Somatic genetic drift and multilevel selection in a clonal seagrass

The architecture of intra-organism mutation rate variation in plants

(2019) Long Wang et al.   PLOS BIOLOGY

Somatic Mutation and Evolution in Plants

(2019) Daniel J. Schoen et al.   Annual Review of Ecology Evolution and Systematics

ape 5.0: an environment for modern phylogenetics and evolutionary analyses in R

(2018) Emmanuel Paradis et al.   BIOINFORMATICS

Quantification of subclonal selection in cancer from bulk sequencing data

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

Mega Clonality in an Aquatic Plant—A Potential Survival Strategy in a Changing Environment

(2018) Eric Bricker et al.   Frontiers in Plant Science

Intraorganismal genetic heterogeneity as a source of genetic variation in modular macroalgae

(2018) Bernabé Santelices et al.   JOURNAL OF PHYCOLOGY

Plant somatic mutations in nature conferring insect and herbicide resistance

(2018) Daniel Simberloff et al.   PEST MANAGEMENT SCIENCE

Neutral tumor evolution?

(2018) Maxime Tarabichi et al.   NATURE GENETICS

Uncertainties in tumor allele frequencies limit power to infer evolutionary pressures

(2017) Javad Noorbakhsh et al.   NATURE GENETICS

Patterns of Stem Cell Divisions Contribute to Plant Longevity

(2016) Agata Burian et al.   CURRENT BIOLOGY

Plant chimeras: The good, the bad, and the ‘Bizzaria’

(2016) Margaret H. Frank et al.   DEVELOPMENTAL BIOLOGY

The genome of the seagrass Zostera marina reveals angiosperm adaptation to the sea

(2016) Jeanine L. Olsen et al.   NATURE

Identification of neutral tumor evolution across cancer types

(2016) Marc J Williams et al.   NATURE GENETICS

Evolution of the Insertion-Deletion Mutation Rate Across the Tree of Life

(2016) Way Sung et al.   G3-Genes Genomes Genetics

Inference of Purifying and Positive Selection in Three Subspecies of Chimpanzees (Pan troglodytes) from Exome Sequencing

(2015) Thomas Bataillon et al.   Genome Biology and Evolution

The evolutionary history of lethal metastatic prostate cancer

(2015) Gunes Gundem et al.   NATURE

Novel R tools for analysis of genome-wide population genetic data with emphasis on clonality

(2015) Zhian N. Kamvar et al.   Frontiers in Genetics

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

Algal mats reduce eelgrass (Zostera marina L.) growth in mixed and monospecific meadows

(2014) Camilla Gustafsson et al.   JOURNAL OF EXPERIMENTAL MARINE BIOLOGY AND ECOLOGY

Genome sequencing of normal cells reveals developmental lineages and mutational processes

(2014) Sam Behjati et al.   NATURE

Pervasive genetic hitchhiking and clonal interference in forty evolving yeast populations

(2013) Gregory I. Lang et al.   NATURE

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

(2013) Kristian Cibulskis et al.   NATURE BIOTECHNOLOGY

A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff

(2012) Pablo Cingolani et al.   FLY

Implications of Extreme Life Span in Clonal Organisms: Millenary Clones in Meadows of the Threatened Seagrass Posidonia oceanica

(2012) Sophie Arnaud-Haond et al.   PLoS One

The variant call format and VCFtools

(2011) P. Danecek et al.   BIOINFORMATICS

CNVnator: An approach to discover, genotype, and characterize typical and atypical CNVs from family and population genome sequencing

(2011) A. Abyzov et al.   GENOME RESEARCH

ggplot2: Elegant Graphics for Data Analysis

(2011) Cedric Ginestet   JOURNAL OF THE ROYAL STATISTICAL SOCIETY SERIES A-STATISTICS IN SOCIETY

Longevity of clonal plants: why it matters and how to measure it

(2010) Lucienne C. de Witte et al.   ANNALS OF BOTANY

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

Widespread genetic mosaicism in the marine angiosperm Zostera marina is correlated with clonal reproduction

(2010) Thorsten B. H. Reusch et al.   EVOLUTIONARY ECOLOGY

Evolution of the mutation rate

(2010) Michael Lynch   TRENDS IN GENETICS

Aging in a Long-Lived Clonal Tree

(2010) Dilara Ally et al.   PLOS BIOLOGY

Mutation Accumulation in Real Branches: Fitness Assays for Genomic Deleterious Mutation Rate and Effect in Large‐Statured Plants

(2009) Stewart T. Schultz et al.   AMERICAN NATURALIST

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

Somatic evolutionary genomics: Mutations during development cause highly variable genetic mosaicism with risk of cancer and neurodegeneration

(2009) S. A. Frank   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA