(Q30010152)

21 May 2017

title

Network evolution: rewiring and signatures of conservation in signaling (English)

1 reference

21 May 2017

Martin Sikora

2

0 references

author name string

Mark G F Sun

1

1 reference

21 May 2017

Michael Costanzo

3

1 reference

21 May 2017

Charles Boone

4

1 reference

21 May 2017

Philip M Kim

5

1 reference

21 May 2017

publication date

15 March 2012

1 reference

PLOS Computational Biology

21 May 2017

published in

1 reference

21 May 2017

volume

8

1 reference

21 May 2017

issue

3

1 reference

21 May 2017

page(s)

e1002411

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Creative Commons Attribution 4.0 International

21 May 2017

copyright license

start time

15 March 2012

1 reference

April 2022 Public Data File from Crossref

copyright status

copyrighted

0 references

cites work

A global protein kinase and phosphatase interaction network in yeast.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3305342

PhosphoGRID: a database of experimentally verified in vivo protein phosphorylation sites from the budding yeast Saccharomyces cerevisiae

22 May 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3305342

Five-vertebrate ChIP-seq reveals the evolutionary dynamics of transcription factor binding

22 May 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3305342

The Pfam protein families database

22 May 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3305342

Bayesian modeling of the yeast SH3 domain interactome predicts spatiotemporal dynamics of endocytosis proteins

22 May 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3305342

Evolution of phosphoregulation: comparison of phosphorylation patterns across yeast species

22 May 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3305342

Jalview Version 2--a multiple sequence alignment editor and analysis workbench

22 May 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3305342

Systematic identification of SH3 domain-mediated human protein-protein interactions by peptide array target screening

22 May 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3305342

A fungal phylogeny based on 42 complete genomes derived from supertree and combined gene analysis

22 May 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3305342

Sequencing of Aspergillus nidulans and comparative analysis with A. fumigatus and A. oryzae

22 May 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3305342

Orthologs, paralogs, and evolutionary genomics

22 May 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3305342

The Yeast Gene Order Browser: combining curated homology and syntenic context reveals gene fate in polyploid species

22 May 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3305342

The Candida Genome Database (CGD), a community resource for Candida albicans gene and protein information

22 May 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3305342

Genome evolution in yeasts

22 May 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3305342

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

22 May 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3305342

The diploid genome sequence of Candida albicans

22 May 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3305342

Prediction and Functional Analysis of Native Disorder in Proteins from the Three Kingdoms of Life

22 May 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3305342

The Ashbya gossypii Genome as a Tool for Mapping the Ancient Saccharomyces cerevisiae Genome

22 May 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3305342

Protein interaction networks by proteome peptide scanning

22 May 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3305342

Network biology: understanding the cell's functional organization

22 May 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3305342

APE: Analyses of Phylogenetics and Evolution in R language

22 May 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3305342

Scansite 2.0: Proteome-wide prediction of cell signaling interactions using short sequence motifs

22 May 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3305342

ELM server: A new resource for investigating short functional sites in modular eukaryotic proteins

22 May 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3305342

Sequencing and comparison of yeast species to identify genes and regulatory elements

22 May 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3305342

Assembly of Cell Regulatory Systems Through Protein Interaction Domains

22 May 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3305342

Topography for independent binding of alpha-helical and PPII-helical ligands to a peroxisomal SH3 domain

22 May 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3305342

Evolution of protein kinase signaling from yeast to man

22 May 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3305342

MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform

22 May 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3305342

Evolutionary rate in the protein interaction network

22 May 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3305342

Phosphoproteome analysis by mass spectrometry and its application to Saccharomyces cerevisiae

22 May 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3305342

The genome sequence of Schizosaccharomyces pombe

22 May 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3305342

SH3 domains: complexity in moderation

22 May 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3305342

Where does fission yeast sit on the tree of life?

22 May 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3305342

Emergence of Scaling in Random Networks

22 May 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3305342

Genome phylogeny based on gene content

22 May 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3305342

Signaling through scaffold, anchoring, and adaptor proteins

22 May 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3305342

SGD: Saccharomyces Genome Database

22 May 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3305342

Basic local alignment search tool

22 May 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3305342

Towards a natural system of organisms: proposal for the domains Archaea, Bacteria, and Eucarya

22 May 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3305342

Measuring the evolutionary rewiring of biological networks

22 May 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3305342

MOTIPS: automated motif analysis for predicting targets of modular 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=3305342

Evolutionary tinkering with conserved components of a transcriptional regulatory network

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3305342

Deciphering protein kinase specificity through large-scale analysis of yeast phosphorylation site motifs

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3305342

Edgetic perturbation models of human inherited disorders

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3305342

Age-dependent evolution of the yeast protein interaction network suggests a limited role of gene duplication and divergence

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3305342

A multidimensional chromatography technology for in-depth phosphoproteome analysis

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3305342

Natural history and evolutionary principles of gene duplication in fungi

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3305342

Divergence of transcription factor binding sites across related yeast species

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3305342

Specificity and evolvability in eukaryotic protein interaction 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=3305342

Relating three-dimensional structures to protein networks provides evolutionary insights

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3305342

Accurate prediction of solvent accessibility using neural networks-based regression.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3305342

An oriented peptide array library (OPAL) strategy to study protein-protein interactions

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3305342

A protein-domain microarray identifies novel protein-protein interactions

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3305342

Identification of potential interaction networks using sequence-based searches for conserved protein-protein interactions or "interologs".

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3305342

AL2CO: calculation of positional conservation in a protein sequence alignment.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3305342

Evolution of transcriptional regulation

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3305342

Large-scale phosphorylation analysis of alpha-factor-arrested Saccharomyces cerevisiae.

3 June 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1002411

Quantitative phosphoproteomics applied to the yeast pheromone signaling pathway

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1002411

Automatic genome-wide reconstruction of phylogenetic gene trees.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1002411

A structural EM algorithm for phylogenetic inference.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1002411

Comparable system-level organization of Archaea and Eukaryotes

21 January 2018

1 reference

12 December 2020

Using substitution probabilities to improve position-specific scoring matrices

1 reference

12 December 2020

Evolving protein interaction networks through gene duplication

1 reference

12 December 2020

The yeast protein interaction network evolves rapidly and contains few redundant duplicate genes

1 reference

12 December 2020

10.1371/JOURNAL.PCBI.1002411

Identifiers

DOI

1 reference

journals/ploscb/SunSCBK12

21 May 2017

DBLP publication ID

1 reference

DBLP Dataset 2021-01-02

28 January 2021

PMC publication ID

3305342

0 references

1 reference