Genome-wide reconstruction of complex structural variants using read clouds

Haplotyping germline and cancer genomes with high-throughput linked-read sequencing

(2016) Grace X Y Zheng et al.   NATURE BIOTECHNOLOGY

Punctuated copy number evolution and clonal stasis in triple-negative breast cancer

(2016) Ruli Gao et al.   NATURE GENETICS

Read clouds uncover variation in complex regions of the human genome

(2015) Alex Bishara et al.   GENOME RESEARCH

An integrated map of structural variation in 2,504 human genomes

(2015) Peter H. Sudmant et al.   NATURE

Cell-lineage heterogeneity and driver mutation recurrence in pre-invasive breast neoplasia

(2015) Ziming Weng et al.   Genome Medicine

The Architecture and Evolution of Cancer Neochromosomes

(2014) Dale W. Garsed et al.   CANCER CELL

Haplotype-resolved whole-genome sequencing by contiguity-preserving transposition and combinatorial indexing

(2014) Sasan Amini et al.   NATURE GENETICS

LUMPY: a probabilistic framework for structural variant discovery

(2014) Ryan M Layer et al.   GENOME BIOLOGY

Diverse Mechanisms of Somatic Structural Variations in Human Cancer Genomes

(2013) Lixing Yang et al.   CELL

Punctuated Evolution of Prostate Cancer Genomes

(2013) Sylvan C. Baca et al.   CELL

Genome evolution during progression to breast cancer

(2013) D. E. Newburger et al.   GENOME RESEARCH

Phenotypic impact of genomic structural variation: insights from and for human disease

(2013) Joachim Weischenfeldt et al.   NATURE REVIEWS GENETICS

The genome sequence of the colonial chordate, Botryllus schlosseri

(2013) Ayelet Voskoboynik et al.   eLife

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

(2012) T. Rausch et al.   BIOINFORMATICS

IDBA-UD: a de novo assembler for single-cell and metagenomic sequencing data with highly uneven depth

(2012) Y. Peng et al.   BIOINFORMATICS

Accurate whole-genome sequencing and haplotyping from 10 to 20 human cells

(2012) Brock A. Peters et al.   NATURE

Complex reorganization and predominant non-homologous repair following chromosomal breakage in karyotypically balanced germline rearrangements and transgenic integration

(2012) Colby Chiang et al.   NATURE GENETICS

Massive Genomic Rearrangement Acquired in a Single Catastrophic Event during Cancer Development

(2011) Philip J. Stephens et al.   CELL

Estimation of rearrangement phylogeny for cancer genomes

(2011) C. D. Greenman et al.   GENOME RESEARCH

Characterizing complex structural variation in germline and somatic genomes

(2011) Aaron R. Quinlan et al.   TRENDS IN GENETICS