Anvi’o: an advanced analysis and visualization platform for ‘omics data

Microbial Community Composition, Functions, and Activities in the Gulf of Mexico 1 Year after the Deepwater Horizon Accident

(2015) Etienne Yergeau et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Elviz – exploration of metagenome assemblies with an interactive visualization tool

(2015) Michael Cantor et al.   BMC BIOINFORMATICS

Bioreactor microbial ecosystems for thiocyanate and cyanide degradation unravelled with genome-resolved metagenomics

(2015) Rose S. Kantor et al.   ENVIRONMENTAL MICROBIOLOGY

Accurate, multi-kb reads resolve complex populations and detect rare microorganisms

(2015) Itai Sharon et al.   GENOME RESEARCH

Arsenic Cycling in Hydrocarbon Plumes: Secondary Effects of Natural Attenuation

(2015) Isabelle M. Cozzarelli et al.   Groundwater

Microbial community successional patterns in beach sands impacted by the Deepwater Horizon oil spill

(2015) Luis M Rodriguez-R et al.   ISME Journal

Gut bacteria are rarely shared by co-hospitalized premature infants, regardless of necrotizing enterocolitis development

(2015) Tali Raveh-Sadka et al.   eLife

Reconstructing rare soil microbial genomes using in situ enrichments and metagenomics

(2015) Tom O. Delmont et al.   Frontiers in Microbiology

Arsenic Cycling in Hydrocarbon Plumes: Secondary Effects of Natural Attenuation

(2015) Isabelle M. Cozzarelli et al.   Groundwater

MetaBAT, an efficient tool for accurately reconstructing single genomes from complex microbial communities

(2015) Dongwan D. Kang et al.   PeerJ

VizBin - an application for reference-independent visualization and human-augmented binning of metagenomic data

(2015) Cedric C Laczny et al.   Microbiome

Binning metagenomic contigs by coverage and composition

(2014) Johannes Alneberg et al.   NATURE METHODS

Comparative Analysis of Functional Metagenomic Annotation and the Mappability of Short Reads

(2014) Rogan Carr et al.   PLoS One

Single-cell genomics reveals features of a Colwellia species that was dominant during the Deepwater Horizon oil spill

(2014) Olivia U. Mason et al.   Frontiers in Microbiology

MaxBin: an automated binning method to recover individual genomes from metagenomes using an expectation-maximization algorithm

(2014) Yu-Wei Wu et al.   Microbiome

Genome sequences of rare, uncultured bacteria obtained by differential coverage binning of multiple metagenomes

(2013) Mads Albertsen et al.   NATURE BIOTECHNOLOGY

A Filtering Method to Generate High Quality Short Reads Using Illumina Paired-End Technology

(2013) A. Murat Eren et al.   PLoS One

UGA is an additional glycine codon in uncultured SR1 bacteria from the human microbiota

(2013) J. H. Campbell et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Metagenomic analysis and metabolite profiling of deep–sea sediments from the Gulf of Mexico following the Deepwater Horizon oil spill

(2013) Nikole E. Kimes et al.   Frontiers in Microbiology

MetAMOS: a modular and open source metagenomic assembly and analysis pipeline

(2013) Todd J Treangen et al.   GENOME BIOLOGY

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

(2012) Y. Peng et al.   BIOINFORMATICS

Time series community genomics analysis reveals rapid shifts in bacterial species, strains, and phage during infant gut colonization

(2012) I. Sharon et al.   GENOME RESEARCH

Metagenome, metatranscriptome and single-cell sequencing reveal microbial response to Deepwater Horizon oil spill

(2012) Olivia U Mason et al.   ISME Journal

Describing microbial communities and performing global comparisons in the ‘omic era

(2012) Tom O Delmont et al.   ISME Journal

MetaSAMS—A novel software platform for taxonomic classification, functional annotation and comparative analysis of metagenome datasets

