Integrative RNA-seq and microarray data analysis reveals GC content and gene length biases in the psoriasis transcriptome

Library preparation methods for next-generation sequencing: Tone down the bias

(2014) Erwin L. van Dijk et al.   EXPERIMENTAL CELL RESEARCH

Coupling mRNA processing with transcription in time and space

(2014) David L. Bentley   NATURE REVIEWS GENETICS

Comparison of RNA-Seq and Microarray in Transcriptome Profiling of Activated T Cells

(2014) Shanrong Zhao et al.   PLoS One

Integrative Biology Approach Identifies Cytokine Targeting Strategies for Psoriasis

(2014) G. K. Perera et al.   Science Translational Medicine

Parallel comparison of Illumina RNA-Seq and Affymetrix microarray platforms on transcriptomic profiles generated from 5-aza-deoxy-cytidine treated HT-29 colon cancer cells and simulated datasets

(2013) Xiao Xu et al.   BMC BIOINFORMATICS

Towards the integration, annotation and association of historical microarray experiments with RNA-seq

(2013) Shweta S Chavan et al.   BMC BIOINFORMATICS

Differential expression analysis for paired RNA-seq data

(2013) Lisa M Chung et al.   BMC BIOINFORMATICS

Dissecting the psoriasis transcriptome: inflammatory- and cytokine-driven gene expression in lesions from 163 patients

(2013) William R Swindell et al.   BMC GENOMICS

Transcription Poisoning by Topoisomerase I Is Controlled by Gene Length, Splice Sites, and miR-142-3p

(2013) S. Solier et al.   CANCER RESEARCH

Creation of Differentiation-Specific Genomic Maps of Human Epidermis through Laser Capture Microdissection

(2013) Nicholas Gulati et al.   JOURNAL OF INVESTIGATIVE DERMATOLOGY

Use of Bru-Seq and BruChase-Seq for genome-wide assessment of the synthesis and stability of RNA

(2013) Michelle T. Paulsen et al.   METHODS

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

(2013) Simon Anders et al.   Nature Protocols

Cross-Study Homogeneity of Psoriasis Gene Expression in Skin across a Large Expression Range

(2013) Jeannette Bigler et al.   PLoS One

IL-17A and IFN-γ Synergistically Induce RNase 7 Expression via STAT3 in Primary Keratinocytes

(2013) Maren Simanski et al.   PLoS One

Dispersion Estimation and Its Effect on Test Performance in RNA-seq Data Analysis: A Simulation-Based Comparison of Methods

(2013) William Michael Landau et al.   PLoS One

Modulation of Epidermal Transcription Circuits in Psoriasis: New Links between Inflammation and Hyperproliferation

(2013) William R. Swindell et al.   PLoS One

Genome-Wide Transcriptional Effects of the Anti-Cancer Agent Camptothecin

(2013) Artur Veloso et al.   PLoS One

Comparison of Microarrays and RNA-Seq for Gene Expression Analyses of Dose-Response Experiments

(2013) Michael B. Black et al.   TOXICOLOGICAL SCIENCES

TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions

(2013) Daehwan Kim et al.   GENOME BIOLOGY

Comprehensive evaluation of differential gene expression analysis methods for RNA-seq data

(2013) Franck Rapaport et al.   GENOME BIOLOGY

A comparison of statistical methods for detecting differentially expressed genes from RNA-seq data

(2012) Vanessa M. Kvam et al.   AMERICAN JOURNAL OF BOTANY

RSeQC: quality control of RNA-seq experiments

(2012) Liguo Wang et al.   BIOINFORMATICS

RNA-seq and microarray complement each other in transcriptome profiling

(2012) Sunitha Kogenaru et al.   BMC GENOMICS

Noncanonical microRNAs and endogenous siRNAs in normal and psoriatic human skin

(2012) Jing Xia et al.   HUMAN MOLECULAR GENETICS

Transcriptional regulatory network for psoriasis

(2012) Xiaonian Lu et al.   JOURNAL OF DERMATOLOGY

Expanding the Psoriasis Disease Profile: Interrogation of the Skin and Serum of Patients with Moderate-to-Severe Psoriasis

