4.7 Review

A comprehensive review and evaluation of computational methods for identifying protein complexes from protein-protein interaction networks

Related references

Note: Only part of the references are listed.
Article Biochemical Research Methods

HITS-PR-HHblits: protein remote homology detection by combining PageRank and Hyperlink-Induced Topic Search

Bin Liu et al.

BRIEFINGS IN BIOINFORMATICS (2020)

Article Biochemical Research Methods

Meta-Path Methods for Prioritizing Candidate Disease miRNAs

Xuan Zhang et al.

IEEE-ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS (2019)

Article Biochemistry & Molecular Biology

SubCellBarCode: Proteome-wide Mapping of Protein Localization and Relocalization

Lukas Minus Orre et al.

MOLECULAR CELL (2019)

Article Biochemistry & Molecular Biology

CORUM: the comprehensive resource of mammalian protein complexes2019

Madalina Giurgiu et al.

NUCLEIC ACIDS RESEARCH (2019)

Review Biochemical Research Methods

A comprehensive review and comparison of different computational methods for protein remote homology detection

Junjie Chen et al.

BRIEFINGS IN BIOINFORMATICS (2018)

Article Biochemical Research Methods

Prediction of potential disease-associated microRNAs using structural perturbation method

Xiangxiang Zeng et al.

BIOINFORMATICS (2018)

Article Biochemistry & Molecular Biology

IDP-CRF: Intrinsically Disordered Protein/Region Identification Based on Conditional Random Fields

Yumeng Liu et al.

INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES (2018)

Article Biochemistry & Molecular Biology

Expansion of the Gene Ontology knowledgebase and resources

S. Carbon et al.

NUCLEIC ACIDS RESEARCH (2017)

Article Biochemical Research Methods

Protein Complex Detection via Effective Integration of Base Clustering Solutions and Co-Complex Affinity Scores

Min Wu et al.

IEEE-ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS (2017)

Article Biochemical Research Methods

Inferring MicroRNA-Disease Associations by Random Walk on a Heterogeneous Network with Multiple Data Sources

Yuansheng Liu et al.

IEEE-ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS (2017)

Article Biochemistry & Molecular Biology

Quantitative analysis of protein interaction network dynamics in yeast

Albi Celaj et al.

MOLECULAR SYSTEMS BIOLOGY (2017)

Article Biochemistry & Molecular Biology

Integration of over 9,000 mass spectrometry experiments builds a global map of human protein complexes

Kevin Drew et al.

MOLECULAR SYSTEMS BIOLOGY (2017)

Article Multidisciplinary Sciences

Architecture of the human interactome defines protein communities and disease networks

Edward L. Huttlin et al.

NATURE (2017)

Article Genetics & Heredity

Probability-based collaborative filtering model for predicting gene-disease associations

Xiangxiang Zeng et al.

BMC MEDICAL GENOMICS (2017)

Article Biochemical Research Methods

Protein complex prediction for large protein protein interaction networks with the Core&Peel method

Marco Pellegrini et al.

BMC BIOINFORMATICS (2016)

Article Biochemical Research Methods

Protein complexes predictions within protein interaction networks using genetic algorithms

Emad Ramadan et al.

BMC BIOINFORMATICS (2016)

Article Biochemical Research Methods

A two-layer integration framework for protein complex detection

Le Ou-Yang et al.

BMC BIOINFORMATICS (2016)

Article Biochemical Research Methods

Construction of dynamic probabilistic protein interaction networks for protein complex identification

Yijia Zhang et al.

BMC BIOINFORMATICS (2016)

Article Biochemical Research Methods

A Novel Machine Learning Method for Cytokine-Receptor Interaction Prediction

Leyi Wei et al.

COMBINATORIAL CHEMISTRY & HIGH THROUGHPUT SCREENING (2016)

Article Biochemical Research Methods

An Empirical Study of Features Fusion Techniques for Protein-Protein Interaction Prediction

Jiancang Zeng et al.

CURRENT BIOINFORMATICS (2016)

Article Biochemical Research Methods

Application of learning to rank to protein remote homology detection

Bin Liu et al.

