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bold: Ragsdale Lab members
Aaron P. Ragsdale, 2023. Human evolution: Neanderthal footprints in African genomes. Current Biology, 33(R1186–R1207).
Mashaal Sohail, María J. Palma-Martinez, Amanda Y. Chong, Consuelo D. Quinto-Cortes, Carmina Barerena-Jonas, Aaron Ragsdale, Santiago G. Medina-Muñoz, ... Andrés Moreno-Estrada, 2023. Mexican Biobank advances population and medical genomics of diverse ancestries. Nature, 622(775-783).
Santiago G. Medina-Muñoz, Diego Ortega-Del Vecchyo, Luis Pablo Cruz-Hervert, Leticia Ferreyra-Reyes, Lourdes Garcia-Garcia, Andrés Moreno-Estrada, Aaron P. Ragsdale, 2023. Demographic Modeling of Admixed Latin American Populations from Whole Genomes. American Journal of Human Genetics, 110:10(1804-1816).
Nigenda-Morales, Sergio F., et al., 2023. The genomic footprint of whaling and isolation in fin whale populations. Nature Communications 14.1: 5465.
Aaron P. Ragsdale, Timothy D. Weaver, Elizabeth G. Atkinson, Eileen Hoal, Marlo Moller, Brenna M. Henn, Simon Gravel, 2023. A weakly structured stem for human origins in Africa. Nature, 617(755-763).
Aaron P. Ragsdale, Kevin R. Thornton, 2023. Multiple sources of uncertainty confound inference of historical human generation times. Molecular Biology and Evolution, doi: 10.1093/molbev/msad160.
M Elise Lauterbur et al, 2023. Expanding the stdpopsim species catalog, and lessons learned for realistic genome simulations. eLife, doi: 10.7554/eLife.84874.
Graham R. Gower, Aaron P. Ragsdale, Gertjan Bisschop, Ryan N. Gutenkunst, Matthew Hartfield, Ekaterina Noskova, Stephan Schiffels, Travis J. Struck, Jerome Kelleher, Kevin Thornton, 2022. Demes: a standard format for demographic models. Genetics, 222(3), iyac131.
Aaron P. Ragsdale, 2022. Local fitness and epistatic effects lead to distinct patterns of linkage disequilibrium in protein-coding genes. Genetics, 221(4), iyac097.
Franz Baumdicker, Gertjan Bisschop, Daniel Goldstein, Graham Gower, Aaron P. Ragsdale, Georgia Tsambos, Sha Zhu, (24 more authors), Jerome Kelleher, 2022. Efficient ancestry and mutation simulation with msprime 1.0. Genetics, 220(3), iyab229.
Kevin A. Bird, Michael A. Hardigan, Aaron P. Ragsdale, Steven J. Knapp, Robert VanBuren, Patrick P. Edger, 2021. Diversification, Spread, and Admixture of Octoploid Strawberry in the Western Hemisphere. American Journal of Botany, 108(11), 2269-2281.
William S. DeWitt, Kameron Decker Harris, Aaron P. Ragsdale, Kelley Harris, 2021. Nonparametric coalescent inference of mutation spectrum history and demography. Proceedings of the National Academy of Sciences (USA), 118(21), e2013798118.
Alex C. McAlvay, Aaron P. Ragsdale, Makenzie E. Mabry, Xinshuai Qi, Kevin A. Bird, Pablo Velaso, Hong An, J. Chris Pires, Eve Emshwiller, 2021. Brassica rapa domestication: Untangling wild and feral forms and convergence of crop morphotypes. Molecular Biology and Evolution 38(8), 3358-3372.
Xin Huang, Alyssa Lyn Fortier, Alec J. Coffman, Travis J. Struck, Megan N. Irby, Jose E. Léon-Burguete, Aaron P. Ragsdale, Ryan N. Gutenkunst, 2019. Inferring genome-wide correlations of mutation fitness effects between populations. Molecular Biology and Evolution, msab162.
Shadi Zabad, Aaron P. Ragsdale, Rosie Sun, Yue Li, Simon Gravel, 2021. Assumptions about frequency-dependent architectures of complex traits bias measures of functional enrichment. Genetic Epidemiology 45(6), 621-632.
The PopSim Consortium (Adrion et al.), 2020. A community-maintained standard library of population genetic models. eLife 9, e54967.
Aaron P. Ragsdale, Dominic Nelson, Simon Gravel, Jerome Kelleher, 2020. Lessons learned from bugs in models of human history. American Journal of Human Genetics 107(4), 583-588.
Dominic Nelson, Jerome Kelleher, Aaron P. Ragsdale, Gil McVean, Simon Gravel, 2020. Accounting for long-range correlations in genome-wide simulations of large cohorts. PLoS Genetics 16(5), e1008619.
Aaron P. Ragsdale, Simon Gravel, 2020. Unbiased Estimation of Linkage Disequilibrium from Unphased Data. Molecular Biology and Evolution 37(3): 923-932.
Aaron P. Ragsdale, Simon Gravel, 2019. Models of archaic admixture and recent history from two-locus statistics. PLOS Genetics 15(6): e1008204.
Aaron P. Ragsdale, Claudia Moreau, Simon Gravel, 2018. Genomic inference using diffusion models and the allele frequency spectrum. Curr. Opinion in Genetics & Devel, 53: 140-147.
Julien Jouganous, Will Long, Aaron P. Ragsdale, Simon Gravel. 2017. Inferring the joint demographic history of multiple populations: beyond the diffusion approximation. Genetics, 206(3): 1549-1567.
Aaron P. Ragsdale, Ryan N. Gutenkunst, 2017. Inferring demographic history using two-locus statistics. Genetics, 206(2): 1037-1048.
Xinshuai Qi, Hong An, Aaron P. Ragsdale, Tara E. Hall, Ryan N. Gutenkunst, J. Chris Pires, Michael S. Barker, 2017. Genomic inferences of domestication events are corroborated by written records in Brassica rapa. Molecular Ecology, 26(13): 3373-3388.
Aaron P. Ragsdale, Alec J. Coffman, PingHsun Hsieh, Travis J. Struck, Ryan N. Gutenkunst, 2016. Triallelic population genomics for inferring correlated fitness effects of same site nonsynonymous mutations. Genetics, 203(1): 513-523.
Brian K. Mannakee, Aaron P. Ragsdale, Mark K. Transtrum, Ryan N. Gutenkunst, 2016. Sloppiness and the geometry of parameter space. in Uncertainty in Biology: a Computational Modeling Approach. Springer, Edited by D Gomez-Cabrero and L Geris.