Deep Learning for Population Genetic Inference

The Drosophila Genome Nexus: A Population Genomic Resource of 623 Drosophila melanogaster Genomes, Including 197 from a Single Ancestral Range Population

(2015) Justin B. Lack et al.   GENETICS

Soft Shoulders Ahead: Spurious Signatures of Soft and Partial Selective Sweeps Result from Linked Hard Sweeps

(2015) D. R. Schrider et al.   GENETICS

Predicting the sequence specificities of DNA- and RNA-binding proteins by deep learning

(2015) Babak Alipanahi et al.   NATURE BIOTECHNOLOGY

Recent Selective Sweeps in North American Drosophila melanogaster Show Signatures of Soft Sweeps

(2015) Nandita R. Garud et al.   PLoS Genetics

The Drosophila Genome Nexus: A Population Genomic Resource of 623 Drosophila melanogaster Genomes, Including 197 from a Single Ancestral Range Population

(2015) Justin B. Lack et al.   GENETICS

Deep learning of the tissue-regulated splicing code

(2014) Michael K. K. Leung et al.   BIOINFORMATICS

The Rhino-Deadlock-Cutoff Complex Licenses Noncanonical Transcription of Dual-Strand piRNA Clusters in Drosophila

(2014) Fabio Mohn et al.   CELL

Reproductive hacking

(2014) C Dustin Rubinstein et al.   FLY

Space–time wiring specificity supports direction selectivity in the retina

(2014) Jinseop S. Kim et al.   NATURE

Computer science: The learning machines

(2014) Nicola Jones   NATURE

Inferring human population size and separation history from multiple genome sequences

(2014) Stephan Schiffels et al.   NATURE GENETICS

The human splicing code reveals new insights into the genetic determinants of disease

(2014) H. Y. Xiong et al.   SCIENCE

A Fast Estimate for the Population Recombination Rate Based on Regression

(2013) K. Lin et al.   GENETICS

Learning Natural Selection from the Site Frequency Spectrum

(2013) R. Ronen et al.   GENETICS

Estimating Variable Effective Population Sizes from Multiple Genomes: A Sequentially Markov Conditional Sampling Distribution Approach

(2013) S. Sheehan et al.   GENETICS

SweeD: Likelihood-Based Detection of Selective Sweeps in Thousands of Genomes

(2013) Pavlos Pavlidis et al.   MOLECULAR BIOLOGY AND EVOLUTION

Adaptive divergence of a transcriptional enhancer between populations of Drosophila melanogaster

(2013) A. Glaser-Schmitt et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Kernel approximate Bayesian computation in population genetic inferences

(2013) Shigeki Nakagome et al.   Statistical Applications in Genetics and Molecular Biology

A Comparative Review of Dimension Reduction Methods in Approximate Bayesian Computation

(2013) M. G. B. Blum et al.   STATISTICAL SCIENCE

Demographic Inference Reveals African and European Admixture in the North American Drosophila melanogaster Population

(2012) P. Duchen et al.   GENETICS

A Novel Approach for Choosing Summary Statistics in Approximate Bayesian Computation

(2012) S. Aeschbacher et al.   GENETICS

Constructing summary statistics for approximate Bayesian computation: semi-automatic approximate Bayesian computation

(2012) Paul Fearnhead et al.   JOURNAL OF THE ROYAL STATISTICAL SOCIETY SERIES B-STATISTICAL METHODOLOGY

A Unified Multitask Architecture for Predicting Local Protein Properties

(2012) Yanjun Qi et al.   PLoS One

Distinguishing between Selective Sweeps from Standing Variation and from a De Novo Mutation

(2012) Benjamin M. Peter et al.   PLoS Genetics

Quantifying the Variation in the Effective Population Size Within a Genome

(2011) Toni I. Gossmann et al.   GENETICS

Joint analysis of demography and selection in population genetics: where do we stand and where could we go?

(2011) JUNRUI LI et al.   MOLECULAR ECOLOGY

Inference of human population history from individual whole-genome sequences

(2011) Heng Li et al.   NATURE

Approximate Bayesian Computation in Evolution and Ecology

(2010) Mark A. Beaumont   Annual Review of Ecology Evolution and Systematics

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

(2010) Gregory Ewing et al.   BIOINFORMATICS

ABCtoolbox: a versatile toolkit for approximate Bayesian computations

(2010) Daniel Wegmann et al.   BMC BIOINFORMATICS

Distinguishing Positive Selection From Neutral Evolution: Boosting the Performance of Summary Statistics

(2010) K. Lin et al.   GENETICS

Searching for Footprints of Positive Selection in Whole-Genome SNP Data From Nonequilibrium Populations

(2010) P. Pavlidis et al.   GENETICS

Likelihood-Free Inference of Population Structure and Local Adaptation in a Bayesian Hierarchical Model

(2010) E. Bazin et al.   GENETICS

On Optimal Selection of Summary Statistics for Approximate Bayesian Computation

(2010) Matthew A Nunes et al.   Statistical Applications in Genetics and Molecular Biology

Adaptive approximate Bayesian computation

(2009) M. A. Beaumont et al.   BIOMETRIKA

Non-linear regression models for Approximate Bayesian Computation

(2009) Michael G. B. Blum et al.   STATISTICS AND COMPUTING

Pervasive Natural Selection in the Drosophila Genome?

(2009) Guy Sella et al.   PLoS Genetics

Inferring the Strength of Selection in Drosophila under Complex Demographic Models

(2008) J. Gonzalez et al.   MOLECULAR BIOLOGY AND EVOLUTION

Genes mirror geography within Europe

(2008) John Novembre et al.   NATURE

Approximately Sufficient Statistics and Bayesian Computation

(2008) Paul Joyce et al.   Statistical Applications in Genetics and Molecular Biology

An Approximate Bayesian Estimator Suggests Strong, Recurrent Selective Sweeps in Drosophila

(2008) Jeffrey D. Jensen et al.   PLoS Genetics