4.6 Article

Unraveling Protein Networks with Power Graph Analysis

Related references

Note: Only part of the references are listed.
Article Biotechnology & Applied Microbiology

Towards zoomable multidimensional maps of the cell

Zhenjun Hu et al.

NATURE BIOTECHNOLOGY (2007)

Article Biochemistry & Molecular Biology

Large-scale mapping of human protein-protein interactions by mass spectrometry

Rob M. Ewing et al.

MOLECULAR SYSTEMS BIOLOGY (2007)

Article Biochemistry & Molecular Biology

New developments in the InterPro database

Nicola J. Mulder et al.

NUCLEIC ACIDS RESEARCH (2007)

Article Multidisciplinary Sciences

Relating three-dimensional structures to protein networks provides evolutionary insights

Philip M. Kim et al.

SCIENCE (2006)

Article Biochemical Research Methods

Protein homology network families reveal step-wise diversification of type III and type IV secretion systems

Duccio Medini et al.

PLOS COMPUTATIONAL BIOLOGY (2006)

Article Biochemistry & Molecular Biology

BLAST: improvements for better sequence analysis

Jian Ye et al.

NUCLEIC ACIDS RESEARCH (2006)

Article Biochemical Research Methods

Integrated assessment and prediction of transcription factor binding

Andreas Beyer et al.

PLOS COMPUTATIONAL BIOLOGY (2006)

Article Biochemistry & Molecular Biology

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

M Arifuzzaman et al.

GENOME RESEARCH (2006)

Article Biochemical Research Methods

XcisClique: analysis of regulatory bicliques

Amrita Pati et al.

BMC BIOINFORMATICS (2006)

Article Biochemical Research Methods

How scale-free are biological networks

Raya Khanin et al.

JOURNAL OF COMPUTATIONAL BIOLOGY (2006)

Article Multidisciplinary Sciences

Proteome survey reveals modularity of the yeast cell machinery

AC Gavin et al.

NATURE (2006)

Article Multidisciplinary Sciences

Global landscape of protein complexes in the yeast Saccharomyces cerevisiae

NJ Krogan et al.

NATURE (2006)

Article Biotechnology & Applied Microbiology

Predicting domain-domain interactions using a parsimony approach

Katia S. Guimaraes et al.

GENOME BIOLOGY (2006)

Article Multidisciplinary Sciences

A protein interaction network of the malaria parasite Plasmodium falciparum

DJ LaCount et al.

NATURE (2005)

Article Multidisciplinary Sciences

Towards a proteome-scale map of the human protein-protein interaction network

JF Rual et al.

NATURE (2005)

Article Biochemistry & Molecular Biology

A human protein-protein interaction network:: A resource for annotating the proteome

U Stelzl et al.

Article Biotechnology & Applied Microbiology

Probabilistic model of the human protein-protein interaction network

DR Rhodes et al.

NATURE BIOTECHNOLOGY (2005)

Article Biotechnology & Applied Microbiology

Effect of sampling on topology predictions of protein-protein interaction networks

JDJ Han et al.

NATURE BIOTECHNOLOGY (2005)

Article Biochemical Research Methods

Identification and characterization of protein subcomplexes in yeast

J Hollunder et al.

PROTEOMICS (2005)

Article Biochemical Research Methods

Filtering high-throughput protein-protein interaction data using a combination of genomic features

A Patil et al.

BMC BIOINFORMATICS (2005)

Article Biochemical Research Methods

Statistical analysis of domains in interacting protein pairs

TMW Nye et al.

BIOINFORMATICS (2005)

Article Multidisciplinary Sciences

Subnets of scale-free networks are not scale-free: Sampling properties of networks

MPH Stumpf et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2005)

Article Biochemical Research Methods

ProViz: protein interaction visualization and exploration

F Iragne et al.

BIOINFORMATICS (2005)

Article Biotechnology & Applied Microbiology

Inferring protein domain interactions from databases of interacting proteins

R Riley et al.