(2012) Mayte Suárez-Fariñas et al.   JOURNAL OF INVESTIGATIVE DERMATOLOGY

Camera: a competitive gene set test accounting for inter-gene correlation

(2012) Di Wu et al.   NUCLEIC ACIDS RESEARCH

A comprehensive comparison of RNA-Seq-based transcriptome analysis from reads to differential gene expression and cross-comparison with microarrays: a case study in Saccharomyces cerevisiae

(2012) Intawat Nookaew et al.   NUCLEIC ACIDS RESEARCH

Summarizing and correcting the GC content bias in high-throughput sequencing

(2012) Yuval Benjamini et al.   NUCLEIC ACIDS RESEARCH

Heterogeneity of Inflammatory and Cytokine Networks in Chronic Plaque Psoriasis

(2012) William R. Swindell et al.   PLoS One

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

Deep sequencing of small RNAs from human skin reveals major alterations in the psoriasis miRNAome

(2011) Cailin E. Joyce et al.   HUMAN MOLECULAR GENETICS

Transcriptional Profiling of Psoriasis Using RNA-seq Reveals Previously Unidentified Differentially Expressed Genes

(2011) Ali Jabbari et al.   JOURNAL OF INVESTIGATIVE DERMATOLOGY

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

(2011) Daniel Bottomly et al.   PLoS One

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

Impact of RNA degradation on gene expression profiling

(2010) Lennart Opitz et al.   BMC Medical Genomics

MicroRNAs and potential target interactions in psoriasis

(2010) John R. Zibert et al.   JOURNAL OF DERMATOLOGICAL SCIENCE

Enhanced Expression and Secretion of Antimicrobial Peptides in Atopic Dermatitis and after Superficial Skin Injury

(2010) Jürgen Harder et al.   JOURNAL OF INVESTIGATIVE DERMATOLOGY

Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation

(2010) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

Biases in Illumina transcriptome sequencing caused by random hexamer priming

(2010) Kasper D. Hansen et al.   NUCLEIC ACIDS RESEARCH

A central role for RNA in the induction and biological activities of type 1 interferons

(2010) Xiao-Ling Li et al.   Wiley Interdisciplinary Reviews-RNA

Differential expression analysis for sequence count data

(2010) Simon Anders et al.   GENOME BIOLOGY

Statistical inferences for isoform expression in RNA-Seq

(2009) Hui Jiang et al.   BIOINFORMATICS

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

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

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

Transcript length bias in RNA-seq data confounds systems biology

(2009) Alicia Oshlack et al.   Biology Direct

Effective treatment of psoriasis with etanercept is linked to suppression of IL-17 signaling, not immediate response TNF genes

(2009) Lisa C. Zaba et al.   JOURNAL OF ALLERGY AND CLINICAL IMMUNOLOGY

Genome-wide scan reveals association of psoriasis with IL-23 and NF-κB pathways

(2009) Rajan P Nair et al.   NATURE GENETICS

Effect of RNA quality on transcript intensity levels in microarray analysis of human post-mortem brain tissues

(2008) Tatiana Popova et al.   BMC GENOMICS

Deep sequencing-based expression analysis shows major advances in robustness, resolution and inter-lab portability over five microarray platforms

(2008) Peter A. C. 't Hoen et al.   NUCLEIC ACIDS RESEARCH

Substantial biases in ultra-short read data sets from high-throughput DNA sequencing

(2008) J. C. Dohm et al.   NUCLEIC ACIDS RESEARCH

Type I Interferon: Potential Therapeutic Target for Psoriasis?

(2008) Yihong Yao et al.   PLoS One

IFN-α Enhances Poly-IC Responses in Human Keratinocytes by Inducing Expression of Cytosolic Innate RNA Receptors: Relevance for Psoriasis

(2007) Errol P. Prens et al.   JOURNAL OF INVESTIGATIVE DERMATOLOGY