(Q33389536)

26 July 2017

Detecting coevolution without phylogenetic trees? Tree-ignorant metrics of coevolution perform as well as tree-aware metrics (English)

1 reference

26 July 2017

0 references

1 reference

4

1 reference

26 July 2017

Rob Knight

6

0 references

J Gregory Caporaso

series ordinal

1

object named as

J Gregory Caporaso

1 reference

26 July 2017

5

Gavin A Huttley

1 reference

26 July 2017

Sandra Smit

2

1 reference

PubMed ID

19055758

26 July 2017

Brett C Easton

series ordinal

3

1 reference

26 July 2017

3 December 2008

1 reference

26 July 2017

BMC Evolutionary Biology

1 reference

26 July 2017

8

1 reference

26 July 2017

327

1 reference

https://scigraph.springernature.com/pub.10.1186/1471-2148-8-327

26 July 2017

0 references

cites work

Bioinformatics assessment of beta-myosin mutations reveals myosin's high sensitivity to mutations

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2637866

Detecting groups of coevolving positions in a molecule: a clustering approach

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2637866

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2637866

Detecting coevolution in and among protein domains

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2637866

PyCogent: a toolkit for making sense from sequence

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2637866

Measuring covariation in RNA alignments: physical realism improves information measures

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2637866

UniFrac: a new phylogenetic method for comparing microbial communities

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2637866

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

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2637866

Context dependence and coevolution among amino acid residues in proteins.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2637866

Solving the protein sequence metric problem

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2637866

The Adaptive Evolution Database (TAED): a phylogeny based tool for comparative genomics

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2637866

On evolutionary conservation of thermodynamic coupling in proteins.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2637866

Using multiple sequence correlation analysis to characterize functionally important protein regions

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2637866

Evolutionarily conserved networks of residues mediate allosteric communication in proteins

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2637866

Exploring a phylogenetic approach for the detection of correlated substitutions in proteins.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2637866

Separation of phylogenetic and functional associations in biological sequences by using the parametric bootstrap

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2637866

Evolutionarily conserved pathways of energetic connectivity in protein families

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2637866

Coevolving protein residues: maximum likelihood identification and relationship to structure.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2637866

Intrahelical side chain interactions in alpha-helices: poor correlation between energetics and frequency.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2637866

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2637866

Helical peptides with three pairs of Asp-Arg and Glu-Arg residues in different orientations and spacings

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2637866

Can three-dimensional contacts in protein structures be predicted by analysis of correlated mutations?

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2637866

CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2637866

Alanine scanning mutagenesis of the alpha-helix 115-123 of phage T4 lysozyme: effects on structure, stability and the binding of solvent

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2637866

Discovering structural correlations in alpha-helices

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2637866

Stabilization of the long central helix of troponin C by intrahelical salt bridges between charged amino acid side chains

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2637866

The neighbor-joining method: a new method for reconstructing phylogenetic trees

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2637866

Helix stabilization by Glu-...Lys+ salt bridges in short peptides of de novo design

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2637866

Aromatic-aromatic interactions and protein stability. Investigation by double-mutant cycles

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2637866

Co-evolving residues in membrane proteins.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2637866

Mutual information without the influence of phylogeny or entropy dramatically improves residue contact prediction.

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2637866

Statistical analysis of intrahelical ionic interactions in alpha-helices and coiled coils.

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2637866

Using information theory to search for co-evolving residues in proteins.

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2637866

Predicting RNA structure using mutual information.

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2637866

Detecting coevolving amino acid sites using Bayesian mutational mapping

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2637866

A model-based approach for detecting coevolving positions in a molecule.

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2637866

Mechanisms and convergence of compensatory evolution in mammalian mitochondrial tRNAs

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2637866

Influence of conservation on calculations of amino acid covariance in multiple sequence alignments

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2637866

Using multiple interdependency to separate functional from phylogenetic correlations in protein alignments

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2637866

Effectiveness of correlation analysis in identifying protein residues undergoing correlated evolution.

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2637866

Inferring functional linkages between proteins from evolutionary scenarios

31 October 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/19055758

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Detecting the coevolution of biosequences--an example of RNA interaction prediction

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/19055758

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Coevolutionary patterns in cytochrome c oxidase subunit I depend on structural and functional context

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/19055758

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1186/1471-2148-8-327

1 reference

PubMed ID

19055758

Dimensions Publication ID

26 July 2017

1 reference

https://scigraph.springernature.com/pub.10.1186/1471-2148-8-327

9 September 2019

1 reference

26 July 2017

1 reference

PubMed ID

19055758