demographic determinants of human microbiome health. Trends Microbiol (2014) 0.81
MDSINE: Microbial Dynamical Systems INference Engine for microbiome time-series analyses. Genome Biol (2016) 0.80
On the Origins and Control of Community Types in the Human Microbiome. PLoS Comput Biol (2016) 0.80
Sociomicrobiology and Pathogenic Bacteria. Microbiol Spectr (2016) 0.76
From cultured to uncultured genome sequences: metagenomics and modeling microbial ecosystems. Cell Mol Life Sci (2015) 0.76
Inferring interactions in complex microbial communities from nucleotide sequence data and environmental parameters. PLoS One (2017) 0.75
Human Microbiome Engineering: The Future and Beyond. J Clin Diagn Res (2015) 0.75
Modeling the Context-Dependent Associations between the Gut Microbiome, Its Environment, and Host Health. MBio (2015) 0.75
Chronic Rhinosinusitis and the Evolving Understanding of Microbial Ecology in Chronic Inflammatory Mucosal Disease. Clin Microbiol Rev (2017) 0.75
Boolean analysis reveals systematic interactions among low-abundance species in the human gut microbiome. PLoS Comput Biol (2017) 0.75
Induction of intestinal Th17 cells by segmented filamentous bacteria. Cell (2009) 20.29
Human gut microbiome viewed across age and geography. Nature (2012) 19.31
The pervasive effects of an antibiotic on the human gut microbiota, as revealed by deep 16S rRNA sequencing. PLoS Biol (2008) 16.57
A framework for human microbiome research. Nature (2012) 11.41
Metagenomic biomarker discovery and explanation. Genome Biol (2011) 11.29
What is flux balance analysis? Nat Biotechnol (2010) 9.01
Gut-residing segmented filamentous bacteria drive autoimmune arthritis via T helper 17 cells. Immunity (2010) 8.90
The human microbiome: at the interface of health and disease. Nat Rev Genet (2012) 7.54
Treg induction by a rationally selected mixture of Clostridia strains from the human microbiota. Nature (2013) 6.77
Gut microbiota in human adults with type 2 diabetes differs from non-diabetic adults. PLoS One (2010) 6.48
UniFrac: an effective distance metric for microbial community comparison. ISME J (2010) 6.43
Metabolic reconstruction for metagenomic data and its application to the human microbiome. PLoS Comput Biol (2012) 6.27
Genomic analysis identifies association of Fusobacterium with colorectal carcinoma. Genome Res (2011) 5.97
Bifidobacteria can protect from enteropathogenic infection through production of acetate. Nature (2011) 5.83
Dysfunction of the intestinal microbiome in inflammatory bowel disease and treatment. Genome Biol (2012) 5.66
Microbiota regulates immune defense against respiratory tract influenza A virus infection. Proc Natl Acad Sci U S A (2011) 5.44
Microbial co-occurrence relationships in the human microbiome. PLoS Comput Biol (2012) 5.35
Vancomycin-resistant Enterococcus domination of intestinal microbiota is enabled by antibiotic treatment in mice and precedes bloodstream invasion in humans. J Clin Invest (2010) 4.95
Genomic variation landscape of the human gut microbiome. Nature (2012) 4.38
Diffusion in biofilms. J Bacteriol (2003) 4.22
Characterizing a model human gut microbiota composed of members of its two dominant bacterial phyla. Proc Natl Acad Sci U S A (2009) 4.09
Inferring correlation networks from genomic survey data. PLoS Comput Biol (2012) 3.80
Ray Meta: scalable de novo metagenome assembly and profiling. Genome Biol (2012) 3.64
MetaVelvet: an extension of Velvet assembler to de novo metagenome assembly from short sequence reads. Nucleic Acids Res (2012) 3.52
Predicting a human gut microbiota's response to diet in gnotobiotic mice. Science (2011) 3.49
Microbial interactions: from networks to models. Nat Rev Microbiol (2012) 3.28
Xenobiotics shape the physiology and gene expression of the active human gut microbiome. Cell (2013) 3.26
The human gut microbiome: ecology and recent evolutionary changes. Annu Rev Microbiol (2011) 3.13
The role of microbiota in infectious disease. Trends Microbiol (2008) 3.11
Cooperation and conflict in microbial biofilms. Proc Natl Acad Sci U S A (2007) 2.79
Intestinal domination and the risk of bacteremia in patients undergoing allogeneic hematopoietic stem cell transplantation. Clin Infect Dis (2012) 2.72
Meta-IDBA: a de Novo assembler for metagenomic data. Bioinformatics (2011) 2.46
Diversity and population structure of sewage-derived microorganisms in wastewater treatment plant influent. Environ Microbiol (2009) 2.20
The microbiota mediates pathogen clearance from the gut lumen after non-typhoidal Salmonella diarrhea. PLoS Pathog (2010) 2.17
Ecological modeling from time-series inference: insight into dynamics and stability of intestinal microbiota. PLoS Comput Biol (2013) 2.16
The role of physiological heterogeneity in microbial population behavior. Nat Chem Biol (2010) 2.04
Intestinal microbiota containing Barnesiella species cures vancomycin-resistant Enterococcus faecium colonization. Infect Immun (2013) 1.85
Metabolic modeling of species interaction in the human microbiome elucidates community-level assembly rules. Proc Natl Acad Sci U S A (2013) 1.84
The microbiome explored: recent insights and future challenges. Nat Rev Microbiol (2013) 1.82
A meta-analysis of changes in bacterial and archaeal communities with time. ISME J (2013) 1.80
Identifying gut microbe-host phenotype relationships using combinatorial communities in gnotobiotic mice. Sci Transl Med (2014) 1.69
Social evolution in multispecies biofilms. Proc Natl Acad Sci U S A (2011) 1.58
iDynoMiCS: next-generation individual-based modelling of biofilms. Environ Microbiol (2011) 1.56
