The gutSMASH web server: automated identification of primary metabolic gene clusters from the gut microbiota

Potential TMA-Producing Bacteria Are Ubiquitously Found in Mammalia

(2020) Silke Rath et al.   Frontiers in Microbiology

A metabolic pathway for bile acid dehydroxylation by the gut microbiome

(2020) Masanori Funabashi et al.   NATURE

1,520 reference genomes from cultivated human gut bacteria enable functional microbiome analyses

(2019) Yuanqiang Zou et al.   NATURE BIOTECHNOLOGY

antiSMASH 5.0: updates to the secondary metabolite genome mining pipeline

(2019) Kai Blin et al.   NUCLEIC ACIDS RESEARCH

Ruminococcus gnavus, a member of the human gut microbiome associated with Crohn’s disease, produces an inflammatory polysaccharide

(2019) Matthew T. Henke et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Species-level functional profiling of metagenomes and metatranscriptomes

(2018) Eric A. Franzosa et al.   NATURE METHODS

A gut bacterial pathway metabolizes aromatic amino acids into nine circulating metabolites

(2017) Dylan Dodd et al.   NATURE

plantiSMASH: automated identification, annotation and expression analysis of plant biosynthetic gene clusters

(2017) Satria A. Kautsar et al.   NUCLEIC ACIDS RESEARCH

The Common Gut Microbe Eubacterium hallii also Contributes to Intestinal Propionate Formation

(2016) Christina Engels et al.   Frontiers in Microbiology

MetaTrans: an open-source pipeline for metatranscriptomics

(2016) Xavier Martinez et al.   Scientific Reports

Small molecules from the human microbiota

(2015) M. S. Donia et al.   SCIENCE

Fast and sensitive protein alignment using DIAMOND

(2014) Benjamin Buchfink et al.   NATURE METHODS

The protein shells of bacterial microcompartment organelles

(2011) Todd O Yeates et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

antiSMASH: rapid identification, annotation and analysis of secondary metabolite biosynthesis gene clusters in bacterial and fungal genome sequences

(2011) Marnix H. Medema et al.   NUCLEIC ACIDS RESEARCH

Prodigal: prokaryotic gene recognition and translation initiation site identification

(2010) Doug Hyatt et al.   BMC BIOINFORMATICS

Ethanolamine utilization in bacterial pathogens: roles and regulation

(2010) Danielle A. Garsin   NATURE REVIEWS MICROBIOLOGY