How data analysis affects power, reproducibility and biological insight of RNA-seq studies in complex datasets

Memory acquisition and retrieval impact different epigenetic processes that regulate gene expression

(2015) Lucia L Peixoto et al.   BMC GENOMICS

Blocking miRNA Biogenesis in Adult Forebrain Neurons Enhances Seizure Susceptibility, Fear Memory, and Food Intake by Increasing Neuronal Responsiveness

(2015) Anna Fiorenza et al.   CEREBRAL CORTEX

Conserved epigenomic signals in mice and humans reveal immune basis of Alzheimer’s disease

(2015) Elizabeta Gjoneska et al.   NATURE

HTSeq--a Python framework to work with high-throughput sequencing data

(2014) S. Anders et al.   BIOINFORMATICS

K‐Lysine acetyltransferase 2a regulates a hippocampal gene expression network linked to memory formation

(2014) Roman M Stilling et al.   EMBO JOURNAL

Histone H2A.Z subunit exchange controls consolidation of recent and remote memory

(2014) Iva B. Zovkic et al.   NATURE

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

(2014) Davide Risso et al.   NATURE BIOTECHNOLOGY

Modulation of learning and memory by cytokines: Signaling mechanisms and long term consequences

(2014) Elissa J. Donzis et al.   NEUROBIOLOGY OF LEARNING AND MEMORY

svaseq: removing batch effects and other unwanted noise from sequencing data

(2014) Jeffrey T. Leek   NUCLEIC ACIDS 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

Functionally diverse dendritic mRNAs rapidly associate with ribosomes following a novel experience

(2014) Joshua A. Ainsley et al.   Nature Communications

Reproducibility of high-throughput mRNA and small RNA sequencing across laboratories

(2013) Peter A C 't Hoen et al.   NATURE BIOTECHNOLOGY

The neuron-specific chromatin regulatory subunit BAF53b is necessary for synaptic plasticity and memory

(2013) Annie Vogel-Ciernia et al.   NATURE NEUROSCIENCE

Count-based differential expression analysis of RNA sequencing data using R and Bioconductor

(2013) Simon Anders et al.   Nature Protocols

NF-κB p50 subunit knockout impairs late LTP and alters long term memory in the mouse hippocampus

(2012) Kensuke Oikawa et al.   BMC NEUROSCIENCE

A comprehensive evaluation of normalization methods for Illumina high-throughput RNA sequencing data analysis

(2012) M.-A. Dillies et al.   BRIEFINGS IN BIOINFORMATICS

NR4A nuclear receptors support memory enhancement by histone deacetylase inhibitors

(2012) Joshua D. Hawk et al.   JOURNAL OF CLINICAL INVESTIGATION

The JAK/STAT Pathway Is Involved in Synaptic Plasticity

(2012) Céline S. Nicolas et al.   NEURON

Using control genes to correct for unwanted variation in microarray data

(2011) J. A. Gagnon-Bartsch et al.   BIOSTATISTICS

GC-Content Normalization for RNA-Seq Data

(2011) Davide Risso et al.   BMC BIOINFORMATICS

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

(2010) James H Bullard et al.   BMC BIOINFORMATICS

Quantitatively and qualitatively different cellular processes are engaged in CA1 during the consolidation and reconsolidation of contextual fear memory

(2010) Philip Barnes et al.   HIPPOCAMPUS

CREB: a multifaceted regulator of neuronal plasticity and protection

(2010) Kensuke Sakamoto et al.   JOURNAL OF NEUROCHEMISTRY

Tackling the widespread and critical impact of batch effects in high-throughput data

(2010) Jeffrey T. Leek et al.   NATURE REVIEWS GENETICS

A Bayesian Framework to Account for Complex Non-Genetic Factors in Gene Expression Levels Greatly Increases Power in eQTL Studies

(2010) Oliver Stegle et al.   PLoS Computational Biology

A scaling normalization method for differential expression analysis of RNA-seq data

(2010) Mark D Robinson et al.   GENOME BIOLOGY

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

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

Mapping and quantifying mammalian transcriptomes by RNA-Seq

(2008) Ali Mortazavi et al.   NATURE METHODS