iGEMS: an integrated model for identification of alternative exon usage events

Diminishing returns in next-generation sequencing (NGS) transcriptome data

(2015) Rex Lei et al.   GENE

Physical Activity, Fitness, Glucose Homeostasis, and Brain Morphology in Twins

(2015) MIRVA ROTTENSTEINER et al.   MEDICINE AND SCIENCE IN SPORTS AND EXERCISE

limma powers differential expression analyses for RNA-sequencing and microarray studies

(2015) Matthew E. Ritchie et al.   NUCLEIC ACIDS RESEARCH

The human transcriptome across tissues and individuals

(2015) M. Mele et al.   SCIENCE

Comparisons of computational methods for differential alternative splicing detection using RNA-seq in plant systems

(2014) Ruolin Liu et al.   BMC BIOINFORMATICS

The Browning of White Adipose Tissue: Some Burning Issues

(2014) Jan Nedergaard et al.   Cell Metabolism

The concordance between RNA-seq and microarray data depends on chemical treatment and transcript abundance

(2014) Charles Wang et al.   NATURE BIOTECHNOLOGY

A comprehensive assessment of RNA-seq accuracy, reproducibility and information content by the Sequencing Quality Control Consortium

(2014)   NATURE BIOTECHNOLOGY

Persistence or change in leisure-time physical activity habits and waist gain during early adulthood: A twin-study

(2014) Mirva Rottensteiner et al.   Obesity

Integrated Exon Level Expression Analysis of Driver Genes Explain Their Role in Colorectal Cancer

(2014) Mohammad Azhar Aziz et al.   PLoS One

Loss of neuronatin promotes “browning” of primary mouse adipocytes while reducing Glut1-mediated glucose disposal

(2013) Valentina Gburcik et al.   AMERICAN JOURNAL OF PHYSIOLOGY-ENDOCRINOLOGY AND METABOLISM

GPViz: dynamic visualization of genomic regions and variants affecting protein domains

(2013) Rene Snajder et al.   BIOINFORMATICS

Reproducible probe-level analysis of the Affymetrix Exon 1.0 ST array with R/Bioconductor

(2013) M. Rodrigo-Domingo et al.   BRIEFINGS IN BIOINFORMATICS

Are all of the human exons alternatively spliced?

(2013) F.-C. Chen   BRIEFINGS IN BIOINFORMATICS

Pfam: the protein families database

(2013) Robert D. Finn et al.   NUCLEIC ACIDS RESEARCH

Molecular Networks of Human Muscle Adaptation to Exercise and Age

(2013) Bethan E. Phillips et al.   PLoS Genetics

Transcriptome analysis of human tissues and cell lines reveals one dominant transcript per gene

(2013) Mar Gonzàlez-Porta et al.   GENOME BIOLOGY

An essential role for Tbx15 in the differentiation of brown and “brite” but not white adipocytes

(2012) Valentina Gburcik et al.   AMERICAN JOURNAL OF PHYSIOLOGY-ENDOCRINOLOGY AND METABOLISM

A systematic comparison and evaluation of high density exon arrays and RNA-seq technology used to unravel the peripheral blood transcriptome of sickle cell disease

(2012) Nalini Raghavachari et al.   BMC Medical Genomics

Detecting differential usage of exons from RNA-seq data

(2012) S. Anders et al.   GENOME RESEARCH

MATS: a Bayesian framework for flexible detection of differential alternative splicing from RNA-Seq data

(2012) Shihao Shen et al.   NUCLEIC ACIDS RESEARCH

The Evolutionary Landscape of Alternative Splicing in Vertebrate Species

(2012) N. L. Barbosa-Morais et al.   SCIENCE

Exon and intron definition in pre-mRNA splicing

(2012) Laura De Conti et al.   Wiley Interdisciplinary Reviews-RNA

Regulation of alternative splicing by the circadian clock and food related cues

(2012) Nicholas J McGlincy et al.   GENOME BIOLOGY

Exon array analysis reveals neuroblastoma tumors have distinct alternative splicing patterns according to stage and MYCN amplification status

(2011) Xiang Guo et al.   BMC Medical Genomics

Comprehensive exon array data processing method for quantitative analysis of alternative spliced variants

(2011) Ping Chen et al.   NUCLEIC ACIDS RESEARCH

BioMart: driving a paradigm change in biological data management

(2011) A. Kasprzyk   Database-The Journal of Biological Databases and Curation

Exon Array Analysis using re-defined probe sets results in reliable identification of alternatively spliced genes in non-small cell lung cancer

(2010) Wolfram Langer et al.   BMC GENOMICS

A transcriptional map of the impact of endurance exercise training on skeletal muscle phenotype

(2010) Pernille Keller et al.   JOURNAL OF APPLIED PHYSIOLOGY

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

(2010) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

Global regulation of alternative splicing during myogenic differentiation

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

Differences in Muscle and Adipose Tissue Gene Expression and Cardio-Metabolic Risk Factors in the Members of Physical Activity Discordant Twin Pairs

(2010) Tuija Leskinen et al.   PLoS One

Integration of microRNA changes in vivo identifies novel molecular features of muscle insulin resistance in type 2 diabetes

(2010) Iain J Gallagher et al.   Genome Medicine

ARH: predicting splice variants from genome-wide data with modified entropy

(2009) Axel Rasche et al.   BIOINFORMATICS

Identifying differential exon splicing using linear models and correlation coefficients

(2009) Sonia H Shah et al.   BMC BIOINFORMATICS

Differential splicing using whole-transcript microarrays

(2009) Mark D Robinson et al.   BMC BIOINFORMATICS

Current-generation high-throughput sequencing: deepening insights into mammalian transcriptomes

(2009) B. J. Blencowe et al.   GENES & DEVELOPMENT

Overestimation of alternative splicing caused by variable probe characteristics in exon arrays

(2009) Dimos Gaidatzis et al.   NUCLEIC ACIDS RESEARCH

Thermogenically competent nonadrenergic recruitment in brown preadipocytes by a PPARγ agonist

(2008) Natasa Petrovic et al.   AMERICAN JOURNAL OF PHYSIOLOGY-ENDOCRINOLOGY AND METABOLISM

FIRMA: a method for detection of alternative splicing from exon array data

(2008) E. Purdom et al.   BIOINFORMATICS

Dissecting an alternative splicing analysis workflow for GeneChip® Exon 1.0 ST Affymetrix arrays

(2008) Cristina Della Beffa et al.   BMC GENOMICS

Alternative Splicing in Colon, Bladder, and Prostate Cancer Identified by Exon Array Analysis

(2008) Kasper Thorsen et al.   MOLECULAR & CELLULAR PROTEOMICS

Tau exon 10 alternative splicing and tauopathies

(2008) Fei Liu et al.   Molecular Neurodegeneration

Alternative isoform regulation in human tissue transcriptomes

(2008) Eric T. Wang et al.   NATURE

Analyzing real-time PCR data by the comparative CT method

(2008) Thomas D Schmittgen et al.   Nature Protocols