Enabling the democratization of the genomics revolution with a fully integrated web-based bioinformatics platform

Supporting community annotation and user collaboration in the integrated microbial genomes (IMG) system

(2016) I-Min A. Chen et al.   BMC GENOMICS

Next-generation sequencing diagnostics of bacteremia in septic patients

(2016) Silke Grumaz et al.   Genome Medicine

Accurate read-based metagenome characterization using a hierarchical suite of unique signatures

(2015) Tracey Allen K. Freitas et al.   NUCLEIC ACIDS RESEARCH

Analysis of the Upper Respiratory Tract Microbiotas as the Source of the Lung and Gastric Microbiotas in Healthy Individuals

(2015) Christine M. Bassis et al.   mBio

Next generation sequencing technology: Advances and applications

(2014) H.P.J. Buermans et al.   BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR BASIS OF DISEASE

Prokka: rapid prokaryotic genome annotation

(2014) T. Seemann   BIOINFORMATICS

RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies

(2014) Alexandros Stamatakis   BIOINFORMATICS

Rapid evaluation and quality control of next generation sequencing data with FaQCs

(2014) Chien-Chi Lo et al.   BMC BIOINFORMATICS

Automated ensemble assembly and validation of microbial genomes

(2014) Sergey Koren et al.   BMC BIOINFORMATICS

Reagent and laboratory contamination can critically impact sequence-based microbiome analyses

(2014) Susannah J Salter et al.   BMC BIOLOGY

Comparative Genomics of Saccharomyces cerevisiae Natural Isolates for Bioenergy Production

(2014) Dana J. Wohlbach et al.   Genome Biology and Evolution

Single-molecule sequencing to track plasmid diversity of hospital-associated carbapenemase-producing Enterobacteriaceae

(2014) S. Conlan et al.   Science Translational Medicine

The microbiome of New World vultures

(2014) Michael Roggenbuck et al.   Nature Communications

Kraken: ultrafast metagenomic sequence classification using exact alignments

(2014) Derrick E Wood et al.   GENOME BIOLOGY

Bacterial Pathogens in the Nasopharynx, Nasal Cavity, and Osteomeatal Complex during Wellness and Viral Infection

(2013) Brad A. Rawlings et al.   American Journal of Rhinology & Allergy

Next-generation sequencing: a challenge to meet the increasing demand for training workshops in Australia

(2013) N. S. Watson-Haigh et al.   BRIEFINGS IN BIOINFORMATICS

Bacillus weihenstephanensischaracteristics are present inBacillus cereusandBacillus mycoidesstrains

(2013) Brahim Soufiane et al.   FEMS MICROBIOLOGY LETTERS

IMG/M 4 version of the integrated metagenome comparative analysis system

(2013) Victor M. Markowitz et al.   NUCLEIC ACIDS RESEARCH

The SEED and the Rapid Annotation of microbial genomes using Subsystems Technology (RAST)

(2013) Ross Overbeek et al.   NUCLEIC ACIDS RESEARCH

PATRIC, the bacterial bioinformatics database and analysis resource

(2013) Alice R. Wattam et al.   NUCLEIC ACIDS RESEARCH

Understanding the limitations of next generation sequencing informatics, an approach to clinical pipeline validation using artificial data sets

(2013) Robert Daber et al.   Cancer Genetics

IDBA-UD: a de novo assembler for single-cell and metagenomic sequencing data with highly uneven depth

(2012) Y. Peng et al.   BIOINFORMATICS

RNA-seq based identification and mutant validation of gene targets related to ethanol resistance in cyanobacterial Synechocystis sp. PCC 6803

(2012) Jiangxin Wang et al.   Biotechnology for Biofuels

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

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

A framework for human microbiome research

(2012)   NATURE

Metagenomic microbial community profiling using unique clade-specific marker genes

(2012) Nicola Segata et al.   NATURE METHODS

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Primer3—new capabilities and interfaces

(2012) Andreas Untergasser et al.   NUCLEIC ACIDS RESEARCH

Novel Bacteriophages Containing a Genome of Another Bacteriophage within Their Genomes

(2012) Maud M. Swanson et al.   PLoS One

Interactive metagenomic visualization in a Web browser

(2011) Brian D Ondov et al.   BMC BIOINFORMATICS

RATT: Rapid Annotation Transfer Tool

(2011) Thomas D. Otto et al.   NUCLEIC ACIDS RESEARCH

Double indexing overcomes inaccuracies in multiplex sequencing on the Illumina platform

(2011) Martin Kircher et al.   NUCLEIC ACIDS RESEARCH

FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments

(2010) Morgan N. Price et al.   PLoS One

jsPhyloSVG: A Javascript Library for Visualizing Interactive and Vector-Based Phylogenetic Trees on the Web

(2010) Samuel A. Smits et al.   PLoS One

Genomic characterization of the Yersinia genus

(2010) Peter E Chen et al.   GENOME BIOLOGY

JBrowse: A next-generation genome browser

(2009) M. E. Skinner et al.   GENOME RESEARCH

Genome-wide association and meta-analysis of bipolar disorder in individuals of European ancestry

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