ReMixT: clone-specific genomic structure estimation in cancer.
Genomic consequences of aberrant DNA repair mechanisms stratify ovarian cancer histotypes.
Divergent modes of clonal spread and intraperitoneal mixing in high-grade serous ovarian cancer.
Systematic analysis of somatic mutations impacting gene expression in 12 tumour types.
Multifocal endometriotic lesions associated with cancer are clonal and carry a high mutation burden.
Dynamics of genomic clones in breast cancer patient xenografts at single-cell resolution.
An RCOR1 loss-associated gene expression signature identifies a prognostically significant DLBCL subgroup.
TITAN: inference of copy number architectures in clonal cell populations from tumor whole-genome sequence data.
PyClone: statistical inference of clonal population structure in cancer.
Distinct evolutionary trajectories of primary high-grade serous ovarian cancers revealed through spatial mutational profiling.
Distinguishing somatic and germline copy number events in cancer patient DNA hybridized to whole-genome SNP genotyping arrays.
DriverNet: uncovering the impact of somatic driver mutations on transcriptional networks in cancer.
Mutation discovery in regions of segmental cancer genome amplifications with CoNAn-SNV: a mixture model for next generation sequencing of tumors.
Integrative analysis of genome-wide loss of heterozygosity and monoallelic expression at nucleotide resolution reveals disrupted pathways in triple-negative breast cancer.
The genomic and transcriptomic architecture of 2,000 breast tumours reveals novel subgroups.
The clonal and mutational evolution spectrum of primary triple-negative breast cancers.
JointSNVMix: a probabilistic model for accurate detection of somatic mutations in normal/tumour paired next-generation sequencing data.
Recurrent somatic DICER1 mutations in nonepithelial ovarian cancers.
Using next-generation sequencing for the diagnosis of rare disorders: a family with retinitis pigmentosa and skeletal abnormalities.
deFuse: an algorithm for gene fusion discovery in tumor RNA-Seq data.
ARID1A mutations in endometriosis-associated ovarian carcinomas.
SNVMix: predicting single nucleotide variants from next-generation sequencing of tumors.