Efficient Coalescent Simulation and Genealogical Analysis for Large Sample Sizes

BGT: efficient and flexible genotype query across many samples

(2015) Heng Li   BIOINFORMATICS

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

(2015) Paul R. Staab et al.   BIOINFORMATICS

Big data: The power of petabytes

(2015) Michael Eisenstein   NATURE

A global reference for human genetic variation

(2015) Richard A. Gibbs et al.   NATURE

The UK10K project identifies rare variants in health and disease

(2015)   NATURE

Large-scale whole-genome sequencing of the Icelandic population

(2015) Daniel F Gudbjartsson et al.   NATURE GENETICS

Big Data: Astronomical or Genomical?

(2015) Zachary D. Stephens et al.   PLOS BIOLOGY

Novel insights into the genetics of smoking behaviour, lung function, and chronic obstructive pulmonary disease (UK BiLEVE): a genetic association study in UK Biobank

(2015) Louise V Wain et al.   Lancet Respiratory Medicine

Efficient haplotype matching and storage using the positional Burrows-Wheeler transform (PBWT)

(2014) R. Durbin   BIOINFORMATICS

Cosi2: an efficient simulator of exact and approximate coalescent with selection

(2014) Ilya Shlyakhter et al.   BIOINFORMATICS

A new method for modeling coalescent processes with recombination

(2014) Ying Wang et al.   BMC BIOINFORMATICS

Critical assessment of coalescent simulators in modeling recombination hotspots in genomic sequences

(2014) Tao Yang et al.   BMC BIOINFORMATICS

The Lengths of Admixture Tracts

(2014) M. Liang et al.   GENETICS

Whole-genome sequence variation, population structure and demographic history of the Dutch population

(2014) Laurent C Francioli et al.   NATURE GENETICS

Inferring human population size and separation history from multiple genome sequences

(2014) Stephan Schiffels et al.   NATURE GENETICS

Distortion of genealogical properties when the sample is very large

(2014) Anand Bhaskar et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Coalescent simulation in continuous space: Algorithms for large neighbourhood size

(2014) J. Kelleher et al.   THEORETICAL POPULATION BIOLOGY

The Impact of Population Demography and Selection on the Genetic Architecture of Complex Traits

(2014) Kirk E. Lohmueller   PLoS Genetics

Demography and the Age of Rare Variants

(2014) Iain Mathieson et al.   PLoS Genetics

Genome-Wide Inference of Ancestral Recombination Graphs

(2014) Matthew D. Rasmussen et al.   PLoS Genetics

Coalescent simulation in continuous space

(2013) Jerome Kelleher et al.   BIOINFORMATICS

ACG: rapid inference of population history from recombining nucleotide sequences

(2013) Brendan D O'Fallon   BMC BIOINFORMATICS

Processing genome scale tabular data with wormtable

(2013) Jerome Kelleher et al.   BMC BIOINFORMATICS

SeqSIMLA: a sequence and phenotype simulation tool for complex disease studies

(2013) Ren-Hua Chung et al.   BMC BIOINFORMATICS

A sequential coalescent algorithm for chromosomal inversions

(2013) S Peischl et al.   HEREDITY

Bringing genome-wide association findings into clinical use

(2013) Teri A. Manolio   NATURE REVIEWS GENETICS

Inference in two dimensions: Allele frequencies versus lengths of shared sequence blocks

(2013) N.H. Barton et al.   THEORETICAL POPULATION BIOLOGY

The Geography of Recent Genetic Ancestry across Europe

(2013) Peter Ralph et al.   PLOS BIOLOGY

Coalescent Tree Imbalance and a Simple Test for Selective Sweeps Based on Microsatellite Variation

(2013) Haipeng Li et al.   PLoS Computational Biology

Inferring Demographic History from a Spectrum of Shared Haplotype Lengths

(2013) Kelley Harris et al.   PLoS Genetics

A New Model for Evolution in a Spatial Continuum

(2012) Nick Barton et al.   ELECTRONIC JOURNAL OF PROBABILITY

Differential confounding of rare and common variants in spatially structured populations

(2012) Iain Mathieson et al.   NATURE GENETICS

NeXML: Rich, Extensible, and Verifiable Representation of Comparative Data and Metadata

