Cosplicing network analysis of mammalian brain RNA-Seq data utilizing WGCNA and Mantel correlations

Transcriptome-wide Landscape of Pre-mRNA Alternative Splicing Associated with Metastatic Colonization

(2014) Zhi-xiang Lu et al.   MOLECULAR CANCER RESEARCH

De-regulation of gene expression and alternative splicing affects distinct cellular pathways in the aging hippocampus

(2014) Roman M. Stilling et al.   Frontiers in Cellular Neuroscience

Selection for Drinking in the Dark Alters Brain Gene Coexpression Networks

(2013) Ovidiu D. Iancu et al.   ALCOHOLISM-CLINICAL AND EXPERIMENTAL RESEARCH

SplicingCompass: differential splicing detection using RNA-Seq data

(2013) Moritz Aschoff et al.   BIOINFORMATICS

Comparative study of RNA-seq- and Microarray-derived coexpression networks in Arabidopsis thaliana

(2013) Federico M. Giorgi et al.   BIOINFORMATICS

Topoisomerases facilitate transcription of long genes linked to autism

(2013) Ian F. King et al.   NATURE

Differential Network Analysis Reveals Genetic Effects on Catalepsy Modules

(2013) Ovidiu D. Iancu et al.   PLoS One

Utilizing RNA-Seq data for de novo coexpression network inference

(2012) Ovidiu D. Iancu et al.   BIOINFORMATICS

A systematic comparison of genome-scale clustering algorithms

(2012) Jeremy J Jay et al.   BMC BIOINFORMATICS

Integrating many co-splicing networks to reconstruct splicing regulatory modules

(2012) Chao Dai et al.   BMC Systems Biology

Function of alternative splicing

(2012) Olga Kelemen et al.   GENE

Genes, behavior and next-generation RNA sequencing

(2012) R. Hitzemann et al.   GENES BRAIN AND BEHAVIOR

Topological domains in mammalian genomes identified by analysis of chromatin interactions

(2012) Jesse R. Dixon et al.   NATURE

Human-Specific Transcriptional Networks in the Brain

(2012) Genevieve Konopka et al.   NEURON

The BioGRID interaction database: 2013 update

(2012) Andrew Chatr-aryamontri et al.   NUCLEIC ACIDS RESEARCH

Comparing Statistical Methods for Constructing Large Scale Gene Networks

(2012) Jeffrey D. Allen et al.   PLoS One

Differential GC Content between Exons and Introns Establishes Distinct Strategies of Splice-Site Recognition

(2012) Maayan Amit et al.   Cell Reports

Statistical Properties of Multivariate Distance Matrix Regression for High-Dimensional Data Analysis

(2012) Matthew A. Zapala et al.   Frontiers in Genetics

Gene networks and haloperidol-induced catalepsy

(2011) O. D. Iancu et al.   GENES BRAIN AND BEHAVIOR

Computational methods for transcriptome annotation and quantification using RNA-seq

(2011) Manuel Garber et al.   NATURE METHODS

Evaluating Gene Expression in C57BL/6J and DBA/2J Mouse Striatum Using RNA-Seq and Microarrays

(2011) Daniel Bottomly et al.   PLoS One

Substance-specific and shared transcription and epigenetic changes in the human hippocampus chronically exposed to cocaine and alcohol

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

Is My Network Module Preserved and Reproducible?

(2011) Peter Langfelder et al.   PLoS Computational Biology

Genetic diversity and striatal gene networks: focus on the heterogeneous stock-collaborative cross (HS-CC) mouse

(2010) Ovidiu D Iancu et al.   BMC GENOMICS

An Alternative Splicing Network Links Cell-Cycle Control to Apoptosis

(2010) Michael J. Moore et al.   CELL

An ESRP-regulated splicing programme is abrogated during the epithelial–mesenchymal transition

(2010) Claude C Warzecha et al.   EMBO JOURNAL

Mammalian microRNAs predominantly act to decrease target mRNA levels

(2010) Huili Guo et al.   NATURE

SFmap: a web server for motif analysis and prediction of splicing factor binding sites

(2010) I. Paz et al.   NUCLEIC ACIDS RESEARCH

Global regulation of alternative splicing during myogenic differentiation

(2010) Christopher S. Bland et al.   NUCLEIC ACIDS RESEARCH

edgeR: a Bioconductor package for differential expression analysis of digital gene expression data

(2009) M. D. Robinson et al.   BIOINFORMATICS

Alternative pre-mRNA splicing switches modulate gene expression in late erythropoiesis

(2009) M. L. Yamamoto et al.   BLOOD

Mapping identifiers for the integration of genomic datasets with the R/Bioconductor package biomaRt

(2009) Steffen Durinck et al.   Nature Protocols

Functional and Evolutionary Insights into Human Brain Development through Global Transcriptome Analysis

(2009) Matthew B. Johnson et al.   NEURON

A computational approach for genome-wide mapping of splicing factor binding sites

(2009) Martin Akerman et al.   GENOME BIOLOGY

Global analysis of alternative splicing regulation by insulin and wingless signaling in Drosophila cells

(2009) Britta Hartmann et al.   GENOME BIOLOGY

Studying alternative splicing regulatory networks through partial correlation analysis

(2009) Liang Chen et al.   GENOME BIOLOGY

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome

(2009) Ben Langmead et al.   GENOME BIOLOGY

WGCNA: an R package for weighted correlation network analysis

(2008) Peter Langfelder et al.   BMC BIOINFORMATICS

A Transcriptome Database for Astrocytes, Neurons, and Oligodendrocytes: A New Resource for Understanding Brain Development and Function

(2008) J. D. Cahoy et al.   JOURNAL OF NEUROSCIENCE

Alternative isoform regulation in human tissue transcriptomes

(2008) Eric T. Wang et al.   NATURE

Deep surveying of alternative splicing complexity in the human transcriptome by high-throughput sequencing

(2008) Qun Pan et al.   NATURE GENETICS