Identification of latent biomarkers in hepatocellular carcinoma by ultra-deep whole-transcriptome sequencing

ENCODE explained

(2012) Joseph R. Ecker et al.   NATURE

The hallmarks of cancer

(2012) Tony Gutschner et al.   RNA Biology

Fluorescence-based alternative splicing reporters for the study of epithelial plasticity in vivo

(2012) J. A. Somarelli et al.   RNA

SpliceTrap: a method to quantify alternative splicing under single cellular conditions

(2011) Jie Wu et al.   BIOINFORMATICS

RNA-sequence analysis of human B-cells

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

Initial impact of the sequencing of the human genome

(2011) Eric S. Lander   NATURE

Peripheral SMN restoration is essential for long-term rescue of a severe spinal muscular atrophy mouse model

(2011) Yimin Hua et al.   NATURE

Computational methods for transcriptome annotation and quantification using RNA-seq

(2011) Manuel Garber et al.   NATURE METHODS

Gene Expression Atlas update--a value-added database of microarray and sequencing-based functional genomics experiments

(2011) M. Kapushesky et al.   NUCLEIC ACIDS RESEARCH

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

(2011) Qichao Huang et al.   PLoS One

A User's Guide to the Encyclopedia of DNA Elements (ENCODE)

(2011)   PLOS BIOLOGY

The Reality of Pervasive Transcription

(2011) Michael B. Clark et al.   PLOS BIOLOGY

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

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

Reduced Expression of Fibroblast Growth Factor Receptor 2IIIb in Hepatocellular Carcinoma Induces a More Aggressive Growth

(2010) Thomas Amann et al.   AMERICAN JOURNAL OF PATHOLOGY

Clinical Implications of Gene Dosage and Gene Expression Patterns in Diploid Breast Carcinoma

(2010) T. Z. Parris et al.   CLINICAL CANCER RESEARCH

Alternative pre-mRNA splicing regulation in cancer: pathways and programs unhinged

(2010) C. J. David et al.   GENES & DEVELOPMENT

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

(2010) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

RNA sequencing: advances, challenges and opportunities

(2010) Fatih Ozsolak et al.   NATURE REVIEWS GENETICS

Ensembl 2011

(2010) P. Flicek et al.   NUCLEIC ACIDS RESEARCH

ArrayExpress update--an archive of microarray and high-throughput sequencing-based functional genomics experiments

(2010) H. Parkinson et al.   NUCLEIC ACIDS RESEARCH

NCBI GEO: archive for functional genomics data sets--10 years on

(2010) T. Barrett et al.   NUCLEIC ACIDS RESEARCH

ConsensusPathDB: toward a more complete picture of cell biology

(2010) Atanas Kamburov et al.   NUCLEIC ACIDS RESEARCH

MapSplice: Accurate mapping of RNA-seq reads for splice junction discovery

(2010) Kai Wang et al.   NUCLEIC ACIDS RESEARCH

Noisy Splicing Drives mRNA Isoform Diversity in Human Cells

(2010) Joseph K. Pickrell et al.   PLoS Genetics

TopHat: discovering splice junctions with RNA-Seq

(2009) Cole Trapnell et al.   BIOINFORMATICS

ESRP1 and ESRP2 Are Epithelial Cell-Type-Specific Regulators of FGFR2 Splicing

(2009) Claude C. Warzecha et al.   MOLECULAR CELL

Large, rare chromosomal deletions associated with severe early-onset obesity

(2009) Elena G. Bochukova et al.   NATURE

Profiling the HeLa S3 transcriptome using randomly primed cDNA and massively parallel short-read sequencing

(2008) Ryan D. Morin et al.   BIOTECHNIQUES

The emerging role of splicing factors in cancer

(2008) Ana Rita Grosso et al.   EMBO REPORTS

A Hot Spot of Genetic Instability in Autism

(2008) Evan E. Eichler et al.   NEW ENGLAND JOURNAL OF MEDICINE

A Global View of Gene Activity and Alternative Splicing by Deep Sequencing of the Human Transcriptome

(2008) M. Sultan et al.   SCIENCE