Multi-tissue Analysis of Co-expression Networks by Higher-Order Generalized Singular Value Decomposition Identifies Functionally Coherent Transcriptional Modules

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

(2014) Wenyuan Li et al.   PLoS Computational Biology

Proteotoxicity and Cardiac Dysfunction — Alzheimer's Disease of the Heart?

(2013) Monte S. Willis et al.   NEW ENGLAND JOURNAL OF MEDICINE

A systemic transcriptome analysis reveals the regulation of neural stem cell maintenance by an E2F1–miRNA feedback loop

(2013) Thomas Palm et al.   NUCLEIC ACIDS RESEARCH

CTen: a web-based platform for identifying enriched cell types from heterogeneous microarray data

(2012) Jason E Shoemaker et al.   BMC GENOMICS

Extension of cortical synaptic development distinguishes humans from chimpanzees and macaques

(2012) X. Liu et al.   GENOME RESEARCH

Association of Stat3 with HSF1 plays a critical role in G-CSF-induced cardio-protection against ischemia/reperfusion injury

(2012) Hong Ma et al.   JOURNAL OF MOLECULAR AND CELLULAR CARDIOLOGY

GSVD Comparison of Patient-Matched Normal and Tumor aCGH Profiles Reveals Global Copy-Number Alterations Predicting Glioblastoma Multiforme Survival

(2012) Cheng H. Lee et al.   PLoS One

Transcriptomes of germinal zones of human and mouse fetal neocortex suggest a role of extracellular matrix in progenitor self-renewal

(2012) S. A. Fietz et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Chapter 5: Network Biology Approach to Complex Diseases

(2012) Dong-Yeon Cho et al.   PLoS Computational Biology

Coexpression Network Analysis in Abdominal and Gluteal Adipose Tissue Reveals Regulatory Genetic Loci for Metabolic Syndrome and Related Phenotypes

(2012) Josine L. Min et al.   PLoS Genetics

A multiple network learning approach to capture system-wide condition-specific responses

(2011) S. Roy et al.   BIOINFORMATICS

Exploring metabolic pathway disruption in the subchronic phencyclidine model of schizophrenia with the Generalized Singular Value Decomposition

(2011) Xiaolin Xiao et al.   BMC Systems Biology

The transcription factors AP-2β and AP-2α are required for survival of sympathetic progenitors and differentiated sympathetic neurons

(2011) Mirko Schmidt et al.   DEVELOPMENTAL BIOLOGY

A Higher-Order Generalized Singular Value Decomposition for Comparison of Global mRNA Expression from Multiple Organisms

(2011) Sri Priya Ponnapalli et al.   PLoS One

Proteins Encoded in Genomic Regions Associated with Immune-Mediated Disease Physically Interact and Suggest Underlying Biology

(2011) Elizabeth J. Rossin et al.   PLoS Genetics

Cross-species common regulatory network inference without requirement for prior gene affiliation

(2010) Amin Moghaddas Gholami et al.   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

DiffCoEx: a simple and sensitive method to find differentially coexpressed gene modules

(2010) Bruno M Tesson et al.   BMC BIOINFORMATICS

Nonresolving Inflammation

(2010) Carl Nathan et al.   CELL

Molecular basis of hereditary cardiomyopathy: abnormalities in calcium sensitivity, stretch response, stress response and beyond

(2010) Akinori Kimura   JOURNAL OF HUMAN GENETICS

A trans-acting locus regulates an anti-viral expression network and type 1 diabetes risk

(2010) Matthias Heinig et al.   NATURE

Network medicine: a network-based approach to human disease

(2010) Albert-László Barabási et al.   NATURE REVIEWS GENETICS

Multi-dimensional correlations for gene coexpression and application to the large-scale data of Arabidopsis

(2009) Kengo Kinoshita et al.   BIOINFORMATICS

Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources

(2009) Da Wei Huang et al.   Nature Protocols

A network view of disease and compound screening

(2009) Eric E. Schadt et al.   NATURE REVIEWS DRUG DISCOVERY

PASTAA: identifying transcription factors associated with sets of co-regulated genes

(2008) Helge G. Roider et al.   BIOINFORMATICS

fdrtool: a versatile R package for estimating local and tail area-based false discovery rates

(2008) K. Strimmer   BIOINFORMATICS

minet: A R/Bioconductor Package for Inferring Large Transcriptional Networks Using Mutual Information

(2008) Patrick E Meyer et al.   BMC BIOINFORMATICS

WGCNA: an R package for weighted correlation network analysis

(2008) Peter Langfelder et al.   BMC BIOINFORMATICS

Multidimensional partitioning and bi-partitioning: analysis and application to gene expression data sets

(2008) Gabriela Kalna et al.   INTERNATIONAL JOURNAL OF COMPUTER MATHEMATICS

Variations in DNA elucidate molecular networks that cause disease

(2008) Yanqing Chen et al.   NATURE

Identification of renal Cd36 as a determinant of blood pressure and risk for hypertension

(2008) Michal Pravenec et al.   NATURE GENETICS

Integrated genomic approaches implicate osteoglycin (Ogn) in the regulation of left ventricular mass

(2008) Enrico Petretto et al.   NATURE GENETICS

Mapping the Genetic Architecture of Gene Expression in Human Liver

(2008) Eric E Schadt et al.   PLOS BIOLOGY

Spectral clustering with eigenvector selection

(2007) Tao Xiang et al.   PATTERN RECOGNITION