Publications

López-Nandam, E., Albright, R., Hanson, E., Sheets, E., & Palumbi, S. (2023). Mutations in coral soma and sperm imply lifelong stem cell renewal and cell lineage selection.. Proceedings of the Royal Society, 290(1991). https://doi.org/10.1098/rspb.2022.1766

Starr, A., Gokhman, D., & Fraser, H. (2023). Accounting for cis-regulatory constraint prioritizes genes likely to affect species-specific traits. Genome Biology, 24(1). https://doi.org/10.1186/s13059-023-02846-8

Chen, H., Turakhia, Y., Bejerano, G., & Kingsley, D. (2023). Whole-genome Comparisons Identify Repeated Regulatory Changes Underlying Convergent Appendage Evolution in Diverse Fish Lineages. Molecular Biology and Evolution, 40(9). https://doi.org/10.1093/molbev/msad188

Armstrong, E., Campana, M., Solari, K., Morgan, S., Ryder, O., Naude, V., Samelius, G., Sharma, K., Hadly, E., & Petrov, D. (2022). Genome report: chromosome-level draft assemblies of the snow leopard, African leopard, and tiger (Panthera uncia, Panthera pardus pardus, and Panthera tigris). G3: Genes|Genomes|Genetics, 12(12). https://doi.org/10.1093/g3journal/jkac277

Patel, R., Musharoff, S., Spence, J., Pimentel, H., Tcheandjieu, C., Mostafavi, H., Sinnott-Armstrong, N., Clarke, S., Smith, C., Durda, P., Taylor, K., Tracy, R., Liu, Y., Johnson, W., Aguet, F., Ardlie, K., Gabriel, S., Smith, J., Nickerson, D., Rich, S., Rotter, J., Tsao, P., Assimes, T., & Pritchard, J. (2022). Genetic interactions drive heterogeneity in causal variant effect sizes for gene expression and complex traits. American Journal of Human Genetics, 109(7), 1286-1297. https://doi.org/10.1016/j.ajhg.2022.05.014

Shen, H., & Feldman, M. (2022). Diversity and its causes: Lewontin on racism, biological determinism and the adaptationist programme. Philosophical Transactions of the Royal Society B, 377(1848). https://doi.org/10.1098/rstb.2020.0417

Liu, X., Rosenberg, N., & Greenbaum, G. (2022). Extracting hierarchical features of cultural variation using network-based clustering. Evolutionary Human Sciences, 4. https://doi.org/10.1017/ehs.2022.15

Cappello, L., Kim, J., Liu, S., & Palacios, J. (2022). Statistical challenges in tracking the evolution of SARS-CoV-2. Statistical Science, 37(2), 162-182. https://doi.org/10.1214/22-STS853

Severson, A., Byrd, B., Mallott, E., Owings, A., DeGiorgio, M., de Flamingh, A., Nijmeh, C., Arellano, M., Leventhal, A., Rosenberg, N., & Malhi, R. (2022). Ancient and modern genomics of the Ohlone Indigenous population of California. Proceedings of the National Academy of Sciences of the United States of America, 119(113). https://doi.org/10.1073/pnas.2111533119

Schull, J., Turakhia, Y., Hemker, J., Daily, W., & Bejerano, G. (2022). Champagne: Automated whole-genome phylogenomic character matrix method using large genomic indels for homoplasy-free inference. Genome Biology and Evolution, 14(3). https://doi.org/10.1093/gbe/evac013

Langdon, Q., Powell, D., Kim, B., Banerjee, S., Payne, C., Dodge, T., Moran, B., Fascinetto-Zago, P., & Schumer, M. (2022). Predictability and parallelism in the contemporary evolution of hybrid genomes. PLoS Genetics, 18(1). https://doi.org/10.1371/journal.pgen.1009914

Liu, X., & Feldman, M. (2021). Effects of cultural transmission of surnaming decisions on the sex ratio at birth. Theoretical Population Biology, 141, 44-53. https://doi.org/10.1016/j.tpb.2021.07.001

Powell, D., Moran, B., Kim, B., Banerjee, S., Aguillon, S., Fascinetto-Zago, P., Langdon, Q., & Schumer, M. (2021). Two new hybrid populations expand the swordtail hybridization model system. Evolution, 75(10), 2524-2539. https://doi.org/10.1111/evo.14337

Moran, B., Payne, C., Langdon, Q., Powell, D., Brandvain, Y., & Schumer, M. (2021). The genomic consequences of hybridization. eLife, 10. https://doi.org/10.7554/eLife.69016

Kim, B., Wang, J., Miller, D., Barmina, O., Delaney, E., Thompson, A., Comeault, A., Peede, D., D’Agostino, E., Pelaez, J., Aguilar, J., Haji, D., Matsunaga, T., Armstrong, E., Zych, M., Ogawa, Y., Stamenkovic-Radak, M., Jelic, M., Veselinovic, M., Tanaskovic, M., Eric, P., Gao, J.-J., Katoh, T., Toda, M., Watabe, H., Watada, M., Davis, J., Moyle, L., Manoli, G., Bertolini, E., Kostal, V., Hawley, S., Takahashi, A., Jones, C., Price, D., Whiteman, N., Kopp, A., Matute, D., & Petrov, D. (2021). Highly contiguous assemblies of 101 drosophilid genomes. eLife, 10. https://doi.org/10.7554/eLife.66405

Kim, J., Edge, M., Goldberg, A., & Rosenberg, N. (2021). Skin deep: The decoupling of genetic admixture levels from phenotypes that differed between source populations. American Journal of Physical Anthropology, 175(2), 406-421. https://doi.org/10.1002/ajpa.24261

Gokhman, D., Agoglia, R., Kinnebrew, M., Gordon, W., Sun, D., Bajpai, V., Naqvi, S., Chen, C., Chan, A., Chen, C., Petrov, D., Ahituv, N., Zhang, H., Mishina, Y., Wysocka, J., Rohatgi, R., & Fraser, H. (2021). Human-chimpanzee fused cells reveal cis-regulatory divergence underlying skeletal evolution. Nature Genetics, 53(4), 467-476. https://doi.org/10.1038/s41588-021-00804-3

Sinnott-Armstrong, N., Naqvi, S., Rivas, M., & Pritchard, J. (2021). GWAS of three molecular traits highlights core genes and pathways alongside a highly polygenic background. eLife, 10. https://doi.org/10.7554/eLife.58615

Boca, S., Huang, L., & Rosenberg, N. (2020). On the heterozygosity of an admixed population. Journal of Mathematical Biology, 81, 1217-1250. https://doi.org/10.1007/s00285-020-01531-9

Kim, J., Rosenberg, N., & Palacios, J. (2020). Distance metrics for ranked evolutionary trees. Proceedings of the National Academy of Sciences of the United States of America, 117(46), 28876-28886. https://doi.org/10.1073/pnas.1922851117