Inferring microbial interaction network from microbiome data using RMN algorithm

Reset of a critically disturbed microbial ecosystem: faecal transplant in recurrent Clostridium difficile infection

(2014) Susana Fuentes et al.   ISME Journal

Identifying Keystone Species in the Human Gut Microbiome from Metagenomic Timeseries Using Sparse Linear Regression

(2014) Charles K. Fisher et al.   PLoS One

Vertical mother-neonate transfer of maternal gut bacteria via breastfeeding

(2013) Ted Jost et al.   ENVIRONMENTAL MICROBIOLOGY

Spatial heterogeneity and co-occurrence patterns of human mucosal-associated intestinal microbiota

(2013) Zhigang Zhang et al.   ISME Journal

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

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

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

Quantitative Profiling of Gut Microbiota of Children With Diarrhea-Predominant Irritable Bowel Syndrome

(2012) Laura Rigsbee et al.   AMERICAN JOURNAL OF GASTROENTEROLOGY

Horizontal gene transfer dynamics and distribution of fitness effects during microbial in silico evolution

(2012) Vadim Mozhayskiy et al.   BMC BIOINFORMATICS

Molecular ecological network analyses

(2012) Ye Deng et al.   BMC BIOINFORMATICS

Competition, Not Cooperation, Dominates Interactions among Culturable Microbial Species

(2012) Kevin R. Foster et al.   CURRENT BIOLOGY

Antagonism influences assembly of a Bacillus guild in a local community and is depicted as a food-chain network

(2012) Rocío-Anaís Pérez-Gutiérrez et al.   ISME Journal

Competition between species can stabilize public-goods cooperation within a species

(2012) Hasan Celiker et al.   Molecular Systems Biology

Microbial interactions: from networks to models

(2012) Karoline Faust et al.   NATURE REVIEWS MICROBIOLOGY

Extended local similarity analysis (eLSA) of microbial community and other time series data with replicates

(2011) Li C Xia et al.   BMC Systems Biology

Social evolution in multispecies biofilms

(2011) S. Mitri et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Phylogenetic Molecular Ecological Network of Soil Microbial Communities in Response to Elevated CO2

(2011) J. Zhou et al.   mBio

Competitive and cooperative metabolic interactions in bacterial communities

(2011) Shiri Freilich et al.   Nature Communications

Inferring genetic interactions via a nonlinear model and an optimization algorithm

(2010) Chung-Ming Chen et al.   BMC Systems Biology

Ecological competition favours cooperation in termite societies

(2010) Judith Korb et al.   ECOLOGY LETTERS

Consumption of Human Milk Oligosaccharides by Gut-Related Microbes

(2010) Angela Marcobal et al.   JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY

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

(2010) Shiri Freilich et al.   NUCLEIC ACIDS RESEARCH

Succession of microbial consortia in the developing infant gut microbiome

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

Functional Molecular Ecological Networks

(2010) J. Zhou et al.   mBio

Convergent temporal dynamics of the human infant gut microbiota

(2009) Pål Trosvik et al.   ISME Journal

Characterizing mixed microbial population dynamics using time-series analysis

(2008) Pål Trosvik et al.   ISME Journal

Characterization of a Streptococcus sp.-Veillonella sp. Community Micromanipulated from Dental Plaque

(2008) N. I. Chalmers et al.   JOURNAL OF BACTERIOLOGY