Beyond modules and hubs: the potential of gene coexpression networks for investigating molecular mechanisms of complex brain disorders

Integrative Analysis of Many Weighted Co-Expression Networks Using Tensor Computation

(2014) Wenyuan Li et al.   PLoS Computational Biology

Spatial and Temporal Mapping of De Novo Mutations in Schizophrenia to a Fetal Prefrontal Cortical Network

(2013) Suleyman Gulsuner et al.   CELL

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

(2013) Bin Zhang et al.   CELL

Biological substrates underpinning diagnosis of major depression

(2013) Etienne Sibille et al.   INTERNATIONAL JOURNAL OF NEUROPSYCHOPHARMACOLOGY

Network models of genome-wide association studies uncover the topological centrality of protein interactions in complex diseases

(2013) Younghee Lee et al.   JOURNAL OF THE AMERICAN MEDICAL INFORMATICS ASSOCIATION

Characterization of drug-induced transcriptional modules: towards drug repositioning and functional understanding

(2013) M. Iskar et al.   Molecular Systems Biology

The Genotype-Tissue Expression (GTEx) project

(2013) John Lonsdale et al.   NATURE GENETICS

Identification of transcriptional regulators in the mouse immune system

(2013) Vladimir Jojic et al.   NATURE IMMUNOLOGY

Gene-pair expression signatures reveal lineage control

(2013) Merja Heinäniemi et al.   NATURE METHODS

Interplay of microRNAs, transcription factors and target genes: linking dynamic expression changes to function

(2013) Petr V. Nazarov et al.   NUCLEIC ACIDS RESEARCH

Structure and dynamics of molecular networks: A novel paradigm of drug discovery

(2013) Peter Csermely et al.   PHARMACOLOGY & THERAPEUTICS

The 3D Organization of the Yeast Genome Correlates with Co-Expression and Reflects Functional Relations between Genes

(2013) Dirar Homouz et al.   PLoS One

When Is Hub Gene Selection Better than Standard Meta-Analysis?

(2013) Peter Langfelder et al.   PLoS One

Genes and pathways underlying regional and cell type changes in Alzheimer's disease

(2013) Jeremy A Miller et al.   Genome Medicine

Dissection of Regulatory Networks that Are Altered in Disease via Differential Co-expression

(2013) David Amar et al.   PLoS Computational Biology

Co-expression Profiling of Autism Genes in the Mouse Brain

(2013) Idan Menashe et al.   PLoS Computational Biology

DNA Methylation Signatures in Development and Aging of the Human Prefrontal Cortex

(2012) Shusuke Numata et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Combing the hairball with BioFabric: a new approach for visualization of large networks

(2012) William JR Longabaugh   BMC BIOINFORMATICS

A systematic comparison of genome-scale clustering algorithms

(2012) Jeremy J Jay et al.   BMC BIOINFORMATICS

Comparison of co-expression measures: mutual information, correlation, and model based indices

(2012) Lin Song et al.   BMC BIOINFORMATICS

Beyond differential expression: the quest for causal mutations and effector molecules

(2012) Nicholas J Hudson et al.   BMC GENOMICS

Identification of microRNA-regulated gene networks by expression analysis of target genes

(2012) Vincenzo Alessandro Gennarino et al.   GENOME RESEARCH

Gene Coexpression Networks in Human Brain Identify Epigenetic Modifications in Alcohol Dependence

(2012) I. Ponomarev et al.   JOURNAL OF NEUROSCIENCE

Studying the differential co-expression of microRNAs reveals significant role of white matter in early Alzheimer's progression

(2012) Malay Bhattacharyya et al.   Molecular BioSystems

An anatomically comprehensive atlas of the adult human brain transcriptome

(2012) Michael J. Hawrylycz et al.   NATURE

Architecture of the human regulatory network derived from ENCODE data

(2012) Mark B. Gerstein et al.   NATURE

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

Molecular signaling network complexity is correlated with cancer patient survivability

(2012) D. Breitkreutz et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Attractor Landscape Analysis Reveals Feedback Loops in the p53 Network That Control the Cellular Response to DNA Damage

(2012) M. Choi et al.   Science Signaling

Alternative α-synuclein transcript usage as a convergent mechanism in Parkinson's disease pathology

(2012) Herve Rhinn et al.   Nature Communications

“Guilt by Association” Is the Exception Rather Than the Rule in Gene Networks

(2012) Jesse Gillis et al.   PLoS Computational Biology

Aging effects on DNA methylation modules in human brain and blood tissue

(2012) Steve Horvath et al.   GENOME BIOLOGY

Integrated analysis of mutations, miRNA and mRNA expression in glioblastoma

(2011) Hua Dong et al.   BMC Systems Biology

Hive plots--rational approach to visualizing networks

(2011) M. Krzywinski et al.   BRIEFINGS IN BIOINFORMATICS

Interactome Networks and Human Disease

(2011) Marc Vidal et al.   CELL

A SURVEY OF CLUSTERING ENSEMBLE ALGORITHMS

(2011) SANDRO VEGA-PONS et al.   INTERNATIONAL JOURNAL OF PATTERN RECOGNITION AND ARTIFICIAL INTELLIGENCE

Large scale microarray profiling and coexpression network analysis of CHO cells identifies transcriptional modules associated with growth and productivity

(2011) Colin Clarke et al.   JOURNAL OF BIOTECHNOLOGY

Major depressive disorder: new clinical, neurobiological, and treatment perspectives

(2011) David J Kupfer et al.   LANCET

Modeling the functional genomics of autism using human neurons

(2011) G Konopka et al.   MOLECULAR PSYCHIATRY

Spatio-temporal transcriptome of the human brain

(2011) Hyo Jung Kang et al.   NATURE

Transcriptomic analysis of autistic brain reveals convergent molecular pathology

(2011) Irina Voineagu et al.   NATURE

Integrated genomic analyses of ovarian carcinoma

(2011) D. Bell et al.   NATURE

Is My Network Module Preserved and Reproducible?

