(Q34510805)

2 August 2017

title

CINPER: an interactive web system for pathway prediction for prokaryotes (English)

1 reference

2 August 2017

0 references

Xizeng Mao

1

1 reference

2 August 2017

Xin Chen

2

1 reference

2 August 2017

Yu Zhang

3

1 reference

2 August 2017

Spencer Pangle

4

1 reference

2 August 2017

Ying Xu

5

1 reference

2 August 2017

language of work or name

English

0 references

publication date

7 December 2012

1 reference

2 August 2017

1 reference

2 August 2017

volume

7

1 reference

2 August 2017

issue

12

1 reference

2 August 2017

page(s)

e51252

1 reference

Creative Commons Attribution 4.0 International

2 August 2017

copyright license

start time

7 December 2012

1 reference

April 2022 Public Data File from Crossref

copyright status

copyrighted

0 references

describes a project that uses

Cytoscape

1 reference

9 June 2022

https://europepmc.org/search?query=(METHODS:'Cytoscape')

based on heuristic

inferred from PubMed Central ID database lookup

cites work

"Guilt by association" is the exception rather than the rule in gene networks

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3517448

Iron utilization in marine cyanobacteria and eukaryotic algae

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3517448

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

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3517448

Comparative transcriptome analysis of Bacillus subtilis responding to dissolved oxygen in adenosine fermentation

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3517448

Thiamin (vitamin B1) biosynthesis and regulation: a rich source of antimicrobial drug targets?

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3517448

The STRING database in 2011: functional interaction networks of proteins, globally integrated and scored

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3517448

Cytoscape Web: an interactive web-based network browser

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3517448

Systematizing the generation of missing metabolic knowledge

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3517448

Computational prediction of the osmoregulation network in Synechococcus sp. WH8102.

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3517448

Pathway Tools version 13.0: integrated software for pathway/genome informatics and systems biology

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3517448

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

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3517448

DOOR: a database for prokaryotic operons

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3517448

NCBI Reference Sequences: current status, policy and new initiatives

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3517448

Presenting and exploring biological pathways with PathVisio

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3517448

The relative value of operon predictions.

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3517448

The RAST Server: rapid annotations using subsystems technology

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3517448

Computational prediction of Pho regulons in cyanobacteria

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3517448

KAAS: an automatic genome annotation and pathway reconstruction server

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3517448

Identifying metabolic enzymes with multiple types of association evidence

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3517448

Computational inference and experimental validation of the nitrogen assimilation regulatory network in cyanobacterium Synechococcus sp. WH 8102.

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3517448

Pathguide: a pathway resource list

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3517448

From genomics to chemical genomics: new developments in KEGG

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3517448

Mapping of orthologous genes in the context of biological pathways: An application of integer programming

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3517448

Expansion of the BioCyc collection of pathway/genome databases to 160 genomes

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3517448

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

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3517448

Comparative genomics analysis of NtcA regulons in cyanobacteria: regulation of nitrogen assimilation and its coupling to photosynthesis

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3517448

Response to oxidative stress involves a novel peroxiredoxin gene in the unicellular cyanobacterium Synechocystis sp. PCC 6803.

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3517448

Bacterial iron homeostasis

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3517448

The biogeochemical cycles of trace metals in the oceans.

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3517448

Missing genes in metabolic pathways: a comparative genomics approach

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3517448

Genes essential to iron transport in the cyanobacterium Synechocystis sp. strain PCC 6803.

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3517448

KEGG: kyoto encyclopedia of genes and genomes

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3517448

Assigning protein functions by comparative genome analysis: Protein phylogenetic profiles

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3517448

A minimal gene set for cellular life derived by comparison of complete bacterial genomes

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3517448

Bacillus subtilis HemY is a peripheral membrane protein essential for protoheme IX synthesis which can oxidize coproporphyrinogen III and protoporphyrinogen IX.

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3517448

Filling gaps in a metabolic network using expression information

7 July 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0051252

Predicting genes for orphan metabolic activities using phylogenetic profiles

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0051252

FieF (YiiP) from Escherichia coli mediates decreased cellular accumulation of iron and relieves iron stress.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0051252

The mechanism of iron homeostasis in the unicellular cyanobacterium synechocystis sp. PCC 6803 and its relationship to oxidative stress

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0051252

10.1371/JOURNAL.PONE.0051252

21 January 2018

Identifiers

DOI

1 reference

2 August 2017

0 references

1 reference

2 August 2017

1 reference