Microbial Co-occurrence Relationships in the Human Microbiome

Building Predictive Models inRUsing thecaretPackage

(2015) Max Kuhn   Journal of Statistical Software

Composition of the adult digestive tract bacterial microbiome based on seven mouth surfaces, tonsils, throat and stool samples

(2012) Nicola Segata et al.   GENOME BIOLOGY

UCHIME improves sensitivity and speed of chimera detection

(2011) Robert C. Edgar et al.   BIOINFORMATICS

Marine bacterial, archaeal and protistan association networks reveal ecological linkages

(2011) Joshua A Steele et al.   ISME Journal

The developing intestinal microbiome and its relationship to health and disease in the neonate

(2011) R Murgas Torrazza et al.   Journal of Perinatology

A Closer Look at Bacteroides: Phylogenetic Relationship and Genomic Implications of a Life in the Human Gut

(2011) Fredrik H. Karlsson et al.   MICROBIAL ECOLOGY

Enterotypes of the human gut microbiome

(2011) Manimozhiyan Arumugam et al.   NATURE

Reducing the Effects of PCR Amplification and Sequencing Artifacts on 16S rRNA-Based Studies

(2011) Patrick D. Schloss et al.   PLoS One

Linking Long-Term Dietary Patterns with Gut Microbial Enterotypes

(2011) G. D. Wu et al.   SCIENCE

Investigating the biological and clinical significance of human dysbioses

(2011) Daniel N. Frank et al.   TRENDS IN MICROBIOLOGY

Bacterial biogeography of the human digestive tract

(2011) Jennifer C. Stearns et al.   Scientific Reports

Bacterial interactions in dental biofilm

(2011) Ruijie Huang et al.   Virulence

Gut microbiome-host interactions in health and disease

(2011) James M Kinross et al.   Genome Medicine

Microbial Eukaryotes in the Human Microbiome: Ecology, Evolution, and Future Directions

(2011) Laura Wegener Parfrey et al.   Frontiers in Microbiology

Moving pictures of the human microbiome

(2011) J Gregory Caporaso et al.   GENOME BIOLOGY

The Human Gut Microbiome: Ecology and Recent Evolutionary Changes

(2010) Jens Walter et al.   Annual Review of Microbiology

Metagenomic Analyses: Past and Future Trends

(2010) Carola Simon et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Success of Self-Administered Home Fecal Transplantation for Chronic Clostridium difficile Infection

(2010) Michael S. Silverman et al.   Clinical Gastroenterology and Hepatology

A global network of coexisting microbes from environmental and whole-genome sequence data

(2010) S. Chaffron et al.   GENOME RESEARCH

Supervised classification of microbiota mitigates mislabeling errors

(2010) Dan Knights et al.   ISME Journal

Creating and characterizing communities of human gut microbes in gnotobiotic mice

(2010) Jeremiah J Faith et al.   ISME Journal

Bacterial 16S Sequence Analysis of Severe Caries in Young Permanent Teeth

(2010) E. L. Gross et al.   JOURNAL OF CLINICAL MICROBIOLOGY

Oral multispecies biofilm development and the key role of cell–cell distance

(2010) Paul E. Kolenbrander et al.   NATURE REVIEWS MICROBIOLOGY

Microbiota restoration: natural and supplemented recovery of human microbial communities

(2010) Gregor Reid et al.   NATURE REVIEWS MICROBIOLOGY

The large-scale organization of the bacterial network of ecological co-occurrence interactions

(2010) Shiri Freilich et al.   NUCLEIC ACIDS RESEARCH

FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments

(2010) Morgan N. Price et al.   PLoS One

Inferring Regulatory Networks from Expression Data Using Tree-Based Methods

(2010) Vân Anh Huynh-Thu et al.   PLoS One

Vaginal microbiome of reproductive-age women

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

Design of 16S rRNA gene primers for 454 pyrosequencing of the human foregut microbiome

(2010) Carlos W Nossa   WORLD JOURNAL OF GASTROENTEROLOGY

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

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

Introducing mothur: Open-Source, Platform-Independent, Community-Supported Software for Describing and Comparing Microbial Communities

(2009) P. D. Schloss et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Defining the healthy "core microbiome" of oral microbial communities

(2009) Egija Zaura et al.   BMC MICROBIOLOGY

Pyramidobacter piscolens gen. nov., sp. nov., a member of the phylum 'Synergistetes' isolated from the human oral cavity

(2009) J. Downes et al.   INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY

What is microbial community ecology?

(2009) Allan Konopka   ISME Journal

Periodontal Therapy Improves Gastric Helicobacter pylori Eradication

(2009) S. Zarić et al.   JOURNAL OF DENTAL RESEARCH

Bacterial Interactions in Dental Biofilm Development

(2009) K. Hojo et al.   JOURNAL OF DENTAL RESEARCH

Getting in Touch with Your Friends

(2009) C. J. Marx   SCIENCE

Topographical and Temporal Diversity of the Human Skin Microbiome

(2009) E. A. Grice et al.   SCIENCE

Bacterial Community Variation in Human Body Habitats Across Space and Time

(2009) E. K. Costello et al.   SCIENCE

The Effect of Diet on the Human Gut Microbiome: A Metagenomic Analysis in Humanized Gnotobiotic Mice

(2009) P. J. Turnbaugh et al.   Science Translational Medicine

Multicellular behavior in bacteria: communication, cooperation, competition and cheating

(2008) Gary M. Dunny et al.   BIOESSAYS

Determination of the Genome Sequence of Porphyromonas gingivalis Strain ATCC 33277 and Genomic Comparison with Strain W83 Revealed Extensive Genome Rearrangements in P. gingivalis

(2008) M. Naito et al.   DNA RESEARCH

A core gut microbiome in obese and lean twins

(2008) Peter J. Turnbaugh et al.   NATURE

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

(2008) Jeroen Raes et al.   NATURE REVIEWS MICROBIOLOGY

The Ribosomal Database Project: improved alignments and new tools for rRNA analysis

(2008) J. R. Cole et al.   NUCLEIC ACIDS RESEARCH

Graph Clustering Via a Discrete Uncoupling Process

(2008) Stijn Van Dongen   SIAM JOURNAL ON MATRIX ANALYSIS AND APPLICATIONS