2025
E. Weine, S.P. Smith, R.K. Knowlton, A. Harpak+. Tradeoffs in Modeling context dependency in Complex Trait Genetics. eLife 2025
S.P. Smith, O.S. Smith, H. Mostafavi, D. Peng, J.J. Berg, M.D. Edge+, A. Harpak+. A litmus test for confounding in polygenic scores. bioRxiv 2025.
M.J. Ming, Changde Cheng, M. Kirkpatrick, A. Harpak+. No Evidence for Sex-Differential Gene Expression Driving Genome-Wide Sex-Differential Natural Selection. American Journal of Human Genetics 2025
2024
J.M. Cole, C.B. Scott, M.M. Johnson, P.R. Golightly, J. Carlson, M.J. Ming, A. Harpak+. M. Kirkpatrick+. The Battle of the Sexes in Humans is Highly Polygenic. PNAS 2024
J.W. Benning*, J. Carlson*, O.S. Smith, Ruth Shaw, A. Harpak+. Confounding Fuels Mininterpretation in Human Genetics . bioRxiv 2024.
J.Y. Wang, N. Lin, M. Zietz, J. Mares, V.M. Narasimhan, P.A. Rathouz, A. Harpak+. Three Open Questions in Polygenic Score Portability. bioRxiv 2024.
A.H. MacQueen*, L. Zhang*, S.P. Smith*, J. Bonette, A.R. Boe, P.A. Fay, F.B. Fritschi, D.B. Lowry, R.B. Mitchell, F.M. Rouquette Jr., Y. Wu, A. Harpak, T.E. Juenger. Diverse Genotype-by-Weather Interactions in Switchgrass. bioRxiv 2024.
K. Hou. Z. Xu, Y. Ding, R. Mandla, Z. Shi, K. Boulier, A. Harpak, B. Pasaniuc. Calibrated prediction intervals for polygenic scores across diverse contexts. Nature Genetics 2024
O.S. Smith, E. Kun, V.M. Narasimhan. HARE: A Python workflow for analyzing genomic feature enrichment in GWAS datasets, JoSS 2024
R. Sotodudeh, S. Trejo, A. Harpak, D. Conley. Does standard adjustment for genomic population structure capture direct genetic effects? bioRxiv 2024
S.P. Smith*. G. Darnell*, D. Udwin, A. Harpak, S. Ramachandran, L. Crawford,. Accounting for statistical non-additive interactions enables the recovery of missing heritability from GWAS summary statistics. eLife 2024.
2023
C. Zhu, M.J. Ming, J.M. Cole, M.D. Edge, M. Kirkpatrick, A. Harpak+. Amplification is the primary mode of gene-by-sex interaction in complex human traits. Cell Genomics 2023. (Press Release)
2022
M. Le, O. Smith, A. Akbari, A. Harpak+, D. Reich+,,, V.M. Narasimhan+. 1,000 ancient genomes uncover 10,000 years of natural selection in Europe. bioRxiv 2022.
2021
A. Harpak+ & M.D. Edge. GWAS deems parents guilty by association. Proceedings of the National Academy of Sciences (PNAS) 2021.
S. Mohammadi*, L. Yang*, A. Harpak*, M. Rodríguez-Ordoñez, S.H. Alvarez, J. Storz, S. Dobler, A., Crawford, P. Andolfatto. Selection maintains co-adapted amino acid substitutions in toxin resistant toad-eating frogs. Current Biology 2021.
A. Harpak+ & M. Przeworski+. The Evolution of Group Differences in Changing Environments. PLoS Biology 2021
Q. Yu, M. Gralka, M. Duvernoy, M. Sousa, A. Harpak, O. Hallatschek. Mutability of demographic noise in microbial range expansions. ISMEJ 2021; (featured in Nature Microbiology Community)
A. Harpak+, N.R. Garud, N.A. Rosenberg, D.A. Petrov, Matthew Combs, P.S. Pennings, J. Munshi-South+. Genetic Adaptation in New York City Rats. Genome Biology and Evolution 2021; (featured in GBE's 40th anniversary special issue, Nature, The Guardian, The Independent, New York Post, Newsweek, The Sun and more)
2020 and earlier
H. Mostafavi*,+, A. Harpak*,+, I. Agarwal, D. Conley, J.K. Pritchard, M. Przeworski+. Variable Prediction Accuracy of Polygenic Scores Within an Ancestry Group. eLife 2020; featured in a VICE article and an eLife Digest)
J.J. Berg*, A. Harpak*, N. Sinnott-Armstrong*, A.M. Jørgensen, H. Mostafavi, Y. Field, E.A. Boyle, X. Zhang, F. Racimo, J.K. Pritchard, G. Coop. Reduced signal for polygenic adaptation of height in UK Biobank. eLife, 2019; featured in an eLife editorial and in Quanta magazine)
E. Glassberg, Z. Gao, A. Harpak, X. Lan, J.K. Pritchard. Measurement of selective constraint on human gene expression. Genetics, 2019; GSA Genetics Spotlight
V. Garcia, E.C. Glassberg, A. Harpak, M.W. Feldman. Finite-sites multiple mutations interference gives rise to wavelet-like oscillations of multilocus linkage disequilibrium. Journal of the Royal Society Interface, 2018
A. Harpak+,*, X. Lan*, Z. Gao, J.K. Pritchard+. Frequent nonallelic gene conversion on the human lineage and its effect on the divergence of gene duplicates. Proceedings of the National Academy of Sciences (PNAS), 2017
R. Sun, Z. Hu, A. Sottoriva, T.A. Graham, A. Harpak, Z. Ma, J.M. Fischer, D. Shibata, C. Curtis. Genetic Diversity in Multi-Region Sequencing Data Reflects the Mode and Tempo of Tumor Evolution. Nature Genetics, 2017
A. Harpak+,*, A. Bhaskar*, J.K. Pritchard. Effects of mutation rate variation on the distribution of allele frequencies in humans. PLoS Genetics, 2016
A. Raj, S. Wang, H. Shim, A. Harpak, Y.I. Li, B. Engelmann, M. Stephens, Y. Gilad, J. K. Pritchard. Thousands of novel translated open reading frames in humans inferred by ribosome footprint profiling. eLife, 2016
A. Harpak+ and G. Sella+. Neutral null models for diversity in serial transfer evolution experiments. Evolution, 2014