Identification of novel point mutations in splicing sites integrating whole-exome and RNA-seq data in myeloproliferative diseases

Evolution and Impact of Subclonal Mutations in Chronic Lymphocytic Leukemia

(2013) Dan A. Landau et al.   CELL

Sensitive detection of somatic point mutations in impure and heterogeneous cancer samples

(2013) Kristian Cibulskis et al.   NATURE BIOTECHNOLOGY

JointSNVMix: a probabilistic model for accurate detection of somatic mutations in normal/tumour paired next-generation sequencing data

(2012) Andrew Roth et al.   BIOINFORMATICS

The application of nonsense-mediated mRNA decay inhibition to the identification of breast cancer susceptibility genes

(2012) Julie K Johnson et al.   BMC CANCER

VarScan 2: Somatic mutation and copy number alteration discovery in cancer by exome sequencing

(2012) D. C. Koboldt et al.   GENOME RESEARCH

Recurrent SETBP1 mutations in atypical chronic myeloid leukemia

(2012) Rocco Piazza et al.   NATURE GENETICS

FusionAnalyser: a new graphical, event-driven tool for fusion rearrangements discovery

(2012) Rocco Piazza et al.   NUCLEIC ACIDS RESEARCH

Screening the human exome: a comparison of whole genome and whole transcriptome sequencing

(2012) Elizabeth T Cirulli et al.   GENOME BIOLOGY

FusionHunter: identifying fusion transcripts in cancer using paired-end RNA-seq

(2011) Yang Li et al.   BIOINFORMATICS

Exome sequencing-based copy-number variation and loss of heterozygosity detection: ExomeCNV

(2011) Jarupon Fah Sathirapongsasuti et al.   BIOINFORMATICS

SomaticSniper: identification of somatic point mutations in whole genome sequencing data

(2011) David E. Larson et al.   BIOINFORMATICS

Whole-exome sequencing identifies somatic mutations of BCOR in acute myeloid leukemia with normal karyotype

(2011) V. Grossmann et al.   BLOOD

Differential expression in RNA-seq: A matter of depth

(2011) S. Tarazona et al.   GENOME RESEARCH

dbNSFP: A lightweight database of human nonsynonymous SNPs and their functional predictions

(2011) Xiaoming Liu et al.   HUMAN MUTATION

Integrative genomics viewer

(2011) James T Robinson et al.   NATURE BIOTECHNOLOGY

Exome sequencing identifies somatic mutations of DNA methyltransferase gene DNMT3A in acute monocytic leukemia

(2011) Xiao-Jing Yan et al.   NATURE GENETICS

Computational methods for transcriptome annotation and quantification using RNA-seq

(2011) Manuel Garber et al.   NATURE METHODS

SomaticSF3B1Mutation in Myelodysplasia with Ring Sideroblasts

(2011) E. Papaemmanuil et al.   NEW ENGLAND JOURNAL OF MEDICINE

Molecular Genetic Analysis of 103 Sporadic Colorectal Tumours in Czech Patients

(2011) Peter Vasovcak et al.   PLoS One

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

(2011) Andrew McPherson et al.   PLoS Computational Biology

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

(2010) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

Somatic mutations altering EZH2 (Tyr641) in follicular and diffuse large B-cell lymphomas of germinal-center origin

(2010) Ryan D Morin et al.   NATURE GENETICS

A method and server for predicting damaging missense mutations

(2010) Ivan A Adzhubei et al.   NATURE METHODS

MutationTaster evaluates disease-causing potential of sequence alterations

(2010) Jana Marie Schwarz et al.   NATURE METHODS

ANNOVAR: functional annotation of genetic variants from high-throughput sequencing data

(2010) K. Wang et al.   NUCLEIC ACIDS RESEARCH

The adaptive significance of unproductive alternative splicing in primates

(2010) A. Skandalis et al.   RNA

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

(2010) Andrea Sboner et al.   GENOME BIOLOGY

Global and unbiased detection of splice junctions from RNA-seq data

(2010) Adam Ameur et al.   GENOME BIOLOGY

Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences

(2010) Jeremy Goecks et al.   GENOME BIOLOGY

TopHat: discovering splice junctions with RNA-Seq

(2009) Cole Trapnell et al.   BIOINFORMATICS

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

The 2008 revision of the World Health Organization (WHO) classification of myeloid neoplasms and acute leukemia: rationale and important changes

(2009) J. W. Vardiman et al.   BLOOD

Identification of deleterious mutations within three human genomes

(2009) S. Chun et al.   GENOME RESEARCH

The cancer genome

(2009) Michael R. Stratton et al.   NATURE

Predicting the effects of coding non-synonymous variants on protein function using the SIFT algorithm

(2009) Prateek Kumar et al.   Nature Protocols

Structural implication of splicing stochastics

(2009) E. Melamud et al.   NUCLEIC ACIDS RESEARCH

Detection of single nucleotide variations in expressed exons of the human genome using RNA-Seq

(2009) Iouri Chepelev et al.   NUCLEIC ACIDS RESEARCH

COSMIC (the Catalogue of Somatic Mutations in Cancer): a resource to investigate acquired mutations in human cancer

(2009) Simon A. Forbes et al.   NUCLEIC ACIDS RESEARCH

A Global View of Cancer-Specific Transcript Variants by Subtractive Transcriptome-Wide Analysis

(2009) Chunjiang He et al.   PLoS One

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome

(2009) Ben Langmead et al.   GENOME BIOLOGY

The variants BRCA1 IVS6-1G>A and BRCA2 IVS15+1G>A lead to aberrant splicing of the transcripts

(2008) Sara Gutiérrez-Enríquez et al.   BREAST CANCER RESEARCH AND TREATMENT

Aberrant RNA splicing and its functional consequences in cancer cells

(2008) J. D. Fackenthal et al.   Disease Models & Mechanisms

Evaluation of in silico splice tools for decision-making in molecular diagnosis

(2008) Claude Houdayer et al.   HUMAN MUTATION

Intronic variants inBRCA1andBRCA2that affect RNA splicing can be reliably selected by splice-site prediction programs

(2008) Maaike P.G. Vreeswijk et al.   HUMAN MUTATION

Frequent somatic mutations of GNAQ in uveal melanoma and blue naevi

(2008) Catherine D. Van Raamsdonk et al.   NATURE

Mapping and quantifying mammalian transcriptomes by RNA-Seq

(2008) Ali Mortazavi et al.   NATURE METHODS

Comparative lesion sequencing provides insights into tumor evolution

(2008) S. Jones et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA