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

Removing technical variability in RNA-seq data using conditional quantile normalization

(2012) K. D. Hansen et al.   BIOSTATISTICS

Local and global factors affecting RNA sequencing analysis

(2011) Edward Sendler et al.   ANALYTICAL BIOCHEMISTRY

Detecting copy number status and uncovering subclonal markers in heterogeneous tumor biopsies

(2011) Fabio Parisi et al.   BMC GENOMICS

Integrative analysis of next generation sequencing for small non-coding RNAs and transcriptional regulation in Myelodysplastic Syndromes

(2011) Dominik Beck et al.   BMC Medical Genomics

Identification of gene fusion transcripts by transcriptome sequencing in BRCA1-mutated breast cancers and cell lines

(2011) Kevin CH Ha et al.   BMC Medical Genomics

Deep RNA sequencing analysis of readthrough gene fusions in human prostate adenocarcinoma and reference samples

(2011) Serban Nacu et al.   BMC Medical Genomics

Design and validation issues in RNA-seq experiments

(2011) Z. Fang et al.   BRIEFINGS IN BIOINFORMATICS

Epigenetics in Alternative Pre-mRNA Splicing

(2011) Reini F. Luco et al.   CELL

A ceRNA Hypothesis: The Rosetta Stone of a Hidden RNA Language?

(2011) Leonardo Salmena et al.   CELL

Accurate identification of A-to-I RNA editing in human by transcriptome sequencing

(2011) J. H. Bahn et al.   GENOME RESEARCH

From GWAS to clinical utility in Parkinson's disease

(2011) Christine Klein et al.   LANCET

AlleleSeq: analysis of allele-specific expression and binding in a network framework

(2011) J. Rozowsky et al.   Molecular Systems Biology

Frequent mutation of histone-modifying genes in non-Hodgkin lymphoma

(2011) Ryan D. Morin et al.   NATURE

Initial impact of the sequencing of the human genome

(2011) Eric S. Lander   NATURE

MHC class II transactivator CIITA is a recurrent gene fusion partner in lymphoid cancers

(2011) Christian Steidl et al.   NATURE

Transcriptome sequencing across a prostate cancer cohort identifies PCAT-1, an unannotated lincRNA implicated in disease progression

(2011) John R Prensner et al.   NATURE BIOTECHNOLOGY

Principles for the post-GWAS functional characterization of cancer risk loci

(2011) Matthew L Freedman et al.   NATURE GENETICS

Whole Transcriptome Sequencing Reveals Gene Expression and Splicing Differences in Brain Regions Affected by Alzheimer's Disease

(2011) Natalie A. Twine et al.   PLoS One

Poly (A)+ Transcriptome Assessment of ERBB2-Induced Alterations in Breast Cell Lines

(2011) Dirce Maria Carraro et al.   PLoS One

Network-Guided Analysis of Genes with Altered Somatic Copy Number and Gene Expression Reveals Pathways Commonly Perturbed in Metastatic Melanoma

(2011) Armand Valsesia et al.   PLoS One

Massive-Scale RNA-Seq Analysis of Non Ribosomal Transcriptome in Human Trisomy 21

(2011) Valerio Costa et al.   PLoS One

RNA-Seq of Human Neurons Derived from iPS Cells Reveals Candidate Long Non-Coding RNAs Involved in Neurogenesis and Neuropsychiatric Disorders

(2011) Mingyan Lin et al.   PLoS One

RNA-Seq Analyses Generate Comprehensive Transcriptomic Landscape and Reveal Complex Transcript Patterns in Hepatocellular Carcinoma

(2011) Qichao Huang et al.   PLoS One

deFuse: An Algorithm for Gene Fusion Discovery in Tumor RNA-Seq Data

(2011) Andrew McPherson et al.   PLoS Computational Biology

An EMT–Driven Alternative Splicing Program Occurs in Human Breast Cancer and Modulates Cellular Phenotype

(2011) Irina M. Shapiro et al.   PLoS Genetics

Identification of fusion genes in breast cancer by paired-end RNA-sequencing

(2011) Henrik Edgren et al.   GENOME BIOLOGY

Analyzing and minimizing PCR amplification bias in Illumina sequencing libraries

(2011) Daniel Aird et al.   GENOME BIOLOGY

TopHat-Fusion: an algorithm for discovery of novel fusion transcripts

(2011) Daehwan Kim et al.   GENOME BIOLOGY

Analysis of transcript and protein overlap in a human osteosarcoma cell line

(2010) Daniel Klevebring et al.   BMC GENOMICS

Fine-Needle Aspiration Biopsies for Gene Expression Ratio-Based Diagnostic and Prognostic Tests in Malignant Pleural Mesothelioma

(2010) A. De Rienzo et al.   CLINICAL CANCER RESEARCH

Copy number variation modifies expression time courses

(2010) E. Chaignat et al.   GENOME RESEARCH

Integrative analysis of the melanoma transcriptome

(2010) M. F. Berger et al.   GENOME RESEARCH

Discovery of non-ETS gene fusions in human prostate cancer using next-generation RNA sequencing

(2010) D. Pflueger et al.   GENOME RESEARCH

Uncovering the Complexity of Transcriptomes with RNA-Seq

(2010) Valerio Costa et al.   JOURNAL OF BIOMEDICINE AND BIOTECHNOLOGY

Understanding the pathogenesis of Alzheimer’s disease: will RNA-Seq realize the promise of transcriptomics?

