(Q36120051)

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:22844541%20AND%20SRC:MED&resulttype=core&format=json

9 February 2020

title

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

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:22844541%20AND%20SRC:MED&resulttype=core&format=json

9 February 2020

main subject

computational biology

1 reference

protein-protein interaction

inferred from title

1 reference

inferred from title

author

Vijaykumar Yogesh Muley

1

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:22844541%20AND%20SRC:MED&resulttype=core&format=json

9 February 2020

Akash Ranjan

2

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:22844541%20AND%20SRC:MED&resulttype=core&format=json

9 February 2020

author name string

Vijaykumar Yogesh Muley

1

1 reference

12 August 2017

Akash Ranjan

2

1 reference

12 August 2017

language of work or name

English

0 references

publication date

26 July 2012

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:22844541%20AND%20SRC:MED&resulttype=core&format=json

9 February 2020

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:22844541%20AND%20SRC:MED&resulttype=core&format=json

9 February 2020

volume

7

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:22844541%20AND%20SRC:MED&resulttype=core&format=json

9 February 2020

issue

7

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:22844541%20AND%20SRC:MED&resulttype=core&format=json

9 February 2020

page(s)

e42057

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:22844541%20AND%20SRC:MED&resulttype=core&format=json

Creative Commons Attribution 4.0 International

9 February 2020

copyright license

start time

26 July 2012

1 reference

April 2022 Public Data File from Crossref

copyright status

copyrighted

0 references

cites work

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1 reference

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2 October 2017

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2 October 2017

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2 October 2017

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2 October 2017

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2 October 2017

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2 October 2017

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2 October 2017

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2 October 2017

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2 October 2017

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2 October 2017

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Modularity of stress response evolution

2 October 2017

1 reference

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Predicting biological networks from genomic data

2 October 2017

1 reference

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High-confidence prediction of global interactomes based on genome-wide coevolutionary networks

2 October 2017

1 reference

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Investigation of factors affecting prediction of protein-protein interaction networks by phylogenetic profiling

2 October 2017

1 reference

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InPrePPI: an integrated evaluation method based on genomic context for predicting protein-protein interactions in prokaryotic genomes

2 October 2017

1 reference

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An improved method for identifying functionally linked proteins using phylogenetic profiles

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3406042

Practical and theoretical advances in predicting the function of a protein by its phylogenetic distribution

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3406042

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

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3406042

Advantages of combined transmembrane topology and signal peptide prediction--the Phobius web server

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3406042

Getting connected: analysis and principles of biological networks

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3406042

Deciphering Protein–Protein Interactions. Part II. Computational Methods to Predict Protein and Domain Interaction Partners

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3406042

Network-based prediction of protein function

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3406042

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

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3406042

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

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3406042

Comparative assessment of performance and genome dependence among phylogenetic profiling methods

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3406042

Ab initio genotype-phenotype association reveals intrinsic modularity in genetic networks

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3406042

Choosing negative examples for the prediction of protein-protein interactions

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3406042

ROCR: visualizing classifier performance in R

2 October 2017

1 reference

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

2 October 2017

1 reference

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Dynamic Complex Formation During the Yeast Cell Cycle

2 October 2017

1 reference

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Functional clues for hypothetical proteins based on genomic context analysis in prokaryotes

2 October 2017

1 reference

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

2 October 2017

1 reference

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Prolinks: a database of protein functional linkages derived from coevolution

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3406042

Network biology: understanding the cell's functional organization

2 October 2017

1 reference

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The Database of Interacting Proteins: 2004 update

2 October 2017

1 reference

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The KEGG resource for deciphering the genome

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3406042

Genome evolution reveals biochemical networks and functional modules

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3406042

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

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3406042

Genetic regulatory mechanisms in the synthesis of proteins

2 October 2017

2 references

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3406042

2 October 2017

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3406042

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

23 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3406042

Genomic functional annotation using co-evolution profiles of gene clusters

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3406042

DIP, the Database of Interacting Proteins: a research tool for studying cellular networks of protein interactions

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3406042

Evolution of gene order conservation in prokaryotes

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3406042

Gene context conservation of a higher order than operons.

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3406042

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

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3406042

Operons in Escherichia coli: genomic analyses and predictions

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3406042

Protein interaction maps for complete genomes based on gene fusion events

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3406042

Assigning protein functions by comparative genome analysis: Protein phylogenetic profiles

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3406042

The use of gene clusters to infer functional coupling

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3406042

Predicting function: from genes to genomes and back

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3406042

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

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3406042

A genomic perspective on protein families

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3406042

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

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3406042

Accurate prediction of protein-protein interactions from sequence alignments using a Bayesian method

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3406042

Computational genetics: finding protein function by nonhomology methods.

2 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3406042

Genome plasticity as a paradigm of eubacteria evolution.

2 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3406042

Conserved clusters of functionally related genes in two bacterial genomes.

2 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3406042

Operons and the effect of genome redundancy in deciphering functional relationships using phylogenetic profiles

2 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3406042

Phylogenetic profiles for the prediction of protein-protein interactions: how to select reference organisms?

23 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3406042

Inferring functional information from domain co-evolution

23 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3406042

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

23 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3406042

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

23 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3406042

Refined phylogenetic profiles method for predicting protein-protein interactions

23 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3406042

23 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3406042

Microbial genescapes: phyletic and functional patterns of ORF distribution among prokaryotes

23 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3406042

Annotation of bacterial genomes using improved phylogenomic profiles

23 September 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/22844541

12 December 2020

inferred from PubMed ID database lookup

Inferring protein interactions from phylogenetic distance matrices

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/22844541

12 December 2020

inferred from PubMed ID database lookup

Gene order is not conserved in bacterial evolution

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/22844541

12 December 2020

inferred from PubMed ID database lookup

Identifiers

DOI

10.1371/JOURNAL.PONE.0042057

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:22844541%20AND%20SRC:MED&resulttype=core&format=json

9 February 2020

0 references

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:22844541%20AND%20SRC:MED&resulttype=core&format=json

9 February 2020

PubMed publication ID

22844541

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:22844541%20AND%20SRC:MED&resulttype=core&format=json