A Comparison of RNA-Seq and Exon Arrays for Whole Genome Transcription Profiling of the L5 Spinal Nerve Transection Model of Neuropathic Pain in the Rat

Maize Gene Atlas Developed by RNA Sequencing and Comparative Evaluation of Transcriptomes Based on RNA Sequencing and Microarrays

(2014) Rajandeep S. Sekhon et al.   PLoS One

A comparison of methods for differential expression analysis of RNA-seq data

(2013) Charlotte Soneson et al.   BMC BIOINFORMATICS

Integration of Genome-wide Approaches Identifies lncRNAs of Adult Neural Stem Cells and Their Progeny In Vivo

(2013) Alexander D. Ramos et al.   Cell Stem Cell

Long Noncoding RNAs: Past, Present, and Future

(2013) J. T. Y. Kung et al.   GENETICS

Peripheral Nerve Injury is Accompanied by Chronic Transcriptome-Wide Changes in the Mouse Prefrontal Cortex

(2013) Sebastian Alvarado et al.   Molecular Pain

A long noncoding RNA contributes to neuropathic pain by silencing Kcna2 in primary afferent neurons

(2013) Xiuli Zhao et al.   NATURE NEUROSCIENCE

PainNetworks: A web-based resource for the visualisation of pain-related genes in the context of their network associations

(2013) James R. Perkins et al.   PAIN

Comparative RNA-Seq and Microarray Analysis of Gene Expression Changes in B-Cell Lymphomas of Canis familiaris

(2013) Marie Mooney et al.   PLoS One

Accuracy of RNA-Seq and its dependence on sequencing depth

(2012) Guoshuai Cai et al.   BMC BIOINFORMATICS

RNA-seq and microarray complement each other in transcriptome profiling

(2012) Sunitha Kogenaru et al.   BMC GENOMICS

RNA-Seq and human complex diseases: recent accomplishments and future perspectives

(2012) Valerio Costa et al.   EUROPEAN JOURNAL OF HUMAN GENETICS

Detecting differential usage of exons from RNA-seq data

(2012) S. Anders et al.   GENOME RESEARCH

Sensory Neuron Downregulation of the Kv9.1 Potassium Channel Subunit Mediates Neuropathic Pain following Nerve Injury

(2012) C. Tsantoulas et al.   JOURNAL OF NEUROSCIENCE

Landscape of transcription in human cells

(2012) Sarah Djebali et al.   NATURE

An integrated encyclopedia of DNA elements in the human genome

(2012)   NATURE

Genetically determined P2X7 receptor pore formation regulates variability in chronic pain sensitivity

(2012) Robert E Sorge et al.   NATURE MEDICINE

RNA-Seq vs Dual- and Single-Channel Microarray Data: Sensitivity Analysis for Differential Expression and Clustering

(2012) Alina Sîrbu et al.   PLoS One

Systems biology approaches to finding novel pain mediators

(2012) Ana Antunes-Martins et al.   Wiley Interdisciplinary Reviews-Systems Biology and Medicine

Microarrays, deep sequencing and the true measure of the transcriptome

(2011) John H Malone et al.   BMC BIOLOGY

Comparing Next-Generation Sequencing and Microarray Technologies in a Toxicological Study of the Effects of Aristolochic Acid on Rat Kidneys

(2011) Zhenqiang Su et al.   CHEMICAL RESEARCH IN TOXICOLOGY

RNA-sequence analysis of human B-cells

(2011) J. M. Toung et al.   GENOME RESEARCH

Differential expression in RNA-seq: A matter of depth

(2011) S. Tarazona et al.   GENOME RESEARCH

Following nerve injury neuregulin-1 drives microglial proliferation and neuropathic pain via the MEK/ERK pathway

(2011) Margarita Calvo et al.   GLIA

MicroRNA modulation in complex regional pain syndrome

(2011) Irina A Orlova et al.   Journal of Translational Medicine

Sequencing technology does not eliminate biological variability

(2011) Kasper D Hansen et al.   NATURE BIOTECHNOLOGY

A Transcriptomic Atlas of Mouse Neocortical Layers

(2011) T. Grant Belgard et al.   NEURON

Ensembl 2012

(2011) P. Flicek et al.   NUCLEIC ACIDS RESEARCH

Patterns of pain: Meta-analysis of microarray studies of pain

(2011) Michael L. LaCroix-Fralish et al.   PAIN

Dynamic Changes in the MicroRNA Expression Profile Reveal Multiple Regulatory Mechanisms in the Spinal Nerve Ligation Model of Neuropathic Pain

