Discovering functional linkages and uncharacterized cellular pathways using phylogenetic profile comparisons: a comprehensive assessment (Q35865281)

10 August 2017

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

1 reference

10 August 2017

1 reference

Teresa M Przytycka

2

0 references

Aravind L Iyer

object named as

L Aravind

series ordinal

3

0 references

author name string

Raja Jothi

series ordinal

1

1 reference

10 August 2017

23 May 2007

1 reference

10 August 2017

1 reference

10 August 2017

8

1 reference

10 August 2017

173

1 reference

Creative Commons Attribution 2.0 Generic

10 August 2017

start time

23 May 2007

1 reference

April 2022 Public Data File from Crossref

copyright status

copyrighted

1 reference

April 2022 Public Data File from Crossref

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11 July 2018

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11 July 2018

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

11 July 2018

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Identification and analysis of evolutionarily cohesive functional modules in protein networks

11 July 2018

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Unique transcriptome signature of Mycobacterium tuberculosis in pulmonary tuberculosis.

11 July 2018

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Life in hot carbon monoxide: the complete genome sequence of Carboxydothermus hydrogenoformans Z-2901

11 July 2018

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Predicting protein-protein interaction by searching evolutionary tree automorphism space

11 July 2018

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Prediction of functional modules based on comparative genome analysis and Gene Ontology application

11 July 2018

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11 July 2018

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Interaction network containing conserved and essential protein complexes in Escherichia coli

11 July 2018

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Making connections between novel transcription factors and their DNA motifs.

11 July 2018

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11 July 2018

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Properties of overlapping genes are conserved across microbial genomes

11 July 2018

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Genome sequence of Haloarcula marismortui: a halophilic archaeon from the Dead Sea

11 July 2018

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'Conserved hypothetical' proteins: prioritization of targets for experimental study

11 July 2018

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Phylogenetic profiling of the Arabidopsis thaliana proteome: what proteins distinguish plants from other organisms?

11 July 2018

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Comprehensive de novo structure prediction in a systems-biology context for the archaea Halobacterium sp. NRC-1

11 July 2018

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Genome-wide identification of genes likely to be involved in human genetic disease

11 July 2018

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11 July 2018

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Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1

11 July 2018

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Prolinks: a database of protein functional linkages derived from coevolution

11 July 2018

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Detection of evolutionarily stable fragments of cellular pathways by hierarchical clustering of phyletic patterns

11 July 2018

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Identification and functional analysis of 'hypothetical' genes expressed in Haemophilus influenzae

11 July 2018

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Quantifying modularity in the evolution of biomolecular systems

11 July 2018

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Comparative analysis of protein domain organization

11 July 2018

1 reference

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A cross-genomic approach for systematic mapping of phenotypic traits to genes

11 July 2018

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The KEGG resource for deciphering the genome

11 July 2018

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Genome evolution reveals biochemical networks and functional modules

11 July 2018

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Visualization and interpretation of protein networks in Mycobacterium tuberculosis based on hierarchical clustering of genome-wide functional linkage maps

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1904249

A protein interaction map of Drosophila melanogaster

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1904249

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

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1904249

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

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1904249

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

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1904249

The balance of driving forces during genome evolution in prokaryotes

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1904249

Comparing bacterial genomes through conservation profiles.

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1904249

The phylogenetic extent of metabolic enzymes and pathways

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1904249

Trait-to-gene: a computational method for predicting the function of uncharacterized genes.

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1904249

STRING: a database of predicted functional associations between proteins

11 July 2018

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MBGD: microbial genome database for comparative analysis

11 July 2018

1 reference

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Algorithms for computing parsimonious evolutionary scenarios for genome evolution, the last universal common ancestor and dominance of horizontal gene transfer in the evolution of prokaryotes

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1904249

Genomic functional annotation using co-evolution profiles of gene clusters

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1904249

The origin and evolution of model organisms

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1904249

Complete genome sequence and comparative genomic analysis of an emerging human pathogen, serotype V Streptococcus agalactiae

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1904249

Comparative analysis of chloroplast genomes: functional annotation, genome-based phylogeny, and deduced evolutionary patterns.

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1904249

Functional organization of the yeast proteome by systematic analysis of protein complexes

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1904249

Predictome: a database of putative functional links between proteins

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1904249

A comprehensive two-hybrid analysis to explore the yeast protein interactome

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1904249

The protein-protein interaction map of Helicobacter pylori

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1904249

Localizing proteins in the cell from their phylogenetic profiles.

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1904249

Co-evolution of proteins with their interaction partners

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1904249

A comprehensive analysis of protein-protein interactions in Saccharomyces cerevisiae

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1904249

Protein interaction maps for complete genomes based on gene fusion events

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1904249

Detecting protein function and protein-protein interactions from genome sequences

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1904249

Assigning protein functions by comparative genome analysis: Protein phylogenetic profiles

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1904249

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

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1904249

Measuring genome evolution

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1904249

A genomic perspective on protein families

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1904249

Conserved clusters of functionally related genes in two bacterial genomes.

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1904249

Basic local alignment search tool

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1904249

Locally defined protein phylogenetic profiles reveal previously missed protein interactions and functional relationships

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1904249

Identification of fungal sphingolipid C9-methyltransferases by phylogenetic profiling

24 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1904249

Inferring functional information from domain co-evolution

24 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1904249

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

24 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1904249

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

24 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1904249

Refined phylogenetic profiles method for predicting protein-protein interactions

24 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1904249

Use of logic relationships to decipher protein network organization

24 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1904249

Improving genome annotations using phylogenetic profile anomaly detection

24 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1904249

Identification of functional links between genes using phylogenetic profiles.

24 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1904249

Co-evolutionary analysis reveals insights into protein-protein interactions.

24 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1904249

24 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1904249

Use of contiguity on the chromosome to predict functional coupling.

24 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1904249

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

24 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1904249

Protein function prediction using the Protein Link EXplorer (PLEX)

24 September 2018

1 reference

12 December 2020

Inferring functional linkages between proteins from evolutionary scenarios

1 reference

12 December 2020

A probabilistic functional network of yeast genes

1 reference

12 December 2020

Exploiting the co-evolution of interacting proteins to discover interaction specificity

1 reference

12 December 2020

Inferring protein interactions from phylogenetic distance matrices

1 reference

12 December 2020

The plant-specific database. Classification of Arabidopsis proteins based on their phylogenetic profile

1 reference

12 December 2020

A domain interaction map based on phylogenetic profiling

1 reference

12 December 2020

An Exponential Core in the Heart of the Yeast Protein Interaction Network

1 reference

12 December 2020

Detection of parallel functional modules by comparative analysis of genome sequences

1 reference

12 December 2020

Identifiers

DOI

10.1186/1471-2105-8-173

1 reference

10 August 2017

journals/bmcbi/JothiPA07

1 reference

DBLP Dataset 2021-01-02

Dimensions Publication ID

28 January 2021

0 references

1 reference

PMC publication ID

1904249

10 August 2017

PubMed publication ID

17521444

1 reference

PMC publication ID

1904249