Publications

Preprints

System drift and speciation, by Josh S Schiffman and Peter L. Ralph, 2021.

Publications

Discovery of Ongoing Selective Sweeps within Anopheles Mosquito Populations Using Deep Learning, by Alexander T. Xue, Daniel R. Schrider, Andrew D. Kern, and the Ag1000G Consortium, in Mol. Biol. Evol., 2021.

Evaluating human autosomal loci for sexually antagonistic viability selection in two large biobanks, by Katja R Kasimatis, Abin Abraham, Peter L Ralph, Andrew D Kern, John A Capra, Patrick C Phillips, in Genetics, 2021.

Quantifying the relationship between genetic diversity and population size suggests natural selection cannot explain Lewontin’s paradox, by Vince Buffalo, in eLife, 2021.

Visualizing population structure with variational autoencoders, by C J Battey, Gabrielle C Coffing, Andrew D Kern, in G3 Genes|Genomes|Genetics, 2021.

A Few Stickleback Suffice for the Transport of Alleles to New Lakes, by Jared Galloway, William A Cresko, Peter Ralph, in G3 Genes|Genomes|Genetics, 2020.

Space is the Place: Effects of Continuous Spatial Structure on Analysis of Population Genetic Data, by CJ Battey, Peter L. Ralph, and Andrew D. Kern, in Genetics, 2020.

Predicting geographic location from genetic variation with deep neural networks, by CJ Battey, Peter L. Ralph, and Andrew D. Kern, in eLife, 2020.

Predicting the Landscape of Recombination Using Deep Learning, by Jeffrey R Adrion, Jared G Galloway, Andrew D Kern, in Molecular Biology and Evolution, 2020.

Widespread selection and gene flow shape the genomic landscape during a radiation of monkeyflowers, by Sean Stankowski, Madeline A. Chase, Allison M. Fuiten, Murillo F. Rodrigues, Peter L. Ralph, and Matthew A Streisfeld, in PLoS Biology, 2019.

An empirical approach to demographic inference with genomic data, by Peter L. Ralph, in Theoretical Population Biology, 2019.

Are populations like a circuit? Comparing isolation by resistance to a new coalescent-based method, by Erik Lundgren and Peter L. Ralph, in Molecular Ecology Resources, 2019.

Local PCA shows how the effect of population structure differs along the genome, by Han Li and Peter Ralph, in Genetics, 2019.

Describes the R package lostruct.

Limits to Genomic Divergence Under Sexually Antagonistic Selection, by Katja R. Kasimatis, Peter L. Ralph and Patrick C. Phillips, in G3, 2019.

Spatial Population Genetics: It’s About Time, by Gideon Bradburd and Peter L. Ralph, in Annual Review of Ecology, Evolution, and Systematics, 2019.

Selected older publications

Supervised machine learning reveals introgressed loci in the genomes of Drosophila simulans and D. sechellia, by Daniel R. Schrider, Julien Ayroles, Daniel R. Matute, Andrew D. Kern, in PLoS Genet, 2018.

Supervised Machine Learning for Population Genetics: A New Paradigm, by Daniel R. Schrider, Andrew D. Kern, in Trends in Genetics, 2018.

diploS/HIC: An Updated Approach to Classifying Selective Sweeps, by Andrew D Kern, Daniel R Schrider, in G3 Genes|Genomes|Genetics, 2018.

Efficient pedigree recording for fast population genetics simulation, by Jerome Kelleher, Kevin Thornton, Jaime Ashander, and Peter Ralph, in PLoS Computational Biology, 2018.

The tools described here are part of tskit.

Tree-sequence recording in SLiM opens new horizons for forward-time simulation of whole genomes, by Benjamin C Haller, Jared Galloway, Jerome Kelleher, Philipp W Messer, and Peter L Ralph., in Molecular Ecology Resources, 2018.

The python package described here is pyslim, and the simulation software is SLiM.

Soft Sweeps Are the Dominant Mode of Adaptation in the Human Genome, by Daniel R. Schrider, Andrew D. Kern, in Molecular Biology and Evolution, 2017.

Exact Calculation of the Joint Allele Frequency Spectrum for Isolation with Migration Models, by Andrew D Kern, Jody Hey, in Genetics, 2017.

S/HIC: Robust Identification of Soft and Hard Sweeps Using Machine Learning, by Daniel R. Schrider, Andrew D. Kern, in PLoS Genetics, 2016.

Effects of Linked Selective Sweeps on Demographic Inference and Model Selection, by Daniel R Schrider, Alexander G Shanku, Andrew D Kern, in Genetics, 2016.

Discoal: flexible coalescent simulations with selection, by Andrew D. Kern, Daniel R. Schrider, in Bioinformatics, 2016.

Soft Shoulders Ahead: Spurious Signatures of Soft and Partial Selective Sweeps Result from Linked Hard Sweeps, by Daniel R Schrider, Fábio K Mendes, Matthew W Hahn, Andrew D Kern, in Genetics, 2015.

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The role of standing variation in geographic convergent adaptation, by Peter Ralph and Graham Coop, in American Naturalist, 2015.

Convergent evolution during local adaptation to patchy landscapes, by Peter Ralph and Graham Coop, in PLoS Genetics, 2015.

Parallel Geographic Variation in Drosophila melanogaster, by Josie A Reinhardt, Bryan Kolaczkowski, Corbin D Jones, David J Begun, Andrew D Kern, in Genetics, 2014.

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The geography of recent genetic ancestry across Europe, by Peter Ralph and Graham Coop,, in PLoS Biology, 2013.

Our summary plus discussion at haldane’s sieve; also discussed at the Loom and nature news)

Genomic Differentiation Between Temperate and Tropical Australian Populations of Drosophila melanogaster, by Bryan Kolaczkowski, Andrew D Kern, Alisha K Holloway, David J Begun, in Genetics, 2011.

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Parallel adaptation: One or many waves of advance of an advantageous allele?, by Peter Ralph and Graham Coop, in Genetics, 2010.

Reviewed by Daniel Wilson, John Hawks, Luke Jostins, and various at Faculty of 1000.

A Population Genetic Hidden Markov Model for Detecting Genomic Regions Under Selection, by A. D. Kern, D. Haussler, in Molecular Biology and Evolution, 2010.

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Human Genome Ultraconserved Elements Are Ultraselected, by S. Katzman, A. D. Kern, G. Bejerano, G. Fewell, L. Fulton, R. K. Wilson, S. R. Salama, D. Haussler, in Science, 2007.

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Population Genomics: Whole-Genome Analysis of Polymorphism and Divergence in Drosophila simulans, by David J Begun, Alisha K Holloway, Kristian Stevens, LaDeana W Hillier, Yu-Ping Poh, Matthew W Hahn, Phillip M Nista, Corbin D Jones, Andrew D Kern, Colin N Dewey, Lior Pachter, Eugene Myers, Charles H Langley, in PLoS Biol, 2007.

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Comparative Genomics of Centrality and Essentiality in Three Eukaryotic Protein-Interaction Networks, by Matthew W. Hahn, Andrew D. Kern, in Molecular Biology and Evolution, 2004.

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Genomic effects of nucleotide substitution in Drosophila simulans, by A. D. Kern, C. D. Jones, D. J. Begun, in Genetics, 2002.

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