(2012) Martha Zakrzewski et al.   JOURNAL OF BIOTECHNOLOGY

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Assessment of Metagenomic Assembly Using Simulated Next Generation Sequencing Data

(2012) Daniel R. Mende et al.   PLoS One

Role for urea in nitrification by polar marine Archaea

(2012) L. Alonso-Saez et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Untangling Genomes from Metagenomes: Revealing an Uncultured Class of Marine Euryarchaeota

(2012) V. Iverson et al.   SCIENCE

Ray Meta: scalable de novo metagenome assembly and profiling

(2012) Sébastien Boisvert et al.   GENOME BIOLOGY

Hydrocarbon-Degrading Bacteria and the Bacterial Community Response in Gulf of Mexico Beach Sands Impacted by the Deepwater Horizon Oil Spill

(2011) Joel E. Kostka et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Oil Biodegradation and Bioremediation: A Tale of the Two Worst Spills in U.S. History

(2011) Ronald M. Atlas et al.   ENVIRONMENTAL SCIENCE & TECHNOLOGY

Individual genome assembly from complex community short-read metagenomic datasets

(2011) Chengwei Luo et al.   ISME Journal

Genomic insights to SAR86, an abundant and uncultivated marine bacterial lineage

(2011) Chris L Dupont et al.   ISME Journal

ggplot2: Elegant Graphics for Data Analysis

(2011) Cedric Ginestet   JOURNAL OF THE ROYAL STATISTICAL SOCIETY SERIES A-STATISTICS IN SOCIETY

Universally Distributed Single-Copy Genes Indicate a Constant Rate of Horizontal Transfer

(2011) Christopher J. Creevey et al.   PLoS One

Natural gas and temperature structured a microbial community response to the Deepwater Horizon oil spill

(2011) M. C. Redmond et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Metagenomic Discovery of Biomass-Degrading Genes and Genomes from Cow Rumen

(2011) M. Hess et al.   SCIENCE

Evaluation of genomic high-throughput sequencing data generated on Illumina HiSeq and Genome Analyzer systems

(2011) André E Minoche et al.   GENOME BIOLOGY

Yersinia pestis genome sequencing identifies patterns of global phylogenetic diversity

(2010) Giovanna Morelli et al.   NATURE GENETICS

Strain-resolved community genomic analysis of gut microbial colonization in a premature infant

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

Deep-Sea Oil Plume Enriches Indigenous Oil-Degrading Bacteria

(2010) Terry C. Hazen et al.   SCIENCE

A Primer on Metagenomics

(2010) John C. Wooley et al.   PLoS Computational Biology

Role of urea in microbial metabolism in aquatic systems: a biochemical and molecular review

(2009) CM Solomon et al.   AQUATIC MICROBIAL ECOLOGY

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

Genome assembly reborn: recent computational challenges

(2009) M. Pop   BRIEFINGS IN BIOINFORMATICS

Hydrocarbon Hydroxylation by Cytochrome P450 Enzymes

(2009) Paul R. Ortiz de Montellano   CHEMICAL REVIEWS

Metagenomics: Read Length Matters

(2008) K. E. Wommack et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

The metagenomics RAST server – a public resource for the automatic phylogenetic and functional analysis of metagenomes

(2008) F Meyer et al.   BMC BIOINFORMATICS

The RAST Server: Rapid Annotations using Subsystems Technology

(2008) Ramy K Aziz et al.   BMC GENOMICS

Velvet: Algorithms for de novo short read assembly using de Bruijn graphs

(2008) D. R. Zerbino et al.   GENOME RESEARCH

Functional metagenomic profiling of nine biomes

(2008) Elizabeth A. Dinsdale et al.   NATURE

Population Genomic Analysis of Strain Variation in Leptospirillum Group II Bacteria Involved in Acid Mine Drainage Formation

(2008) Sheri L Simmons et al.   PLOS BIOLOGY