Publications
CEHG members work across diverse areas in the life sciences. On this page you'll find selected publications from over the years.
Publications
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Featured publication
Stable population structure in Europe since the Iron Age, despite high mobility
A Stanford Medicine team led by CEHG Co-Director Jonathan Pritchard analyzed thousands of genomes, including those newly sequenced from 204 skeletons, to gain insight into how and where people moved during the Roman Empire.
Selected publications from CEHG research
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- Shiff, C., & Rosen, N. (2026). Enumeration of rooted binary perfect phylogenies. Discrete Applied Math. https://doi.org/10.1016/j.dam.2025.10.053
- Ramachandran, S., & Rosenberg, N. (2026). Reflections on the Human Genome Diversity Project: a conversation with Marcus W. Feldman, Henry T. Greely, and Mary-Claire King. Genetics. https://doi.org/10.1093/genetics/iyaf273
- Payne, C., Ly, D., Rodriguez-Soto, R., Powell, D., Robles, N., Gunn, T., Baczenas, J., Bergman, A., Pollock, A., Moran, B., Baker, J., Reznick, D., & Schumer, M. (2026). Recent evolution of large offspring size and post-fertilization nutrient provisioning in swordtails. Proceedings Biological Sciences. https://doi.org/10.1098/rspb.2025.1945
- Laursen, R., Chen, H., Demaray, J., Pelka, K., & Engelhardt, B. (2026). Neighborhood nonnegative matrix factorization identifies patterns and spatially-variable genes in large-scale spatial transcriptomics data. Genome Biology. https://doi.org/10.1186/s13059-025-03846-6
- Ota, M., Spence, J., Zeng, T., Dann, E., Milind, N., Marson, A., & Pritchard, J. (2025). Causal modelling of gene effects from regulators to programs to traits. Nature, 650(8101), 399-408. https://doi.org/10.1038/s41586-025-09866-3
- Fortier, A., & Pritchard, J. (2025). The primate Major Histocompatibility Complex as a case study of gene family evolution. Elife. https://doi.org/10.7554/eLife.103545
- Frayer, M., Robles, N., Rodriguez-Barrera, M. ., Coughlan, J., & Schumer, M. (2025). The molecular evolutionary basis of species formation revisited. Trends in Genetics, 41(12), 1068-1095. https://doi.org/10.1016/j.tig.2025.07.003
- Starr, A., Palmer, M., & Fraser, H. (2025). In silico genome transplants and the cis-regulatory basis of biodiversity. Trends in Genetics. https://doi.org/10.1016/j.tig.2025.10.012
- Lappo, E., & Rosenberg, N. (2025). Coalescent theory of the ψ directionality index. G3 (Bethesda), 15(11). https://doi.org/10.1093/g3journal/jkaf202
- Dawood, M., Heavner, B., Wheeler, M., Ungar, R., LoTempio, J., Wiel, L., Berger, S., Bernstein, J., Chong, J., Delot, E., Eichler, E., Lupski, J., Shojaie, A., Talkowski, M., Wagner, A., Wei, C.-L., Wellington, C., Wheeler, M., Members, G. P. ., Carvalho, C., Gibbs, R., Gifford, C., May, S., Miller, D., Rehm, H., Samocha, K., Sedlazeck, F., Vilain, E., O’Donnell-Luria, A., Posey, J., Chadwick, L., Bamshad, M., & Montgomery, S. (2025). GREGoR: accelerating genomics for rare diseases. Nature, 647(8089), 331-342. https://doi.org/10.1038/s41586-025-09613-8
- Pasca, S., Arlotta, P., Campbell, P., Charo, A., Evans, J., Farahany, N., Gage, F., Godfrey-Smith, P., Hyun, I., Kriegstein, A., Melloni, L., Ming, G.-L., Moreno, J., Sugarman, J., Temple, S., Testa, G., & Greely, H. (2025). The need for a global effort to attend to human neural organoid and assembloid research. Science, 390(6773), 574-577. https://doi.org/10.1126/science.aeb1510
- Spence, J., Mostafavi, H., Ota, M., Milind, N., Giorgjieva, T., Smith, C., Simons, Y., Sella, G., & Pritchard, J. (2025). Specificity, length and luck drive gene rankings in association studies. Nature, 649(8098), 918-925. https://doi.org/10.1038/s41586-025-09703-7
- Li, W., Hung, P.-H., Matsui, T., Levy, S., & Sherlock, G. (2025). Scaling DNA engineering. Trends in Biotechnology, 43(10). https://doi.org/10.1016/j.tibtech.2025.05.002
- Gjorgjieva, T., & Rosenberg, N. (2025). Toward minimal SNP sets for record-matching with CODIS STR profiles. European Journal of Human Genetics. https://doi.org/10.1038/s41431-025-01941-7
- Robles, N., Moran, B., Barreras, M. ., Jofre, G. ., Gunn, T., Iverson, E., Beskid, S., Baczenas, J., Sedghifar, A., Andolfatto, P., Powell, D., Brandvain, Y., Havird, J., Rosenthal, G., & Schumer, M. (2025). Admixture Mapping Reveals Evidence for Multiple Mitonuclear Incompatibilities in Swordtail Fish Hybrids. Molecular Ecology. https://doi.org/10.1111/mec.70106
- Robles, N., Moran, B., Rodriguez-Barrera, M. ., Jofre, G. ., Gunn, T., Iverson, E., Beskid, S., Baczenas, J., Sedghifar, A., Andolfatto, P., Powell, D., Brandvain, Y., Havird, J., Rosenthal, G., & Schumer, M. (2025). Admixture Mapping Reveals Evidence for Multiple Mitonuclear Incompatibilities in Swordtail Fish Hybrids. Molecular Ecology, 34(22), 1068-1095. https://doi.org/10.1111/mec.70106
- Karageorgi, M., Lyulina, A., Bitter, M., Lappo, E., Greenblum, S., Mouza, Z., Tran, C., Huynh, A., Oken, H., Schmidt, P., & Petrov, D. (2025). Beneficial reversal of dominance maintains a large-effect resistance polymorphism under fluctuating insecticide selection. Nature Ecology & Evolution, 9(11), 2145-2160. https://doi.org/10.1038/s41559-025-02853-x
- Aguirre, M., Spence, J., Sella, G., & Pritchard, J. (2025). . Gene regulatory network structure informs the distribution of perturbation effects. PloS Computational Biology. https://doi.org/10.1101/2025.08.12.669924
- Kasser, S., Nala, K., Fortunato, L., & Feldman, M. (2025). Not by Selection Alone: Expanding the Scope of Gene-Culture Coevolution. Evolutionary Anthropology, 34(3). https://doi.org/10.1002/evan.70007
- Fogarty, L., Zhang, S., & Feldman, M. (2025). Gene-culture association and coevolution. Theoretical Population Biology, 165, 62-71. https://doi.org/10.1016/j.tpb.2025.08.003