Courses Taught
Number | Name | Level |
|---|---|---|
BIOL 2296 | Genetics | Undergraduate |
BIOL 3403 | Genomic Biology | Undergraduate |
BIOL 4391 | Accelerated Research in Biology | Undergraduate |
BIOL 5403 | Genomics | Graduate |
BIOL 5509 | Computational Genomics | Graduate |
BIOL 8210 | Seminar | Graduate |
Selected Publications
Recent
Ritchie, A., Stark, T., & Liberles, D. (2021). Inferring the number and position of changes in selective regime in a non-equilibrium mutation-selection framework. BMC Ecology and Evolution, 21(1). doi: 10.1186/s12862-021-01770-4.
Harman, J., Cuff, A., Settele, J., Jacobus, L., Liberles, D., & Traulsen, A. (2021). Inaugural BMC Ecology and Evolution image competition: the winning images. BMC Ecology and Evolution, 21(1). doi: 10.1186/s12862-021-01886-7.
Harman, J., Cuff, A., Settele, J., Jacobus, L., Liberles, D., & Traulsen, A. (2021). Correction to: Inaugural BMC Ecology and Evolution image competition: the winning images (BMC Ecology and Evolution, (2021), 21, 1, (157), 10.1186/s12862-021-01886-7). BMC Ecology and Evolution, 21(1). doi: 10.1186/s12862-021-01891-w.
Stark, T., Kaufman, R., Maltepes, M., Chi, P., & Liberles, D. (2021). Detecting Selection on Segregating Gene Duplicates in a Population. Journal of Molecular Evolution, 89(8), 554-564. doi: 10.1007/s00239-021-10024-2.
Stark, T.L. & Liberles, D.A. (2021). Characterizing Amino Acid Substitution with Complete Linkage of Sites on a Lineage. Genome Biology and Evolution, 13(10), evab225. doi: 10.1093/gbe/evab225.
Selberg, A., Gaucher, E., & Liberles, D. (2021). Ancestral Sequence Reconstruction: From Chemical Paleogenetics to Maximum Likelihood Algorithms and Beyond. Journal of Molecular Evolution, 89(3), 157-164. doi: 10.1007/s00239-021-09993-1.
Goldman, A. & Liberles, D. (2021). The Journal of Molecular Evolution Turns 50. Journal of Molecular Evolution, 89(3), 119-121. doi: 10.1007/s00239-021-10000-w.
Liberles, D. (2021). 2020 Zuckerkandl Prize. Journal of Molecular Evolution, 89(1-2), 1. doi: 10.1007/s00239-020-09990-w.
Chi, P., Kosater, W., & Liberles, D. (2020). Detecting signatures of positive selection against a backdrop of compensatory processes. Molecular Biology and Evolution, 37(11), 3353-3362. doi: 10.1093/molbev/msaa161.
Wilson, A., Kosater, W., & Liberles, D. (2020). Evolutionary Processes and Biophysical Mechanisms: Revisiting Why Evolved Proteins Are Marginally Stable. Journal of Molecular Evolution, 88(5), 415-417. doi: 10.1007/s00239-020-09948-y.
Diao, J., Stark, T., Liberles, D., O’Reilly, M., & Holland, B. (2020). Level-dependent QBD models for the evolution of a family of gene duplicates. Stochastic Models, 36(2), 285-311. doi: 10.1080/15326349.2019.1680296.
Liberles, D., Chang, B., Geiler-Samerotte, K., Goldman, A., Hey, J., Kaçar, B., Meyer, M., Murphy, W., Posada, D., & Storfer, A. (2020). Emerging Frontiers in the Study of Molecular Evolution. Journal of Molecular Evolution, 88(3), 211-226. doi: 10.1007/s00239-020-09932-6.
Liberles, D. (2020). 2019 Zuckerkandl Prize. Journal of Molecular Evolution, 88(2), 121. doi: 10.1007/s00239-019-09924-1.
Northover, D., Shank, S., & Liberles, D. (2020). Characterizing lineage-specific evolution and the processes driving genomic diversification in chordates. BMC Evolutionary Biology, 20(1). doi: 10.1186/s12862-020-1585-y.
Liberles, D. (2019). A New Editorial Beginning at Journal of Molecular Evolution. Journal of Molecular Evolution, 87(2-3), 69-71. doi: 10.1007/s00239-019-09888-2.
Yohe, L., Liu, L., Dávalos, L., & Liberles, D. (2019). Protocols for the Molecular Evolutionary Analysis of Membrane Protein Gene Duplicates. In Methods in Molecular Biology, 1851 (pp. 49-62). doi: 10.1007/978-1-4939-8736-8_3.
Fragata, I., Blanckaert, A., Louro, M.D., Liberles, D., & Bank, C. (2019). Evolution in the light of fitness landscape theory. Trends in Ecology and Evolution, 34(1), 69-82. doi: 10.1016/j.tree.2018.10.009.
Liberles, D. & Teufel, A. (2018). Evolution and structure of proteins and proteomes. Genes, 9(12). doi: 10.3390/genes9120583.
Teufel, A., Ritchie, A., Wilke, C., & Liberles, D. (2018). Using the mutation-selection framework to characterize selection on protein sequences. Genes, 9(8). doi: 10.3390/genes9080409.
Platt, A., Weber, C., & Liberles, D. (2018). Protein evolution depends on multiple distinct population size parameters. BMC Evolutionary Biology, 18(1). doi: 10.1186/s12862-017-1085-x.
Chi, P., Kim, D., Lai, J., Bykova, N., Weber, C., Kubelka, J., & Liberles, D. (2018). A new parameter-rich structure-aware mechanistic model for amino acid substitution during evolution. Proteins: Structure, Function and Bioinformatics, 86(2), 218-228. doi: 10.1002/prot.25429.
Liberles, D. & Holland, B. (2018). Evolutionary models. In Encyclopedia of Bioinformatics and Computational Biology: ABC of Bioinformatics, 1-3 (pp. 712-718). doi: 10.1016/B978-0-12-809633-8.20256-2.
Arenas, M., Weber, C., Liberles, D., & Bastolla, U. (2017). ProtASR: An Evolutionary Framework for Ancestral Protein Reconstruction with Selection on Folding Stability. Systematic Biology, 66(6), 1054-1064. doi: 10.1093/sysbio/syw121.
Hermansen, R., Oswald, B., Knight, S., Shank, S., Northover, D., Korunes, K., Michel, S., & Liberles, D. (2017). The Adaptive Evolution Database (TAED): A New Release of a Database of Phylogenetically Indexed Gene Families from Chordates. Journal of Molecular Evolution, 85(1-2), 46-56. doi: 10.1007/s00239-017-9806-8.
Orlenko, A., Chi, P., & Liberles, D. (2017). Characterizing the roles of changing population size and selection on the evolution of flux control in metabolic pathways. BMC Evolutionary Biology, 17(1). doi: 10.1186/s12862-017-0962-7.
Stark, T., Liberles, D., Holland, B., & O’Reilly, M. (2017). Analysis of a mechanistic Markov model for gene duplicates evolving under subfunctionalization. BMC Evolutionary Biology, 17(1), 1-16. doi: 10.1186/s12862-016-0848-0.