A reverse metabolic approach to weaning: in silico identification of immune-beneficial infant gut bacteria, mining their metabolism for prebiotic feeds and sourcing these feeds in the natural product space

Community metabolic modeling approaches to understanding the gut microbiome: Bridging biochemistry and ecology

(2017) Helena Mendes-Soares et al.   FREE RADICAL BIOLOGY AND MEDICINE

Lactate- and acetate-based cross-feeding interactions between selected strains of lactobacilli, bifidobacteria and colon bacteria in the presence of inulin-type fructans

(2017) Frédéric Moens et al.   INTERNATIONAL JOURNAL OF FOOD MICROBIOLOGY

Influence of diet on the gut microbiome and implications for human health

(2017) Rasnik K. Singh et al.   Journal of Translational Medicine

Maternal inheritance of bifidobacterial communities and bifidophages in infants through vertical transmission

(2017) Sabrina Duranti et al.   Microbiome

Evolution of gut microbiota composition from birth to 24 weeks in the INFANTMET Cohort

(2017) Cian J. Hill et al.   Microbiome

Evolution of gut Bifidobacterium population in healthy Japanese infants over the first three years of life: a quantitative assessment

(2017) Ravinder Nagpal et al.   Scientific Reports

RevEcoR: an R package for the reverse ecology analysis of microbiomes

(2016) Yang Cao et al.   BMC BIOINFORMATICS

Bifidobacterial inulin-type fructan degradation capacity determines cross-feeding interactions between bifidobacteria and Faecalibacterium prausnitzii

(2016) Frédéric Moens et al.   INTERNATIONAL JOURNAL OF FOOD MICROBIOLOGY

Generation of genome-scale metabolic reconstructions for 773 members of the human gut microbiota

(2016) Stefanía Magnúsdóttir et al.   NATURE BIOTECHNOLOGY

The microbiome in early life: implications for health outcomes

(2016) Sabrina Tamburini et al.   NATURE MEDICINE

Database Resources of the National Center for Biotechnology Information

(2016)   NUCLEIC ACIDS RESEARCH

The Infant Microbiome

(2016) Irene Yang et al.   NURSING RESEARCH

Genome Analysis and Characterisation of the Exopolysaccharide Produced by Bifidobacterium longum subsp. longum 35624™

(2016) Friedrich Altmann et al.   PLoS One

Genomics of the Genus Bifidobacterium Reveals Species-Specific Adaptation to the Glycan-Rich Gut Environment

(2015) Christian Milani et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

NetCooperate: a network-based tool for inferring host-microbe and microbe-microbe cooperation

(2015) Roie Levy et al.   BMC BIOINFORMATICS

Dynamics and Stabilization of the Human Gut Microbiome during the First Year of Life

(2015) Fredrik Bäckhed et al.   Cell Host & Microbe

In Utero and Early-Life Exposure to Ambient Air Toxics and Childhood Brain Tumors: A Population-Based Case–Control Study in California, USA

(2015) Ondine S. von Ehrenstein et al.   ENVIRONMENTAL HEALTH PERSPECTIVES

BiGG Models: A platform for integrating, standardizing and sharing genome-scale models

(2015) Zachary A. King et al.   NUCLEIC ACIDS RESEARCH

Linking Microbiota to Human Diseases: A Systems Biology Perspective

(2015) Hao Wu et al.   TRENDS IN ENDOCRINOLOGY AND METABOLISM

tmChem: a high performance approach for chemical named entity recognition and normalization

(2015) Robert Leaman et al.   Journal of Cheminformatics

GNormPlus: An Integrative Approach for Tagging Genes, Gene Families, and Protein Domains

(2015) Chih-Hsuan Wei et al.   Biomed Research International

Dietary Modulation of Gut Microbiota Contributes to Alleviation of Both Genetic and Simple Obesity in Children

(2015) Chenhong Zhang et al.   EBioMedicine

Role of the Microbiota in Immunity and Inflammation

(2014) Yasmine Belkaid et al.   CELL

Diversity and dynamics of bacteriocins from human microbiome

(2014) Jinshui Zheng et al.   ENVIRONMENTAL MICROBIOLOGY

An integrated catalog of reference genes in the human gut microbiome

(2014) Junhua Li et al.   NATURE BIOTECHNOLOGY

Acute Obtundation in a 9-Month-Old Patient

(2014) Suzanne M. Edmunds et al.   PEDIATRIC EMERGENCY CARE

Development of the preterm infant gut microbiome: a research priority

(2014) Maureen W Groer et al.   Microbiome

DNorm: disease name normalization with pairwise learning to rank

(2013) R. Leaman et al.   BIOINFORMATICS

tmVar: a text mining approach for extracting sequence variants in biomedical literature

(2013) C.-H. Wei et al.   BIOINFORMATICS

PubTator: a web-based text mining tool for assisting biocuration

(2013) Chih-Hsuan Wei et al.   NUCLEIC ACIDS RESEARCH

Mother-to-Infant Transmission of Intestinal Bifidobacterial Strains Has an Impact on the Early Development of Vaginally Delivered Infant's Microbiota

(2013) Hiroshi Makino et al.   PLoS One

Metabolic modeling of species interaction in the human microbiome elucidates community-level assembly rules

(2013) R. Levy et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

NetSeed: a network-based reverse-ecology tool for calculating the metabolic interface of an organism with its environment

(2012) R. Carr et al.   BIOINFORMATICS

Human gut microbiome viewed across age and geography

(2012) Tanya Yatsunenko et al.   NATURE

Bacteriocin Production: a Probiotic Trait?

(2011) Alleson Dobson et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Cultured Representatives of Two Major Phylogroups of Human Colonic Faecalibacterium prausnitzii Can Utilize Pectin, Uronic Acids, and Host-Derived Substrates for Growth

(2011) Mireia Lopez-Siles et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Immunostimulatory effect of faecal Bifidobacterium species of breast-fed and formula-fed infants in a peripheral blood mononuclear cell/Caco-2 co-culture system

(2011) T. Pozo-Rubio et al.   BRITISH JOURNAL OF NUTRITION

Intestinal microbiota in human health and disease: the impact of probiotics

(2011) Jacoline Gerritsen et al.   Genes and Nutrition

Cross-feeding between bifidobacteria and butyrate-producing colon bacteria explains bifdobacterial competitiveness, butyrate production, and gas production

(2011) Luc De Vuyst et al.   INTERNATIONAL JOURNAL OF FOOD MICROBIOLOGY

Determinants of the human infant intestinal microbiota after the introduction of first complementary foods in infant samples from five European centres

(2011) M. Fallani et al.   MICROBIOLOGY-SGM

High-throughput generation, optimization and analysis of genome-scale metabolic models

(2010) Christopher S Henry et al.   NATURE BIOTECHNOLOGY

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

The NIH Human Microbiome Project

(2009) et al.   GENOME RESEARCH

Topological Signatures of Species Interactions in Metabolic Networks

(2009) Elhanan Borenstein et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

The interaction between predation and competition

(2008) Peter Chesson et al.   NATURE