Computationally efficient demographic history inference from allele frequencies with supervised machine learning

Autor: Linh N. Tran, Connie K. Sun, Travis J. Struck, Mathews Sajan, Ryan N. Gutenkunst

Inferring past demographic history of natural populations from genomic data is of central concern in many studies across research fields. Previously, our group had developed dadi, a widely used demographic history inference method based on the allele

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_________::5549c60fa6c4156fea1c1aaaea4d7826
https://doi.org/10.1101/2023.05.24.542158

Demes: a standard format for demographic models

Autor: Graham Gower, Aaron P. Ragsdale, Gertjan Bisschop, Ryan N. Gutenkunst, Matthew Hartfield, Ekaterina Noskova, Stephan Schiffels, Travis J. Struck, Jerome Kelleher, Kevin R. Thornton

Publikováno v: Genetics, vol 222, iss 3
Gower, G, Ragsdale, A P, Bisschop, G, Gutenkunst, R N, Hartfield, M, Noskova, E, Schiffels, S, Struck, T J, Kelleher, J & Thornton, K R 2022, ' Demes : a standard format for demographic models ', Genetics, vol. 222, no. 3, iyac131 . https://doi.org/10.1093/genetics/iyac131
Genetics
Gower, G, Ragsdale, A P, Gutenkunst, R N, Hartfield, M, Noskova, E, Struck, T J, Kelleher, J & Thornton, K R 2022, ' Demes : A standard format for demographic models ', Genetics, vol. 222, no. 3, iyac131 . https://doi.org/10.1093/genetics/iyac131

Understanding the demographic history of populations is a key goal in population genetics, and with improving methods and data, ever more complex models are being proposed and tested. Demographic models of current interest typically consist of a set

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::7f86bafdd942c25c10dd2acbe7562d47
https://doi.org/10.1093/genetics/iyac131

Demogenomic modeling of the timing and the processes of early European farmers differentiation

Autor: Laura Winkelbach, Fokke Gerritsen, Maxime Brami, Maria Teschler-Nicola, Christina Papageorgopoulou, Laurent Excoffier, Jens Blöcher, Joachim Pechtl, Andrea Zeeb-Lanz, Nina Marchi, Susanne Kreutzer, Eva Lenneis, Yoan Diekmann, Elissavet Ganiatsou, Travis J. Struck, Valérie Piuz, Vivian Link, Joris Peters, Joachim Burger, Necmi Karul, Sofija Stefanović, Adamandia Kapopoulou, Albert Pukaj, Zuzana Hofmanová, Sevasti Triantaphyllou, Daniel Wegmann, Alexandre Thiéry, Sylwia M. Figarska, Carlos S. Reyna-Blanco, Ilektra Schulz, Ryan N. Gutenkunst

The precise genetic origins of the first Neolithic farming populations, as well as the processes and the timing of their differentiation, remain largely unknown. Based on demogenomic modeling of high-quality ancient genomes, we show that the early fa

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_________::65049f633e12bf17593578f5f8e55a81
https://doi.org/10.1101/2020.11.23.394502

A community-maintained standard library of population genetic models

Autor: Christopher C. Kyriazis, Bernard Y. Kim, Adam Siepel, Graham Gower, Franz Baumdicker, Patrick F. McKenzie, Christopher B. Cole, Jeffrey R. Adrion, Noah Dukler, Jedidiah Carlson, Arun Durvasula, Peter L. Ralph, Georgia Tsambos, Travis J. Struck, Fernando Racimo, Kirk E. Lohmueller, Diego Ortega-Del Vecchyo, Jerome Kelleher, Reed A. Cartwright, Philipp W. Messer, Simon Gravel, Daniel R. Schrider, Ryan N. Gutenkunst, Ilan Gronau, Ariella L. Gladstein, Jared Galloway, Andrew D. Kern, Ekaterina Noskova, Aaron P. Ragsdale

Publikováno v: Adrion, J R, Cole, C B, Dukler, N, Galloway, J G, Gladstein, A L, Gower, G, Kyriazis, C C, Ragsdale, A P, Tsambos, G, Baumdicker, F, Carlson, J, Cartwright, R A, Durvasula, A, Gronau, I, Kim, B Y, McKenzie, P, Messer, P W, Noskova, E, Ortega-Del Vecchyo, D, Racimo, F, Struck, T J, Gravel, S, Gutenkunst, R N, Lohmueller, K E, Ralph, P L, Schrider, D R, Siepel, A, Kelleher, J & Kern, A D 2020, ' A community-maintained standard library of population genetic models ', eLife, vol. 9, 54967 . https://doi.org/10.7554/eLife.54967
eLife, Vol 9 (2020)
eLife

The explosion in population genomic data demands ever more complex modes of analysis, and increasingly these analyses depend on sophisticated simulations. Recent advances in population genetic simulation have made it possible to simulate large and co

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::4678f5b75f7315bef4c6521aa389be2e

The impact of genome-wide association studies on biomedical research publications

Autor: Brian K. Mannakee, Travis J. Struck, Ryan N. Gutenkunst

Publikováno v: Human Genomics
Human Genomics, Vol 12, Iss 1, Pp 1-9 (2018)

The past decade has seen major investment in genome-wide association studies (GWAS), with the goal of identifying and motivating research on novel genes involved in complex human disease. To assess whether this goal is being met, we quantified the ef

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::2a4c0145c82eed1243388efbeb217d41
https://doi.org/10.1101/106773