The Genomes On Line Database (GOLD) in 2007: status of genomic and metagenomic projects and their associated metadata

By K. Liolios, Konstantinos Mavrommatis, Nektarios Tavernarakis, Nikos Kyrpides. 2008

412 citations recorded by the source corpus.

View Paper: https://www.semanticscholar.org/paper/da981d0a072c321367f333141b338ada16b385a2

How researchers see this paper

The researchers whose trusted networks rank it highest, strongest advocate first. Every researcher gets a different order.

Citations in the corpus

The Harvest suite for rapid core-genome alignment and visualization of thousands of intraspecific microbial genomes (2014, background): “With the number of publically available genomes currently doubling every 18 months [1], and genome quality improving with the arrival of new technologies, we set out to solve the problem of aligning thousands of closely-related whole genomes.”
Identification of direct residue contacts in protein–protein interaction by message passing (2009, background): “Rapid increase in the number of sequenced bacterial genomes in the past decade [resulting in 700 completed genome projects to date (4)] has fueled the increasing use of covariance-based methods of sequence analysis for protein structure studies.”
Inference of direct residue contacts in two-component signaling. (2010, background): “In the light of the number of bacterial genomes that have been sequenced ( 1000) or whose sequence is in the works ( 3500) (Liolios et al., 2008), such methods are starting to become amenable for those proteins, which are encoded by the majority of bacterial genomes.”
Insights from 20 years of bacterial genome sequencing (2015, background): “As of October 2014, the GOLD (Pagani et al. 2012) contains 544 metagenomics studies associated with 6726metagenome samples andMG-RASTsystem holds 150,039 metagenomic samples, of which 20,415 are publically available.”
A Phylogeny-Based Benchmarking Test for Orthology Inference Reveals the Limitations of Function-Based Validation (2014, unknown): “0) [1].”
A large-scale evaluation of computational protein function prediction (2013, unknown): “For a given target protein i and some decision threshold t ∈ [0, 1], the precision and recall were calculated as”
BIGSdb: Scalable analysis of bacterial genome variation at the population level (2010, background): “Many of the genomes hosted in online databases [42-44] have detailed and comprehensive annotation, but what these databases have in common is that for any particular species they contain very few genomes (Figure 4) and the analysis is geared specifically to the attributes of the sequence itself…”
The genome sequence of Bifidobacterium longum subsp. infantis reveals adaptations for milk utilization within the infant microbiome (2008, background): “These results are consistent with the utilization pathway reconstructed from the genome sequence, as the 9-carbon carbohydrate backbone of N-acetyl-[2-13C]neuraminic acid was metabolized into 3-carbon [2-13]pyruvate, plus unlabeled N-acetylmannosamine (ManNAc).”
From Principal Component to Direct Coupling Analysis of Coevolution in Proteins: Low-Eigenvalue Modes are Needed for Structure Prediction (2012, unknown): “ts, and improves our capacity of extracting residue contacts in this case. Introduction Thanks to the constant progresses in DNA sequencing techniques, by now more than 4,400 full genomes aresequenced[1], resultingin morethan 3.6107 knownprotein sequences[2], which areclassiﬁedinto more than 14,000 ”
The Genomes OnLine Database (GOLD) v.4: status of genomic and metagenomic projects and their associated metadata (2011, background): “As of September 2011, 11 472 projects have been registered, versus 5843 in September 2009 (5), 2905 in September 2007 (4) and 1575 in September 2005 (3) (Figure 1A).”
Genetic Engineering of Algae for Enhanced Biofuel Production (2010, background): “Most of these come from the manipulation of E. coli, in which the overexpression and deletion of entire metabolic pathways are feasible.”