Estimation of spatial demographic maps from polymorphism data using a neural network
bioRxiv. 2024.
Smith CC, G Patterson, PL Ralph, AD Kern.
disperseNN2: a neural network for estimating dispersal rate from georeferenced polymorphism data.
BMC Bioinformatics. 2023.
Smith CC, Kern AD.
Dispersal inference from population genetic variation using a convolutional neural network.
Genetics. 2023.
Smith CC, Silas Tittes, Ralph PL, Kern AD.
Machine learning speeds up genetic structure analysis.
Nature Computational Science. 2023. (invited review; not peer-reviewed)
Smith CC.
Gene expression and alternative splicing may contribute to adaptive divergence in sunflower ecotypes.
Heredity. 2023.
Innes P, Smith CC, Goebl A, Kane NC.
Expanding the stdpopsim species catalogue, and lessons learned from realistic genome simulations.
eLife. 2023.
Lauterbur ME, Cavassim MIA, Gladstein AL, Gower G, Pope NS, Tsambos G, Adrion J, Belsare S, Biddanda A, Caudill V, Cury J, Echevarria I, Haller BC, Hasan AR, Huang X, Iasi LNM, Noskova E, Jana Obs ̆teter J, Pavinato VAC, Pearson A, Peede D, Perez MF, Rodrigues MF, Smith CC, Spence JP, Anastasia Teterina, Silas Tittes, Unneberg P, Vazquez JM, Waples RK, Wohns AW, Wong Y, Baumdicker F, Cartwright RA, Gorjanc G, Gutenkunst RN, Kelleher J, Kern AD, Ragsdale AP, Ralph PL, Schrider DR, Gronau I.
A migratory divide spanning two continents is associated with genomic and ecological divergence.
Evolution. 2022.
Turbek SP, Schield DR, Scordato ES, Contina A, Da XW, Liu Y, Liu Y, Pagani-Núñez E, Ren QM, Smith CC, Stricker CA, Wunder M, Zonana DM, Safran RJ.
Aberrant RNA splicing due to genetic incompatibilities in sunflower hybrids.
Evolution. 2021.
Smith CC, Rieseberg LH, Hulke BS, Kane NC.
Sex-linked genetic diversity and differentiation in a globally distributed avian species complex.
Molecular Ecology. 2021.
Schield DR, Scordato ES, Smith CC, Carter JK, Cherkaoui SI, Gombobaatar S, Hajib S, Hanane S, Hund AK, Koyama K, Liang W, Liu Y, Magri N, Rubtsov A, Sheta B, Turbek S, Wilkins M, Yu L, Safran RJ.
The gut microbiota response to helminth infection depends on host sex and genotype.
The ISME Journal. 2020.
Ling F, Steinel N, Weber J, Ma L, Smith CC, Correa D, Zhu B, Bolnick D, Wang G.
Migratory divides coincide with reproductive barriers across replicated avian hybrid zones above the Tibetan Plateau.
Ecology Letters. 2020.
Scordato ES, Smith CC, Semenov GA, Liu Y, Wilkins MR, Liang W, Rubtsov A, Sundev G, Koyama K, Turbek SP, Wunder MB, Stricker CA, Safran RJ.
Leveraging whole genome sequencing data for demographic inference with approximate Bayesian computation.
Molecular Ecology Resources. 2020.
Smith CC, Flaxman SM.
Unifying Theoretical and Empirical Perspectives on Genomic Differentiation.
Trends in Ecology and Evolution. 2019.
Semenov GA, Safran RJ, Smith CC, Turbek SP, Mullen SP, Flaxman SM.
Demographic inference in barn swallows using whole-genome data shows signal for bottleneck and subspecies differentiation during the Holocene.
Molecular Ecology. 2018.
Smith CC, Flaxman SM, Scordato ES, Kane NC, Hund AK, Sheta BM, Safran RJ.
Genetics of alternative splicing evolution during sunflower domestication.
Proceedings of the National Academy of Sciences. 2018.
Smith CC, Tittes S, Mendieta JP, Collier-zans E, Rowe HC, Rieseberg LH, Kane NC.
Book Review: Molecular population genetics. Matthew Hahn.
Molecular Ecology. 2018. (invited review)
Smith CC, Scordato ES, Taylor SA, Tittes S, Vergara D. (all authors contributed equally)
Effects of assortative mate choice on the genomic and morphological structure of a hybrid zone between two bird subspecies.
Molecular Ecology. 2017.
Semenov GA, Scordato ES, Khaydarov DR, Smith CC, Kane NC, Safran RJ.
Dietary input of microbes and host genetic variation shape among-population differences in stickleback gut microbiota.
The ISME journal. 2015.
Smith CC, Snowberg LK, Caporaso JG, Knight R, Bolnick DI.
Wolbachia do not live by reproductive manipulation alone: infection polymorphism in Drosophila suzukii and D. subpulchrella.
Molecular Ecology. 2014.
Hamm CA, Begun DJ, Vo A, Smith CC, Saelao P, Shaver AO, Jaenike J, Turelli M.