Comprehensive curation and analysis of global interaction networks in Saccharomyces cerevisiae (Q24675519)

13

0 references

Bobby-Joe Breitkreutz

4

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Ashton Breitkreutz

2

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Kara Dolinski

18

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Lorrie Boucher

3

0 references

Teresa Reguly

1

Teresa Reguly

0 references

Nizar N Batada

Nizar N Batada

19

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Trey Ideker

17

Trey Ideker

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Rose Oughtred

9

Rose Oughtred

0 references

Mike Tyers

20

Mike Tyers

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author name string

Gary C Hon

5

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Chad L Myers

6

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Ainslie Parsons

7

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Helena Friesen

8

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Amy Tong

10

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Chris Stark

11

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Yuen Ho

12

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Brenda Andrews

14

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Charles Boone

15

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Olga G Troyanskya

describes a project that uses

16

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language of work or name

English

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publication date

2006

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1 reference

5

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page(s)

11

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issue

4

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Cytoscape

Cytoscape

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CZ Software Mentions: A large dataset of software mentions in the biomedical literature

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Formation of regulatory patterns during signal propagation in a Mammalian cellular network

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Motifs, themes and thematic maps of an integrated Saccharomyces cerevisiae interaction network

7 April 2017

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Consolidating the set of known human protein-protein interactions in preparation for large-scale mapping of the human interactome

7 April 2017

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Ontological visualization of protein-protein interactions

7 April 2017

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Inparanoid: a comprehensive database of eukaryotic orthologs

7 April 2017

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Reactome: a knowledgebase of biological pathways

7 April 2017

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Textpresso: an ontology-based information retrieval and extraction system for biological literature

7 April 2017

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A comprehensive evolutionary classification of proteins encoded in complete eukaryotic genomes

7 April 2017

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IntAct: an open source molecular interaction database

7 April 2017

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

7 April 2017

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Protein complexes and functional modules in molecular networks

7 April 2017

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The COG database: an updated version includes eukaryotes

7 April 2017

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PreBIND and Textomy--mining the biomedical literature for protein-protein interactions using a support vector machine

7 April 2017

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The GRID: the General Repository for Interaction Datasets

7 April 2017

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Osprey: a network visualization system

7 April 2017

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An automated method for finding molecular complexes in large protein interaction networks

7 April 2017

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No simple dependence between protein evolution rate and the number of protein-protein interactions: only the most prolific interactors tend to evolve slowly

7 April 2017

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

7 April 2017

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

7 April 2017

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KEGG: kyoto encyclopedia of genes and genomes

7 April 2017

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Cluster analysis and display of genome-wide expression patterns

7 April 2017

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Comprehensive identification of cell cycle-regulated genes of the yeast Saccharomyces cerevisiae by microarray hybridization

7 April 2017

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

7 April 2017

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Discovery of biological networks from diverse functional genomic data

7 April 2017

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Global analysis of protein localization in budding yeast

7 April 2017

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The Gene Ontology (GO) database and informatics resource

7 April 2017

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Global analysis of protein expression in yeast

7 April 2017

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Functional profiling of the Saccharomyces cerevisiae genome

7 April 2017

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Systematic identification of protein complexes in Saccharomyces cerevisiae by mass spectrometry

7 April 2017

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

7 April 2017

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Genomic expression programs in the response of yeast cells to environmental changes

7 April 2017

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A comprehensive analysis of protein-protein interactions in Saccharomyces cerevisiae

7 April 2017

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Emergence of Scaling in Random Networks

7 April 2017

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Collective dynamics of 'small-world' networks

7 April 2017

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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1561585

Exploring the metabolic and genetic control of gene expression on a genomic scale

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1561585

Global landscape of protein complexes in the yeast Saccharomyces cerevisiae

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1561585

Proteome survey reveals modularity of the yeast cell machinery

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1561585

Exploration of the function and organization of the yeast early secretory pathway through an epistatic miniarray profile

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1561585

Transcriptional regulatory code of a eukaryotic genome

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1561585

Global mapping of the yeast genetic interaction network

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1561585

New components of a system for phosphate accumulation and polyphosphate metabolism in Saccharomyces cerevisiae revealed by genomic expression analysis

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1561585

Functional discovery via a compendium of expression profiles

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1561585

Two yeast forkhead genes regulate the cell cycle and pseudohyphal growth

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1561585

Toward a protein-protein interaction map of the budding yeast: A comprehensive system to examine two-hybrid interactions in all possible combinations between the yeast proteins