(2011) Peter Langfelder et al.   PLoS Computational Biology

Variance of Gene Expression Identifies Altered Network Constraints in Neurological Disease

(2011) Jessica C. Mar et al.   PLoS Genetics

Is human blood a good surrogate for brain tissue in transcriptional studies?

(2010) Chaochao Cai et al.   BMC GENOMICS

Toward the dynamic interactome: it's about time

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

Coexpression Network Analysis Identifies Transcriptional Modules Related to Proastrocytic Differentiation and Sprouty Signaling in Glioma

(2010) A. E. Ivliev et al.   CANCER RESEARCH

Coexpression network analysis of neural tissue reveals perturbations in developmental processes in schizophrenia

(2010) A. Torkamani et al.   GENOME RESEARCH

Meta-analysis of lineage-specific gene expression signatures in mouse leukocyte populations

(2010) Neil A. Mabbott et al.   IMMUNOBIOLOGY

Altered Gene Synchrony Suggests a Combined Hormone-Mediated Dysregulated State in Major Depression

(2010) Chris Gaiteri et al.   PLoS One

From ‘differential expression’ to ‘differential networking’ – identification of dysfunctional regulatory networks in diseases

(2010) Alberto de la Fuente   TRENDS IN GENETICS

Relationship between gene co-expression and sharing of transcription factor binding sites in Drosophila melanogaster

(2009) A. Marco et al.   BIOINFORMATICS

Analyzing miRNA co-expression networks to explore TF-miRNA regulation

(2009) Sanghamitra Bandyopadhyay et al.   BMC BIOINFORMATICS

Genomic analysis reveals a tight link between transcription factor dynamics and regulatory network architecture

(2009) Raja Jothi et al.   Molecular Systems Biology

Line graphs, link partitions, and overlapping communities

(2009) T. S. Evans et al.   PHYSICAL REVIEW E

Community detection in graphs

(2009) Santo Fortunato   PHYSICS REPORTS-REVIEW SECTION OF PHYSICS LETTERS

Network Properties of Complex Human Disease Genes Identified through Genome-Wide Association Studies

(2009) Fredrik Barrenas et al.   PLoS One

Localized network centrality and essentiality in the yeast–protein interaction network

(2009) Keunwan Park et al.   PROTEOMICS

Comprehensive Mapping of Long-Range Interactions Reveals Folding Principles of the Human Genome

(2009) E. Lieberman-Aiden et al.   SCIENCE

A Differential Wiring Analysis of Expression Data Correctly Identifies the Gene Containing the Causal Mutation

(2009) Nicholas J. Hudson et al.   PLoS Computational Biology

Aging Mice Show a Decreasing Correlation of Gene Expression within Genetic Modules

(2009) Lucinda K. Southworth et al.   PLoS Genetics

Multi-tissue coexpression networks reveal unexpected subnetworks associated with disease

(2009) Radu Dobrin et al.   GENOME BIOLOGY

Differential variability analysis of gene expression and its application to human diseases

(2008) J. W.K. Ho et al.   BIOINFORMATICS

WGCNA: an R package for weighted correlation network analysis

(2008) Peter Langfelder et al.   BMC BIOINFORMATICS

A comparative study of different machine learning methods on microarray gene expression data

(2008) Mehdi Pirooznia et al.   BMC GENOMICS

Insights into the Organization of Biochemical Regulatory Networks Using Graph Theory Analyses

(2008) Avi Ma'ayan   JOURNAL OF BIOLOGICAL CHEMISTRY

A Systems Level Analysis of Transcriptional Changes in Alzheimer's Disease and Normal Aging

(2008) J. A. Miller et al.   JOURNAL OF NEUROSCIENCE

The liver pharmacological and xenobiotic gene response repertoire

(2008) Georges Natsoulis et al.   Molecular Systems Biology

Ripples from neighbouring transcription

(2008) Miki Ebisuya et al.   NATURE CELL BIOLOGY

Network pharmacology: the next paradigm in drug discovery

(2008) Andrew L Hopkins   Nature Chemical Biology

Functional organization of the transcriptome in human brain

(2008) Michael C Oldham et al.   NATURE NEUROSCIENCE

Major Depressive Disorder

(2008) R.H. Belmaker et al.   NEW ENGLAND JOURNAL OF MEDICINE

Network properties of genes harboring inherited disease mutations

(2008) I. Feldman et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A survey of visualization tools for biological network analysis

(2008) Georgios A Pavlopoulos et al.   BioData Mining

Variations in the transcriptome of Alzheimer's disease reveal molecular networks involved in cardiovascular diseases

(2008) Monika Ray et al.   GENOME BIOLOGY