Subclonal reconstruction of tumors by using machine learning and population genetics

Pan-cancer analysis of whole genomes

(2020)   NATURE

The evolutionary history of 2,658 cancers

(2020) Moritz Gerstung et al.   NATURE

A community effort to create standards for evaluating tumor subclonal reconstruction

(2020) Adriana Salcedo et al.   NATURE BIOTECHNOLOGY

Resolving genetic heterogeneity in cancer

(2019) Samra Turajlic et al.   NATURE REVIEWS GENETICS

Evolutionary Trajectories of IDHWT Glioblastomas Reveal a Common Path of Early Tumorigenesis Instigated Years ahead of Initial Diagnosis

(2019) Verena Körber et al.   CANCER CELL

Tracing Oncogene Rearrangements in the Mutational History of Lung Adenocarcinoma

(2019) Jake June-Koo Lee et al.   CELL

Spatially constrained tumour growth affects the patterns of clonal selection and neutral drift in cancer genomic data

(2019) Ketevan Chkhaidze et al.   PLoS Computational Biology

Longitudinal molecular trajectories of diffuse glioma in adults

(2019) Floris P. Barthel et al.   NATURE

The Evolutionary Landscape of Localized Prostate Cancers Drives Clinical Aggression

(2018) Shadrielle Melijah G. Espiritu et al.   CELL

Quantification of subclonal selection in cancer from bulk sequencing data

(2018) Marc J. Williams et al.   NATURE GENETICS

The evolutionary landscape of colorectal tumorigenesis

(2018) William Cross et al.   Nature Ecology & Evolution

Between-region genetic divergence reflects the mode and tempo of tumor evolution

(2017) Ruping Sun et al.   NATURE GENETICS

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

Universal Asymptotic Clone Size Distribution for General Population Growth

(2016) Michael D. Nicholson et al.   BULLETIN OF MATHEMATICAL BIOLOGY

Measuring cancer evolution from the genome

(2016) Trevor A Graham et al.   JOURNAL OF PATHOLOGY

Identification of neutral tumor evolution across cancer types

(2016) Marc J Williams et al.   NATURE GENETICS

Genetic drift, selection and the evolution of the mutation rate

(2016) Michael Lynch et al.   NATURE REVIEWS GENETICS

Excess of mutational jackpot events in expanding populations revealed by spatial Luria–Delbrück experiments

(2016) Diana Fusco et al.   Nature Communications

Pan-cancer analysis of intratumor heterogeneity as a prognostic determinant of survival

(2016) Luc G.T. Morris et al.   Oncotarget

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

(2015) Nicholas E. Navin   GENOME RESEARCH

The evolutionary history of lethal metastatic prostate cancer

(2015) Gunes Gundem et al.   NATURE

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

(2015) Noemi Andor et al.   NATURE MEDICINE

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

(2015) Amit G Deshwar et al.   GENOME BIOLOGY

Optimizing Cancer Genome Sequencing and Analysis

(2015) Malachi Griffith et al.   Cell Systems

Scaling Solution in the Large Population Limit of the General Asymmetric Stochastic Luria–Delbrück Evolution Process

(2014) David A. Kessler et al.   JOURNAL OF STATISTICAL PHYSICS

PyClone: statistical inference of clonal population structure in cancer

(2014) Andrew Roth et al.   NATURE METHODS

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

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

Population genetics of neutral mutations in exponentially growing cancer cell populations

(2013) Rick Durrett   ANNALS OF APPLIED PROBABILITY

Large population solution of the stochastic Luria-Delbruck evolution model

(2013) D. A. Kessler et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Life History of 21 Breast Cancers

(2012) Serena Nik-Zainal et al.   CELL

The clonal and mutational evolution spectrum of primary triple-negative breast cancers

(2012) Sohrab P. Shah et al.   NATURE

Clonal evolution in cancer

(2012) Mel Greaves et al.   NATURE

Bayesian Estimation of Beta Mixture Models with Variational Inference

(2011) Zhanyu Ma et al.   IEEE TRANSACTIONS ON PATTERN ANALYSIS AND MACHINE INTELLIGENCE

Power-Law Distributions in Empirical Data

(2009) Aaron Clauset et al.   SIAM REVIEW