Quantitative assessment of gene expression network module-validation methods
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Title
Quantitative assessment of gene expression network module-validation methods
Authors
Keywords
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Journal
Scientific Reports
Volume 5, Issue 1, Pages -
Publisher
Springer Nature
Online
2015-10-16
DOI
10.1038/srep15258
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Note: Only part of the references are listed.- Gene co-expression network analysis identifies porcine genes associated with variation in Salmonella shedding
- (2014) Arun Kommadath et al. BMC GENOMICS
- Spatiotemporal positioning of multipotent modules in diverse biological networks
- (2014) Yinying Chen et al. CELLULAR AND MOLECULAR LIFE SCIENCES
- Integrative Analysis of Many Weighted Co-Expression Networks Using Tensor Computation
- (2014) Wenyuan Li et al. PLoS Computational Biology
- Discovery and analysis of consistent active sub-networks in cancers
- (2013) Raj K Gaire et al. BMC BIOINFORMATICS
- A novel subgradient-based optimization algorithm for blockmodel functional module identification
- (2013) Yijie Wang et al. BMC BIOINFORMATICS
- Discovering protein complexes in protein interaction networks via exploring the weak ties effect
- (2013) Xiaoke Ma et al. BMC Systems Biology
- Dynamical patterning modules in plant development and evolution
- (2013) Valeria Hernández-Hernández et al. INTERNATIONAL JOURNAL OF DEVELOPMENTAL BIOLOGY
- MGclus: network clustering employing shared neighbors
- (2013) Oliver Frings et al. Molecular BioSystems
- A Modular Organization of the Human Intestinal Mucosal Microbiota and Its Association with Inflammatory Bowel Disease
- (2013) Maomeng Tong et al. PLoS One
- Optimization criteria and biological process enrichment in homologous multiprotein modules
- (2013) L. Hodgkinson et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- Maximal information component analysis: a novel non-linear network analysis method
- (2013) Christoph D. Rau et al. Frontiers in Genetics
- Robustness and accuracy of functional modules in integrated network analysis
- (2012) Daniela Beisser et al. BIOINFORMATICS
- A systems biology approach to the global analysis of transcription factors in colorectal cancer
- (2012) Meeta P Pradhan et al. BMC CANCER
- Metabolic Flux-Based Modularity using Shortest Retroactive distances
- (2012) Gautham Vivek Sridharan et al. BMC Systems Biology
- Spotlight: Assembly of protein complexes by integrating graph clustering methods
- (2012) Chia-Hao Chin et al. GENE
- Identification of Hierarchical and Overlapping Functional Modules in PPI Networks
- (2012) Jianxin Wang et al. IEEE TRANSACTIONS ON NANOBIOSCIENCE
- Prediction of Human Disease-Related Gene Clusters by Clustering Analysis
- (2012) Peng Gang Sun et al. International Journal of Biological Sciences
- An Integrative Approach to Infer Regulation Programs in a Transcription Regulatory Module Network
- (2012) Jianlong Qi et al. JOURNAL OF BIOMEDICINE AND BIOTECHNOLOGY
- An integrated approach to identify causal network modules of complex diseases with application to colorectal cancer
- (2012) Zhenshu Wen et al. JOURNAL OF THE AMERICAN MEDICAL INFORMATICS ASSOCIATION
- The core regulation module of stress-responsive regulatory networks in yeast
- (2012) Dongsan Kim et al. NUCLEIC ACIDS RESEARCH
- Identifying protein interaction subnetworks by a bagging Markov random field-based method
- (2012) Li Chen et al. NUCLEIC ACIDS RESEARCH
- Regulatory Snapshots: Integrative Mining of Regulatory Modules from Expression Time Series and Regulatory Networks
- (2012) Joana P. Gonçalves et al. PLoS One
- Functional Annotation of Hierarchical Modularity
- (2012) Kanchana Padmanabhan et al. PLoS One
- A Gene Co-Expression Network in Whole Blood of Schizophrenia Patients Is Independent of Antipsychotic-Use and Enriched for Brain-Expressed Genes
- (2012) Simone de Jong et al. PLoS One
- Identifying Responsive Modules by Mathematical Programming: An Application to Budding Yeast Cell Cycle
- (2012) Zhenshu Wen et al. PLoS One
- Coexpression network analysis in chronic hepatitis B and C hepatic lesions reveals distinct patterns of disease progression to hepatocellular carcinoma
- (2012) Danning He et al. Journal of Molecular Cell Biology
- Posterior Association Networks and Functional Modules Inferred from Rich Phenotypes of Gene Perturbations
- (2012) Xin Wang et al. PLoS Computational Biology
- Network-Assisted Investigation of Combined Causal Signals from Genome-Wide Association Studies in Schizophrenia
- (2012) Peilin Jia et al. PLoS Computational Biology
- A systems genetic analysis of high density lipoprotein metabolism and network preservation across mouse models
- (2011) Peter Langfelder et al. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR AND CELL BIOLOGY OF LIPIDS
- Defining an informativeness metric for clustering gene expression data
- (2011) Jessica C. Mar et al. BIOINFORMATICS
- Modular analysis of the probabilistic genetic interaction network
- (2011) Lin Hou et al. BIOINFORMATICS
- A quantitative analysis of monochromaticity in genetic interaction networks
- (2011) Chien-Hsiang Hsu et al. BMC BIOINFORMATICS
- Efficient α, β-motif finder for identification of phenotype-related functional modules
- (2011) Matthew C Schmidt et al. BMC BIOINFORMATICS
