Comprehensive characterization of complex structural variations in cancer by directly comparing genome sequence reads

Chromoplexy: A New Category of Complex Rearrangements in the Cancer Genome

(2013) Michael M. Shen   CANCER CELL

Punctuated Evolution of Prostate Cancer Genomes

(2013) Sylvan C. Baca et al.   CELL

Criteria for Inference of Chromothripsis in Cancer Genomes

(2013) Jan O. Korbel et al.   CELL

Mutational landscape and significance across 12 major cancer types

(2013) Cyriac Kandoth et al.   NATURE

Signatures of mutational processes in human cancer

(2013) Ludmil B. Alexandrov et al.   NATURE

Development and validation of a clinical cancer genomic profiling test based on massively parallel DNA sequencing

(2013) Garrett M Frampton et al.   NATURE BIOTECHNOLOGY

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

(2013) Kristian Cibulskis et al.   NATURE BIOTECHNOLOGY

Recurrent somatic alterations of FGFR1 and NTRK2 in pilocytic astrocytoma

(2013) David T W Jones et al.   NATURE GENETICS

IntOGen-mutations identifies cancer drivers across tumor types

(2013) Abel Gonzalez-Perez et al.   NATURE METHODS

Landscape of somatic mutations and clonal evolution in mantle cell lymphoma

(2013) S. Bea et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

DELLY: structural variant discovery by integrated paired-end and split-read analysis

(2012) T. Rausch et al.   BIOINFORMATICS

Genome Sequencing of Pediatric Medulloblastoma Links Catastrophic DNA Rearrangements with TP53 Mutations

(2012) Tobias Rausch et al.   CELL

Background Mutations in Parental Cells Account for Most of the Genetic Heterogeneity of Induced Pluripotent Stem Cells

(2012) Margaret A. Young et al.   Cell Stem Cell

An integrated map of genetic variation from 1,092 human genomes

(2012)   NATURE

Recurrent mutation of the ID3 gene in Burkitt lymphoma identified by integrated genome, exome and transcriptome sequencing

(2012)   NATURE GENETICS

Primer3—new capabilities and interfaces

(2012) Andreas Untergasser et al.   NUCLEIC ACIDS RESEARCH

ART: a next-generation sequencing read simulator

(2011) Weichun Huang et al.   BIOINFORMATICS

Whole-genome sequencing identifies recurrent mutations in chronic lymphocytic leukaemia

(2011) Xose S. Puente et al.   NATURE

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

(2011) Jianmin Wang et al.   NATURE METHODS

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

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

Effect of read-mapping biases on detecting allele-specific expression from RNA-sequencing data

(2009) Jacob F. Degner et al.   BIOINFORMATICS

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

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

Circos: An information aesthetic for comparative genomics

(2009) M. Krzywinski et al.   GENOME RESEARCH

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

(2009) Ken Chen et al.   NATURE METHODS