[PDF][PDF] The genomic origins of the world's first farmers

…, SM Figarska, E Ganiatsou, A Pukaj, TJ Struck… - Cell, 2022 - cell.com
The precise genetic origins of the first Neolithic farming populations in Europe and Southwest
Asia, as well as the processes and the timing of their differentiation, remain largely …

A community-maintained standard library of population genetic models

…, D Ortega-Del Vecchyo, F Racimo, TJ Struck… - elife, 2020 - elifesciences.org
The explosion in population genomic data demands ever more complex modes of analysis,
and increasingly, these analyses depend on sophisticated simulations. Recent advances in …

Inferring genome-wide correlations of mutation fitness effects between populations

…, AL Fortier, AJ Coffman, TJ Struck… - Molecular Biology …, 2021 - academic.oup.com
The effect of a mutation on fitness may differ between populations depending on environmental
and genetic context, but little is known about the factors that underlie such differences. …

Demes: a standard format for demographic models

…, E Noskova, S Schiffels, TJ Struck, J Kelleher… - Genetics, 2022 - academic.oup.com
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 …

Triallelic population genomics for inferring correlated fitness effects of same site nonsynonymous mutations

AP Ragsdale, AJ Coffman, PH Hsieh, TJ Struck… - Genetics, 2016 - academic.oup.com
The distribution of mutational effects on fitness is central to evolutionary genetics. Typical
univariate distributions, however, cannot model the effects of multiple mutations at the same site…

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

TJ Struck, BK Mannakee, RN Gutenkunst - Human Genomics, 2018 - Springer
The past decade has seen major investment in genome-wide association studies (GWAS).
Among the many goals of GWAS, a major one is to identify and motivate research on novel …

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

LN Tran, CK Sun, TJ Struck, M Sajan, RN Gutenkunst - bioRxiv, 2023 - ncbi.nlm.nih.gov
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 …

Testing whether metazoan tyrosine loss was driven by selection against promiscuous phosphorylation

S Pandya, TJ Struck, BK Mannakee… - Molecular biology …, 2015 - academic.oup.com
Protein tyrosine phosphorylation is a key regulatory modification in metazoans, and the
corresponding kinase enzymes have diversified dramatically. This diversification is correlated …

[HTML][HTML] dadi-cli: Automated and distributed population genetic model inference from allele frequency spectra

X Huang, TJ Struck, SW Davey, RN Gutenkunst - bioRxiv, 2023 - ncbi.nlm.nih.gov
dadi is a popular software package for inferring models of demographic history and natural
selection from population genomic data. But using dadi requires Python scripting and manual …

DFEnitely different: genome-wide characterization of differences in mutation fitness effects between populations

AL Fortier, AJ Coffman, TJ Struck, MN Irby… - bioRxiv, 2019 - biorxiv.org
The effect of a mutation on fitness may differ between populations, depending on environmental
and genetic context. Experimental studies have shown that such differences exist, but …