BreaKmer: detection of structural variation in targeted massively parallel sequencing data using kmers

LUMPY: a probabilistic framework for structural variant discovery

(2014) Ryan M Layer et al.   GENOME BIOLOGY

DNA Sequencing of Cancer: What Have We Learned?

(2013) Juliann Chmielecki et al.   Annual Review of Medicine

Diverse Mechanisms of Somatic Structural Variations in Human Cancer Genomes

(2013) Lixing Yang et al.   CELL

Existing and Emerging Technologies for Tumor Genomic Profiling

(2013) Laura E. MacConaill   JOURNAL OF CLINICAL ONCOLOGY

The MLL recombinome of acute leukemias in 2013

(2013) C Meyer et al.   LEUKEMIA

Genomic sequencing of meningiomas identifies oncogenic SMO and AKT1 mutations

(2013) Priscilla K Brastianos et al.   NATURE GENETICS

Genomic and Epigenomic Landscapes of Adult De Novo Acute Myeloid Leukemia

(2013)   NEW ENGLAND JOURNAL OF MEDICINE

SoftSearch: Integration of Multiple Sequence Features to Identify Breakpoints of Structural Variations

(2013) Steven N. Hart et al.   PLoS One

Cancer Genome Landscapes

(2013) B. Vogelstein et al.   SCIENCE

Are Results of Targeted Gene Sequencing Ready to Be Used for Clinical Decision Making for Patients with Acute Myelogenous Leukemia?

(2013) Arati V. Rao et al.   Current Hematologic Malignancy Reports

Analysis of insertion-deletion from deep-sequencing data: software evaluation for optimal detection

(2012) J. A. Neuman et al.   BRIEFINGS IN BIOINFORMATICS

SOAPindel: Efficient identification of indels from short paired reads

(2012) S. Li et al.   GENOME RESEARCH

Comprehensive molecular characterization of human colon and rectal cancer

(2012)   NATURE

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Prognostic Relevance of Integrated Genetic Profiling in Acute Myeloid Leukemia

(2012) Jay P. Patel et al.   NEW ENGLAND JOURNAL OF MEDICINE

Chapter 6: Structural Variation and Medical Genomics

(2012) Benjamin J. Raphael   PLoS Computational Biology

CREST maps somatic structural variation in cancer genomes with base-pair resolution

(2011) Jianmin Wang et al.   NATURE METHODS

Genome structural variation discovery and genotyping

(2011) Can Alkan et al.   NATURE REVIEWS GENETICS

High-Throughput Detection of Actionable Genomic Alterations in Clinical Tumor Samples by Targeted, Massively Parallel Sequencing

(2011) Nikhil Wagle et al.   Cancer Discovery

Fast and accurate long-read alignment with Burrows–Wheeler transform

(2010) Heng Li et al.   BIOINFORMATICS

Clinical Implications of the Cancer Genome

(2010) Laura E. MacConaill et al.   JOURNAL OF CLINICAL ONCOLOGY

Pindel: a pattern growth approach to detect break points of large deletions and medium sized insertions from paired-end short reads

(2009) K. Ye et al.   BIOINFORMATICS

Predicting drug susceptibility of non–small cell lung cancers based on genetic lesions

(2009) Martin L. Sos et al.   JOURNAL OF CLINICAL INVESTIGATION

Computational methods for discovering structural variation with next-generation sequencing

(2009) Paul Medvedev et al.   NATURE METHODS

BreakDancer: an algorithm for high-resolution mapping of genomic structural variation

(2009) Ken Chen et al.   NATURE METHODS

Chromosomal translocations: revisited yet again

(2008) J. D. Rowley   BLOOD