Publications and Preprints

I am happy to provide PDFs for any paper listed here upon email request.

For publications with more than a handful of authors, only the first few authors are listed.
A list of publications is also available through Google Scholar

* indicates equal contribution
† indicates co-corresponding author
& indicates authors are listed alphabetically

Preprints

• Gerlach, P. A.*^†, Milind, N.*^†, Spence, J. P.^†, and Pritchard, J. K.^† High false sign rates in transcriptome-wide association studies. bioRxiv preprint.

• Judd, J.^†, Spence, J. P.^†, Milind, N., Kachuri, L., Witte, J. S., and Pritchard, J. K.^† Allele frequencies at recessive disease genes are mainly determined by pleiotropic effects in heterozygotes. bioRxiv preprint.

• Aguirre, M.^†, Spence, J. P.^†, Sella, G.^†, and Pritchard, J. K.^† Regulatory network topology and the genetic architecture of gene expression. bioRxiv preprint.

• Milind, N.^†, Smith, C. J., Zhu, H., Spence, J. P.^†, and Pritchard, J. K.^† Buffering and non-monotonic behavior of gene dosage response curves for human complex traits. medRxiv preprint.

• Mualim, K. S.*, Spence, J. P.*, Weiß, C. L.*, Selmoni, O., Lin, M., and Expósito-Alonso, M. Genetic diversity loss in the Anthropocene will continue long after habitat destruction ends. bioRxiv preprint.

2025

• Ota, M.^†, Spence, J. P., Zeng, T., Dann, E., Milind, N., Marson, A.^†, and Pritchard, J. K.^† Causal modelling of gene effects from regulators to programs to traits. Nature (2025). [research briefing]

• Spence, J. P.*^†, Mostafavi, H.*^†, Ota, M.^†, Milind, N., Gjorgjieva, T., Smith, C. J., Simons, Y. B., Sella, G., and Pritchard, J. K.^† Specificity, length and luck drive gene rankings in association studies. Nature (2025). [research briefing] [research highlight]

• Judd, J., Spence, J. P., Pritchard, J. K., Kachuri, L., and Witte, J. S. Investigating the role of neighborhood socioeconomic status and germline genetics on prostate cancer risk. HGG Advances (2025).

• Aguirre, M.^†, Spence, J. P.^†, Sella, G.^†, and Pritchard, J. K.^† Gene regulatory network structure informs the distribution of perturbation effects. PLoS Computational Biology (2025).

• Schraiber, J. G., Spence, J. P., and Edge, M. D. Estimation of demography and mutation rates from one million haploid genomes. American Journal of Human Genetics (2025).

• Smith, C. J.^†, Strausz, S.^†, FinnGen, Spence, J. P.^†, Ollila, H. M.^†, and Pritchard, J. K.^† Haplotype analysis reveals pleiotropic disease associations in the HLA region. American Journal of Human Genetics (2025).

• Batra, S. S.*, Cabrera, A.*, Spence, J. P.*, Goell, H., Anand, S. S., Hilton, I. B., and Song, Y. S. Predicting the effects of CRIS citationPR-Cas9-based epigenome editing. eLife (2025).

2024

• Patel, R. A.^†, Weiß, C. L., Zhu, H., Mostafavi, H., Simons, Y. B., Spence, J. P.^†, and Pritchard, J. K.^† Characterizing selection on complex traits through conditional frequency spectra. Genetics (2024).

• Czech, L. Spence, J. P., and Expósito-Alonso, M. grenedalf: population genetic statistics for the next generation of pool sequencing. Bioinformatics (2024).

• Rothschild, D.*, Susanto, T. T.*, Sui, X.*, Spence, J. P., Rangan, R., Genuth, N. R., Sinnott-Armstrong, N., Wang, X., Pritchard, J. K.^†, and Barna, M.^† Diversity of ribosomes at the level of rRNA variation associated with human health and disease. Cell Genomics (2024).

• Zeng, T.* ^{, †}, Spence, J. P.* ^{, †}, Mostafavi, H., and Pritchard, J. K.^† Bayesian estimation of gene constraint from an evolutionary model with gene features. Nature Genetics (2024).

• Antonio, M. L.*, Weiß, C. L.*, Gao, Z.*, Sawyer, S.*, Oberreiter, V, Moots, H. M., Spence, J. P., et al. Stable population structure in Europe since the Iron Age, despite high mobility. eLife (2024).

• Aw, A. J., Spence, J. P., and Song, Y. S. A simple and flexible test of sample exchangeability with applications to statistical genomics. Annals of Applied Statistics (2024).

2023

• Mostafavi, H.^†, Spence, J. P., Naqvi, S., and Pritchard, J. K.^†. Systematic differences in discovery of genetic effects on gene expression and complex traits. Nature Genetics (2023).

• Spence, J. P.^†, Zeng, T., Mostafavi, H., and Pritchard, J. K. Scaling the Discrete-time Wright-Fisher model to biobank-scale datasets. Genetics (2023).

• Moots, H. M., Antonio, M. L.*, Sawyer, S.*, Spence, J. P.*, Oberreiter, V.*, Weiß, C. L.*, Lucci, M.*, Cherifi, Y. M. S.*, et al. A genetic history of continuity and mobility in the Iron Age central Mediterranean. Nature Ecology & Evolution, Vol. 7 (2023) 1515-1524.

• Schreiber, J.*, Boix, C.*, et al. The ENCODE Imputation Challenge: A critical assessment of methods for cross-cell type imputation of epigenomic profiles. Genome Biology, Vol. 24 (2023).

• Fan, S.*, Spence, J. P.*, Feng, Y., Hansen, M. E. B., Terhorst, J., Beltrame, M. H., Ranciaro, A., Hirbo, J., Beggs, W., Thomas, N., Nyambo, T., Mpoloka, S. W., Mokone, G. G., Njamnshi, A., Folkunang, C., Meskel, D. W., Belay, G., Song, Y. S., and Tishkoff, S. A. Whole-genome sequencing reveals a complex African population demographic history and signatures of local adaptation. Cell, Vol. 186, Issue 5 (2023).

• Lauterbur, M. E., et al. Expanding the stdpopsim catalog, and lessons learned for realistic genome simulations. eLife reviewed preprint (2023).

2022

• Spence, J. P.^†, Sinnott-Armstrong, N., Assimes, T., and Pritchard, J. K.^† A flexible modeling and inference framework for estimating variant effect sizes from GWAS summary statistics. bioRxiv.

• Czech, L.*, Peng, Y.*, Spence, J. P., et al. Monitoring rapid evolution of plant populations at scale with Pool-sequencing. bioRxiv.

• Expósito-Alonso, M., Booker, T. R.^&, Czech, L.^&, Gillespie, L.^&, Hately, S.^&, Kyriazis, C. C.^&, Lang, P. L. M.^&, Leventhal, L.^&, Nogues-Bravo, D.^&, Pagowski, V.^&, Ruffley, M.^&, Spence, J. P.^&, Toro Arana, S. E.^&, Weiß, C. L.^&, and Zess, E.^& Genetic diversity loss in the Anthropocene. Science, Vol. 377, Issue 6613 (2022).

• Patel, R. A.*, Musharoff, S. A.*, Spence, J. P., et al. Genetic interactions drive heterogeneity in causal variant effect sizes for gene expression and complex traits. American Journal of Human Genetics (2022).

2021

• Naqvi, S.*, Sleyp, Y.*, Hoskens, H., Indencleef, K., Spence, J. P., et al. Shared heritability of human face and brain shape. Nature Genetics (2021).

2020

• Spence, J. P. Flexible mean field variational inference using mixtures of non-overlapping exponential families. Advances in Neural Information Processing Systems 33 (NeurIPS 2020).

2019

• Spence, J. P.^† and Song, Y. S.^† Inference and analysis of population-specific fine-scale recombination maps across 26 diverse human populations. Science Advances, Vol. 5, No. 10, eaaw9206 (2019). [Method: pyrho]

• Steinrücken, M., Kamm, J., Spence, J. P., and Song, Y. S. Inference of complex population histories using whole-genome sequences from multiple populations. PNAS, Vol. 116, No. 34 (2019) 17115-17120. [Method: dical2]

2018

• Chan, J., Perrone, V., Spence, J. P., Jenkins, P., Mathieson, S., and Song Y. S. A likelihood-free inference framework for population genetic data using exchangeable neural networks. Advances in Neural Information Processing Systems 31 (NeurIPS 2018).

• Moreno-Mayar, J. V.*, Vinner, L.*, de Barros Damgaard, P.*, de la Fuente C.*, Chan, J.*, Spence, J. P.*, et al. Early human dispersals within the Americas. Science, Vol. 362, Issue 6419 (2018).

• Steinrücken, M., Spence, J. P., Kamm, J. A., Wieczorek, E. and Song, Y. S. Model-based detection and analysis of introgressed Neanderthal ancestry in modern humans. Molecular Ecology, Vol. 27, No. 19 (2018) 3873-3888.

• Spence, J. P., Steinrücken, M., Terhorst, J., and Song, Y. S. Inference of population history using coalescent HMMs: review and outlook. Current Opinion in Genetics & Development, Vol. 53 (2018) 70-76.

2016

• Mallick et al. The Simons Genome Diversity Project: 300 genomes from 142 diverse populations. Nature, Vol. 538 (2016) 201-206.

• Kamm, J. A.*, Spence, J. P.*, Chan, J., and Song, Y. S. Two-locus likelihoods under variable population size and fine-scale recombination rate estimation. Genetics, Vol. 203, No. 3 (2016) 1381-1399.

• Spence, J. P.*, Kamm, J. A.*, and Song, Y. S. The site frequency spectrum for general coalescents. Genetics, Vol. 202, No. 4 (2016) 1549-1561.