(2011) David von Schack et al.   PLoS One

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

(2011) Daniel Bottomly et al.   PLoS One

Profile of MicroRNAs following Rat Sciatic Nerve Injury by Deep Sequencing: Implication for Mechanisms of Nerve Regeneration

(2011) Bin Yu et al.   PLoS One

From RNA-seq reads to differential expression results

(2011) Alicia Oshlack et al.   GENOME BIOLOGY

A framework for oligonucleotide microarray preprocessing

(2010) Benilton S. Carvalho et al.   BIOINFORMATICS

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

(2010) James H Bullard et al.   BMC BIOINFORMATICS

A comparison of massively parallel nucleotide sequencing with oligonucleotide microarrays for global transcription profiling

(2010) James R Bradford et al.   BMC GENOMICS

Multiple chronic pain states are associated with a common amino acid–changing allele in KCNS1

(2010) Michael Costigan et al.   BRAIN

mRNA-seq with agnostic splice site discovery for nervous system transcriptomics tested in chronic pain

(2010) P. Hammer et al.   GENOME RESEARCH

Transcribed dark matter: meaning or myth?

(2010) C. P. Ponting et al.   HUMAN MOLECULAR GENETICS

Neuregulin-ErbB Signaling Promotes Microglial Proliferation and Chemotaxis Contributing to Microgliosis and Pain after Peripheral Nerve Injury

(2010) M. Calvo et al.   JOURNAL OF NEUROSCIENCE

Small RNAs Control Sodium Channel Expression, Nociceptor Excitability, and Pain Thresholds

(2010) J. Zhao et al.   JOURNAL OF NEUROSCIENCE

Alternative expression analysis by RNA sequencing

(2010) Malachi Griffith et al.   NATURE METHODS

Into the unknown: expression profiling without genome sequence information in CHO by next generation sequencing

(2010) Fabian Birzele et al.   NUCLEIC ACIDS RESEARCH

Differential expression analysis for sequence count data

(2010) Simon Anders et al.   GENOME BIOLOGY

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

A close examination of double filtering with fold change and t test in microarray analysis

(2009) Song Zhang et al.   BMC BIOINFORMATICS

Estimating accuracy of RNA-Seq and microarrays with proteomics

(2009) Xing Fu et al.   BMC GENOMICS

T-Cell Infiltration and Signaling in the Adult Dorsal Spinal Cord Is a Major Contributor to Neuropathic Pain-Like Hypersensitivity

(2009) M. Costigan et al.   JOURNAL OF NEUROSCIENCE

Profiling of dynamically changed gene expression in dorsal root ganglia post peripheral nerve injury and a critical role of injury-induced glial fibrillary acetic protein in maintenance of pain behaviors

(2009) Doo-sik Kim et al.   PAIN

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

(2009) Ben Langmead et al.   GENOME BIOLOGY

Next-Generation DNA Sequencing Methods

(2008) Elaine R. Mardis   Annual Review of Genomics and Human Genetics

Comparison of dorsal root ganglion gene expression in rat models of traumatic and HIV-associated neuropathic pain

(2008) Klio Maratou et al.   EUROPEAN JOURNAL OF PAIN

RNA-seq: An assessment of technical reproducibility and comparison with gene expression arrays

(2008) J. C. Marioni et al.   GENOME RESEARCH

Origins, Actions and Dynamic Expression Patterns of the Neuropeptide VGF in Rat Peripheral and Central Sensory Neurones Following Peripheral Nerve Injury

(2008) Andrew Moss et al.   Molecular Pain

Mapping and quantifying mammalian transcriptomes by RNA-Seq

(2008) Ali Mortazavi et al.   NATURE METHODS

RNA-Seq: a revolutionary tool for transcriptomics

(2008) Zhong Wang et al.   NATURE REVIEWS GENETICS