Assessing reliability of intra-tumor heterogeneity estimates from single sample whole exome sequencing data

Integrative inference of subclonal tumour evolution from single-cell and bulk sequencing data

(2019) Salem Malikic et al.   Nature Communications

Deconvolution and phylogeny inference of structural variations in tumor genomic samples

(2018) Jesse Eaton et al.   BIOINFORMATICS

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

(2018) Charissa Kim et al.   CELL

Distribution-based measures of tumor heterogeneity are sensitive to mutation calling and lack strong clinical predictive power

(2018) Javad Noorbakhsh et al.   Scientific Reports

Single-cell DNA sequencing reveals a late-dissemination model in metastatic colorectal cancer

(2017) Marco L. Leung et al.   GENOME RESEARCH

Tumour heterogeneity and resistance to cancer therapies

(2017) Ibiayi Dagogo-Jack et al.   Nature Reviews Clinical Oncology

The evolution of tumour phylogenetics: principles and practice

(2017) Russell Schwartz et al.   NATURE REVIEWS GENETICS

TRACERx Renal: tracking renal cancer evolution through therapy

(2017) Samra Turajlic et al.   Nature Reviews Urology

Ensembl 2018

(2017) Daniel R Zerbino et al.   NUCLEIC ACIDS RESEARCH

Clonal cooperativity in heterogenous cancers

(2017) Hengbo Zhou et al.   SEMINARS IN CELL & DEVELOPMENTAL BIOLOGY

Principles of Reconstructing the Subclonal Architecture of Cancers

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

Association Between Genomic Metrics and Immune Infiltration in Triple-Negative Breast Cancer

(2017) Thomas Karn et al.   JAMA Oncology

New paradigms in clonal evolution: punctuated equilibrium in cancer

(2016) William CH Cross et al.   JOURNAL OF PATHOLOGY

COSMIC: somatic cancer genetics at high-resolution

(2016) Simon A. Forbes et al.   NUCLEIC ACIDS RESEARCH

The somatic mutation profiles of 2,433 breast cancers refines their genomic and transcriptomic landscapes

(2016) Bernard Pereira et al.   Nature Communications

Pan-cancer analysis of the extent and consequences of intratumor heterogeneity

(2015) Noemi Andor et al.   NATURE MEDICINE

TCGAbiolinks: an R/Bioconductor package for integrative analysis of TCGA data

(2015) Antonio Colaprico et al.   NUCLEIC ACIDS RESEARCH

Clonal status of actionable driver events and the timing of mutational processes in cancer evolution

(2015) Nicholas McGranahan et al.   Science Translational Medicine

Systematic pan-cancer analysis of tumour purity

(2015) Dvir Aran et al.   Nature Communications

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

(2015) Amit G Deshwar et al.   GENOME BIOLOGY

Clonal evolution in breast cancer revealed by single nucleus genome sequencing

(2014) Yong Wang et al.   NATURE

Genomic architecture and evolution of clear cell renal cell carcinomas defined by multiregion sequencing

(2014) Marco Gerlinger et al.   NATURE GENETICS

PyClone: statistical inference of clonal population structure in cancer

(2014) Andrew Roth et al.   NATURE METHODS

Dissecting the clonal origins of childhood acute lymphoblastic leukemia by single-cell genomics

(2014) Charles Gawad et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Cancer Evolution: Mathematical Models and Computational Inference

(2014) Niko Beerenwinkel et al.   SYSTEMATIC BIOLOGY

Tumor Evolution in Response to Chemotherapy: Phenotype versus Genotype

(2014) Nicholas E. Navin   Cell Reports

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

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

EXPANDS: expanding ploidy and allele frequency on nested subpopulations

(2013) Noemi Andor et al.   BIOINFORMATICS

Spatiotemporal Dynamics of Intratumoral Immune Cells Reveal the Immune Landscape in Human Cancer

(2013) Gabriela Bindea et al.   IMMUNITY

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

(2013) Kristian Cibulskis et al.   NATURE BIOTECHNOLOGY

Clonal competition with alternating dominance in multiple myeloma

(2012) J. J. Keats et al.   BLOOD

The Life History of 21 Breast Cancers

(2012) Serena Nik-Zainal et al.   CELL

Absolute quantification of somatic DNA alterations in human cancer

(2012) Scott L Carter et al.   NATURE BIOTECHNOLOGY

MATH, a novel measure of intratumor genetic heterogeneity, is high in poor-outcome classes of head and neck squamous cell carcinoma

(2012) Edmund A. Mroz et al.   ORAL ONCOLOGY

Support vector methods for survival analysis: a comparison between ranking and regression approaches

(2011) Vanya Van Belle et al.   ARTIFICIAL INTELLIGENCE IN MEDICINE

survcomp: an R/Bioconductor package for performance assessment and comparison of survival models

(2011) Markus S. Schröder et al.   BIOINFORMATICS

Tumour evolution inferred by single-cell sequencing

(2011) Nicholas Navin et al.   NATURE