Cross-species cluster co-conservation: a new method for generating protein interaction networks (Q38280669)

1 September 2017

Cross-species cluster co-conservation: a new method for generating protein interaction networks (English)

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1 September 2017

4

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1 September 2017

Anis Karimpour-Fard

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1 September 2017

Corrella S Detweiler

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1 September 2017

Kimberly D Erickson

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1 September 2017

Ryan T Gill

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1 September 2017

1 January 2007

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1 September 2017

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1 September 2017

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1 September 2017

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1 September 2017

R185

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describes a project that uses

1 September 2017

Cytoscape

object named as

Cytoscape

2 references

9 June 2022

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

inferred from PubMed Central ID database lookup

CZ Software Mentions: A large dataset of software mentions in the biomedical literature

exact match

https://scigraph.springernature.com/pub.10.1186/gb-2007-8-9-r185

0 references

cites work

SCALEs: multiscale analysis of library enrichment

1 reference

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The Rcs phosphorelay system is specific to enteric pathogens/commensals and activates ydeI, a gene important for persistent Salmonella infection of mice

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2375023

YOGY: a web-based, integrated database to retrieve protein orthologs and associated Gene Ontology terms

6 September 2017

1 reference

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Effect of Motility on Surface Colonization and Reproductive Success of Pseudomonas fluorescens in Dual-Dilution Continuous Culture and Batch Culture Systems

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2375023

Predicting functional gene links from phylogenetic-statistical analyses of whole genomes

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2375023

Pseudomonas aeruginosa Genome Database and PseudoCAP: facilitating community-based, continually updated, genome annotation

6 September 2017

1 reference

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MorA defines a new class of regulators affecting flagellar development and biofilm formation in diverse Pseudomonas species

6 September 2017

1 reference

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GGDEF and EAL domains inversely regulate cyclic di-GMP levels and transition from sessility to motility

6 September 2017

1 reference

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Prolinks: a database of protein functional linkages derived from coevolution

6 September 2017

1 reference

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FimX, a multidomain protein connecting environmental signals to twitching motility in Pseudomonas aeruginosa

6 September 2017

1 reference

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Cytoscape: a software environment for integrated models of biomolecular interaction networks

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2375023

Biofilm formation at the air-liquid interface by the Pseudomonas fluorescens SBW25 wrinkly spreader requires an acetylated form of cellulose.

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2375023

Inference of protein function and protein linkages in Mycobacterium tuberculosis based on prokaryotic genome organization: a combined computational approach

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2375023

Bacterial type III secretion systems are ancient and evolved by multiple horizontal-transfer events

6 September 2017

2 references

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6 September 2017

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2375023

STRING: a database of predicted functional associations between proteins

31 August 2018

1 reference

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Genomic functional annotation using co-evolution profiles of gene clusters

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2375023

Predictome: a database of putative functional links between proteins

6 September 2017

1 reference

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6 September 2017

1 reference

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Complete genome sequence of Pseudomonas aeruginosa PAO1, an opportunistic pathogen

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2375023

Homology a personal view on some of the problems

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2375023

Detecting protein function and protein-protein interactions from genome sequences

6 September 2017

1 reference

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Type III secretion machines: bacterial devices for protein delivery into host cells

6 September 2017

1 reference

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Assigning protein functions by comparative genome analysis: Protein phylogenetic profiles

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2375023

Type III protein secretion systems in bacterial pathogens of animals and plants

6 September 2017

1 reference

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Bacterial locomotion and signal transduction.

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2375023

Molecular mechanisms of bacterial virulence: type III secretion and pathogenicity islands

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2375023

Escherichia coli fliAZY operon

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2375023

FlhA, a component of the flagellum assembly apparatus of Pseudomonas aeruginosa, plays a role in internalization by corneal epithelial cells

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2375023

Gene co-regulation is highly conserved in the evolution of eukaryotes and prokaryotes

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2375023

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

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2375023

Systematic characterization of Escherichia coli genes/ORFs affecting biofilm formation.

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2375023

Differential gene expression shows natural brominated furanones interfere with the autoinducer-2 bacterial signaling system of Escherichia coli

23 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2375023

In vitro characterization of FlgB, FlgC, FlgF, FlgG, and FliE, flagellar basal body proteins of Salmonella

31 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2375023

Protein function prediction using the Protein Link EXplorer (PLEX)

31 August 2018

1 reference

12 December 2020

Signal decay through a reverse phosphorelay in the Arc two-component signal transduction system

1 reference

12 December 2020

A domain interaction map based on phylogenetic profiling

1 reference

12 December 2020

Genetic analysis of Escherichia coli biofilm formation: roles of flagella, motility, chemotaxis and type I pili

1 reference

12 December 2020

Identifiers

DOI

10.1186/GB-2007-8-9-R185

1 reference

Dimensions Publication ID

1 September 2017

0 references

1 reference

1 September 2017

PubMed publication ID

17803817

1 reference