Published in Genome Res on May 07, 2010
Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol (2014) 27.48
From RNA-seq reads to differential expression results. Genome Biol (2010) 5.77
A comparison of methods for differential expression analysis of RNA-seq data. BMC Bioinformatics (2013) 4.36
ReCount: a multi-experiment resource of analysis-ready RNA-seq gene count datasets. BMC Bioinformatics (2011) 3.12
Shrinkage estimation of dispersion in Negative Binomial models for RNA-seq experiments with small sample size. Bioinformatics (2013) 1.23
Microarray analysis of rat sensory ganglia after local inflammation implicates novel cytokines in pain. PLoS One (2012) 0.96
Criticality and degeneracy in injury-induced changes in primary afferent excitability and the implications for neuropathic pain. Elife (2014) 0.95
Diametrically opposite methylome-transcriptome relationships in high- and low-CpG promoter genes in postmitotic neural rat tissue. Epigenetics (2012) 0.95
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. Mol Pain (2014) 0.95
Epigenetics and the transition from acute to chronic pain. Pain Med (2012) 0.93
Dispersion estimation and its effect on test performance in RNA-seq data analysis: a simulation-based comparison of methods. PLoS One (2013) 0.93
SERE: single-parameter quality control and sample comparison for RNA-Seq. BMC Genomics (2012) 0.92
subSeq: determining appropriate sequencing depth through efficient read subsampling. Bioinformatics (2014) 0.91
Using a priori knowledge to align sequencing reads to their exact genomic position. Nucleic Acids Res (2012) 0.91
Evaluation of phenoxybenzamine in the CFA model of pain following gene expression studies and connectivity mapping. Mol Pain (2010) 0.89
Itch-associated peptides: RNA-Seq and bioinformatic analysis of natriuretic precursor peptide B and gastrin releasing peptide in dorsal root and trigeminal ganglia, and the spinal cord. Mol Pain (2014) 0.86
Genome-wide transcriptional profiling of skin and dorsal root ganglia after ultraviolet-B-induced inflammation. PLoS One (2014) 0.86
Analgesia by inhibiting tetrahydrobiopterin synthesis. Curr Opin Pharmacol (2011) 0.85
Plasticity of DNA methylation in a nerve injury model of pain. Epigenetics (2015) 0.83
Identification of 3' gene ends using transcriptional and genomic conservation across vertebrates. BMC Genomics (2012) 0.81
DAFS: a data-adaptive flag method for RNA-sequencing data to differentiate genes with low and high expression. BMC Bioinformatics (2014) 0.80
Neonatal pain: What's age got to do with it? Surg Neurol Int (2014) 0.78
Pain's peptide signature. Pain (2012) 0.78
Transcriptomic Approaches to Neural Repair. J Neurosci (2015) 0.78
Selective repression of gene expression in neuropathic pain by the neuron-restrictive silencing factor/repressor element-1 silencing transcription (NRSF/REST). Neurosci Lett (2015) 0.77
Cooperativity between remote sites of ectopic spiking allows afterdischarge to be initiated and maintained at different locations. J Comput Neurosci (2015) 0.77
Phosphoinositide signaling in somatosensory neurons. Adv Biol Regul (2015) 0.76
Interleukin-1β pre-treated bone marrow stromal cells alleviate neuropathic pain through CCL7-mediated inhibition of microglial activation in the spinal cord. Sci Rep (2017) 0.75
FHF2 isoforms differentially regulate Nav1.6-mediated resurgent sodium currents in dorsal root ganglion neurons. Pflugers Arch (2016) 0.75
Phospholipase C δ4 regulates cold sensitivity in mice. J Physiol (2016) 0.75
LPEseq: Local-Pooled-Error Test for RNA Sequencing Experiments with a Small Number of Replicates. PLoS One (2016) 0.75
DGEclust: differential expression analysis of clustered count data. Genome Biol (2015) 0.75
stageR: a general stage-wise method for controlling the gene-level false discovery rate in differential expression and differential transcript usage. Genome Biol (2017) 0.75
Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol (2009) 235.12
Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nat Methods (2008) 126.81
Accurate whole human genome sequencing using reversible terminator chemistry. Nature (2008) 90.20
TopHat: discovering splice junctions with RNA-Seq. Bioinformatics (2009) 81.13
Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature (2007) 75.09
Genome-wide mapping of in vivo protein-DNA interactions. Science (2007) 64.92
RNA-seq: an assessment of technical reproducibility and comparison with gene expression arrays. Genome Res (2008) 62.07
RNA-Seq: a revolutionary tool for transcriptomics. Nat Rev Genet (2009) 58.77
Alternative isoform regulation in human tissue transcriptomes. Nature (2008) 52.76
The transcriptional landscape of the yeast genome defined by RNA sequencing. Science (2008) 48.99
Stem cell transcriptome profiling via massive-scale mRNA sequencing. Nat Methods (2008) 31.04
The MicroArray Quality Control (MAQC) project shows inter- and intraplatform reproducibility of gene expression measurements. Nat Biotechnol (2006) 30.90
A global view of gene activity and alternative splicing by deep sequencing of the human transcriptome. Science (2008) 29.99
Deep surveying of alternative splicing complexity in the human transcriptome by high-throughput sequencing. Nat Genet (2008) 24.51
Dynamic repertoire of a eukaryotic transcriptome surveyed at single-nucleotide resolution. Nature (2008) 18.84
Antisense transcription in the mammalian transcriptome. Science (2005) 15.69
Sequence census methods for functional genomics. Nat Methods (2007) 7.38
Genome-wide mapping of alternative splicing in Arabidopsis thaliana. Genome Res (2009) 5.24
Dark matter in the genome: evidence of widespread transcription detected by microarray tiling experiments. Trends Genet (2005) 4.56
Distinct DNA methylation patterns characterize differentiated human embryonic stem cells and developing human fetal liver. Genome Res (2009) 4.11
GTP cyclohydrolase and tetrahydrobiopterin regulate pain sensitivity and persistence. Nat Med (2006) 3.38
Replicate high-density rat genome oligonucleotide microarrays reveal hundreds of regulated genes in the dorsal root ganglion after peripheral nerve injury. BMC Neurosci (2002) 3.21
Genomic convergence analysis of schizophrenia: mRNA sequencing reveals altered synaptic vesicular transport in post-mortem cerebellum. PLoS One (2008) 2.22
Small proline-rich repeat protein 1A is expressed by axotomized neurons and promotes axonal outgrowth. J Neurosci (2002) 2.01
Sensory neuron targeting by self-complementary AAV8 via lumbar puncture for chronic pain. Proc Natl Acad Sci U S A (2008) 1.73
Peptide neurotransmitters activate a cation channel complex of NALCN and UNC-80. Nature (2008) 1.71
Coupling gene chip analyses and rat genetic variances in identifying potential target genes that may contribute to neuropathic allodynia development. J Neurochem (2003) 1.50
Segmental spinal nerve ligation model of neuropathic pain. Methods Mol Med (2004) 1.24
Comparison of gene expression profiles in neuropathic and inflammatory pain. J Physiol Pharmacol (2006) 1.09
Intrathecal gene transfer by adeno-associated virus for pain. Curr Opin Mol Ther (2005) 0.99
Exploiting microarrays to reveal differential gene expression in the nervous system. Genome Biol (2003) 0.90
Dorsal horn-enriched genes identified by DNA microarray, in situ hybridization and immunohistochemistry. BMC Neurosci (2002) 0.81
Accurate whole human genome sequencing using reversible terminator chemistry. Nature (2008) 90.20
Alternative isoform regulation in human tissue transcriptomes. Nature (2008) 52.76
The MicroArray Quality Control (MAQC) project shows inter- and intraplatform reproducibility of gene expression measurements. Nat Biotechnol (2006) 30.90