GENOME BIOLOGY (2005)

Article Biochemistry & Molecular Biology

The ProDom database of protein domain families: more emphasis on 3D

C Bru et al.

NUCLEIC ACIDS RESEARCH (2005)

Article Biochemistry & Molecular Biology

Evolution of the multifunctional protein tyrosine phosphatase family

B Pils et al.

MOLECULAR BIOLOGY AND EVOLUTION (2004)

Article Multidisciplinary Sciences

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

SM Li et al.

SCIENCE (2004)

Article Physics, Fluids & Plasmas

Topological generalizations of network motifs

N Kashtan et al.

PHYSICAL REVIEW E (2004)

Article Biochemical Research Methods

Modeling interactome: scale-free or geometric?

N Przulj et al.

BIOINFORMATICS (2004)

Article Biochemistry & Molecular Biology

Protein interaction networks by proteome peptide scanning

C Landgraf et al.

PLOS BIOLOGY (2004)

Article Biochemical Research Methods

Protein complex prediction via cost-based clustering

AD King et al.

BIOINFORMATICS (2004)

Review Genetics & Heredity

Duplication and divergence: The evolution of new genes and old ideas

JS Taylor et al.

ANNUAL REVIEW OF GENETICS (2004)

Article Genetics & Heredity

Gene regulatory network growth by duplication

SA Teichmann et al.

NATURE GENETICS (2004)

Article Biotechnology & Applied Microbiology

A Drosophila protein-interaction map centered on cell-cycle regulators

CA Stanyon et al.

GENOME BIOLOGY (2004)

Article Biotechnology & Applied Microbiology

Modular decomposition of protein-protein interaction networks

J Gagneur et al.

GENOME BIOLOGY (2004)

Article Multidisciplinary Sciences

A protein interaction map of Drosophila melanogaster

L Giot et al.

SCIENCE (2003)

Article Biochemistry & Molecular Biology

Assigning function to yeast proteins by integration of technologies

TR Hazbun et al.

MOLECULAR CELL (2003)

Article Biochemical Research Methods

Integrative approach for computationally inferring protein domain interactions

SK Ng et al.

BIOINFORMATICS (2003)

Article Biochemistry & Molecular Biology

Topological structure analysis of the protein-protein interaction network in budding yeast

DB Bu et al.

NUCLEIC ACIDS RESEARCH (2003)

Article Biochemical Research Methods

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

GD Bader et al.

BMC BIOINFORMATICS (2003)

Article Biochemistry & Molecular Biology

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

P Shannon et al.

GENOME RESEARCH (2003)

Article Biotechnology & Applied Microbiology

Osprey: a network visualization system

BJ Breitkreutz et al.

GENOME BIOLOGY (2003)

Article Multidisciplinary Sciences

Transcriptional regulatory networks in Saccharomyces cerevisiae

TI Lee et al.

SCIENCE (2002)

Article Multidisciplinary Sciences

Network motifs: Simple building blocks of complex networks

R Milo et al.

SCIENCE (2002)

Article Biotechnology & Applied Microbiology

Analyzing yeast protein-protein interaction data obtained from different sources

GD Bader et al.

NATURE BIOTECHNOLOGY (2002)

Article Biochemistry & Molecular Biology

Inferring domain-domain interactions from protein-protein interactions

MH Deng et al.

GENOME RESEARCH (2002)

Article Multidisciplinary Sciences

Specificity and stability in topology of protein networks

S Maslov et al.

SCIENCE (2002)

Article Multidisciplinary Sciences

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

T Ito et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2001)

Article Biochemistry & Molecular Biology

A DNA damage-induced p53 serine 392 kinase complex contains CK2, hSpt16, and SSRP1

DM Keller et al.

MOLECULAR CELL (2001)

Article Multidisciplinary Sciences

The protein-protein interaction map of Helicobacter pylori

JC Rain et al.

NATURE (2001)

Article Cell Biology

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

AP Gasch et al.

MOLECULAR BIOLOGY OF THE CELL (2000)

Article Multidisciplinary Sciences

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

T Ito et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2000)