A Profile Hidden Markov Model to investigate the distribution and frequency of LanB-encoding lantibiotic modification genes in the human oral and gut microbiome

Fast and sensitive taxonomic classification for metagenomics with Kaiju

(2016) Peter Menzel et al.   Nature Communications

Temporal Stability of the Salivary Microbiota in Oral Health

(2016) Daniel Belstrøm et al.   PLoS One

A large scale prediction of bacteriocin gene blocks suggests a wide functional spectrum for bacteriocins

(2015) James T. Morton et al.   BMC BIOINFORMATICS

In silico identification of bacteriocin gene clusters in the gastrointestinal tract, based on the Human Microbiome Project’s reference genome database

(2015) Calum J. Walsh et al.   BMC MICROBIOLOGY

Composition and temporal stability of the gut microbiota in older persons

(2015) Ian B Jeffery et al.   ISME Journal

antiSMASH 3.0—a comprehensive resource for the genome mining of biosynthetic gene clusters

(2015) Tilmann Weber et al.   NUCLEIC ACIDS RESEARCH

A Systematic Analysis of Biosynthetic Gene Clusters in the Human Microbiome Reveals a Common Family of Antibiotics

(2014) Mohamed S. Donia et al.   CELL

Diversity and dynamics of bacteriocins from human microbiome

(2014) Jinshui Zheng et al.   ENVIRONMENTAL MICROBIOLOGY

Beneficial modulation of the gut microbiota

(2014) Calum J. Walsh et al.   FEBS LETTERS

Modulation of Gut Microbiota in the Management of Metabolic Disorders: The Prospects and Challenges

(2014) Omotayo Erejuwa et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Novel bacteriocins from lactic acid bacteria (LAB): various structures and applications

(2014) Rodney H Perez et al.   Microbial Cell Factories

Structure and mechanism of the tRNA-dependent lantibiotic dehydratase NisB

(2014) Manuel A. Ortega et al.   NATURE

Autoregressive Higher-Order Hidden Markov Models: Exploiting Local Chromosomal Dependencies in the Analysis of Tumor Expression Profiles

(2014) Michael Seifert et al.   PLoS One

Profile Hidden Markov Models for the Detection of Viruses within Metagenomic Sequence Data

(2014) Peter Skewes-Cox et al.   PLoS One

A coupled hidden Markov model for disease interactions

(2013) Chris Sherlock et al.   JOURNAL OF THE ROYAL STATISTICAL SOCIETY SERIES C-APPLIED STATISTICS

BAGEL3: automated identification of genes encoding bacteriocins and (non-)bactericidal posttranslationally modified peptides

(2013) Auke J. van Heel et al.   NUCLEIC ACIDS RESEARCH

In vitro activity of the nisin dehydratase NisB

(2013) N. Garg et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Long-Term Stability of the Human Gut Microbiota

(2013) J. J. Faith et al.   SCIENCE

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

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

The Impact of the Gut Microbiota on Human Health: An Integrative View

(2012) Jose C. Clemente et al.   CELL

Ribosomally synthesized and post-translationally modified peptide natural products: overview and recommendations for a universal nomenclature

(2012) Paul G. Arnison et al.   NATURAL PRODUCT REPORTS

Structure, function and diversity of the healthy human microbiome

(2012)   NATURE

The role of the gut microbiota in nutrition and health

(2012) Harry J. Flint et al.   Nature Reviews Gastroenterology & Hepatology

Phylogenetic identification of bacterial MazF toxin protein motifs among probiotic strains and foodborne pathogens and potential implications of engineered probiotic intervention in food

(2012) Xianghe Yan et al.   Cell and Bioscience

Artemis: an integrated platform for visualization and analysis of high-throughput sequence-based experimental data

(2011) T. Carver et al.   BIOINFORMATICS

The Pfam protein families database

(2011) M. Punta et al.   NUCLEIC ACIDS RESEARCH

Metagenomics of the intestinal microbiota: potential applications

(2010) S. Dusko Ehrlich   GASTROENTEROLOGIE CLINIQUE ET BIOLOGIQUE

A human gut microbial gene catalogue established by metagenomic sequencing

(2010) Junjie Qin et al.   NATURE

Effect of broad- and narrow-spectrum antimicrobials on Clostridium difficile and microbial diversity in a model of the distal colon

(2010) M. C. Rea et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Discovery of Unique Lanthionine Synthetases Reveals New Mechanistic and Evolutionary Insights

(2010) Yuki Goto et al.   PLOS BIOLOGY

Hidden Markov Models and their Applications in Biological Sequence Analysis

(2009) Byung-Jun Yoon   CURRENT GENOMICS

Thiostrepton Biosynthesis: Prototype for a New Family of Bacteriocins

(2009) Wendy L. Kelly et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY