COCO-CL: hierarchical clustering of homology relations based on evolutionary correlations (Q35106134)

6 August 2017

title

COCO-CL: hierarchical clustering of homology relations based on evolutionary correlations (English)

1 reference

6 August 2017

main subject

hierarchical clustering

1 reference

Elena Zotenko

2

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Teresa M. Przytycka

object named as

Teresa M Przytycka

series ordinal

4

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author name string

Raja Jothi

series ordinal

1

1 reference

6 August 2017

Asba Tasneem

series ordinal

3

1 reference

6 August 2017

language of work or name

English

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publication date

24 January 2006

1 reference

6 August 2017

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6 August 2017

volume

22

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6 August 2017

issue

7

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6 August 2017

page(s)

779-788

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Protein molecular function prediction by Bayesian phylogenomics

6 August 2017

cites work

1 reference

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Predicting protein-protein interaction by searching evolutionary tree automorphism space

9 July 2018

1 reference

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Conserved patterns of protein interaction in multiple species

9 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1620014

CDD: a Conserved Domain Database for protein classification

9 July 2018

1 reference

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Annotation transfer between genomes: protein-protein interologs and protein-DNA regulogs

9 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1620014

The COG database: an updated version includes eukaryotes

9 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1620014

OrthoMCL: Identification of Ortholog Groups for Eukaryotic Genomes

9 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1620014

Phylogenetic analysis and gene functional predictions: phylogenomics in action

9 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1620014

RIO: analyzing proteomes by automated phylogenomics using resampled inference of orthologs

9 July 2018

1 reference

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Cross-referencing eukaryotic genomes: TIGR Orthologous Gene Alignments (TOGA)

9 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1620014

Automated ortholog inference from phylogenetic trees and calculation of orthology reliability

9 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1620014

Automatic clustering of orthologs and in-paralogs from pairwise species comparisons

9 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1620014

Co-evolution of proteins with their interaction partners

9 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1620014

Homology a personal view on some of the problems

9 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1620014

The COG database: a tool for genome-scale analysis of protein functions and evolution

9 July 2018

1 reference

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Evolution of aminoacyl-tRNA synthetases--analysis of unique domain architectures and phylogenetic trees reveals a complex history of horizontal gene transfer events.

9 July 2018

1 reference

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Comparison of the complete protein sets of worm and yeast: orthology and divergence

9 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1620014

Modular evolution of the Glx-tRNA synthetase family--rooting of the evolutionary tree between the bacteria and archaea/eukarya branches

9 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1620014

Evolutionary parameters of the transcribed mammalian genome: an analysis of 2,820 orthologous rodent and human sequences

9 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1620014

A genomic perspective on protein families

9 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1620014

From gene to organismal phylogeny: reconciled trees and the gene tree/species tree problem

9 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1620014

Reconstruction of ancient molecular phylogeny

9 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1620014

Evolution of the Glx-tRNA synthetase family: the glutaminyl enzyme as a case of horizontal gene transfer

9 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1620014

Distinguishing Homologous from Analogous Proteins

9 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1620014

Basic local alignment search tool

9 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1620014

Multiple ribonuclease H-encoding genes in the Caenorhabditis elegans genome contrasts with the two typical ribonuclease H-encoding genes in the human genome

9 July 2018

1 reference

https://api.crossref.org/works/10.1093/BIOINFORMATICS/BTL009

Signal peptide peptidase- and ClpP-like proteins of Bacillus subtilis required for efficient translocation and processing of secretory proteins.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093/BIOINFORMATICS/BTL009

NOTUNG: a program for dating gene duplications and optimizing gene family trees

21 January 2018

1 reference

https://api.crossref.org/works/10.1093/BIOINFORMATICS/BTL009

Tree pattern matching in phylogenetic trees: automatic search for orthologs or paralogs in homologous gene sequence databases

21 January 2018

1 reference

https://api.crossref.org/works/10.1093/BIOINFORMATICS/BTL009

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1093/BIOINFORMATICS/BTL009

A biologically consistent model for comparing molecular phylogenies.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093/BIOINFORMATICS/BTL009

21 January 2018

1 reference

https://api.crossref.org/works/10.1093/BIOINFORMATICS/BTL009

Towards detection of orthologues in sequence databases

21 January 2018

1 reference

https://api.crossref.org/works/10.1093/BIOINFORMATICS/BTL009

A simple algorithm to infer gene duplication and speciation events on a gene tree.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093/BIOINFORMATICS/BTL009

Orthology, paralogy and proposed classification for paralog subtypes

21 January 2018

1 reference

https://api.crossref.org/works/10.1093/BIOINFORMATICS/BTL009

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

21 January 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/16434444

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Hierarchical clustering schemes

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/16434444

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Gene descent, duplication, and horizontal transfer in the evolution of glutamyl- and glutaminyl-tRNA synthetases

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/16434444

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1093/BIOINFORMATICS/BTL009

1 reference

journals/bioinformatics/JothiZTP06

6 August 2017

DBLP publication ID

1 reference

DBLP Dataset 2021-01-02

28 January 2021

1 reference

6 August 2017

1 reference