Gomez-Simmonds, A., Annavajhala, M. K., Seeram, D., Hokunson, T. W., Park, H., & Uhlemann, A.-C. (2024). Genomic epidemiology of carbapenem-resistant Enterobacterales at a New York City hospital over a 10-year period reveals complex plasmid-clone dynamics and evidence for frequent horizontal transfer ofblaKPC. Genome Research, 34(11), 1895–1907. https://doi.org/10.1101/gr.279355.124

Narechania, A., Bobo, D., Deitz, K., DeSalle, R., Planet, P. J., & Mathema, B. (2024). Rapid SARS-CoV-2 surveillance using clinical, pooled, or wastewater sequence as a sensor for population change. Genome Research, 34(10), 1651–1660. https://doi.org/10.1101/gr.278594.123

Park, C., Mani, S., Beltran-Velez, N., Maurer, K., Huang, T., Li, S., Gohil, S., Livak, K. J., Knowles, D. A., Wu, C. J., & Azizi, E. (2024). A Bayesian framework for inferring dynamic intercellular interactions from time-series single-cell data. Genome Research, 34(9), 1384–1396. https://doi.org/10.1101/gr.279126.124

Xu, C., Bao, S., Wang, Y., Li, W., Chen, H., Shen, Y., Jiang, T., & Zhang, C. (2024). Reference-informed prediction of alternative splicing and splicing-altering mutations from sequences. Genome Research, 34(7), 1052–1065. https://doi.org/10.1101/gr.279044.124

Lorig-Roach, R., Meredith, M., Monlong, J., Jain, M., Olsen, H., McNulty, B., Porubsky, D., Montague, T., Lucas, J., Condon, C., Eizenga, J. M., Juul, S., McKenzie, S., Simmonds, S. E., Park, J., Asri, M., Koren, S., Eichler, E., Axel, R., … Paten, B. (2024). Phased nanopore assembly with Shasta and modular graph phasing with GFAse. Genome Research. https://doi.org/10.1101/gr.278268.123

Chen, H., Hu, B., Horth, C., Bareke, E., Rosenbaum, P., Kwon, S. Y., Sirois, J., Weinberg, D. N., Robison, F. M., Garcia, B. A., Lu, C., Pastor, W. A., & Majewski, J. (2022). H3K36 dimethylation shapes the epigenetic interaction landscape by directing repressive chromatin modifications in embryonic stem cells. Genome Research. https://doi.org/10.1101/gr.276383.121

Jin, B., Capra, J. A., Benchek, P., Wheeler, N., Naj, A. C., Hamilton-Nelson, K. L., Farrell, J. J., Leung, Y. Y., Kunkle, B., Vadarajan, B., Schellenberg, G. D., Mayeux, R., Wang, L.-S., Farrer, L. A., Pericak-Vance, M. A., Martin, E. R., Haines, J. L., Crawford, D. C., & Bush, W. S. (2022). An association test of the spatial distribution of rare missense variants within protein structures identifies Alzheimer’s disease–related patterns. Genome Research, 32(4), 778–790. https://doi.org/10.1101/gr.276069.121

Joseph, T. A., Chlenski, P., Litman, A., Korem, T., & Pe’er, I. (2022). Accurate and robust inference of microbial growth dynamics from metagenomic sequencing reveals personalized growth rates. Genome Research, 32(3), 558–568. https://doi.org/10.1101/gr.275533.121

Edwards, M. M., Zuccaro, M. V., Sagi, I., Ding, Q., Vershkov, D., Benvenisty, N., Egli, D., & Koren, A. (2021). Delayed DNA replication in haploid human embryonic stem cells. Genome Research, 31(12), 2155–2169. https://doi.org/10.1101/gr.275953.121