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

SubCellBarCode: Proteome-wide Mapping of Protein Localization and Relocalization

(2019) Lukas Minus Orre et al.   MOLECULAR CELL

BioSeq-Analysis2.0: an updated platform for analyzing DNA, RNA and protein sequences at sequence level and residue level based on machine learning approaches

(2019) Bin Liu et al.   NUCLEIC ACIDS RESEARCH

Prediction of potential disease-associated microRNAs using structural perturbation method

(2018) Xiangxiang Zeng et al.   BIOINFORMATICS

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

(2018) Yumeng Liu et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

CORUM: the comprehensive resource of mammalian protein complexes—2019

(2018) Madalina Giurgiu et al.   NUCLEIC ACIDS RESEARCH

STRING v11: protein–protein association networks with increased coverage, supporting functional discovery in genome-wide experimental datasets

(2018) Damian Szklarczyk et al.   NUCLEIC ACIDS RESEARCH

Meta-path methods for prioritizing candidate disease miRNAs

(2017) Xuan Zhang et al.   IEEE-ACM Transactions on Computational Biology and Bioinformatics

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

(2017) Min Wu et al.   IEEE-ACM Transactions on Computational Biology and Bioinformatics

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

(2017) Yuansheng Liu et al.   IEEE-ACM Transactions on Computational Biology and Bioinformatics

Quantitative analysis of protein interaction network dynamics in yeast

(2017) Albi Celaj et al.   Molecular Systems Biology

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

(2017) Kevin Drew et al.   Molecular Systems Biology

Architecture of the human interactome defines protein communities and disease networks

(2017) Edward L. Huttlin et al.   NATURE

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

(2016) Marco Pellegrini et al.   BMC BIOINFORMATICS

Protein complexes predictions within protein interaction networks using genetic algorithms

(2016) Emad Ramadan et al.   BMC BIOINFORMATICS

A two-layer integration framework for protein complex detection

(2016) Le Ou-Yang et al.   BMC BIOINFORMATICS

Construction of dynamic probabilistic protein interaction networks for protein complex identification

(2016) Yijia Zhang et al.   BMC BIOINFORMATICS

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

(2016) Junjie Chen et al.   BRIEFINGS IN BIOINFORMATICS

A novel machine learning method for cytokine-receptor interaction prediction

(2016) Leyi Wei et al.   COMBINATORIAL CHEMISTRY & HIGH THROUGHPUT SCREENING

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

(2016) Jiancang Zeng et al.   Current Bioinformatics

Detection of overlapping protein complexes in gene expression, phenotype and pathways of Saccharomyces cerevisiae using Prorank based Fuzzy algorithm

(2016) P. Manikandan et al.   GENE

Expansion of the Gene Ontology knowledgebase and resources

(2016)   NUCLEIC ACIDS RESEARCH

Application of learning to rank to protein remote homology detection

(2015) Bin Liu et al.   BIOINFORMATICS

A Human Interactome in Three Quantitative Dimensions Organized by Stoichiometries and Abundances

(2015) Marco Y. Hein et al.   CELL

The BioPlex Network: A Systematic Exploration of the Human Interactome

(2015) Edward L. Huttlin et al.   CELL

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

(2015) Bingjing Cai et al.   IEEE-ACM Transactions on Computational Biology and Bioinformatics

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

(2015) Wei Zhang et al.   IEEE-ACM Transactions on Computational Biology and Bioinformatics

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

(2015) Wei Peng et al.   IEEE-ACM Transactions on Computational Biology and Bioinformatics

Detecting Protein Complexes from Signed Protein-Protein Interaction Networks

(2015) Le Ou-Yang et al.   IEEE-ACM Transactions on Computational Biology and Bioinformatics

Fundamentals of protein interaction network mapping

(2015) J. Snider et al.   Molecular Systems Biology

Panorama of ancient metazoan macromolecular complexes

(2015) Cuihong Wan et al.   NATURE

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

(2015) Eileen Marie Hanna et al.   PLoS One

An efficient protein complex mining algorithm based on Multistage Kernel Extension

(2014) Xianjun Shen et al.   BMC BIOINFORMATICS

MAE-FMD: Multi-agent evolutionary method for functional module detection in protein-protein interaction networks

(2014) Jun Ji et al.   BMC BIOINFORMATICS

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

(2014) Xiao-Fei Zhang et al.   BMC BIOINFORMATICS

Detecting temporal protein complexes from dynamic protein-protein interaction networks

(2014) Le Ou-Yang et al.   BMC BIOINFORMATICS

Detecting protein complexes in protein interaction networks using a ranking algorithm with a refined merging procedure

(2014) Eileen Hanna et al.   BMC BIOINFORMATICS

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

(2014) Ben Teng et al.   BRIEFINGS IN BIOINFORMATICS

Detecting Protein Complexes Based on Uncertain Graph Model

(2014) Bihai Zhao et al.   IEEE-ACM Transactions on Computational Biology and Bioinformatics

Functional module identification in protein interaction networks by interaction patterns

(2013) Yijie Wang et al.   BIOINFORMATICS

Combining evolutionary information extracted from frequency profiles with sequence-based kernels for protein remote homology detection

(2013) Bin Liu et al.   BIOINFORMATICS

Identifying conserved protein complexes between species by constructing interolog networks

(2013) Phi-Vu Nguyen et al.   BMC BIOINFORMATICS

Protein complex detection using interaction reliability assessment and weighted clustering coefficient

