Publications

Preprints

Accurate Detection of Incomplete Lineage Sorting via Supervised Machine Learning, by Benjamin Rosenzweig, Andrew D. Kern, Matthew W. Hahn, 2023.

Shared evolutionary processes shape landscapes of genomic variation in the great apes, by Murillo F. Rodrigues, Andrew D Kern, and Peter L Ralph, 2023.

Evaluating evidence for co-geography in the Anopheles Plasmodium host-parasite system, by Clara T Rehmann, Peter L Ralph, and Andrew D Kern, 2023.

A Quantitative Genetic Model of Background Selection in Humans, by Vince Buffalo and Andrew D. Kern, 2023.

slendr: a framework for spatio-temporal population genomic simulations on geographic landscapes, by Martin Petr, Benjamin C. Haller, Peter L. Ralph, and Fernando Racimo, 2022.

Publications

disperseNN2: a neural network for estimating dispersal distance from georeferenced polymorphism data, by Chris C. R. Smith and Andrew D. Kern, in BMC Bioinformatics, 2023.

Describes the software package disperseNN2.

Dispersal inference from population genetic variation using a convolutional neural network, by Chris C. R. Smith, Silas Tittes, Peter L. Ralph, Andrew D. Kern, in Genetics, 2023.

Describes the software package disperseNN.

Standing genetic variation and chromosome differences drove rapid ecotype formation in a major malaria mosquito, by Scott T. Small, Carlo Costantini, N’Fale Sagnon, Moussa W. Guelbeogo, Scott J. Emrich, Andrew D. Kern, Michael C. Fontaine, Nora J. Besansky, in Proc. Natl. Acad. Sci. U.S.A., 2023.

Expanding the stdpopsim species catalog, and lessons learned for realistic genome simulations, by M. Elise Lauterbur, Maria Izabel A. Cavassim, Ariella L. Gladstein, Graham Gower, Nathaniel S. Pope, Georgia Tsambos, Jeffrey Adrion, Saurabh Belsare, Arjun Biddanda, Victoria Caudill, Jean Cury, Ignacio Echevarria, Benjamin C. Haller, Ahmed R. Hasan, Xin Huang, Leonardo Nicola Martin Iasi, Ekaterina Noskova, Jana Obšteter, Vitor Antonio Corrêa Pavinato, Alice Pearson, David Peede, Manolo F. Perez, Murillo F. Rodrigues, Chris C.R. Smith, Jeffrey P. Spence, Anastasia Teterina, Silas Tittes, Per Unneberg, Juan Manuel Vazquez, Ryan K. Waples, Anthony Wilder Wohns, Yan Wong, Franz Baumdicker, Reed A. Cartwright, Gregor Gorjanc, Ryan N. Gutenkunst, Jerome Kelleher, Andrew D. Kern, Aaron P. Ragsdale, Peter L. Ralph, Daniel R. Schrider, Ilan Gronau, in eLife, 2023.

Cell types and molecular architecture of the octopus visual system, by Jeremea O. Songco-Casey, Gabrielle C. Coffing, Denise M. Piscopo, Judit R. Pungor, Andrew D. Kern, Adam C. Miller, and Cristopher M. Niell, in Current Biology, 2022.

System drift and speciation, by Josh S Schiffman and Peter L. Ralph, in Evolution, 2022.

Enabling Inference for Context-Dependent Models of Mutation by Bounding the Propagation of Dependency, by Frederick A. Matsen, Peter L. Ralph, in Journal of Computational Biology, 2022.

Efficient ancestry and mutation simulation with msprime 1.0, by Franz Baumdicker, Gertjan Bisschop, Daniel Goldstein, Graham Gower, Aaron P Ragsdale, Georgia Tsambos, Sha Zhu, Bjarki Eldon, E Castedo Ellerman, Jared G Galloway, Ariella L Gladstein, Gregor Gorjanc, Bing Guo, Ben Jeffery, Warren W Kretzschumar, Konrad Lohse, Michael Matschiner, Dominic Nelson, Nathaniel S Pope, Consuelo D Quinto-Cortés, Murillo F Rodrigues, Kumar Saunack, Thibaut Sellinger, Kevin Thornton, Hugo van Kemenade, Anthony W Wohns, Yan Wong, Simon Gravel, Andrew D Kern, Jere Koskela, Peter L Ralph, Jerome Kelleher, in Genetics, 2022.

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.

Describes the software package ‘locator’.

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.

|| journal || code

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.

|| journal

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.

|| journal

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.

|| journal || code

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.

|| journal

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.

|| journal

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.

|| journal

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

|| journal