ContEst16S: an algorithm that identifies contaminated prokaryotic genomes using 16S RNA gene sequences

How Next-Generation Sequencing and Multiscale Data Analysis Will Transform Infectious Disease Management

(2015) Theodore R. Pak et al.   CLINICAL INFECTIOUS DISEASES

CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes

(2015) Donovan H. Parks et al.   GENOME RESEARCH

ProDeGe: a computational protocol for fully automated decontamination of genomes

(2015) Kristin Tennessen et al.   ISME Journal

Large-scale contamination of microbial isolate genomes by Illumina PhiX control

(2015) Supratim Mukherjee et al.   Standards in Genomic Sciences

Integrating genomics into the taxonomy and systematics of the Bacteria and Archaea

(2014) J. Chun et al.   INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY

Rfam 12.0: updates to the RNA families database

(2014) Eric P. Nawrocki et al.   NUCLEIC ACIDS RESEARCH

Infernal 1.1: 100-fold faster RNA homology searches

(2013) E. P. Nawrocki et al.   BIOINFORMATICS

Assuring the quality of next-generation sequencing in clinical laboratory practice

(2012) Amy S Gargis et al.   NATURE BIOTECHNOLOGY

Mutational robustness of 16S ribosomal RNA, shown by experimental horizontal gene transfer in Escherichia coli

(2012) K. Kitahara et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Abundant Human DNA Contamination Identified in Non-Primate Genome Databases

(2011) Mark S. Longo et al.   PLoS One

Fast Identification and Removal of Sequence Contamination from Genomic and Metagenomic Datasets

(2011) Robert Schmieder et al.   PLoS One

Limitations of next-generation genome sequence assembly

(2010) Can Alkan et al.   NATURE METHODS

Comparative genomics reveals mechanism for short-term and long-term clonal transitions in pandemic Vibrio cholerae

(2009) J. Chun et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA