Publications

Engel, S., Aleksander, S., Nash, R., Wong, E., Weng, S., Miyasato, S., Sherlock, G., & Cherry, J. (2025). Saccharomyces Genome Database: advances in genome annotation, expanded biochemical pathways, and other key enhancements. . Genetics, 229(3). https://doi.org/10.1093/genetics/iyae185

Preising, G., Gunn, T., Baczenas, J., Powell, D., Dodge, T., Sewell, S., Pollock, A., Kairuz, J., Savage, M., Lu, Y., Fitschen-Brown, M., Meyer, A., Schartel, M., Cummings, M., Thakur, S., Inman, C., Rios-Cardenas, O., Morris, M., Tobler, M., & Schumer, M. (2024). Recurrent evolution of small body size and loss of the sword ornament in Northern swordtail fish. Evolution. https://doi.org/doi.org/10.1093/evolut/qpae124

Marderstein, A., Zuani, M., Moeller, R., Bezney, J., Padhi, E., Wong, S., Coorens, T., Xie, Y., Xue, H. ., Montgomery, S., & Cvejic, A. (2024). Single-cell multi-omics map of human fetal blood in Down syndrome. Nature, 634. https://doi.org/10.1038/s41586-024-07946-4

Armstrong, E., Mooney, J., Solari, K., Kim, B., Barsh, G., Grant, V., Greenbaum, G., Kaelin, C., Panchenko, K., Pickrell, J., Rosenberg, N., Ryder, O., Yokoyama, T., Ramakrishnan, U., Petrov, D., & Hadley, E. (2024). Unraveling the genomic diversity and admixture history of captive tigers in the United States. PNAS, 121(39). https://doi.org/doi.org/10.1073/pnas.2402924121

Jena, S., Verma, A., & Engelhardt, B. (2024). Answering open questions in biology using spatial genomics and structured methods. BMC Bioinformatics, 25. https://doi.org/10.1186/s12859-024-05912-5

Du, K., Ricci, J., Lu, Y., Garcia-Olazabal, M., Walter, R., Warren, W., Dodge, T., Schumer, M., Park, H., Meyer, A., & Schartl, M. (2024). Phylogenomic analyses of all species of swordtail fishes (genus Xiphophorus) show that hybridization preceded speciation.. Nature Communications, 15(6609). https://doi.org/10.1038/s41467-024-50852-6

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

Agranat-Tamir, L., Mooney, J., & Rosenberg, N. (2024). Counting the genetic ancestors from source populations in members of an admixed population.. Genetics, 226(2). https://doi.org/10.1093/genetics/iyae011

Antonio, M., Weiß, C., Gao, Z., Sawyer, S., Oberreiter, V., Moots, H., Spence, J., Cheronet, O., Zagorc, B., (+ 88 Authors, ), & 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