Discovering Condition-Specific Gene Co-Expression Patterns Using Gaussian Mixture Models: A Cancer Case Study

lnCaNet: pan-cancer co-expression network for human lncRNA and cancer genes

(2016) Yining Liu et al.   BIOINFORMATICS

Large-scale gene co-expression network as a source of functional annotation for cattle genes

(2016) Hamid Beiki et al.   BMC GENOMICS

petal: Co-expression network modelling in R

(2016) Juli Petereit et al.   BMC Systems Biology

InterPro in 2017—beyond protein family and domain annotations

(2016) Robert D. Finn et al.   NUCLEIC ACIDS RESEARCH

Co-expression analysis of high-throughput transcriptome sequencing data with Poisson mixture models

(2015) Andrea Rau et al.   BIOINFORMATICS

Systematic noise degrades gene co-expression signals but can be corrected

(2015) Saskia Freytag et al.   BMC BIOINFORMATICS

Pegasus, a workflow management system for science automation

(2015) Ewa Deelman et al.   Future Generation Computer Systems-The International Journal of eScience

The Reactome pathway Knowledgebase

(2015) Antonio Fabregat et al.   NUCLEIC ACIDS RESEARCH

The Pfam protein families database: towards a more sustainable future

(2015) Robert D. Finn et al.   NUCLEIC ACIDS RESEARCH

Normalization of RNA-seq data using factor analysis of control genes or samples

(2014) Davide Risso et al.   NATURE BIOTECHNOLOGY

OMIM.org: Online Mendelian Inheritance in Man (OMIM®), an online catalog of human genes and genetic disorders

(2014) Joanna S. Amberger et al.   NUCLEIC ACIDS RESEARCH

ArrayExpress update—simplifying data submissions

(2014) Nikolay Kolesnikov et al.   NUCLEIC ACIDS RESEARCH

A combination of gene expression ranking and co-expression network analysis increases discovery rate in large-scale mutant screens for novelArabidopsis thalianaabiotic stress genes

(2014) Vanessa Ransbotyn et al.   PLANT BIOTECHNOLOGY JOURNAL

Systematic tracking of dysregulated modules identifies novel genes in cancer

(2013) Sriganesh Srihari et al.   BIOINFORMATICS

Maximizing capture of gene co-expression relationships through pre-clustering of input expression samples: an Arabidopsis case study

(2013) F Feltus et al.   BMC Systems Biology

Correlating transcriptional networks to breast cancer survival: a large-scale coexpression analysis

(2013) Colin Clarke et al.   CARCINOGENESIS

Integration of Cancer Gene Co-expression Network and Metabolic Network To Uncover Potential Cancer Drug Targets

(2013) Jingqi Chen et al.   JOURNAL OF PROTEOME RESEARCH

Systems genetics approaches to understand complex traits

(2013) Mete Civelek et al.   NATURE REVIEWS GENETICS

Correction: Proteomic Identification of Mitochondrial Targets of Arginase in Human Breast Cancer

(2013) Rajan Singh et al.   PLoS One

linkcomm: an R package for the generation, visualization, and analysis of link communities in networks of arbitrary size and type

(2011) Alex T. Kalinka et al.   BIOINFORMATICS

Sequencing of a QTL-rich region of the Theobroma cacao genome using pooled BACs and the identification of trait specific candidate genes

(2011) Frank A Feltus et al.   BMC GENOMICS

Impact of gene expression noise on organismal fitness and the efficacy of natural selection

(2011) Z. Wang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Evaluation of statistical methods for normalization and differential expression in mRNA-Seq experiments

(2010) James H Bullard et al.   BMC BIOINFORMATICS

Identification of a gene module associated with BMD through the integration of network analysis and genome-wide association data

(2010) Charles R Farber   JOURNAL OF BONE AND MINERAL RESEARCH

Link communities reveal multiscale complexity in networks

(2010) Yong-Yeol Ahn et al.   NATURE

Rational association of genes with traits using a genome-scale gene network for Arabidopsis thaliana

(2010) Insuk Lee et al.   NATURE BIOTECHNOLOGY

Genomewide Association Studies and Assessment of the Risk of Disease

(2010) Teri A. Manolio   NEW ENGLAND JOURNAL OF MEDICINE

NCBI GEO: archive for functional genomics data sets--10 years on

(2010) T. Barrett et al.   NUCLEIC ACIDS RESEARCH

The Association of Multiple Interacting Genes with Specific Phenotypes in Rice Using Gene Coexpression Networks

(2010) Stephen P. Ficklin et al.   PLANT PHYSIOLOGY

Methods for merging Gaussian mixture components

(2010) Christian Hennig   Advances in Data Analysis and Classification

Differential expression analysis for sequence count data

(2010) Simon Anders et al.   GENOME BIOLOGY

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

(2009) Da Wei Huang et al.   Nature Protocols

Systems genetics analysis of cancer susceptibility: from mouse models to humans

(2009) David Quigley et al.   NATURE REVIEWS GENETICS

The genetics of quantitative traits: challenges and prospects

(2009) Trudy F. C. Mackay et al.   NATURE REVIEWS GENETICS

Combining partial correlation and an information theory approach to the reversed engineering of gene co-expression networks

(2008) Antonio Reverter et al.   BIOINFORMATICS

WGCNA: an R package for weighted correlation network analysis

(2008) Peter Langfelder et al.   BMC BIOINFORMATICS

Genome-wide association studies for complex traits: consensus, uncertainty and challenges

(2008) Mark I. McCarthy et al.   NATURE REVIEWS GENETICS