BIOINFORMATICS (2015)

Article Biochemistry & Molecular Biology

The BioPlex Network: A Systematic Exploration of the Human Interactome

Edward L. Huttlin et al.

Article Biochemical Research Methods

Identification of Protein Complexes from Tandem Affinity Purification/Mass Spectrometry Data via Biased Random Walk

Bingjing Cai et al.

IEEE-ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS (2015)

Article Biochemical Research Methods

A New Method for Detecting Protein Complexes based on the Three Node Cliques

Wei Zhang et al.

IEEE-ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS (2015)

Article Biochemical Research Methods

Identification of Protein Complexes Using Weighted PageRank-Nibble Algorithm and Core-Attachment Structure

Wei Peng et al.

IEEE-ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS (2015)

Article Biochemical Research Methods

Detecting Protein Complexes from Signed Protein-Protein Interaction Networks

Le Ou-Yang et al.

IEEE-ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS (2015)

Review Biochemistry & Molecular Biology

Fundamentals of protein interaction network mapping

Jamie Snider et al.

MOLECULAR SYSTEMS BIOLOGY (2015)

Article Multidisciplinary Sciences

Panorama of ancient metazoan macromolecular complexes

Cuihong Wan et al.

NATURE (2015)

Article Biochemical Research Methods

Network inference from AP-MS data: computational challenges and solutions

Ben Teng et al.

BRIEFINGS IN BIOINFORMATICS (2015)

Article Multidisciplinary Sciences

Detecting Protein Complexes in Protein Interaction Networks Modeled as Gene Expression Biclusters

Eileen Marie Hanna et al.

PLOS ONE (2015)

Proceedings Paper Computer Science, Artificial Intelligence

Regularizing predicted complexes by mutually exclusive protein-protein interactions

Osamu Maruyama et al.

PROCEEDINGS OF THE 2015 IEEE/ACM INTERNATIONAL CONFERENCE ON ADVANCES IN SOCIAL NETWORKS ANALYSIS AND MINING (ASONAM 2015) (2015)

Article Biochemical Research Methods

Functional module identification in protein interaction networks by interaction patterns

Yijie Wang et al.

BIOINFORMATICS (2014)

Article Biochemical Research Methods

An efficient protein complex mining algorithm based on Multistage Kernel Extension

Xianjun Shen et al.

BMC BIOINFORMATICS (2014)

Article Biochemical Research Methods

Detecting overlapping protein complexes based on a generative model with functional and topological properties

Xiao-Fei Zhang et al.

BMC BIOINFORMATICS (2014)

Article Biochemical Research Methods

Detecting temporal protein complexes from dynamic protein-protein interaction networks

Le Ou-Yang et al.

BMC BIOINFORMATICS (2014)

Article Biochemical Research Methods

Identifying protein complexes and functional modules-from static PPI networks to dynamic PPI networks

Bolin Chen et al.

BRIEFINGS IN BIOINFORMATICS (2014)

Article Biochemical Research Methods

Detecting Protein Complexes Based on Uncertain Graph Model

Bihai Zhao et al.

IEEE-ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS (2014)

Review Biochemical Research Methods

Dynamic protein interaction network construction and applications

Jianxin Wang et al.

PROTEOMICS (2014)

Article Biochemical Research Methods

Identifying conserved protein complexes between species by constructing interolog networks

Phi-Vu Nguyen et al.

BMC BIOINFORMATICS (2013)

Article Biochemical Research Methods

Protein complex detection using interaction reliability assessment and weighted clustering coefficient

Nazar Zaki et al.

BMC BIOINFORMATICS (2013)

Article Mathematical & Computational Biology

PPSampler2: Predicting protein complexes more accurately and efficiently by sampling

Chasanah Kusumastuti Widita et al.

BMC SYSTEMS BIOLOGY (2013)

Article Biochemistry & Molecular Biology

Protein-protein interaction networks: the puzzling riches

Shoshana J. Wodak et al.