High density DNA methylation array with single CpG site resolution. Genomics (2011) 10.35
Elucidation of the small RNA component of the transcriptome. Science (2005) 8.66
Carrier testing for severe childhood recessive diseases by next-generation sequencing. Sci Transl Med (2011) 8.20
Full-length mRNA-Seq from single-cell levels of RNA and individual circulating tumor cells. Nat Biotechnol (2012) 7.37
Mammalian microRNAs: experimental evaluation of novel and previously annotated genes. Genes Dev (2010) 7.14
Metagenomic discovery of biomass-degrading genes and genomes from cow rumen. Science (2011) 6.93
A highly annotated whole-genome sequence of a Korean individual. Nature (2009) 6.91
Global identification of microRNA-target RNA pairs by parallel analysis of RNA ends. Nat Biotechnol (2008) 6.18
Ab initio construction of a eukaryotic transcriptome by massively parallel mRNA sequencing. Proc Natl Acad Sci U S A (2009) 6.01
High-resolution analysis of parent-of-origin allelic expression in the mouse brain. Science (2010) 5.91
Genome-wide mapping of DNase hypersensitive sites using massively parallel signature sequencing (MPSS). Genome Res (2005) 5.71
Chimeric transcript discovery by paired-end transcriptome sequencing. Proc Natl Acad Sci U S A (2009) 5.30
Exogenous plant MIR168a specifically targets mammalian LDLRAP1: evidence of cross-kingdom regulation by microRNA. Cell Res (2011) 4.55
PRG-1 and 21U-RNAs interact to form the piRNA complex required for fertility in C. elegans. Mol Cell (2008) 4.48
Distinct DNA methylation patterns characterize differentiated human embryonic stem cells and developing human fetal liver. Genome Res (2009) 4.11
Parkin mediates nonclassical, proteasomal-independent ubiquitination of synphilin-1: implications for Lewy body formation. J Neurosci (2005) 3.92
Genome, epigenome and RNA sequences of monozygotic twins discordant for multiple sclerosis. Nature (2010) 3.90
Monitoring chronic lymphocytic leukemia progression by whole genome sequencing reveals heterogeneous clonal evolution patterns. Blood (2012) 3.63
Multiplexed RNA structure characterization with selective 2'-hydroxyl acylation analyzed by primer extension sequencing (SHAPE-Seq). Proc Natl Acad Sci U S A (2011) 3.30
Ketamine-induced neuronal cell death in the perinatal rhesus monkey. Toxicol Sci (2007) 3.22
Transcriptome-wide regulation of pre-mRNA splicing and mRNA localization by muscleblind proteins. Cell (2012) 3.20
Transcriptome profiling of human and murine ESCs identifies divergent paths required to maintain the stem cell state. Stem Cells (2005) 3.16
RNA-ligase-dependent biases in miRNA representation in deep-sequenced small RNA cDNA libraries. RNA (2011) 3.00
Base-pair resolution DNA methylation sequencing reveals profoundly divergent epigenetic landscapes in acute myeloid leukemia. PLoS Genet (2012) 2.94
A five-microRNA signature identified from genome-wide serum microRNA expression profiling serves as a fingerprint for gastric cancer diagnosis. Eur J Cancer (2010) 2.84
Molecular Evidence of Sexual Transmission of Ebola Virus. N Engl J Med (2015) 2.71
Direct measurement of DNA affinity landscapes on a high-throughput sequencing instrument. Nat Biotechnol (2011) 2.60
Cohesin-mediated interactions organize chromosomal domain architecture. EMBO J (2013) 2.48
Noncanonical compensation of zygotic X transcription in early Drosophila melanogaster development revealed through single-embryo RNA-seq. PLoS Biol (2011) 2.43
Serum microRNA expression profile as a biomarker in the diagnosis and prognosis of pancreatic cancer. Clin Chem (2011) 2.42
An atlas of human gene expression from massively parallel signature sequencing (MPSS). Genome Res (2005) 2.39
Genome sequencing and analysis of the Tasmanian devil and its transmissible cancer. Cell (2012) 2.37
