MicroScope in 2017: an expanding and evolving integrated resource for community expertise of microbial genomes (Q36207277)

12 August 2017

MicroScope in 2017: an expanding and evolving integrated resource for community expertise of microbial genomes (English)

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12 August 2017

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13

Claudine Médigue

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Alexandre Renaux

object named as

Alexandre Renaux

8

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Alexandra Calteau

object named as

Alexandra Calteau

2

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author name string

David Vallenet

1

1 reference

12 August 2017

Stéphane Cruveiller

3

1 reference

12 August 2017

Mathieu Gachet

4

1 reference

12 August 2017

Aurélie Lajus

5

1 reference

12 August 2017

Adrien Josso

6

1 reference

12 August 2017

Jonathan Mercier

7

1 reference

12 August 2017

Johan Rollin

9

1 reference

12 August 2017

Zoe Rouy

10

1 reference

12 August 2017

David Roche

11

1 reference

12 August 2017

Claude Scarpelli

12

1 reference

12 August 2017

language of work or name

English

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publication date

29 November 2016

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12 August 2017

Nucleic Acids Research

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12 August 2017

45

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12 August 2017

D1

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12 August 2017

D517-D528

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Creative Commons Attribution-NonCommercial 4.0 International

12 August 2017

start time

28 November 2016

1 reference

April 2022 Public Data File from Crossref

copyright status

copyrighted

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cites work

NCBI prokaryotic genome annotation pipeline

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5210572

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

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5210572

The revisited genome of Pseudomonas putida KT2440 enlightens its value as a robust metabolic chassis

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5210572

MG-RAST, a Metagenomics Service for Analysis of Microbial Community Structure and Function

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5210572

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

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5210572

The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases.

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5210572

KEGG as a reference resource for gene and protein annotation

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5210572

Ten years of maintaining and expanding a microbial genome and metagenome analysis system

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5210572

Minimum Information about a Biosynthetic Gene cluster.

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5210572

A novel method of consensus pan-chromosome assembly and large-scale comparative analysis reveal the highly flexible pan-genome of Acinetobacter baumannii

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5210572

Big Data: Astronomical or Genomical?

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5210572

antiSMASH 3.0-a comprehensive resource for the genome mining of biosynthetic gene clusters

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5210572

HAMAP in 2015: updates to the protein family classification and annotation system

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5210572

Updates in Rhea--a manually curated resource of biochemical reactions

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5210572

Prokka: rapid prokaryotic genome annotation

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5210572

PATRIC, the bacterial bioinformatics database and analysis resource

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5210572

Genomic analysis of smooth tubercle bacilli provides insights into ancestry and pathoadaptation of Mycobacterium tuberculosis

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5210572

MicroScope--an integrated microbial resource for the curation and comparative analysis of genomic and metabolic data

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5210572

The ChEBI reference database and ontology for biologically relevant chemistry: enhancements for 2013

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5210572

Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5210572

Artemis: an integrated platform for visualization and analysis of high-throughput sequence-based experimental data

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5210572

UniPathway: a resource for the exploration and annotation of metabolic pathways

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5210572

WikiPathways: building research communities on biological pathways

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5210572

Ultra-fast sequence clustering from similarity networks with SiLiX.

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5210572

MicroScope: a platform for microbial genome annotation and comparative genomics

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5210572

From a consortium sequence to a unified sequence: the Bacillus subtilis 168 reference genome a decade later

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5210572

The National Center for Biotechnology Information's Protein Clusters Database

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5210572

A gene wiki for community annotation of gene function

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5210572

Calling on a million minds for community annotation in WikiProteins

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5210572

The minimum information about a genome sequence (MIGS) specification

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5210572

A complete collection of single-gene deletion mutants of Acinetobacter baylyi ADP1.

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5210572

The RAST Server: rapid annotations using subsystems technology

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5210572

TIGRFAMs and Genome Properties: tools for the assignment of molecular function and biological process in prokaryotic genomes

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5210572

MaGe: a microbial genome annotation system supported by synteny results

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5210572

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

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5210572

GenDB--an open source genome annotation system for prokaryote genomes

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5210572

TM4: a free, open-source system for microarray data management and analysis

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5210572

The automatic annotation of bacterial genomes

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5210572

Novel metabolic features in Acinetobacter baylyi ADP1 revealed by a multiomics approach

29 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5210572

Epistasis and allele specificity in the emergence of a stable polymorphism in Escherichia coli.

22 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5210572

An updated metabolic view of the Bacillus subtilis 168 genome

22 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5210572

antiSMASH: rapid identification, annotation and analysis of secondary metabolite biosynthesis gene clusters in bacterial and fungal genome sequences

22 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5210572

TM4 microarray software suite

22 September 2018

1 reference

Crossref

https://api.crossref.org/works/10.1093%2FNAR%2FGKW1101

Accurate Microbial Genome Annotation Using an Integrated and User-Friendly Environment for Community Expertise of Gene Functions: The MicroScope Platform

21 January 2018

1 reference

Crossref

https://api.crossref.org/works/10.1093%2FNAR%2FGKW1101

A System for Automated Bacterial (genome) Integrated Annotation--SABIA

21 January 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/27899624

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1093/NAR/GKW1101

1 reference

journals/nar/VallenetCCGLJMR17

12 August 2017

1 reference

DBLP Dataset 2021-01-02

28 January 2021

1 reference

12 August 2017

1 reference