Ancient bacteria of the Ötzi’s microbiome: a genomic tale from the Copper Age

The 5300-year-old Helicobacter pylori genome of the Iceman

(2016) F. Maixner et al.   SCIENCE

Clostridium perfringens Enterotoxin: Action, Genetics, and Translational Applications

(2016) John Freedman et al.   Toxins

Gut microbiota composition and Clostridium difficile infection in hospitalized elderly individuals: a metagenomic study

(2016) Christian Milani et al.   Scientific Reports

Exploring Vertical Transmission of Bifidobacteria from Mother to Child

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

Comparative genomics of Pseudomonas fluorescens subclade III strains from human lungs

(2015) Brittan S. Scales et al.   BMC GENOMICS

VFDB 2016: hierarchical and refined dataset for big data analysis—10 years on

(2015) Lihong Chen et al.   NUCLEIC ACIDS RESEARCH

Genomic analyses of Clostridium perfringens isolates from five toxinotypes

(2015) Karl A. Hassan et al.   RESEARCH IN MICROBIOLOGY

Microbiology, Genomics, and Clinical Significance of the Pseudomonas fluorescens Species Complex, an Unappreciated Colonizer of Humans

(2014) Brittan S. Scales et al.   CLINICAL MICROBIOLOGY REVIEWS

Ancient human genomes suggest three ancestral populations for present-day Europeans

(2014) Iosif Lazaridis et al.   NATURE

Pathogens and host immunity in the ancient human oral cavity

(2014) Christina Warinner et al.   NATURE GENETICS

Paleomicrobiology: Revealing Fecal Microbiomes of Ancient Indigenous Cultures

(2014) Raul J. Cano et al.   PLoS One

Pseudomonas fluorescens can induce and divert the human β-defensin-2 secretion in intestinal epithelial cells to enhance its virulence

(2013) Amar Madi et al.   ARCHIVES OF MICROBIOLOGY

Sequencing ancient calcified dental plaque shows changes in oral microbiota with dietary shifts of the Neolithic and Industrial revolutions

(2013) Christina J Adler et al.   NATURE GENETICS

Control of pathogens and pathobionts by the gut microbiota

(2013) Nobuhiko Kamada et al.   NATURE IMMUNOLOGY

The Transporter Classification Database

(2013) Milton H. Saier et al.   NUCLEIC ACIDS RESEARCH

The carbohydrate-active enzymes database (CAZy) in 2013

(2013) Vincent Lombard et al.   NUCLEIC ACIDS RESEARCH

The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of Pathway/Genome Databases

(2013) Ron Caspi et al.   NUCLEIC ACIDS RESEARCH

Pfam: the protein families database

(2013) Robert D. Finn et al.   NUCLEIC ACIDS RESEARCH

Assessing the Fecal Microbiota: An Optimized Ion Torrent 16S rRNA Gene-Based Analysis Protocol

(2013) Christian Milani et al.   PLoS One

Genome-Wide Comparison of Medieval and Modern Mycobacterium leprae

(2013) V. J. Schuenemann et al.   SCIENCE

Emerging genetic patterns of the european neolithic: Perspectives from a late neolithic bell beaker burial site in Germany

(2012) Esther J. Lee et al.   AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY

Metagenomics of human microbiome: beyond 16s rDNA

(2012) M.J. Gosalbes et al.   CLINICAL MICROBIOLOGY AND INFECTION

SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing

(2012) Anton Bankevich et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

Insights from Characterizing Extinct Human Gut Microbiomes

(2012) Raul Y. Tito et al.   PLoS One

New insights into the Tyrolean Iceman's origin and phenotype as inferred by whole-genome sequencing

(2012) Andreas Keller et al.   Nature Communications

RAPSearch2: a fast and memory-efficient protein similarity search tool for next-generation sequencing data

(2011) Y. Zhao et al.   BIOINFORMATICS

PGAP: pan-genomes analysis pipeline

(2011) Yongbing Zhao et al.   BIOINFORMATICS

mapDamage: testing for damage patterns in ancient DNA sequences

(2011) Aurelien Ginolhac et al.   BIOINFORMATICS

Integrative analysis of environmental sequences using MEGAN4

(2011) D. H. Huson et al.   GENOME RESEARCH

A draft genome of Yersinia pestis from victims of the Black Death

(2011) Kirsten I. Bos et al.   NATURE

Double indexing overcomes inaccuracies in multiplex sequencing on the Illumina platform

(2011) Martin Kircher et al.   NUCLEIC ACIDS RESEARCH

Genomes of the Most Dangerous Epidemic Bacteria Have a Virulence Repertoire Characterized by Fewer Genes but More Toxin-Antitoxin Modules

(2011) Kalliopi Georgiades et al.   PLoS One

Count: evolutionary analysis of phylogenetic profiles with parsimony and likelihood

(2010) M. Csuos   BIOINFORMATICS

Prodigal: prokaryotic gene recognition and translation initiation site identification

(2010) Doug Hyatt et al.   BMC BIOINFORMATICS

progressiveMauve: Multiple Genome Alignment with Gene Gain, Loss and Rearrangement

(2010) Aaron E. Darling et al.   PLoS One

Pseudomonas extremaustralis sp. nov., a Poly(3-hydroxybutyrate) Producer Isolated from an Antarctic Environment

(2009) Nancy I. López et al.   CURRENT MICROBIOLOGY

Clostridial toxins

(2009) Michel R Popoff et al.   Future Microbiology

Microbiomic analysis of the bifidobacterial population in the human distal gut

(2009) Francesca Turroni et al.   ISME Journal

Shifting the genomic gold standard for the prokaryotic species definition

(2009) Michael Richter et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

An effective method for isolation of DNA from pig faeces and comparison of five different methods

(2008) Jun-ni Tang et al.   JOURNAL OF MICROBIOLOGICAL METHODS

The occurrence of cpb2-toxigenic Clostridium perfringens and the possible role of the β2-toxin in enteric disease of domestic animals, wild animals and humans

(2008) Alphons J.A.M. van Asten et al.   VETERINARY JOURNAL