publications and preprints

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

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: How genes are prioritized by rare and common variant association studies bioRxiv preprint. [.pdf]
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.
Schraiber, J. G., Spence, J. P., and Edge, M. D. Estimation of demography and mutation rates from one million haploid genomes. bioRxiv preprint.
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. medRxiv preprint.
Smith, C. J.†, Strausz, S.†, FinnGenn, Spence, J. P.†, Ollila, H. M.†, and Pritchard, J. K.† Haplotype analysis reveals pleiotropic disease associations in the HLA region. medRxiv preprint.
Aguirre, M.†, Spence, J. P.†, Sella, G.†, and Pritchard, J. K.† Gene regulatory network structure informs the distribution of perturbation effects. bioRxiv preprint.
Batra, S. S.*, Cabrera, A.*, Spence, J. P.*, Hilton, I. B., and Song, Y. S. Predicting the effects of CRISPR-Cas9-based epigenome editing. bioRxiv preprint.
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 preprint.
Czech, L.*, Peng, Y.*, Spence, J. P., et al. Monitoring rapid evolution of plant populations at scale with Pool-sequencing. bioRxiv preprint.

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). [.pdf] [supplement] [.ris]
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). [.pdf] [supplement] [.ris]
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). [.pdf] [.ris]
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). [.pdf] [supplement] [.ris]

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). [.pdf] [supplement] [.ris]
Spence, J. P.†, Zeng, T., Mostafavi, H., and Pritchard, J. K. Scaling the Discrete-time Wright-Fisher model to biobank-scale datasets. Genetics (2023). [.pdf] [.ris]
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. [.pdf] [.ris]
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). [.pdf] [.ris]
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). [.pdf] [.ris]
Lauterbur, M. E., et al. Expanding the stdpopsim catalog, and lessons learned for realistic genome simulations. eLife reviewed preprint (2023).

2022

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). [.pdf] [supplement] [.ris]
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). [.pdf] [supplement] [.ris]

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). [.pdf] [supplement] [.ris]

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). [.pdf] [supplement] [.ris]

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). [.pdf] [supplement] [.ris] [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. [.pdf] [supplement] [.ris] [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). [.pdf] [supplement] [.ris]
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). [.pdf] [supplement] [.ris]
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. [.pdf] [supplement] [.ris]
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. [.pdf] [.ris]

2016

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