Genomes OnLine Database (GOLD) v.6: data updates and feature enhancements

Identification and genome reconstruction of abundant distinct taxa in microbiomes from one thermophilic and three mesophilic production-scale biogas plants

(2016) Yvonne Stolze et al.   Biotechnology for Biofuels

SAR11 bacteria linked to ocean anoxia and nitrogen loss

(2016) Despina Tsementzi et al.   NATURE

Uncovering Earth’s virome

(2016) David Paez-Espino et al.   NATURE

Global metagenomic survey reveals a new bacterial candidate phylum in geothermal springs

(2016) Emiley A. Eloe-Fadrosh et al.   Nature Communications

The standard operating procedure of the DOE-JGI Metagenome Annotation Pipeline (MAP v.4)

(2016) Marcel Huntemann et al.   Standards in Genomic Sciences

Recurring patterns in bacterioplankton dynamics during coastal spring algae blooms

(2016) Hanno Teeling et al.   eLife

A new view of the tree of life

(2016) Laura A. Hug et al.   Nature Microbiology

International Code of Nomenclature of Prokaryotes

(2015) Charles T Parker et al.   INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY

ProDeGe: a computational protocol for fully automated decontamination of genomes

(2015) Kristin Tennessen et al.   ISME Journal

GenBank

(2015) Karen Clark et al.   NUCLEIC ACIDS RESEARCH

EBI metagenomics in 2016 - an expanding and evolving resource for the analysis and archiving of metagenomic data

(2015) Alex Mitchell et al.   NUCLEIC ACIDS RESEARCH

Database resources of the National Center for Biotechnology Information

(2015)   NUCLEIC ACIDS RESEARCH

Discovery of Novel Plant Interaction Determinants from the Genomes of 163 Root Nodule Bacteria

(2015) Rekha Seshadri et al.   Scientific Reports

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

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

The standard operating procedure of the DOE-JGI Microbial Genome Annotation Pipeline (MGAP v.4)

(2015) Marcel Huntemann et al.   Standards in Genomic Sciences

Big Data: Astronomical or Genomical?

(2015) Zachary D. Stephens et al.   PLOS BIOLOGY

Metazen – metadata capture for metagenomes

(2015) Jared Bischof et al.   Standards in Genomic Sciences

BioTextQuest + : a knowledge integration platform for literature mining and concept discovery

(2014) Nikolas Papanikolaou et al.   BIOINFORMATICS

Impact of single-cell genomics and metagenomics on the emerging view of extremophile “microbial dark matter”

(2014) Brian P. Hedlund et al.   EXTREMOPHILES

Obtaining genomes from uncultivated environmental microorganisms using FACS–based single-cell genomics

(2014) Christian Rinke et al.   Nature Protocols

The Genomes OnLine Database (GOLD) v.5: a metadata management system based on a four level (meta)genome project classification

(2014) T.B.K. Reddy et al.   NUCLEIC ACIDS RESEARCH

Genomic Encyclopedia of Type Strains, Phase I: The one thousand microbial genomes (KMG-I) project

(2014) Nikos C. Kyrpides et al.   Standards in Genomic Sciences

Toward richer metadata for microbial sequences: replacing strain-level NCBI taxonomy taxids with BioProject, BioSample and Assembly records

(2014) Scott Federhen et al.   Standards in Genomic Sciences

Genomic Standards Consortium Projects

(2014) Dawn Field et al.   Standards in Genomic Sciences

Genomic Encyclopedia of Bacteria and Archaea: Sequencing a Myriad of Type Strains

(2014) Nikos C. Kyrpides et al.   PLOS BIOLOGY

Insights into the phylogeny and coding potential of microbial dark matter

(2013) Christian Rinke et al.   NATURE

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

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

IMG 4 version of the integrated microbial genomes comparative analysis system

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

PATRIC, the bacterial bioinformatics database and analysis resource

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

MycoCosm portal: gearing up for 1000 fungal genomes

(2013) Igor V. Grigoriev et al.   NUCLEIC ACIDS RESEARCH

StrainInfo introduces electronic passports for microorganisms

(2013) Bert Verslyppe et al.   SYSTEMATIC AND APPLIED MICROBIOLOGY

The State of Standards in Genomic Sciences

(2012) George M. Garrity   Standards in Genomic Sciences

Minimum information about a marker gene sequence (MIMARKS) and minimum information about any (x) sequence (MIxS) specifications

(2011) Pelin Yilmaz et al.   NATURE BIOTECHNOLOGY

The sequence read archive: explosive growth of sequencing data

(2011) Y. Kodama et al.   NUCLEIC ACIDS RESEARCH

The NCBI Taxonomy database

(2011) S. Federhen   NUCLEIC ACIDS RESEARCH

A Catalog of Reference Genomes from the Human Microbiome

(2010) et al.   SCIENCE

A phylogeny-driven genomic encyclopaedia of Bacteria and Archaea

(2009) Dongying Wu et al.   NATURE

The Genomes On Line Database (GOLD) in 2009: status of genomic and metagenomic projects and their associated metadata

(2009) Konstantinos Liolios et al.   NUCLEIC ACIDS RESEARCH

Genomic sequencing of single microbial cells from environmental samples

(2008) Thomas Ishoey et al.   CURRENT OPINION IN MICROBIOLOGY