CURRENT OPINION IN STRUCTURAL BIOLOGY (2013)

Article Genetics & Heredity

Sampling strategy for protein complex prediction using cluster size frequency

Daisuke Tatsuke et al.

Article Biochemical Research Methods

Protein Complex Prediction in Large Ontology Attributed Protein-Protein Interaction Networks

Yijia Zhang et al.

IEEE-ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS (2013)

Review Biochemical Research Methods

A SURVEY OF COMPUTATIONAL METHODS FOR PROTEIN COMPLEX PREDICTION FROM PROTEIN INTERACTION NETWORKS

Sriganesh Srihari et al.

JOURNAL OF BIOINFORMATICS AND COMPUTATIONAL BIOLOGY (2013)

Article Biochemical Research Methods

Identifying functional modules in interaction networks through overlapping Markov clustering

Yu-Keng Shih et al.

BIOINFORMATICS (2012)

Article Biochemical Research Methods

Identifying Protein Complexes From Interactome Based on Essential Proteins and Local Fitness Method

Jianxin Wang et al.

IEEE TRANSACTIONS ON NANOBIOSCIENCE (2012)

Article Biochemical Research Methods

Protein Complexes Discovery Based on Protein-Protein Interaction Data via a Regularized Sparse Generative Network Model

Xiao-Fei Zhang et al.

IEEE-ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS (2012)

Article Biochemical Research Methods

Identification of Essential Proteins Based on Edge Clustering Coefficient

Jianxin Wang et al.

IEEE-ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS (2012)

Article Biochemical Research Methods

Detecting overlapping protein complexes in protein-protein interaction networks

Tamas Nepusz et al.

NATURE METHODS (2012)

Article Biochemistry & Molecular Biology

MINT, the molecular interaction database: 2012 update

Luana Licata et al.

NUCLEIC ACIDS RESEARCH (2012)

Article Multidisciplinary Sciences

Multiplex assay for condition-dependent changes in protein-protein interactions

Ulrich Schlecht et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2012)

Article Biochemistry & Molecular Biology

Detection of protein complexes using a protein ranking algorithm

Nazar Zaki et al.

PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS (2012)

Article Biochemical Research Methods

Identification of protein complexes from co-immunoprecipitation data

Guy Geva et al.

BIOINFORMATICS (2011)

Article Biochemical Research Methods

Construction of co-complex score matrix for protein complex prediction from AP-MS data

Zhipeng Xie et al.

BIOINFORMATICS (2011)

Article Biochemical Research Methods

A comparison of the functional modules identified from time course and static PPI network data

Xiwei Tang et al.

BMC BIOINFORMATICS (2011)

Article Biochemical Research Methods

A Fast Hierarchical Clustering Algorithm for Functional Modules Discovery in Protein Interaction Networks

Jianxin Wang et al.

IEEE-ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS (2011)

Article Biochemical Research Methods

Ontology integration to identify protein complex in protein interaction networks

Bo Xu et al.

PROTEOME SCIENCE (2011)

Article Biochemical Research Methods

SPICi: a fast clustering algorithm for large biological networks

Peng Jiang et al.

BIOINFORMATICS (2010)

Article Biochemical Research Methods

Protein complex prediction via verifying and reconstructing the topology of domain-domain interactions

Yosuke Ozawa et al.

BMC BIOINFORMATICS (2010)

Article Biochemical Research Methods

Discover Protein Complexes in Protein-Protein Interaction Networks Using Parametric Local Modularity

Jongkwang Kim et al.

BMC BIOINFORMATICS (2010)

Article Biotechnology & Applied Microbiology

Computational approaches for detecting protein complexes from protein interaction networks: a survey

Xiaoli Li et al.

BMC GENOMICS (2010)

Article Mathematical & Computational Biology

Discovering conditional co-regulated protein complexes by integrating diverse data sources

Fei Luo et al.

BMC SYSTEMS BIOLOGY (2010)

Review Biochemical Research Methods

Toward the dynamic interactome: it's about time

Teresa M. Przytycka et al.

