Exploiting locational and topological overlap model to identify modules in protein interaction networks

SMILE: a novel procedure for subcellular module identification with localisation expansion

(2018) Lixin Cheng et al.   IET Systems Biology

Full Characterization of Localization Diversity in the Human Protein Interactome

(2017) Lixin Cheng et al.   JOURNAL OF PROTEOME RESEARCH

ICN: a normalization method for gene expression data considering the over-expression of informative genes

(2016) Lixin Cheng et al.   Molecular BioSystems

HIPPIE v2.0: enhancing meaningfulness and reliability of protein–protein interaction networks

(2016) Gregorio Alanis-Lobato et al.   NUCLEIC ACIDS RESEARCH

CrossNorm: a novel normalization strategy for microarray data in cancers

(2016) Lixin Cheng et al.   Scientific Reports

Prediction of problematic complexes from PPI networks: sparse, embedded, and small complexes

(2015) Chern Han Yong et al.   Biology Direct

A dual role of p53 in the control of autophagy

(2014) Ezgi Tasdemir et al.   Autophagy

ComPPI: a cellular compartment-specific database for protein–protein interaction network analysis

(2014) Daniel V. Veres et al.   NUCLEIC ACIDS RESEARCH

The BioGRID interaction database: 2015 update

(2014) Andrew Chatr-aryamontri et al.   NUCLEIC ACIDS RESEARCH

RAID: a comprehensive resource for human RNA-associated (RNA-RNA/RNA-protein) interaction

(2014) X. Zhang et al.   RNA

Connect the dots

(2013) Yifei Li et al.   Autophagy

Integrated Systems Approach Identifies Genetic Nodes and Networks in Late-Onset Alzheimer’s Disease

(2013) Bin Zhang et al.   CELL

Simple Topological Features Reflect Dynamics and Modularity in Protein Interaction Networks

(2013) Yuri Pritykin et al.   PLoS Computational Biology

Detecting overlapping protein complexes in protein-protein interaction networks

(2012) Tamás Nepusz et al.   NATURE METHODS

Interactome Networks and Human Disease

(2011) Marc Vidal et al.   CELL

Protein localization as a principal feature of the etiology and comorbidity of genetic diseases

(2011) S. Park et al.   Molecular Systems Biology

ncFANs: a web server for functional annotation of long non-coding RNAs

(2011) Q. Liao et al.   NUCLEIC ACIDS RESEARCH

Discovering approximate-associated sequence patterns for protein–DNA interactions

(2010) Tak-Ming Chan et al.   BIOINFORMATICS

Recent advances in clustering methods for protein interaction networks

(2010) Jianxin Wang et al.   BMC GENOMICS

MIPS: curated databases and comprehensive secondary data resources in 2010

(2010) H. Werner Mewes et al.   NUCLEIC ACIDS RESEARCH

A human functional protein interaction network and its application to cancer data analysis

(2010) Guanming Wu et al.   GENOME BIOLOGY

Human Cancer Protein-Protein Interaction Network: A Structural Perspective

(2009) Gozde Kar et al.   PLoS Computational Biology

WGCNA: an R package for weighted correlation network analysis

(2008) Peter Langfelder et al.   BMC BIOINFORMATICS

Regulation of autophagy by cytoplasmic p53

(2008) Ezgi Tasdemir et al.   NATURE CELL BIOLOGY

Human Protein Reference Database--2009 update

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

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

(2008) H. Yu et al.   SCIENCE