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

A combinatorial approach for analyzing intra-tumor heterogeneity from high-throughput sequencing data

(2014) Iman Hajirasouliha et al.   BIOINFORMATICS

Inferring clonal evolution of tumors from single nucleotide somatic mutations

(2014) Wei Jiao et al.   BMC BIOINFORMATICS

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

(2014) Gavin Ha et al.   GENOME RESEARCH

Genome sequencing of normal cells reveals developmental lineages and mutational processes

(2014) Sam Behjati et al.   NATURE

Global optimization of somatic variant identification in cancer genomes with a global community challenge

(2014) Paul C Boutros et al.   NATURE GENETICS

PyClone: statistical inference of clonal population structure in cancer

(2014) Andrew Roth et al.   NATURE METHODS

High-Definition Reconstruction of Clonal Composition in Cancer

(2014) Andrej Fischer et al.   Cell Reports

Inferring Clonal Composition from Multiple Sections of a Breast Cancer

(2014) Habil Zare et al.   PLoS Computational Biology

SciClone: Inferring Clonal Architecture and Tracking the Spatial and Temporal Patterns of Tumor Evolution

(2014) Christopher A. Miller et al.   PLoS Computational Biology

Clonal Architecture of Secondary Acute Myeloid Leukemia Defined by Single-Cell Sequencing

(2014) Andrew E. O. Hughes et al.   PLoS Genetics

PurBayes: estimating tumor cellularity and subclonality in next-generation sequencing data

(2013) Nicholas B. Larson et al.   BIOINFORMATICS

EXPANDS: expanding ploidy and allele frequency on nested subpopulations

(2013) Noemi Andor et al.   BIOINFORMATICS

Evolution and Impact of Subclonal Mutations in Chronic Lymphocytic Leukemia

(2013) Dan A. Landau et al.   CELL

Selection and adaptation during metastatic cancer progression

(2013) Christoph A. Klein   NATURE

Tumour heterogeneity in the clinic

(2013) Philippe L. Bedard et al.   NATURE

The causes and consequences of genetic heterogeneity in cancer evolution

(2013) Rebecca A. Burrell et al.   NATURE

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

(2013) Kristian Cibulskis et al.   NATURE BIOTECHNOLOGY

The Cancer Genome Atlas Pan-Cancer analysis project

(2013) John N Weinstein et al.   NATURE GENETICS

The Implications of Clonal Genome Evolution for Cancer Medicine

(2013) Samuel Aparicio et al.   NEW ENGLAND JOURNAL OF MEDICINE

TrAp: a tree approach for fingerprinting subclonal tumor composition

(2013) Francesco Strino et al.   NUCLEIC ACIDS RESEARCH

SomatiCA: Identifying, Characterizing and Quantifying Somatic Copy Number Aberrations from Cancer Genome Sequencing Data

(2013) Mengjie Chen et al.   PLoS One

THetA: inferring intra-tumor heterogeneity from high-throughput DNA sequencing data

(2013) Layla Oesper et al.   GENOME BIOLOGY

Strelka: accurate somatic small-variant calling from sequenced tumor–normal sample pairs

(2012) Christopher T. Saunders et al.   BIOINFORMATICS

Monitoring chronic lymphocytic leukemia progression by whole genome sequencing reveals heterogeneous clonal evolution patterns

(2012) A. Schuh et al.   BLOOD

The Life History of 21 Breast Cancers

(2012) Serena Nik-Zainal et al.   CELL

Clonal evolution in relapsed acute myeloid leukaemia revealed by whole-genome sequencing

(2012) Li Ding et al.   NATURE

Absolute quantification of somatic DNA alterations in human cancer

(2012) Scott L Carter et al.   NATURE BIOTECHNOLOGY

Intratumor Heterogeneity and Branched Evolution Revealed by Multiregion Sequencing

(2012) Marco Gerlinger et al.   NEW ENGLAND JOURNAL OF MEDICINE

Correcting for cancer genome size and tumour cell content enables better estimation of copy number alterations from next-generation sequence data

(2011) Arief Gusnanto et al.   BIOINFORMATICS

Hallmarks of Cancer: The Next Generation

(2011) Douglas Hanahan et al.   CELL

Copy number variation detection in whole-genome sequencing data using the Bayesian information criterion

(2011) R. Xi et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

(2010) Heng Li et al.   BIOINFORMATICS

Tracing the tumor lineage

(2010) Nicholas E. Navin et al.   Molecular Oncology

Genomic Analysis of the Clonal Origins of Relapsed Acute Lymphoblastic Leukemia

(2008) C. G. Mullighan et al.   SCIENCE