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1561585

The transcriptional program of sporulation in budding yeast

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1561585

Systematic genetic analysis with ordered arrays of yeast deletion mutants

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1561585

A protein interaction map of Drosophila melanogaster

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1561585

Development of human protein reference database as an initial platform for approaching systems biology in humans

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1561585

Specificity and stability in topology of protein networks

7 April 2017

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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1561585

Correlation between transcriptome and interactome mapping data from Saccharomyces cerevisiae

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1561585

Transcriptional remodeling in response to iron deprivation in Saccharomyces cerevisiae

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1561585

A Bayesian Networks Approach for Predicting Protein-Protein Interactions from Genomic Data

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1561585

A map of the interactome network of the metazoan C. elegans

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1561585

Comparative assessment of large-scale data sets of protein-protein interactions

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1561585

Network motifs in the transcriptional regulation network of Escherichia coli

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1561585

Lethality and centrality in protein networks

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1561585

Error and attack tolerance of complex networks

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1561585

Global analysis of protein phosphorylation in yeast

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1561585

Evidence for dynamically organized modularity in the yeast protein-protein interaction network

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1561585

The HUPO PSI's molecular interaction format--a community standard for the representation of protein interaction data

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1561585

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

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1561585

BIND: the Biomolecular Interaction Network Database

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1561585

Hierarchical organization of modularity in metabolic networks

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1561585

Evolutionary rate in the protein interaction network

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1561585

MINT: a Molecular INTeraction database

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1561585

MIPS: a database for genomes and protein sequences

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1561585

A new approach to decoding life: systems biology

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1561585

Integrated genomic and proteomic analyses of a systematically perturbed metabolic network

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1561585

Some protein interaction data do not exhibit power law statistics

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1561585

Systematic interpretation of genetic interactions using protein networks

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1561585

Conserved patterns of protein interaction in multiple species

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1561585

Transcriptional networks: reverse-engineering gene regulation on a global scale

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1561585

Combining biological networks to predict genetic interactions

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1561585

Harvesting the genome's bounty: integrative genomics

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1561585

FTICR mass spectrometry for qualitative and quantitative bioanalyses.

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1561585

Stochastic model of protein-protein interaction: why signaling proteins need to be colocalized

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1561585

The yeast cell-cycle network is robustly designed

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1561585

Increasing specificity in high-throughput yeast two-hybrid experiments

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1561585

Does Selection Mold Molecular Networks?

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1561585

On the number of protein-protein interactions in the yeast proteome

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1561585

Functional genomics and proteomics: charting a multidimensional map of the yeast cell

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1561585

A Bayesian framework for combining heterogeneous data sources for gene function prediction (in Saccharomyces cerevisiae).

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1561585

Schizosaccharomyces pombe essential genes: a pilot study.

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1561585

Modular organization of cellular networks

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1561585

Analyzing yeast protein-protein interaction data obtained from different sources

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1561585

Genome-wide analysis of gene expression regulated by the calcineurin/Crz1p signaling pathway in Saccharomyces cerevisiae

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1561585

Essential genes are more evolutionarily conserved than are nonessential genes in bacteria

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1561585

Genomic expression responses to DNA-damaging agents and the regulatory role of the yeast ATR homolog Mec1p

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1561585

Whole-genome expression analysis of snf/swi mutants of Saccharomyces cerevisiae

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1561585

The Yeast Protein Database (YPD): a curated proteome database for Saccharomyces cerevisiae

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1561585

The synthetic genetic interaction spectrum of essential genes

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1561585

A Robust Toolkit for Functional Profiling of the Yeast Genome

28 November 2018

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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1561585

Modeling interactome: scale-free or geometric?

28 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1561585

Gaining confidence in high-throughput protein interaction networks

28 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1561585

DNA helicase gene interaction network defined using synthetic lethality analyzed by microarray

28 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1561585

Global architecture of genetic interactions on the protein network.

28 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1561585

The FlyBase database of the Drosophila genome projects and community literature.

28 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1561585

Essential Genes Are More Evolutionarily Conserved Than Are Nonessential Genes in Bacteria

28 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1561585

Is there a bias in proteome research?

28 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1561585

A probabilistic functional network of yeast genes

28 November 2018

1 reference

12 December 2020

Life cycles of successful genes

1 reference

12 December 2020

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

1 reference

12 December 2020

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

1 reference

12 December 2020

Identifiers

DOI

10.1186/JBIOL36

1 reference

Dimensions Publication ID

4425487

1052859865

0 references

4425487

1 reference

1 reference

1 reference