- A novel method to identify cooperative functional modules: study of module coordination in the Saccharomyces cerevisiae cell cycle
- (2011) Jeh-Ting Hsu et al. BMC BIOINFORMATICS
- Assessing the functional coherence of modules found in multiple-evidence networks from Arabidopsis
- (2011) Artem Lysenko et al. BMC BIOINFORMATICS
- Identification of dysfunctional modules and disease genes in congenital heart disease by a network-based approach
- (2011) Danning He et al. BMC GENOMICS
- A systems biology model of the regulatory network in Populus leaves reveals interacting regulators and conserved regulation
- (2011) Nathaniel Street et al. BMC PLANT BIOLOGY
- DENSE: efficient and prior knowledge-driven discovery of phenotype-associated protein functional modules
- (2011) Willam Hendrix et al. BMC Systems Biology
- Biological interaction networks are conserved at the module level
- (2011) Guy E Zinman et al. BMC Systems Biology
- Biological network motif detection and evaluation
- (2011) Wooyoung Kim et al. BMC Systems Biology
- Network for Activation of Human Endothelial Cells by Oxidized Phospholipids
- (2011) Casey E. Romanoski et al. CIRCULATION RESEARCH
- ModuleSearch: finding functional modules in a protein–protein interaction network
- (2011) Guangyu Cui et al. COMPUTER METHODS IN BIOMECHANICS AND BIOMEDICAL ENGINEERING
- Identifying disease genes and module biomarkers by differential interactions
- (2011) Xiaoping Liu et al. JOURNAL OF THE AMERICAN MEDICAL INFORMATICS ASSOCIATION
- The emergence of modularity in biological systems
- (2011) Dirk M. Lorenz et al. Physics of Life Reviews
- Assessing the Biological Significance of Gene Expression Signatures and Co-Expression Modules by Studying Their Network Properties
- (2011) Pablo Minguez et al. PLoS One
- Is My Network Module Preserved and Reproducible?
- (2011) Peter Langfelder et al. PLoS Computational Biology
- A hub-attachment based method to detect functional modules from confidence-scored protein interactions and expression profiles
- (2010) Chia-Hao Chin et al. BMC BIOINFORMATICS
- svdPPCS: an effective singular value decomposition-based method for conserved and divergent co-expression gene module identification
- (2010) Wensheng Zhang et al. BMC BIOINFORMATICS
- Investigating the validity of current network analysis on static conglomerate networks by protein network stratification
- (2010) Minlu Zhang et al. BMC BIOINFORMATICS
- Recent advances in clustering methods for protein interaction networks
- (2010) Jianxin Wang et al. BMC GENOMICS
- Inferring modules from human protein interactome classes
- (2010) Elisabetta Marras et al. BMC Systems Biology
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- (2010) Zhiao Shi et al. BMC Systems Biology
- Toward the dynamic interactome: it's about time
- (2010) T. M. Przytycka et al. BRIEFINGS IN BIOINFORMATICS
- Gene Coexpression Network Topology of Cardiac Development, Hypertrophy, and Failure
- (2010) Frederick E. Dewey et al. Circulation-Cardiovascular Genetics
- Coexpression Analysis of Tomato Genes and Experimental Verification of Coordinated Expression of Genes Found in a Functionally Enriched Coexpression Module
- (2010) S. Ozaki et al. DNA RESEARCH
- Modularity measure of networks with overlapping communities
- (2010) A. Lázár et al. EPL
- Module Discovery by Exhaustive Search for Densely Connected, Co-Expressed Regions in Biomolecular Interaction Networks
- (2010) Recep Colak et al. PLoS One
- Protein Interaction Networks—More Than Mere Modules
- (2010) Stefan Pinkert et al. PLoS Computational Biology
- Pathway identification by network pruning in the metabolic network of Escherichia coli
- (2009) P. Gerlee et al. BIOINFORMATICS
- Enumeration of condition-dependent dense modules in protein interaction networks
- (2009) Elisabeth Georgii et al. BIOINFORMATICS
- Identifying functional modules using expression profiles and confidence-scored protein interactions
- (2009) Igor Ulitsky et al. BIOINFORMATICS
- Reverse engineering module networks by PSO-RNN hybrid modeling
- (2009) Yuji Zhang et al. BMC GENOMICS
- Identifying responsive functional modules from protein-protein interaction network
- (2009) Zikai Wu et al. MOLECULES AND CELLS
- Dynamic modularity in protein interaction networks predicts breast cancer outcome
- (2009) Ian W Taylor et al. NATURE BIOTECHNOLOGY
- Identifying functional modules in protein-protein interaction networks: an integrated exact approach
- (2008) M. T. Dittrich et al. BIOINFORMATICS
- WGCNA: an R package for weighted correlation network analysis
- (2008) Peter Langfelder et al. BMC BIOINFORMATICS
- Modifying the DPClus algorithm for identifying protein complexes based on new topological structures
- (2008) Min Li et al. BMC BIOINFORMATICS
- Gene module level analysis: identification to networks and dynamics
- (2008) Xuewei Wang et al. CURRENT OPINION IN BIOTECHNOLOGY
- GraphWeb: mining heterogeneous biological networks for gene modules with functional significance
- (2008) J. Reimand et al. NUCLEIC ACIDS RESEARCH
- Identifying network communities with a high resolution
- (2008) Jianhua Ruan et al. PHYSICAL REVIEW E
- Human Gene Coexpression Landscape: Confident Network Derived from Tissue Transcriptomic Profiles
- (2008) Carlos Prieto et al. PLoS One
- Using Dynamic Gene Module Map Analysis To Identify Targets That Modulate Free Fatty Acid Induced Cytotoxicity
- (2007) Z. Li et al. BIOTECHNOLOGY PROGRESS
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