(Q34562914)

3 August 2017

title

Evaluation of physical and functional protein-protein interaction prediction methods for detecting biological pathways (English)

1 reference

protein-protein interaction

3 August 2017

main subject

1 reference

based on heuristic

inferred from title

author

Vijaykumar Yogesh Muley

object named as

Vijaykumar Yogesh Muley

series ordinal

1

0 references

Akash Ranjan

object named as

Akash Ranjan

series ordinal

2

0 references

language of work or name

English

0 references

publication date

17 January 2013

1 reference

3 August 2017

1 reference

3 August 2017

volume

8

1 reference

3 August 2017

issue

1

1 reference

3 August 2017

page(s)

e54325

1 reference

Creative Commons Attribution 4.0 International

3 August 2017

copyright license

start time

17 January 2013

1 reference

April 2022 Public Data File from Crossref

copyright status

copyrighted

0 references

cites work

Effect of reference genome selection on the performance of computational methods for genome-wide protein-protein interaction prediction

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3547882

Comparison of phylogenetic trees through alignment of embedded evolutionary distances

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3547882

Global functional atlas of Escherichia coli encompassing previously uncharacterized proteins

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3547882

Predicting protein linkages in bacteria: which method is best depends on task

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3547882

Multiple sequence alignment using ClustalW and ClustalX

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3547882

Coordinating assembly of a bacterial macromolecular machine

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3547882

Many Microbe Microarrays Database: uniformly normalized Affymetrix compendia with structured experimental metadata

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3547882

Discovering functional linkages and uncharacterized cellular pathways using phylogenetic profile comparisons: a comprehensive assessment

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3547882

Inferring genome-wide functional linkages in E. coli by combining improved genome context methods: comparison with high-throughput experimental data

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3547882

NCBI reference sequences (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3547882

Finding function: evaluation methods for functional genomic data

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3547882

Large-scale identification of protein-protein interaction of Escherichia coli K-12

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3547882

Evaluation of different biological data and computational classification methods for use in protein interaction prediction

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3547882

ROCR: visualizing classifier performance in R

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3547882

Nebulon: a system for the inference of functional relationships of gene products from the rearrangement of predicted 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=3547882

Interaction network containing conserved and essential protein complexes in Escherichia coli

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3547882

Analysis of genomic context: prediction of functional associations from conserved bidirectionally transcribed gene pairs

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3547882

The KEGG resource for deciphering the genome

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3547882

Genome evolution reveals biochemical networks and functional modules

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3547882

A Bayesian Networks Approach for Predicting Protein-Protein Interactions from Genomic Data

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3547882

Discovery of uncharacterized cellular systems by genome-wide analysis of functional linkages

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3547882

Comparative assessment of large-scale data sets of protein-protein interactions

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3547882

Relating whole-genome expression data with protein-protein interactions

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3547882

Comparative genomics and bioenergetics

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3547882

Correlation between transcriptome and interactome mapping data from Saccharomyces cerevisiae

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3547882

How signals are heard during bacterial chemotaxis: protein-protein interactions in sensory signal propagation

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3547882

Gene context conservation of a higher order than 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=3547882

Predicting protein function by genomic context: quantitative evaluation and qualitative inferences

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3547882

Computational genetics: finding protein function by nonhomology methods.

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3547882

Operons in Escherichia coli: genomic analyses and 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=3547882

A combined algorithm for genome-wide prediction of protein function

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3547882

Detecting protein function and protein-protein interactions from genome sequences

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3547882

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=3547882

The use of gene clusters to infer functional coupling

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3547882

Predicting function: from genes to genomes and back

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3547882

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

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3547882

A genomic perspective on protein families

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3547882

Gapped BLAST and PSI-BLAST: a new generation of protein database search programs

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3547882

Conserved clusters of functionally related genes in two 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=3547882

Complete genome sequences of cellular life forms: glimpses of theoretical evolutionary genomics

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3547882

7 July 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0054325

Assessing protein co-evolution in the context of the tree of life assists in the prediction of the interactome.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0054325

Origin and evolution of metabolic pathways

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0054325

The inference of protein-protein interactions by co-evolutionary analysis is improved by excluding the information about the phylogenetic relationships

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0054325

Transcriptome Complexity in a Genome-Reduced Bacterium

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0054325

Annotation of bacterial genomes using improved phylogenomic profiles

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0054325

Gene order is not conserved in bacterial evolution

21 January 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/23349851

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1371/JOURNAL.PONE.0054325

1 reference

release_5nhihhkup5hltgmlxfpjhfhj5q

3 August 2017

0 references

1 reference

Fatcat

https://api.fatcat.wiki/v0/release/5nhihhkup5hltgmlxfpjhfhj5q

mapped directly with Wikidata item

24 November 2022

based on heuristic

PMC publication ID

3547882

1 reference

3 August 2017

1 reference