BRIEFINGS IN BIOINFORMATICS (2010)

Article Biochemical Research Methods

Enumeration of condition-dependent dense modules in protein interaction networks

Elisabeth Georgii et al.

BIOINFORMATICS (2009)

Article Biochemical Research Methods

Complex discovery from weighted PPI networks

Guimei Liu et al.

BIOINFORMATICS (2009)

Article Biochemical Research Methods

RRW: repeated random walks on genome-scale protein networks for local cluster discovery

Kathy Macropol et al.

BMC BIOINFORMATICS (2009)

Article Biochemical Research Methods

A core-attachment based method to detect protein complexes in PPI networks

Min Wu et al.

BMC BIOINFORMATICS (2009)

Article Biochemical Research Methods

Revealing Biological Modules via Graph Summarization

Saket Navlakha et al.

JOURNAL OF COMPUTATIONAL BIOLOGY (2009)

Article Biochemical Research Methods

Predicting Protein Complexes from PPI Data: A Core-Attachment Approach

Henry C. M. Leung et al.

JOURNAL OF COMPUTATIONAL BIOLOGY (2009)

Article Biochemical Research Methods

Bootstrapping the Interactome: Unsupervised Identification of Protein Complexes in Yeast

Caroline C. Friedel et al.

JOURNAL OF COMPUTATIONAL BIOLOGY (2009)

Article Biochemistry & Molecular Biology

Up-to-date catalogues of yeast protein complexes

Shuye Pu et al.

NUCLEIC ACIDS RESEARCH (2009)

Article Biochemistry & Molecular Biology

Human Protein Reference Database-2009 update

T. S. Keshava Prasad et al.

NUCLEIC ACIDS RESEARCH (2009)

Article Biochemical Research Methods

Ensemble non-negative matrix factorization methods for clustering proteinprotein interactions

Derek Greene et al.

BIOINFORMATICS (2008)

Article Biochemical Research Methods

Protein complex identification by supervised graph local clustering

Yanjun Qi et al.

BIOINFORMATICS (2008)

Article Biochemical Research Methods

A structural approach for finding functional modules from large biological networks

Mutlu Mete et al.

BMC BIOINFORMATICS (2008)

Review Biochemistry & Molecular Biology

Evolution and dynamics of protein interactions and networks

Emmanuel D. Levy et al.

CURRENT OPINION IN STRUCTURAL BIOLOGY (2008)

Article Multidisciplinary Sciences

Estimating the size of the human interactome

Michael P. H. Stumpf et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2008)

Article Multidisciplinary Sciences

Global alignment of multiple protein interaction networks with application to functional orthology detection

Rohit Singh et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2008)

Article Multidisciplinary Sciences

High-quality binary protein interaction map of the yeast interactome network

Haiyuan Yu et al.

SCIENCE (2008)

Article Mathematical & Computational Biology

USING INDIRECT PROTEIN–PROTEIN INTERACTIONS FOR PROTEIN COMPLEX PREDICTION

HON NIAN CHUA et al.

Journal of Bioinformatics and Computational Biology (2008)

Article Biochemical Research Methods

Growing functional modules from a seed protein via integration of protein interaction and gene expression data

Ioannis A. Maraziotis et al.

BMC BIOINFORMATICS (2007)

Review Biochemistry & Molecular Biology

Inference of macromolecular assemblies from crystalline state

Evgeny Krissinel et al.

JOURNAL OF MOLECULAR BIOLOGY (2007)

Article Biochemical Research Methods

An ensemble framework for clustering protein-protein interaction networks

Sitaram Asur et al.

BIOINFORMATICS (2007)

Article Biochemical Research Methods

Identification of functional modules from conserved ancestral protein-protein interactions

Janusz Dutkowski et al.

BIOINFORMATICS (2007)

Article Biochemical Research Methods

WI-PHI: A weighted yeast interactorne enriched for direct physical interactions

Lars Kiemer et al.

PROTEOMICS (2007)

Article Biochemical Research Methods

Identifying functional modules in the physical interactome of Saccharomyces cerevisiae

Shuye Pu et al.

