SEED servers: high-performance access to the SEED genomes, annotations, and metabolic models (Q30485765)

13 August 2017

SEED servers: high-performance access to the SEED genomes, annotations, and metabolic models (English)

1 reference

13 August 2017

1 reference

13 August 2017

Ross Overbeek

1 reference

13 August 2017

Scott Devoid

1 reference

13 August 2017

Terrence Disz

1 reference

13 August 2017

Robert A Edwards

1 reference

13 August 2017

Christopher S Henry

1 reference

13 August 2017

Gary J Olsen

1 reference

13 August 2017

Robert Olson

1 reference

13 August 2017

Bruce Parrello

1 reference

13 August 2017

Gordon D Pusch

1 reference

13 August 2017

Rick L Stevens

1 reference

13 August 2017

Veronika Vonstein

1 reference

13 August 2017

Fangfang Xia

1 reference

13 August 2017

language of work or name

English

0 references

publication date

24 October 2012

1 reference

13 August 2017

1 reference

13 August 2017

1 reference

13 August 2017

1 reference

13 August 2017

e48053

1 reference

Creative Commons CC0 License

13 August 2017

start time

24 October 2012

1 reference

April 2022 Public Data File from Crossref

copyrighted, dedicated to the public domain by copyright holder

0 references

cites work

Real time metagenomics: using k-mers to annotate metagenomes

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3480482

PhiSpy: a novel algorithm for finding prophages in bacterial genomes that combines similarity- and composition-based strategies

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3480482

BioProject and BioSample databases at NCBI: facilitating capture and organization of metadata

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3480482

The Genomes OnLine Database (GOLD) v.4: status of genomic and metagenomic projects and their associated metadata

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3480482

The UniProt-GO Annotation database in 2011.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3480482

Origins of the E. coli strain causing an outbreak of hemolytic-uremic syndrome in Germany

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3480482

Genome sequence analyses of two isolates from the recent Escherichia coli outbreak in Germany reveal the emergence of a new pathotype: Entero-Aggregative-Haemorrhagic Escherichia coli (EAHEC)

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3480482

Connecting genotype to phenotype in the era of high-throughput sequencing.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3480482

The pseudogenes of Mycobacterium leprae reveal the functional relevance of gene order within operons

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3480482

High-throughput generation, optimization and analysis of genome-scale metabolic models

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3480482

Accessing the SEED genome databases via Web services API: tools for programmers

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3480482

Beyond the HapMap Genotypic Data: Prospects of Deep Resequencing Projects

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3480482

FIGfams: yet another set of protein families

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3480482

iBsu1103: a new genome-scale metabolic model of Bacillus subtilis based on SEED annotations

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3480482

Origins and evolutionary genomics of the 2009 swine-origin H1N1 influenza A epidemic

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3480482

A flood of microbial genomes-do we need more?

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3480482

Emergence of a novel swine-origin influenza A (H1N1) virus in humans

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3480482

Group contribution method for thermodynamic analysis of complex metabolic networks

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3480482

KEGG Atlas mapping for global analysis of metabolic pathways

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3480482

The RAST Server: rapid annotations using subsystems technology

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3480482

Annotation of bacterial and archaeal genomes: improving accuracy and consistency

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3480482

Evolution of the core and pan-genome of Streptococcus: positive selection, recombination, and genome composition

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3480482

Toward the automated generation of genome-scale metabolic networks in the SEED.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3480482

The subsystems approach to genome annotation and its use in the project to annotate 1000 genomes

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3480482

20 June 2018

The microbial pan-genome

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3480482

Environmental genome shotgun sequencing of the Sargasso Sea

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3480482

The KEGG resource for deciphering the genome

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3480482

UniProt: the Universal Protein knowledgebase

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3480482

The effects of alternate optimal solutions in constraint-based genome-scale metabolic models

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3480482

The Genome sequence of the SARS-associated coronavirus

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3480482

Genome-scale metabolic model of Helicobacter pylori 26695.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3480482

The KEGG databases at GenomeNet

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3480482

Genome alignment, evolution of prokaryotic genome organization, and prediction of gene function using genomic context

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3480482

Genomics: what is realistically achievable?

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3480482

Gene ontology: tool for the unification of biology

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3480482

The use of gene clusters to infer functional coupling

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3480482

Conservation of gene order: a fingerprint of proteins that physically interact

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3480482

Inferring Functional Relationships from Conservation of Gene Order

20 June 2018

1 reference

Crossref

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0048053

Pathogen microevolution in high resolution

21 January 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3480482

Use of contiguity on the chromosome to predict functional coupling.

26 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3480482

Biolog phenotype microarrays

26 November 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/23110173

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Sequencing the species pan-genome

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/23110173

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1371/JOURNAL.PONE.0048053

1 reference

13 August 2017

0 references

1 reference

13 August 2017

PubMed publication ID

23110173

1 reference