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

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.
Czech, L. Spence, J. P., and Expósito-Alonso, M. grenedalf: population genetic statistics for the next generation of pool sequencing arXiv preprint.
Zeng, T.* ^, †, Spence, J. P.* ^, †, Mostafavi, H., and Pritchard, J. K.† Bayesian estimation of gene constraint from an evolutionary model with gene features. bioRxiv preprint.
Rothschild, D.*, Susanto, T. T.*, Spence, J. P., Genuth, N. R., Sinnott-Armstrong, N., Pritchard, J. K., and Barna, M. A comprehensive rRNA variation atlas in health and disease. bioRxiv preprint. [.pdf]
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

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]