PROTEOMICS (2007)

Article Biochemical Research Methods

Toward a comprehensive atlas of the physical interactome of Saccharomyces cerevisiae

Sean R. Collins et al.

MOLECULAR & CELLULAR PROTEOMICS (2007)

Article Biochemical Research Methods

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

Eitan Hirsh et al.

BIOINFORMATICS (2007)

Review Biochemistry & Molecular Biology

The value of high quality protein-protein interaction networks for systems biology

Ulrich Stelzl et al.

CURRENT OPINION IN CHEMICAL BIOLOGY (2006)

Article Biochemical Research Methods

Evaluation of clustering algorithms for protein-protein interaction networks

Sylvain Brohee et al.

BMC BIOINFORMATICS (2006)

Article Biochemical Research Methods

Detecting functional modules in the yeast protein-protein interaction network

Jingchun Chen et al.

BIOINFORMATICS (2006)

Article Biochemistry & Molecular Biology

Combining functional and topological properties to identify core modules in Protein Interaction Networks

Zelmina Lubovac et al.

PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS (2006)

Article Biochemical Research Methods

A direct comparison of protein interaction confidence assignment schemes

Silpa Suthram et al.

BMC BIOINFORMATICS (2006)

Article Multidisciplinary Sciences

Modularity and community structure in networks

M. E. J. Newman

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2006)

Article Biochemical Research Methods

CFinder:: locating cliques and overlapping modules in biological networks

B Adamcsek et al.

BIOINFORMATICS (2006)

Article Biochemical Research Methods

Development and implementation of an algorithm for detection of protein complexes in large interaction networks

Md Altaf-Ul-Amin et al.

BMC BIOINFORMATICS (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 Biology

The origins and evolution of functional modules: lessons from protein complexes

JB Pereira-Leal et al.

PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES (2006)

Article Biochemical Research Methods

Protein-protein interaction assays: eliminating false positive interactions

TN Nguyen et al.

NATURE METHODS (2006)

Article Biochemistry & Molecular Biology

BioGRID: a general repository for interaction datasets

Chris Stark et al.

NUCLEIC ACIDS RESEARCH (2006)

Article Biochemical Research Methods

Identification of protein complexes by comparative analysis of yeast and bacterial protein interaction data

R Sharan et al.

JOURNAL OF COMPUTATIONAL BIOLOGY (2005)

Article Biochemistry & Molecular Biology

CYGD: the comprehensive Yeast Genome Database

U Guldener et al.

NUCLEIC ACIDS RESEARCH (2005)

Article Multidisciplinary Sciences

Defining and identifying communities in networks

F Radicchi et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2004)

Article Biochemical Research Methods

Functional topology in a network of protein interactions

N Przulj et al.

BIOINFORMATICS (2004)

Review Genetics & Heredity

Network biology:: Understanding the cell's functional organization

AL Barabási et al.

NATURE REVIEWS GENETICS (2004)

Article Biochemical Research Methods

Protein complex prediction via cost-based clustering

AD King et al.

BIOINFORMATICS (2004)

Article Biochemistry & Molecular Biology

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

HY Yu et al.

GENOME RESEARCH (2004)

Article Multidisciplinary Sciences

Protein complexes and functional modules in molecular networks

V Spirin et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (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 Multidisciplinary Sciences

Community structure in social and biological networks

M Girvan et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2002)

Article Multidisciplinary Sciences

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

C von Mering et al.

NATURE (2002)

Article Biochemistry & Molecular Biology

An efficient algorithm for large-scale detection of protein families

AJ Enright et al.

NUCLEIC ACIDS RESEARCH (2002)

Article Biochemistry & Molecular Biology

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

I Xenarios et al.

NUCLEIC ACIDS RESEARCH (2002)

Article Biochemistry & Molecular Biology

MIPS: a database for genomes and protein sequences

HW Mewes et al.

NUCLEIC ACIDS RESEARCH (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 Biotechnology & Applied Microbiology

A network of protein-protein interactions in yeast

B Schwikowski et al.

NATURE BIOTECHNOLOGY (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)