(2013) Nazar Zaki et al.   BMC BIOINFORMATICS

PPSampler2: Predicting protein complexes more accurately and efficiently by sampling

(2013) Chasanah Kusumastuti Widita et al.   BMC Systems Biology

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

(2013) B. Chen et al.   BRIEFINGS IN BIOINFORMATICS

Protein–protein interaction networks: the puzzling riches

(2013) Shoshana J Wodak et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

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

(2013) Yijia Zhang et al.   IEEE-ACM Transactions on Computational Biology and Bioinformatics

Clustering based on multiple biological information: approach for predicting protein complexes

(2013) Xiwei Tang et al.   IET Systems Biology

Negatome 2.0: a database of non-interacting proteins derived by literature mining, manual annotation and protein structure analysis

(2013) Philipp Blohm et al.   NUCLEIC ACIDS RESEARCH

Detection of protein complexes using a protein ranking algorithm

(2013) Nazar Zaki et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Dynamic protein interaction network construction and applications

(2013) Jianxin Wang et al.   PROTEOMICS

Identifying functional modules in interaction networks through overlapping Markov clustering

(2012) Y.-K. Shih et al.   BIOINFORMATICS

Sampling strategy for protein complex prediction using cluster size frequency

(2012) Daisuke Tatsuke et al.   GENE

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

(2012) Jianxin Wang et al.   IEEE TRANSACTIONS ON NANOBIOSCIENCE

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

(2012) Xiao-Fei Zhang et al.   IEEE-ACM Transactions on Computational Biology and Bioinformatics

Detecting overlapping protein complexes in protein-protein interaction networks

(2012) Tamás Nepusz et al.   NATURE METHODS

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

(2012) U. Schlecht et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Construction and application of dynamic protein interaction network based on time course gene expression data

(2012) Jianxin Wang et al.   PROTEOMICS

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

(2012) SRIGANESH SRIHARI et al.   Journal of Bioinformatics and Computational Biology

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

(2011) Zhipeng Xie et al.   BIOINFORMATICS

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

(2011) Xiwei Tang et al.   BMC BIOINFORMATICS

Identification of Essential Proteins Based on Edge Clustering Coefficient

(2011) Jianxin Wang et al.   IEEE-ACM Transactions on Computational Biology and Bioinformatics

MINT, the molecular interaction database: 2012 update

(2011) Luana Licata et al.   NUCLEIC ACIDS RESEARCH

Ontology integration to identify protein complex in protein interaction networks

(2011) Bo Xu et al.   Proteome Science

Detecting protein complexes and functional modules from protein interaction networks: A graph entropy approach

(2011) Edward Casey Kenley et al.   PROTEOMICS

Identification of protein complexes from co-immunoprecipitation data

(2010) Guy Geva et al.   BIOINFORMATICS

SPICi: a fast clustering algorithm for large biological networks

(2010) Peng Jiang et al.   BIOINFORMATICS

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

(2010) Yosuke Ozawa et al.   BMC BIOINFORMATICS

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

(2010) Jongkwang Kim et al.   BMC BIOINFORMATICS

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

(2010) Xiaoli Li et al.   BMC GENOMICS

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

(2010) Fei Luo et al.   BMC Systems Biology

Toward the dynamic interactome: it's about time

(2010) T. M. Przytycka et al.   BRIEFINGS IN BIOINFORMATICS

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

(2010) Jianxin Wang et al.   IEEE-ACM Transactions on Computational Biology and Bioinformatics

Enumeration of condition-dependent dense modules in protein interaction networks

(2009) Elisabeth Georgii et al.   BIOINFORMATICS

Complex discovery from weighted PPI networks

(2009) Guimei Liu et al.   BIOINFORMATICS

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

(2009) Kathy Macropol et al.   BMC BIOINFORMATICS

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

(2009) Min Wu et al.   BMC BIOINFORMATICS

Revealing Biological Modules via Graph Summarization

(2009) Saket Navlakha et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

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

(2009) Henry C.M. Leung et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

Bootstrapping the Interactome: Unsupervised Identification of Protein Complexes in Yeast

(2009) Caroline C. Friedel et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

Ensemble non-negative matrix factorization methods for clustering protein–protein interactions

(2008) Derek Greene et al.   BIOINFORMATICS

Protein complex identification by supervised graph local clustering

(2008) Y. Qi et al.   BIOINFORMATICS

A structural approach for finding functional modules from large biological networks

(2008) Mutlu Mete et al.   BMC BIOINFORMATICS

Modifying the DPClus algorithm for identifying protein complexes based on new topological structures

(2008) Min Li et al.   BMC BIOINFORMATICS

Evolution and dynamics of protein interactions and networks

(2008) Emmanuel D Levy et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Up-to-date catalogues of yeast protein complexes

(2008) Shuye Pu et al.   NUCLEIC ACIDS RESEARCH

Human Protein Reference Database--2009 update

(2008) T. S. Keshava Prasad et al.   NUCLEIC ACIDS RESEARCH

Estimating the size of the human interactome

(2008) M. P. H. Stumpf et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

(2008) R. Singh et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

High-Quality Binary Protein Interaction Map of the Yeast Interactome Network

(2008) H. Yu et al.   SCIENCE

USING INDIRECT PROTEIN–PROTEIN INTERACTIONS FOR PROTEIN COMPLEX PREDICTION

(2008) HON NIAN CHUA et al.   Journal of Bioinformatics and Computational Biology