Inference of past demography, dormancy and self-fertilization rates from whole genome sequence data

Robust Design for Coalescent Model Inference

(2019) Kris V Parag et al.   SYSTEMATIC BIOLOGY

Genomic structure of the native inhabitants of Peninsular Malaysia and North Borneo suggests complex human population history in Southeast Asia

(2018) Chee-Wei Yew et al.   HUMAN GENETICS

Effects of population- and seed bank size fluctuations on neutral evolution and efficacy of natural selection

(2018) Lukas Heinrich et al.   THEORETICAL POPULATION BIOLOGY

Persistent seed banking as eco-evolutionary determinant of plant nucleotide diversity: novel population genetics insights

(2018) Aurélien Tellier   NEW PHYTOLOGIST

The IICR and the non-stationary structured coalescent: towards demographic inference with arbitrary changes in population structure

(2018) Willy Rodríguez et al.   HEREDITY

Madeiran Arabidopsis thaliana Reveals Ancient Long-Range Colonization and Clarifies Demography in Eurasia

(2017) Andrea Fulgione et al.   MOLECULAR BIOLOGY AND EVOLUTION

African genomes illuminate the early history and transition to selfing inArabidopsis thaliana

(2017) Arun Durvasula et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Spontaneous Mutation Accumulation inDaphnia pulexin Selection-Free vs. Competitive Environments

(2016) Jullien M. Flynn et al.   MOLECULAR BIOLOGY AND EVOLUTION

Robust and scalable inference of population history from hundreds of unphased whole genomes

(2016) Jonathan Terhorst et al.   NATURE GENETICS

Determinants of genetic diversity

(2016) Hans Ellegren et al.   NATURE REVIEWS GENETICS

Effects of the population pedigree on genetic signatures of historical demographic events

(2016) John Wakeley et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Multiple alleles at a single locus control seed dormancy in Swedish Arabidopsis

(2016) Envel Kerdaffrec et al.   eLife

scrm: efficiently simulating long sequences using the approximated coalescent with recombination

(2015) Paul R. Staab et al.   BIOINFORMATICS

Complete Genomes Reveal Signatures of Demographic and Genetic Declines in the Woolly Mammoth

(2015) Eleftheria Palkopoulou et al.   CURRENT BIOLOGY

Bayesian Nonparametric Inference of Population Size Changes from Sequential Genealogies

(2015) J. A. Palacios et al.   GENETICS

Signatures of positive selection: from selective sweeps at individual loci to subtle allele frequency changes in polygenic adaptation

(2015) Wolfgang Stephan   MOLECULAR ECOLOGY

Inferring human population size and separation history from multiple genome sequences

(2014) Stephan Schiffels et al.   NATURE GENETICS

A Critical Assessment of Storytelling: Gene Ontology Categories and the Importance of Validating Genomic Scans

(2012) Pavlos Pavlidis et al.   MOLECULAR BIOLOGY AND EVOLUTION

Germ banks affect the inference of past demographic events

(2012) Daniel Živković et al.   MOLECULAR ECOLOGY

Spindle Assembly and Spatial Distribution of γ-tubulin during Abortive Meiosis and Cleavage Division in the Parthenogenetic Water FleaDaphnia pulex

(2012) Chizue Hiruta et al.   ZOOLOGICAL SCIENCE

A New Isolation with Migration Model along Complete Genomes Infers Very Different Divergence Processes among Closely Related Great Ape Species

(2012) Thomas Mailund et al.   PLoS Genetics

The recombination landscape in Arabidopsis thaliana F2 populations

(2011) P A Salomé et al.   HEREDITY

Inference of human population history from individual whole-genome sequences

(2011) Heng Li et al.   NATURE

Whole-genome sequencing of multiple Arabidopsis thaliana populations

(2011) Jun Cao et al.   NATURE GENETICS

Microbial seed banks: the ecological and evolutionary implications of dormancy

(2011) Jay T. Lennon et al.   NATURE REVIEWS MICROBIOLOGY

Inference of seed bank parameters in two wild tomato species using ecological and genetic data

(2011) A. Tellier et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Abortive meiosis in the oogenesis of parthenogenetic Daphnia pulex

(2010) Chizue Hiruta et al.   CHROMOSOME RESEARCH

The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data

(2010) A. McKenna et al.   GENOME RESEARCH

The Rate and Molecular Spectrum of Spontaneous Mutations in Arabidopsis thaliana

(2010) S. Ossowski et al.   SCIENCE

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