Items where Subject is "population genetics"

Paper

Adrion, JR, Cole, C. B., Dukler, N., Galloway, JG, Gladstein, AL, Gower, G, Kyriazis, CC, Ragsdale, AP, Tsambos, G, Baumdicker, F, Carlson, J., Cartwright, R. A., Durvasula, A, Gronau, I., Kim, BY, McKenzie, P, Messer, PW, Noskova, E, Ortega-Del Vecchyo, D., Racimo, F, Struck, TJ, Gravel, S, Gutenkunst, R. N., Lohmueller, K. E., Ralph, PL, Schrider, D. R., Siepel, A., Kelleher, J. E., Kern, A. D. (June 2020) A Community-Maintained Standard Library of Population Genetic Models. Elife, 9. ISSN 2050-084X (Electronic)2050-084X (Linking)

Bienvenu, François, Akcay, Erol, Legendre, Stéphane, McCandlish, David (June 2017) The genealogical decomposition of a matrix population model with applications to the aggregation of stages. Theoretical Population Biology, 115. pp. 69-80.

Cano, Alejandro V, Gitschlag, Bryan L, Rozhoňová, Hana, Stoltzfus, Arlin, McCandlish, David M, Payne, Joshua L (May 2023) Mutation bias and the predictability of evolution. Philosophical Transactions of the Royal Society B: Biological Sciences, 378 (1877). p. 20220055. ISSN 0962-8436

Crow, Megan, Suresh, Hamsini, Lee, John, Gillis, Jesse (November 2020) Coexpression reveals conserved mechanisms of transcriptional cell identity. BioRxiv. (Unpublished)

Devos, Katrien M, Qi, Peng, Bahri, Bochra A, Gimode, Davis M, Jenike, Katharine, Manthi, Samuel J, Lule, Dagnachew, Lux, Thomas, Martinez-Bello, Liliam, Pendergast, Thomas H, Plott, Chris, Saha, Dipnarayan, Sidhu, Gurjot S, Sreedasyam, Avinash, Wang, Xuewen, Wang, Hao, Wright, Hallie, Zhao, Jianxin, Deshpande, Santosh, de Villiers, Santie, Dida, Mathews M, Grimwood, Jane, Jenkins, Jerry, Lovell, John, Mayer, Klaus FX, Mneney, Emmarold E, Ojulong, Henry F, Schatz, Michael C, Schmutz, Jeremy, Song, Bo, Tesfaye, Kassahun, Odeny, Damaris A (June 2023) Genome analyses reveal population structure and a purple stigma color gene candidate in finger millet. Nature Communications, 14 (1). p. 3694. ISSN 2041-1723

Dukler, Noah, Mughal, Mehreen R, Ramani, Ritika, Huang, Yi-Fei, Siepel, Adam (July 2022) Extreme purifying selection against point mutations in the human genome. Nature Communications, 13 (1). p. 4312. ISSN 2041-1723

Hejase, Hussein A, Mo, Ziyi, Campagna, Leonardo, Siepel, Adam (November 2021) A Deep-Learning Approach for Inference of Selective Sweeps from the Ancestral Recombination Graph. Molecular Biology and Evolution. ISSN 0737-4038

Hu, Ying, Colantonio, Vincent, Müller, Bárbara SF, Leach, Kristen A, Nanni, Adalena, Finegan, Christina, Wang, Bo, Baseggio, Matheus, Newton, Carter J, Juhl, Emily M, Hislop, Lillian, Gonzalez, Juan M, Rios, Esteban F, Hannah, L Curtis, Swarts, Kelly, Gore, Michael A, Hennen-Bierwagen, Tracie A, Myers, Alan M, Settles, A Mark, Tracy, William F, Resende, Marcio FR (February 2021) Genome assembly and population genomic analysis provide insights into the evolution of modern sweet corn. Nature Communications, 12 (1). p. 1227. ISSN 2041-1723

Huang, Y. F., Gulko, B., Siepel, A. (April 2017) Fast, scalable prediction of deleterious noncoding variants from functional and population genomic data. Nat Genet, 49 (4). pp. 618-624. ISSN 1061-4036

Hubisz, M., Siepel, A. (January 2020) Inference of Ancestral Recombination Graphs Using ARGweaver. Methods Mol Biol, 2090. pp. 231-266. ISSN 1064-3745

Kato, M., Vasco, D. A., Sugino, R., Narushima, D., Krasnitz, A. (September 2017) Sweepstake evolution revealed by population-genetic analysis of copy-number alterations in single genomes of breast cancer. R Soc Open Sci, 4 (9). p. 171060. ISSN 2054-5703 (Print)2054-5703

Kent, C. F., Dey, A., Patel, H., Tsvetkov, N., Tiwari, T., MacPhail, V. J., Gobeil, Y., Harpur, B. A., Gurtowski, J., Schatz, M. C., Colla, S. R., Zayed, A. (August 2018) Conservation Genomics of the Declining North American Bumblebee Bombus terricola Reveals Inbreeding and Selection on Immune Genes. Front Genet, 9. p. 316. ISSN 1664-8021 (Print)1664-8021

Krittanawong, Chayakrit, Johnson, Kipp W, Choi, Edward, Kaplin, Scott, Venner, Eric, Murugan, Mullai, Wang, Zhen, Glicksberg, Benjamin S, Amos, Christopher I, Schatz, Michael C, Tang, WH Wilson (February 2022) Artificial Intelligence and Cardiovascular Genetics. Life, 12 (2). p. 279. ISSN 2075-1729

McCandlish, D. M., Epstein, C. L., Plotkin, J. B. (February 2015) Formal properties of the probability of fixation: identities, inequalities and approximations. Theor Popul Biol, 99. pp. 98-113. ISSN 1096-0325 (Electronic)0040-5809 (Linking)

McCandlish, D. M., Otwinowski, J., Plotkin, J. B. (September 2015) Detecting epistasis from an ensemble of adapting populations. Evolution, 69 (9). pp. 2359-70. ISSN 1558-5646 (Electronic)0014-3820 (Linking)

Mo, Ziyi, Siepel, Adam (September 2023) Domain-adaptive neural networks improve supervised machine learning based on simulated population genetic data. bioRxiv. (Submitted)

Ranallo-Benavidez, T Rhyker, Lemmon, Zachary, Soyk, Sebastian, Aganezov, Sergey, Salerno, William J, McCoy, Rajiv C, Lippman, Zachary B, Schatz, Michael C, Sedlazeck, Fritz J (May 2021) Optimized sample selection for cost-efficient long-read population sequencing. Genome Research, 31 (5). pp. 910-918. ISSN 1088-9051

Scheinfeldt, L. B., Soi, S., Lambert, C., Ko, W. Y., Coulibaly, A., Ranciaro, A., Thompson, S., Hirbo, J., Beggs, W., Ibrahim, M., Nyambo, T., Omar, S., Woldemeskel, D., Belay, G., Froment, A., Kim, J., Tishkoff, S. A. (March 2019) Genomic evidence for shared common ancestry of East African hunting-gathering populations and insights into local adaptation. Proc Natl Acad Sci U S A, 116 (10). pp. 4166-4175. ISSN 0027-8424

Vranken, S, Scheben, A, Batley, J, Wernberg, T, Coleman, MA (October 2022) Genomic consequences and selection efficacy in sympatric sexual versus asexual kelps. Frontiers in Marine Science, 9. ISSN 2296-7745

Werner, Jonathan M, Hover, John, Gillis, Jesse (October 2024) Population variability in X-chromosome inactivation across 10 mammalian species. Nature Communications, 15 (1). p. 8991. ISSN 2041-1723 (Public Dataset)

Werner, Jonathan M, Hover, John, Gillis, Jesse (October 2023) Population variability in X-chromosome inactivation across 9 mammalian species. (Submitted)

Xue, Alexander T, Schrider, Daniel R, Kern, Andrew D, Ag1000g Consortium (March 2021) Discovery of Ongoing Selective Sweeps within Anopheles Mosquito Populations Using Deep Learning. Molecular Biology and Evolution, 38 (3). pp. 1168-1183. ISSN 0737-4038

Book Section

Fano, Ugo, Caspari, Ernst W., Demerec, Milislav (1950) Genetics. In: Medical Physics. Medical Physics, 2 . Year Book Publishers Inc., Chicago, pp. 365-384.

Thesis

Ziyi, Mo (January 2024) Scalable and robust deep-learning methods power evolutionary-genetic studies of biobank-scale population genomic data. PhD thesis, Cold Spring Harbor Laboratory.