Reconstructing ancestral gene content by coevolution (Q28749459)

3

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Eytan Ruppin

5

object named as

Eytan Ruppin

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author name string

Hadas Birin

2

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Martin Kupiec

Co-evolutionary networks of genes and cellular processes across fungal species

4

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language of work or name

English

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publication date

January 2010

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published in

Genome Research

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volume

20

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issue

1

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page(s)

122-32

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cites work

1 reference

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16 March 2017

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More taxa are not necessarily better for the reconstruction of ancestral character states

16 March 2017

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16 March 2017

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Sea Anemone Genome Reveals Ancestral Eumetazoan Gene Repertoire and Genomic Organization

16 March 2017

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16 March 2017

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Reconstructing contiguous regions of an ancestral genome

16 March 2017

1 reference

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Comprehensive curation and analysis of global interaction networks in Saccharomyces cerevisiae

16 March 2017

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A metabolic network in the evolutionary context: multiscale structure and modularity

16 March 2017

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Identification and classification of conserved RNA secondary structures in the human genome

16 March 2017

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Large-scale identification of protein-protein interaction of Escherichia coli K-12

16 March 2017

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Global landscape of protein complexes in the yeast Saccharomyces cerevisiae

16 March 2017

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Proteome survey reveals modularity of the yeast cell machinery

16 March 2017

1 reference

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Reconstructing large regions of an ancestral mammalian genome in silico

16 March 2017

1 reference

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The COG database: an updated version includes eukaryotes

16 March 2017

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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

16 March 2017

1 reference

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

16 March 2017

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A fast algorithm for joint reconstruction of ancestral amino acid sequences

16 March 2017

1 reference

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16 March 2017

The universal ancestor

1 reference

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PAML: a program package for phylogenetic analysis by maximum likelihood

16 March 2017

1 reference

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A new method of inference of ancestral nucleotide and amino acid sequences

16 March 2017

1 reference

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Evolutionarily conserved pathways of energetic connectivity in protein families

16 March 2017

1 reference

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Saccharomyces Genome Database (SGD) provides tools to identify and analyze sequences from Saccharomyces cerevisiae and related sequences from other organisms

7 April 2017

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Evolutionary relationship of archaebacteria, eubacteria, and eukaryotes inferred from phylogenetic trees of duplicated genes

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2798824

Co-evolutionary rates of functionally related yeast genes.

9 May 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2798824

Genome evolution in cyanobacteria: the stable core and the variable shell

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2798824

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

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2798824

Detecting coevolution in and among protein domains

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2798824

Natural history and evolutionary principles of gene duplication in fungi

3 June 2018

1 reference

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Modular co-evolution of metabolic networks

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2798824

Ancestral genome sizes specify the minimum rate of lateral gene transfer during prokaryote evolution.

3 June 2018

1 reference

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Comparison of protein interaction networks reveals species conservation and divergence

3 June 2018

1 reference

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A minimal estimate for the gene content of the last universal common ancestor--exobiology from a terrestrial perspective

3 June 2018

1 reference

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The evolution of A-, F-, and V-type ATP synthases and ATPases: reversals in function and changes in the H+/ATP coupling ratio

3 June 2018

1 reference

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Ancestral sequence reconstruction in primate mitochondrial DNA: compositional bias and effect on functional inference.

3 June 2018

1 reference

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Computational inference of scenarios for alpha-proteobacterial genome evolution

3 June 2018

1 reference

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Comparative genomics, minimal gene-sets and the last universal common ancestor

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2798824

Escherichia coli YidC is a membrane insertase for Sec-independent proteins

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2798824

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2798824

Reconstruction of metabolic networks from genome data and analysis of their global structure for various organisms

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2798824

Analyzing yeast protein-protein interaction data obtained from different sources

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2798824

Functional genomics of Escherichia coli in Japan

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2798824

The nature of the last universal common ancestor

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2798824

RNA secondary structure prediction using stochastic context-free grammars and evolutionary history

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2798824

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2798824

Secondary structure of 16S ribosomal RNA.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2798824

Higher order structure in ribosomal RNA

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2798824

Evolution of the vacuolar H+-ATPase: implications for the origin of eukaryotes

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2798824

Reconstruction of ancestral genomic sequences using likelihood

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2798824

Identification of conserved protein complexes based on a model of protein network evolution.

27 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2798824

Constrained models of evolution lead to improved prediction of functional linkage from correlated gain and loss of genes.

27 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2798824

The coordinated evolution of yeast proteins is constrained by functional modularity

27 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2798824

Estimating and improving protein interaction error rates.

27 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2798824

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

27 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2798824

Identification of functional links between genes using phylogenetic profiles.

27 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2798824

Multiple Maxima of Likelihood in Phylogenetic Trees: An Analytic Approach

27 November 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/19948819

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

A probabilistic functional network of yeast genes

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/19948819

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/19948819

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1101/GR.096115.109

1 reference

4860307

4860307

1 reference

1 reference

1 reference