EcoCyc: fusing model organism databases with systems biology (Q34311072)

1 August 2017

title

EcoCyc: fusing model organism databases with systems biology (English)

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1 August 2017

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23

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24

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Martin Peralta-Gil

3

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Julio Collado-Vides

Julio Collado-Vides

21

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Alberto Santos-Zavaleta

Alberto Santos-Zavaleta

4

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Markus Krummenacker

10

Markus Krummenacker

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1 August 2017

César Bonavides-Martínez

6

César Bonavides-Martínez

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1 August 2017

5

Socorro Gama-Castro

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1 August 2017

Ingrid M Keseler

1

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Amanda Mackie

2

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1 August 2017

Carol Fulcher

7

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Araceli M Huerta

8

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Anamika Kothari

9

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Mario Latendresse

11

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Luis Muñiz-Rascado

12

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Quang Ong

13

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Suzanne Paley

14

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Imke Schröder

15

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Alexander G Shearer

16

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Pallavi Subhraveti

17

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Mike Travers

18

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Deepika Weerasinghe

19

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Verena Weiss

20

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Robert P Gunsalus

22

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1 August 2017

language of work or name

English

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publication date

9 November 2012

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1 August 2017

published in

Nucleic Acids Research

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1 August 2017

volume

41

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1 August 2017

issue

Database issue

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1 August 2017

page(s)

D605-12

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Creative Commons Attribution-NonCommercial 3.0 Unported

1 August 2017

copyright license

start time

4 October 2016

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April 2022 Public Data File from Crossref

copyright status

copyrighted

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cites work

RegPrecise web services interface: programmatic access to the transcriptional regulatory interactions in bacteria reconstructed by comparative genomics

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3531154

Comparative multi-omics systems analysis of Escherichia coli strains B and K-12

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3531154

Construction and completion of flux balance models from pathway databases

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3531154

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

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3531154

The evolution of metabolic networks of E. coli

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3531154

Direct regulation of Escherichia coli ribosomal protein promoters by the transcription factors ppGpp and DksA

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3531154

FITBAR: a web tool for the robust prediction of prokaryotic regulons

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3531154

Theoretical and empirical quality assessment of transcription factor-binding motifs

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3531154

Genome scale reconstruction of a Salmonella metabolic model: comparison of similarity and differences with a commensal Escherichia coli strain

6 July 2018

1 reference

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Control of bacterial transcription, translation and replication by (p)ppGpp

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3531154

Multidimensional annotation of the Escherichia coli K-12 genome

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3531154

Multicopy suppression underpins metabolic evolvability

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3531154

A genome-scale metabolic reconstruction for Escherichia coli K-12 MG1655 that accounts for 1260 ORFs and thermodynamic information

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3531154

Tractor_DB (version 2.0): a database of regulatory interactions in gamma-proteobacterial genomes

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3531154

Experimental and computational assessment of conditionally essential genes in Escherichia coli

6 July 2018

1 reference

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Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants: the Keio collection

6 July 2018

1 reference

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Highly accurate genome sequences of Escherichia coli K-12 strains MG1655 and W3110

6 July 2018

1 reference

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Escherichia coli K-12: a cooperatively developed annotation snapshot--2005

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3531154

TCDB: the Transporter Classification Database for membrane transport protein analyses and information

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3531154

DksA potentiates direct activation of amino acid promoters by ppGpp

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3531154

Experimental Determination and System Level Analysis of Essential Genes in Escherichia coli MG1655

6 July 2018

1 reference

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Phenotype microarrays for high-throughput phenotypic testing and assay of gene function

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3531154

Mechanism of regulation of transcription initiation by ppGpp. I. Effects of ppGpp on transcription initiation in vivo and in vitro

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3531154

The complete genome sequence of Escherichia coli K-12

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3531154

Characterization of the specific pyruvate transport system in Escherichia coli K-12.

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3531154

ppGpp and DksA likely regulate the activity of the extracytoplasmic stress factor sigmaE in Escherichia coli by both direct and indirect mechanisms.

6 July 2018

1 reference

Crossref

https://api.crossref.org/works/10.1093%2FNAR%2FGKS1027

PRODORIC (release 2009): a database and tool platform for the analysis of gene regulation in prokaryotes

21 January 2018

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Crossref

https://api.crossref.org/works/10.1093%2FNAR%2FGKS1027

Sigma70 promoters in Escherichia coli: specific transcription in dense regions of overlapping promoter-like signals.

21 January 2018

1 reference

Crossref

https://api.crossref.org/works/10.1093%2FNAR%2FGKS1027

DksA: a critical component of the transcription initiation machinery that potentiates the regulation of rRNA promoters by ppGpp and the initiating NTP

21 January 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/23143106

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1093/NAR/GKS1027

1 reference

journals/nar/KeselerMPSGBFHKKLMOPSSSTWWCGPK13

1 August 2017

DBLP publication ID

1 reference

DBLP Dataset 2021-01-02

28 January 2021

1 reference

1 August 2017

1 reference