Characterizing allele- and haplotype-specific copy numbers in single cells with CHISEL

SCOPE: A Normalization and Copy-Number Estimation Method for Single-Cell DNA Sequencing

(2020) Rujin Wang et al.   Cell Systems

Clonal Decomposition and DNA Replication States Defined by Scaled Single-Cell Genome Sequencing

(2019) Emma Laks et al.   CELL

Genomic and Functional Approaches to Understanding Cancer Aneuploidy

(2018) Alison M. Taylor et al.   CANCER CELL

Chemoresistance Evolution in Triple-Negative Breast Cancer Delineated by Single-Cell Sequencing

(2018) Charissa Kim et al.   CELL

Linking transcriptional and genetic tumor heterogeneity through allele analysis of single-cell RNA-seq data

(2018) Jean Fan et al.   GENOME RESEARCH

Genome doubling shapes the evolution and prognosis of advanced cancers

(2018) Craig M. Bielski et al.   NATURE GENETICS

Comparison of phasing strategies for whole human genomes

(2018) Yongwook Choi et al.   PLoS Genetics

Scalable whole-genome single-cell library preparation without preamplification

(2017) Hans Zahn et al.   NATURE METHODS

Tracking the Evolution of Non–Small-Cell Lung Cancer

(2017) Mariam Jamal-Hanjani et al.   NEW ENGLAND JOURNAL OF MEDICINE

Principles of Reconstructing the Subclonal Architecture of Cancers

(2017) Stefan C. Dentro et al.   Cold Spring Harbor Perspectives in Medicine

Landscape of somatic mutations in 560 breast cancer whole-genome sequences

(2016) Serena Nik-Zainal et al.   NATURE

Reference-based phasing using the Haplotype Reference Consortium panel

(2016) Po-Ru Loh et al.   NATURE GENETICS

A reference panel of 64,976 haplotypes for genotype imputation

(2016)   NATURE GENETICS

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

(2016) Ruli Gao et al.   NATURE GENETICS

Next-generation genotype imputation service and methods

(2016) Sayantan Das et al.   NATURE GENETICS

Single-cell genome sequencing: current state of the science

(2016) Charles Gawad et al.   NATURE REVIEWS GENETICS

FACETS: allele-specific copy number and clonal heterogeneity analysis tool for high-throughput DNA sequencing

(2016) Ronglai Shen et al.   NUCLEIC ACIDS RESEARCH

Inferring the Mutational History of a Tumor Using Multi-state Perfect Phylogeny Mixtures

(2016) Mohammed El-Kebir et al.   Cell Systems

Biological and Therapeutic Impact of Intratumor Heterogeneity in Cancer Evolution

(2015) Nicholas McGranahan et al.   CANCER CELL

The first five years of single-cell cancer genomics and beyond

(2015) Nicholas E. Navin   GENOME RESEARCH

Whole genomes redefine the mutational landscape of pancreatic cancer

(2015) Nicola Waddell et al.   NATURE

Interactive analysis and assessment of single-cell copy-number variations

(2015) Tyler Garvin et al.   NATURE METHODS

PhyloWGS: Reconstructing subclonal composition and evolution from whole-genome sequencing of tumors

(2015) Amit G Deshwar et al.   GENOME BIOLOGY

TITAN: inference of copy number architectures in clonal cell populations from tumor whole-genome sequence data

(2014) Gavin Ha et al.   GENOME RESEARCH

Clonal evolution in breast cancer revealed by single nucleus genome sequencing

(2014) Yong Wang et al.   NATURE

PyClone: statistical inference of clonal population structure in cancer

(2014) Andrew Roth et al.   NATURE METHODS

Allele-specific copy number profiling by next-generation DNA sequencing

(2014) Hao Chen et al.   NUCLEIC ACIDS RESEARCH

High-Definition Reconstruction of Clonal Composition in Cancer

(2014) Andrej Fischer et al.   Cell Reports

Algorithms to Model Single Gene, Single Chromosome, and Whole Genome Copy Number Changes Jointly in Tumor Phylogenetics

(2014) Salim Akhter Chowdhury et al.   PLoS Computational Biology

Phylogenetic Quantification of Intra-tumour Heterogeneity

(2014) Roland F. Schwarz et al.   PLoS Computational Biology

The causes and consequences of genetic heterogeneity in cancer evolution

(2013) Rebecca A. Burrell et al.   NATURE

Pan-cancer patterns of somatic copy number alteration

(2013) Travis I Zack et al.   NATURE GENETICS

Emerging landscape of oncogenic signatures across human cancers

(2013) Giovanni Ciriello et al.   NATURE GENETICS

The Life History of 21 Breast Cancers

(2012) Serena Nik-Zainal et al.   CELL

Integrative analysis of genome-wide loss of heterozygosity and monoallelic expression at nucleotide resolution reveals disrupted pathways in triple-negative breast cancer

(2012) G. Ha et al.   GENOME RESEARCH

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

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

Absolute quantification of somatic DNA alterations in human cancer

(2012) Scott L Carter et al.   NATURE BIOTECHNOLOGY

A statistical framework for SNP calling, mutation discovery, association mapping and population genetical parameter estimation from sequencing data

(2011) H. Li   BIOINFORMATICS

Tumour evolution inferred by single-cell sequencing

(2011) Nicholas Navin et al.   NATURE

Copy neutral loss of heterozygosity: a novel chromosomal lesion in myeloid malignancies

(2010) C. O'Keefe et al.   BLOOD

The landscape of somatic copy-number alteration across human cancers

(2010) Rameen Beroukhim et al.   NATURE

Allele-specific copy number analysis of tumors

(2010) P. Van Loo et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

PICNIC: an algorithm to predict absolute allelic copy number variation with microarray cancer data

(2009) C. D. Greenman et al.   BIOSTATISTICS

A comprehensive catalogue of somatic mutations from a human cancer genome

(2009) Erin D. Pleasance et al.   NATURE

Genome Alteration Print (GAP): a tool to visualize and mine complex cancer genomic profiles obtained by SNP arrays

(2009) Tatiana Popova et al.   GENOME BIOLOGY

What is the expectation maximization algorithm?

(2008) Chuong B Do et al.   NATURE BIOTECHNOLOGY

Prevalence of copy-number neutral LOH in glioblastomas revealed by genomewide analysis of laser-microdissected tissues

(2008) Daisuke Kuga et al.   NEURO-ONCOLOGY

Segmentation-based detection of allelic imbalance and loss-of-heterozygosity in cancer cells using whole genome SNP arrays

(2008) Johan Staaf et al.   GENOME BIOLOGY