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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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- Sherkow, J., Cook-Deegan, R., & Greely, H. (2024). The Myriad Decision at 10. Annual Review of Genomics and Human Genetics, 25. https://doi.org/10.1146/annurev-genom-010323-011239
- Wang, B., Starr, A., & Fraser, H. (2024). Cell-type-specific cis-regulatory divergence in gene expression and chromatin accessibility revealed by human-chimpanzee hybrid cells. eLife, 12. https://doi.org/10.7554/eLife.89594
- Smail, C., & Montgomery, S. (2024). RNA Sequencing in Disease Diagnosis. Annual Review of Genomics and Human Genetics, 25. https://doi.org/10.1146/annurev-genom-021623-121812
- Cotter, D., Severson, A., Kang, J., Godrej, H., Carmi, S., & Rosenberg, N. (2024). Modeling the effects of consanguinity on autosomal and X-chromosomal runs of homozygosity and identity-by-descent sharing. G3 (Bethesda), 14(2). https://doi.org/10.1093/g3journal/jkad264
- Antonio, M., Weiß, C., Gao, Z., Sawyer, S., Oberreiter, V., Moots, H., Spence, J., Cheronet, O., Zagorc, B., & Pritchard, J. (2024). Stable population structure in Europe since the Iron Age, despite high mobility. eLife, 13. https://doi.org/10.7554/eLife.79714
- Pettie, K., Mumbach, M., Lee, A., Ayroles, J., Chang, H., Kasowski, M., & Fraser, H. (2024). Chromatin activity identifies differential gene regulation across human ancestries. Genome Biology, 25(21). https://doi.org/10.1186/s13059-024-03165-2
- Ungar, R., Goddard , P., Jensen, T., Degalez, F., Smith, K., Jin, C., Bonner, Undiagnosed Diseases Network, D., Bernstein, J., Wheeler, M., & Montgomery, S. (2024). Impact of genome build on RNA-seq interpretation and diagnostics. medRvix. https://doi.org/10.1101/2024.01.11.24301165
- Moran, B., Payne, C., Powell, D., Iverson, E., Donny, A., Banerjee, S., Langdon, Q., Gunn, T., Rodriguez-Soto, R., Madero, A., Baczenas, J., Kleczko, K., Liu, F., Matney, R., Singhal, K., Leib, R., Hernandez-Perez, O., Corbett-Detig, R., Frydman, J., Gifford, C., Schartl, M., Havird, J., & Schumer, M. (2024). A lethal mitonuclear incompatibility in complex I of natural hybrids. Nature, 626(7997), 119-127. https://doi.org/10.1038/s41586-023-06895-8
- Lappo, E., & Rosenberg, N. (2024). Solving the Arizona search problem by imputation. iScience, 27(2). https://doi.org/10.1016/j.isci.2024.108831
- Chaung, K., Baharav, T., Henderson, G., Zheludev, I. ., Wang, P., & Salzman, J. (2023). SPLASH: A statistical, reference-free genomic algorithm unifies biological discovery.. Cell, 186(25), 5440-5456. https://doi.org/10.1016/j.cell.2023.10.028
- Chen, V., Johnson, M., Lucas Hérissant, L., Humphrey, P., Yuan, D., Li, Y., Agarwala, A., Hoelscher, S., Petrov, D., Desai, M., & Sherlock, G. (2023). Evolution of haploid and diploid populations reveals common, strong, and variable pleiotropic effects in non-home environments.. eLife, 12. https://doi.org/10.7554/eLife.92899
- Li, T., Ferarro, N., Strober, B., Aguet, F., Kasela, S., Arvanitis, M., Ni, B., Wiel, L., Hershberg, E., Ardlie, K., Arking, D., Beer, R., Brody, J., Blackwell, T., Clish, C., Gabriel, S., Robert, G., Guo, X., Gupta, N., Johnson, W. C., & Montgomery, S. (2023). The functional impact of rare variation across the regulatory cascade. Cell Genomics, 3(10). https://doi.org/10.1016/j.xgen.2023.100401
- Moots, H., Antonio, M., Sawyer, S., Spence, J., Oberreiter, V. ., Wei, C., Lucci, M., Cherifi, Y., La Pastina, F., Genchi, F. ., Praxmeier, E. ., Zagorc, B., Cheronet, O., Özdoğan, K., Demetz, L., Amrani, S., Candilio, F., De Angelis, D., Gasperetti, G. ., Fernandes, D., Gao, Z., Fantar, M., Coppa, A., Pritchard, J., & Pinhasi, R. (2023). A genetic history of continuity and mobility in the Iron Age central Mediterranean. Nature Ecology & Evolution, 7, 1515–1524. https://doi.org/10.1038/s41559-023-02143-4
- Jones, A., Townes, F. W., Li, D., & Engelhardt, B. (2023). Alignment of spatial genomics data using deep Gaussian processes. Nature Methods, 20, 1379–1387. https://doi.org/10.1038/s41592-023-01972-2
- Mooney, J., Agranat-Tamir, L., Pritchard, J. ., & Rosenberg, N. (2023). On the number of genealogical ancestors tracing to the source groups of an admixed population. Genetics, 224(3). https://doi.org/10.1093/genetics/iyad079
- Kachuri, L., Hoffman, T., Jiang, Y., Berndt, S., Shelley, J., Schaffer, K., Machiela, M., Freedman, N., Huang, W.-Y., Li, S., Easterlin, R., Goodman, P., Till, C., Thompson, I., Lilja, H., Van Den Eeden, S., Chanock, S., Haiman, C., Conti, D., Klein, R., Mosley, J., Graff, R., & Witte, J. (2023). Genetically adjusted PSA levels for prostate cancer screening.. Nature Medicine, 29, pages 1412-. https://doi.org/10.1038/s41591-023-02277-9
- Kinsler, G., Schmidlin, K., Newell, D., Eder, R., Apodaca, S., Lam, G., Petrov, D., & Geiler-Samerotte, K. (2023). Extreme Sensitivity of Fitness to Environmental Conditions: Lessons from #1BigBatch. Journal of Molecular Evolution , 91, 293–310. https://doi.org/10.1007/s00239-023-10114-3
- Samyak, R., & Palacios, J. (2023). Statistical summaries of unlabelled evolutionary trees. Biometrika, 111, 171–193.
- Denton, K., Ram, Y., & Feldman, M. (2023). Conditions that favour cumulative cultural evolution. Philosophical Transactions of the Royal Society B, 378(1872). https://doi.org/10.1098/rstb.2021.0400
- Mathur, S., & Rosenberg, N. (2023). All galls are divided into three or more parts: recursive enumeration of labeled histories for galled trees. Algorithms for Molecular Biology, 18(1). https://doi.org/10.1186/s13015-023-00224-4