A mutation in TGFB3 associated with a syndrome of low muscle mass, growth retardation, distal arthrogryposis and clinical features overlapping with Marfan and Loeys-Dietz syndrome. Am J Med Genet A (2013) 2.35
Expression profile of microRNAs in serum: a fingerprint for esophageal squamous cell carcinoma. Clin Chem (2010) 2.34
From single-cell to cell-pool transcriptomes: stochasticity in gene expression and RNA splicing. Genome Res (2013) 2.23
A microsatellite-based, gene-rich linkage map reveals genome structure, function and evolution in Gossypium. Genetics (2007) 2.23
Genomic convergence analysis of schizophrenia: mRNA sequencing reveals altered synaptic vesicular transport in post-mortem cerebellum. PLoS One (2008) 2.22
Diagnostic potential of saliva: current state and future applications. Clin Chem (2011) 2.20
MPSS profiling of human embryonic stem cells. BMC Dev Biol (2004) 2.17
Integrated analysis of gene expression, CpG island methylation, and gene copy number in breast cancer cells by deep sequencing. PLoS One (2011) 2.16
Construction of Parallel Analysis of RNA Ends (PARE) libraries for the study of cleaved miRNA targets and the RNA degradome. Nat Protoc (2009) 2.12
Identification of ten serum microRNAs from a genome-wide serum microRNA expression profile as novel noninvasive biomarkers for nonsmall cell lung cancer diagnosis. Int J Cancer (2011) 2.01
Fat deposition in dilated cardiomyopathy assessed by CMR. JACC Cardiovasc Imaging (2013) 2.00
Studying arrhythmogenic right ventricular dysplasia with patient-specific iPSCs. Nature (2013) 2.00
Increased serum and urinary microRNAs in children with idiopathic nephrotic syndrome. Clin Chem (2013) 1.86
Poly[[(pentaethylenehexamine)manganese(II)] [hepta-mu-selenido-tritin(IV)]]: a tin-selenium net with remarkable flexibility. Acta Crystallogr C (2009) 1.80
A novel bioinformatics pipeline for identification and characterization of fusion transcripts in breast cancer and normal cell lines. Nucleic Acids Res (2011) 1.77
Prolonged exposure to ketamine increases neurodegeneration in the developing monkey brain. Int J Dev Neurosci (2009) 1.76
Sensory neuron targeting by self-complementary AAV8 via lumbar puncture for chronic pain. Proc Natl Acad Sci U S A (2008) 1.73
Estrogen receptor alpha controls a gene network in luminal-like breast cancer cells comprising multiple transcription factors and microRNAs. Am J Pathol (2010) 1.73
MicroRNA-138 suppresses epithelial-mesenchymal transition in squamous cell carcinoma cell lines. Biochem J (2011) 1.67
Comparative methylome analysis of benign and malignant peripheral nerve sheath tumors. Genome Res (2011) 1.60
Transcriptome analysis of Pseudomonas syringae identifies new genes, noncoding RNAs, and antisense activity. J Bacteriol (2010) 1.59
Cyclin-dependent kinase inhibition by the KLF6 tumor suppressor protein through interaction with cyclin D1. Cancer Res (2004) 1.57
Somatic mutation of CDKN1B in small intestine neuroendocrine tumors. Nat Genet (2013) 1.56
Highly sensitive and specific microRNA expression profiling using BeadArray technology. Nucleic Acids Res (2008) 1.54
Comparison of single-surgeon series of transperitoneal laparoendoscopic single-site surgery and standard laparoscopic adrenalectomy. Urology (2012) 1.51
Association analyses identify multiple new lung cancer susceptibility loci and their interactions with smoking in the Chinese population. Nat Genet (2012) 1.49
Modeling and automation of sequencing-based characterization of RNA structure. Proc Natl Acad Sci U S A (2011) 1.49
Duplex-specific nuclease efficiently removes rRNA for prokaryotic RNA-seq. Nucleic Acids Res (2011) 1.48
The association between IGF1 CA repeat polymorphisms and breast cancer risk: a meta-analysis. Breast Cancer Res Treat (2011) 1.42
Identification of seven serum microRNAs from a genome-wide serum microRNA expression profile as potential noninvasive biomarkers for malignant astrocytomas. Int J Cancer (2012) 1.41