The evolution of mutualism in gut microbiota via host epithelial selection. PLoS Biol (2012) 1.55
OptCom: a multi-level optimization framework for the metabolic modeling and analysis of microbial communities. PLoS Comput Biol (2012) 1.48
Identifying keystone species in the human gut microbiome from metagenomic timeseries using sparse linear regression. PLoS One (2014) 1.37
Mass spectrometry: from proteomics to metabolomics and lipidomics. Chem Soc Rev (2009) 1.34
Obesity and the gut microbiota. J Clin Gastroenterol (2011) 1.31
Mathematical modeling of primary succession of murine intestinal microbiota. Proc Natl Acad Sci U S A (2013) 1.27
Particle-based multidimensional multispecies biofilm model. Appl Environ Microbiol (2004) 1.26
Cutting through the complexity of cell collectives. Proc Biol Sci (2013) 1.20
A three-dimensional computer model of four hypothetical mechanisms protecting biofilms from antimicrobials. Appl Environ Microbiol (2006) 1.19
Modulation of the gut microbiota by nutrients with prebiotic properties: consequences for host health in the context of obesity and metabolic syndrome. Microb Cell Fact (2011) 1.16
A comprehensive metatranscriptome analysis pipeline and its validation using human small intestine microbiota datasets. BMC Genomics (2013) 1.15
Understanding the interactions between bacteria in the human gut through metabolic modeling. Sci Rep (2013) 1.14
The effects of operational and environmental variations on anaerobic wastewater treatment systems: a review. Bioresour Technol (2005) 1.11
Towards a predictive systems-level model of the human microbiome: progress, challenges, and opportunities. Curr Opin Biotechnol (2013) 1.10
Community flux balance analysis for microbial consortia at balanced growth. PLoS One (2013) 1.08
Strategies for representing metabolic pathways within biochemical systems theory: reversible pathways. Math Biosci (1989) 1.08
Multi-scale individual-based model of microbial and bioconversion dynamics in aerobic granular sludge. Environ Sci Technol (2007) 1.06
Inferring dynamic signatures of microbes in complex host ecosystems. PLoS Comput Biol (2012) 1.01
A reliable simulator for dynamic flux balance analysis. Biotechnol Bioeng (2012) 0.98
The evolution of bacteriocin production in bacterial biofilms. Am Nat (2011) 0.96
Effect of different salt adaptation strategies on the microbial diversity, activity, and settling of nitrifying sludge in sequencing batch reactors. Appl Microbiol Biotechnol (2011) 0.94
Social interaction, noise and antibiotic-mediated switches in the intestinal microbiota. PLoS Comput Biol (2012) 0.94
Acetate-producing bifidobacteria protect the host from enteropathogenic infection via carbohydrate transporters. Gut Microbes (2012) 0.93
Growth dependence of conjugation explains limited plasmid invasion in biofilms: an individual-based modelling study. Environ Microbiol (2011) 0.92
Incorporating microbial ecology into the metabolic modelling of polyphosphate accumulating organisms and glycogen accumulating organisms. Water Res (2010) 0.91
Escherichia coli adapts to tetracycline resistance plasmid (pBR322) by mutating endogenous potassium transport: in silico hypothesis testing. FEMS Microbiol Ecol (2012) 0.86
Kinetic modelling of lactate utilization and butyrate production by key human colonic bacterial species. FEMS Microbiol Ecol (2011) 0.86
A three-dimensional computer model analysis of three hypothetical biofilm detachment mechanisms. Biotechnol Bioeng (2007) 0.85
Mathematical modelling of carbohydrate degradation by human colonic microbiota. J Theor Biol (2010) 0.84
Microbial community engineering for biopolymer production from glycerol. Appl Microbiol Biotechnol (2011) 0.82
Heterogeneity of intracellular polymer storage states in enhanced biological phosphorus removal (EBPR)--observation and modeling. Environ Sci Technol (2012) 0.81
The granule size distribution in an anammox-based granular sludge reactor affects the conversion--implications for modeling. Biotechnol Bioeng (2012) 0.80
Identification of functionally relevant populations in enhanced biological phosphorus removal processes based on intracellular polymers profiles and insights into the metabolic diversity and heterogeneity. Environ Sci Technol (2012) 0.80
Critical review of activated sludge modeling: state of process knowledge, modeling concepts, and limitations. Biotechnol Bioeng (2012) 0.79
Multi-species nitrifying biofilm model (MSNBM) including free ammonia and free nitrous acid inhibition and oxygen limitation. Biotechnol Bioeng (2010) 0.77
Multidimensional modeling of biofilm development and fluid dynamics in a hydrogen-based, membrane biofilm reactor (MBfR). Water Res (2013) 0.76
Effects of the antimicrobial tylosin on the microbial community structure of an anaerobic sequencing batch reactor. Biotechnol Bioeng (2011) 0.76
Integrated modelling of sewer system and wastewater treatment plant for investigating the impacts of chemical dosing in sewers. Water Sci Technol (2012) 0.76
Activated sludge pilot plant: comparison between experimental and predicted concentration profiles using three different modelling approaches. Water Res (2011) 0.76
Model-based evaluation of competition between polyphosphate- and glycogen-accumulating organisms. Water Res (2007) 0.76
Mathematical modeling of wastewater decolorization in a trickle-bed bioreactor. J Biotechnol (2011) 0.76
Using a carbon-based ASM3 EAWAG Bio-P for modelling the enhanced biological phosphorus removal in anaerobic/aerobic activated sludge systems. Bioprocess Biosyst Eng (2010) 0.75