(2012) Rutger A. Vos et al.   SYSTEMATIC BIOLOGY

Simulation of Molecular Data under Diverse Evolutionary Scenarios

(2012) Miguel Arenas   PLoS Computational Biology

Inference of Population Structure using Dense Haplotype Data

(2012) Daniel John Lawson et al.   PLoS Genetics

fastsimcoal: a continuous-time coalescent simulator of genomic diversity under arbitrarily complex evolutionary scenarios

(2011) Laurent Excoffier et al.   BIOINFORMATICS

HAPGEN2: simulation of multiple disease SNPs

(2011) Zhan Su et al.   BIOINFORMATICS

phenosim - A software to simulate phenotypes for testing in genome-wide association studies

(2011) Torsten Günther et al.   BMC BIOINFORMATICS

An Overview of Population Genetic Data Simulation

(2011) Xiguo Yuan et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

O3-5.2 UK biobank: the need for large prospective epidemiological studies

(2011) R. Collins   JOURNAL OF EPIDEMIOLOGY AND COMMUNITY HEALTH

Inference of human population history from individual whole-genome sequences

(2011) Heng Li et al.   NATURE

GCTA: A Tool for Genome-wide Complex Trait Analysis

(2010) Jian Yang et al.   AMERICAN JOURNAL OF HUMAN GENETICS

MSMS: a coalescent simulation program including recombination, demographic structure and selection at a single locus

(2010) Gregory Ewing et al.   BIOINFORMATICS

DendroPy: a Python library for phylogenetic computing

(2010) J. Sukumaran et al.   BIOINFORMATICS

ETE: a python Environment for Tree Exploration

(2010) Jaime Huerta-Cepas et al.   BMC BIOINFORMATICS

A NEW MODEL FOR EXTINCTION AND RECOLONIZATION IN TWO DIMENSIONS: QUANTIFYING PHYLOGEOGRAPHY

(2010) Nicholas H. Barton et al.   EVOLUTION

Recovering Population Parameters from a Single Gene Genealogy: An Unbiased Estimator of the Growth Rate

(2010) Yosef E. Maruvka et al.   MOLECULAR BIOLOGY AND EVOLUTION

Biopython: freely available Python tools for computational molecular biology and bioinformatics

(2009) P. J. A. Cock et al.   BIOINFORMATICS

Extended Newick: it is time for a standard representation of phylogenetic networks

(2009) Gabriel Cardona et al.   BMC BIOINFORMATICS

mbs: modifying Hudson's ms software to generate samples of DNA sequences with a biallelic site under selection

(2009) Kosuke M Teshima et al.   BMC BIOINFORMATICS

Coalescent Simulation of Intracodon Recombination

(2009) M. Arenas et al.   GENETICS

Fast model-based estimation of ancestry in unrelated individuals

(2009) D. H. Alexander et al.   GENOME RESEARCH

Sequential Markov coalescent algorithms for population models with demographic structure

(2009) A. Eriksson et al.   THEORETICAL POPULATION BIOLOGY

Inferring the Joint Demographic History of Multiple Populations from Multidimensional SNP Frequency Data

(2009) Ryan N. Gutenkunst et al.   PLoS Genetics

Designing Genome-Wide Association Studies: Sample Size, Power, Imputation, and the Choice of Genotyping Chip

(2009) Chris C. A. Spencer et al.   PLoS Genetics

PhyloNet: a software package for analyzing and reconstructing reticulate evolutionary relationships

(2008) Cuong Than et al.   BMC BIOINFORMATICS

Simulation of Genomes: A Review

(2008) Antonio Carvajal-Rodriguez   CURRENT GENOMICS

Fast and flexible simulation of DNA sequence data

(2008) G. K. Chen et al.   GENOME RESEARCH

Proportionally more deleterious genetic variation in European than in African populations

(2008) Kirk E. Lohmueller et al.   NATURE

Genes mirror geography within Europe

(2008) John Novembre et al.   NATURE

Genome-wide association studies for complex traits: consensus, uncertainty and challenges

(2008) Mark I. McCarthy et al.   NATURE REVIEWS GENETICS