(2010) Greg T. Sutherland et al.   JOURNAL OF NEUROCHEMISTRY

Transcriptome profiling in neurodegenerative disease

(2010) Eliza Courtney et al.   JOURNAL OF NEUROSCIENCE METHODS

Nutritional genomics era: opportunities toward a genome-tailored nutritional regimen

(2010) Valerio Costa et al.   JOURNAL OF NUTRITIONAL BIOCHEMISTRY

Transcriptome genetics using second generation sequencing in a Caucasian population

(2010) Stephen B. Montgomery et al.   NATURE

Epigenetics as a unifying principle in the aetiology of complex traits and diseases

(2010) Arturas Petronis   NATURE

Understanding mechanisms underlying human gene expression variation with RNA sequencing

(2010) Joseph K. Pickrell et al.   NATURE

Gene-expression-based prognostic assays for breast cancer

(2010) Chungyeul Kim et al.   Nature Reviews Clinical Oncology

RNA sequencing: advances, challenges and opportunities

(2010) Fatih Ozsolak et al.   NATURE REVIEWS GENETICS

Next-generation genomics: an integrative approach

(2010) R. David Hawkins et al.   NATURE REVIEWS GENETICS

Missing heritability and strategies for finding the underlying causes of complex disease

(2010) Evan E. Eichler et al.   NATURE REVIEWS GENETICS

The Genetics of Alzheimer Disease: Back to the Future

(2010) Lars Bertram et al.   NEURON

Tumor Transcriptome Sequencing Reveals Allelic Expression Imbalances Associated with Copy Number Alterations

(2010) Brian B. Tuch et al.   PLoS One

Age-Correlated Gene Expression in Normal and Neurodegenerative Human Brain Tissues

(2010) Kajia Cao et al.   PLoS One

The study of eQTL variations by RNA-seq: from SNPs to phenotypes

(2010) Jacek Majewski et al.   TRENDS IN GENETICS

FusionSeq: a modular framework for finding gene fusions by analyzing Paired-End RNA-Sequencing data

(2010) Andrea Sboner et al.   GENOME BIOLOGY

miR-34a, a microRNA up-regulated in a double transgenic mouse model of Alzheimer's disease, inhibits bcl2 translation

(2009) Xiaoying Wang et al.   BRAIN RESEARCH BULLETIN

Parkinson's Disease Patient-Derived Induced Pluripotent Stem Cells Free of Viral Reprogramming Factors

(2009) Frank Soldner et al.   CELL

Application of serial analysis of gene expression to the study of human genetic disease

(2009) Martin P. Horan   HUMAN GENETICS

Cancer genome sequencing: a review

(2009) E. R. Mardis et al.   HUMAN MOLECULAR GENETICS

Short non-coding RNA biology and neurodegenerative disorders: novel disease targets and therapeutics

(2009) M. S. Weinberg et al.   HUMAN MOLECULAR GENETICS

Genome-wide analysis of allelic expression imbalance in human primary cells by high-throughput transcriptome resequencing

(2009) Graham A. Heap et al.   HUMAN MOLECULAR GENETICS

Direct RNA sequencing

(2009) Fatih Ozsolak et al.   NATURE

The cancer genome

(2009) Michael R. Stratton et al.   NATURE

Next-generation gap

(2009) John D McPherson   NATURE METHODS

Sequencing technologies — the next generation

(2009) Michael L. Metzker   NATURE REVIEWS GENETICS

Mapping complex disease traits with global gene expression

(2009) William Cookson et al.   NATURE REVIEWS GENETICS

pH measurement as quality control on humanpost mortembrain tissue: a study of the BrainNet Europe consortium

(2009) C. M. Monoranu et al.   NEUROPATHOLOGY AND APPLIED NEUROBIOLOGY

Alterations in corticostriatal synaptic plasticity in mice overexpressing human α-synuclein

(2009) J.B. Watson et al.   NEUROSCIENCE

Massive transcriptional start site analysis of human genes in hypoxia cells

(2009) Katsuya Tsuchihara et al.   NUCLEIC ACIDS RESEARCH

Parkinson’s disease: A genetic perspective

(2008) Andrea C. Belin et al.   FEBS Journal

Identification of dysregulated genes in lymphocytes from children with Down syndrome

(2008) Cesar A. Sommer et al.   GENOME

Genome-wide detection and analysis of hippocampus core promoters using DeepCAGE

(2008) E. Valen et al.   GENOME RESEARCH

Genetics of gene expression and its effect on disease

(2008) Valur Emilsson et al.   NATURE

The beginning of the end for microarrays?

(2008) Jay Shendure   NATURE METHODS

High-Resolution Mapping of Expression-QTLs Yields Insight into Human Gene Regulation

(2008) Jean-Baptiste Veyrieras et al.   PLoS Genetics