Measuring the distribution of fitness effects in somatic evolution by combining clonal dynamics with dN/dS ratios

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

Measuring Clonal Evolution in Cancer with Genomics

(2019) Marc J. Williams et al.   Annual Review of Genomics and Human Genetics

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

New Insights from Studies of Clonal Hematopoiesis

(2018) Christopher J. Gibson et al.   CLINICAL CANCER RESEARCH

Mapping the in vivo fitness landscape of lung adenocarcinoma tumor suppression in mice

(2018) Zoë N. Rogers et al.   NATURE GENETICS

Quantification of subclonal selection in cancer from bulk sequencing data

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

The effects of mutational processes and selection on driver mutations across cancer types

(2018) Daniel Temko et al.   Nature Communications

Comprehensive Characterization of Cancer Driver Genes and Mutations

(2018) Matthew H. Bailey et al.   CELL

OUP accepted manuscript

(2018)   JNCI-Journal of the National Cancer Institute

Population dynamics of normal human blood inferred from somatic mutations

(2018) Henry Lee-Six et al.   NATURE

Detecting repeated cancer evolution from multi-region tumor sequencing data

(2018) Giulio Caravagna et al.   NATURE METHODS

Somatic mutant clones colonize the human esophagus with age

(2018) Iñigo Martincorena et al.   SCIENCE

brms: An R Package for Bayesian Multilevel Models Using Stan

(2017) Paul-Christian Bürkner   Journal of Statistical Software

Bayesian inference of negative and positive selection in human cancers

(2017) Donate Weghorn et al.   NATURE GENETICS

Julia: A Fresh Approach to Numerical Computing

(2017) Jeff Bezanson et al.   SIAM REVIEW

Mutational Signatures Are Critical for Proper Estimation of Purifying Selection Pressures in Cancer Somatic Mutation Data When Using the dN/dS Metric

(2017) Jimmy Van den Eynden et al.   Frontiers in Genetics

The Ecology and Evolution of Cancer: The Ultra-Microevolutionary Process

(2016) Chung-I Wu et al.   Annual Review of Genetics

Universal Asymptotic Clone Size Distribution for General Population Growth

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

Identification of neutral tumor evolution across cancer types

(2016) Marc J Williams et al.   NATURE GENETICS

Constrained positive selection on cancer mutations in normal skin

(2016) Iñigo Martincorena et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Reply to Martincorena et al.: Evidence for constrained positive selection of cancer mutations in normal skin is lacking

(2016) Benjamin D. Simons   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Practical Bayesian model evaluation using leave-one-out cross-validation and WAIC

(2016) Aki Vehtari et al.   STATISTICS AND COMPUTING

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

(2016) Diana Fusco et al.   Nature Communications

Quantifying Clonal and Subclonal Passenger Mutations in Cancer Evolution

(2016) Ivana Bozic et al.   PLoS Computational Biology

A Big Bang model of human colorectal tumor growth

(2015) Andrea Sottoriva et al.   NATURE GENETICS

Deep sequencing as a probe of normal stem cell fate and preneoplasia in human epidermis

(2015) Benjamin D. Simons   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Extremely high genetic diversity in a single tumor points to prevalence of non-Darwinian cell evolution

(2015) Shaoping Ling et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

High burden and pervasive positive selection of somatic mutations in normal human skin

(2015) I. Martincorena et al.   SCIENCE

Differentiation imbalance in single oesophageal progenitor cells causes clonal immortalization and field change

(2014) Maria P. Alcolea et al.   NATURE CELL BIOLOGY

Population genetics of neutral mutations in exponentially growing cancer cell populations

(2013) Rick Durrett   ANNALS OF APPLIED PROBABILITY

Why Time Matters: Codon Evolution and the Temporal Dynamics of dN/dS

(2013) Carina F. Mugal et al.   MOLECULAR BIOLOGY AND EVOLUTION

Mutational heterogeneity in cancer and the search for new cancer-associated genes

(2013) Michael S. Lawrence et al.   NATURE

Defining Stem Cell Dynamics in Models of Intestinal Tumor Initiation

(2013) L. Vermeulen et al.   SCIENCE

Stochastic homeostasis in human airway epithelium is achieved by neutral competition of basal cell progenitors

(2013) Vitor H Teixeira et al.   eLife

Snakemake--a scalable bioinformatics workflow engine

(2012) J. Koster et al.   BIOINFORMATICS

A Single Progenitor Population Switches Behavior to Maintain and Repair Esophageal Epithelium

(2012) D. P. Doupe et al.   SCIENCE

Universal patterns of stem cell fate in cycling adult tissues

(2011) A. M. Klein et al.   DEVELOPMENT

Spatial structure increases the waiting time for cancer

(2011) Erik A Martens et al.   NEW JOURNAL OF PHYSICS

Intestinal Stem Cell Replacement Follows a Pattern of Neutral Drift

(2010) C. Lopez-Garcia et al.   SCIENCE

Stochastic fate of p53-mutant epidermal progenitor cells is tilted toward proliferation by UV B during preneoplasia

(2009) A. M. Klein et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Population Genetics of dN/dS

(2008) Sergey Kryazhimskiy et al.   PLoS Genetics