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David A Liberles

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David A Liberles

  • College of Science and Technology

    • Biology

      • Professor

Courses Taught

Number

Name

Level

BIOL 3403

Genomic Biology

Undergraduate

BIOL 5403

Genomics

Graduate

BIOL 8210

Seminar

Graduate

Selected Publications

Recent

  • McCloskey, N.S., Mammedova, A., & Liberles, D.A. (2024). PEMPS: a phylogenetic software tool to model the evolution of metabolic pathways. BMC Bioinformatics, 25(1), 244. England. 10.1186/s12859-024-05867-7

  • Weisman, C.M., Minh, B.Q., & Liberles, D.A. (2024). 2023 Zuckerkandl Prize. J Mol Evol, 92(1), 1-2. Germany. 10.1007/s00239-024-10153-4

  • Williams, R.A. & Liberles, D.A. (2024). A Dynamic Programming Approach for the Alignment of Molecules. Cold Spring Harbor Laboratory. doi: 10.1101/2024.01.23.576849.

  • McCloskey, N.S., Mammedova, A., & Liberles, D.A. (2024). PEMPS: A Phylogenetic Software Tool to Model the Evolution of Metabolic Pathways. Cold Spring Harbor Laboratory. doi: 10.1101/2024.01.04.574206.

  • Wilson, A.E. & Liberles, D.A. (2023). Expectations of duplicate gene retention under the gene duplicability hypothesis. BMC Ecol Evol, 23(1), 76. England. 10.1186/s12862-023-02174-2

  • Liberles, D.A. (2023). A Genomic Conceptualization of Species. J Mol Evol, 91(4), 379-381. Germany. 10.1007/s00239-023-10111-6

  • Luzuriaga-Neira, A.R., Ritchie, A.M., Payne, B.L., Carrillo-Parramon, O., Liberles, D.A., & Alvarez-Ponce, D. (2023). Highly Abundant Proteins Are Highly Thermostable. Genome Biol Evol, 15(7). England. 10.1093/gbe/evad112

  • Wilson, A.E. & Liberles, D.A. (2023). Dosage balance acts as a time-dependent selective barrier to subfunctionalization. BMC Ecol Evol, 23(1), 14. England. 10.1186/s12862-023-02116-y

  • Liberles, D.A. (2023). The Memory Problem for Neutral Mutational Models of Evolution. J Mol Evol, 91(1), 2-5. Germany. 10.1007/s00239-022-10084-y

  • Liberles, D.A., Alvarez-Ponce, D., Meyer, M.M., Minh, B.Q., & Silva, J.C. (2023). 2022 Zuckerkandl Prize. J Mol Evol, 91(1), 1. Germany. 10.1007/s00239-022-10089-7

  • Assis, R., Conant, G., Holland, B., Liberles, D.A., O'Reilly, M.M., & Wilson, A.E. (2023). Models for the retention of duplicate genes and their biological underpinnings. F1000Res, 12, 1400. England. 10.12688/f1000research.141786.2

  • Henry, C.N., Piper, K., Wilson, A.E., Miraszek, J.L., Probst, C.S., Rong, Y., & Liberles, D.A. (2022). WGDTree: a phylogenetic software tool to examine conditional probabilities of retention following whole genome duplication events. BMC Bioinformatics, 23(1), 505. England. 10.1186/s12859-022-05042-w

  • Krishnamurthy, R., Goldman, A.D., Liberles, D.A., Rogers, K.L., & Tor, Y. (2022). Nucleobases in Meteorites to Nucleobases in RNA and DNA? J Mol Evol, 90(5), 328-331. Germany. 10.1007/s00239-022-10069-x

  • Liberles, D.A., Meyer, M.M., Rest, J.S., & Teufel, A.I. (2022). 2021 Zuckerkandl Prize. J Mol Evol, 90(1), 1. Germany. 10.1007/s00239-021-10041-1

  • Stark, T.L., Kaufman, R.S., Maltepes, M.A., Chi, P.B., & Liberles, D.A. (2021). Detecting Selection on Segregating Gene Duplicates in a Population. J Mol Evol, 89(8), 554-564. Germany. 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 Biol Evol, 13(10). England. 10.1093/gbe/evab225

  • Harman, J.L., Cuff, A.L., Settele, J., Jacobus, L.M., Liberles, D.A., & Traulsen, A. (2021). Correction to: Inaugural BMC Ecology and Evolution image competition: the winning images. BMC Ecol Evol, 21(1), 174. England. 10.1186/s12862-021-01891-w

  • Harman, J.L., Cuff, A.L., Settele, J., Jacobus, L.M., Liberles, D.A., & Traulsen, A. (2021). Inaugural BMC Ecology and Evolution image competition: the winning images. BMC Ecol Evol, 21(1), 157. England. 10.1186/s12862-021-01886-7

  • Selberg, A.G., Gaucher, E.A., & Liberles, D.A. (2021). Ancestral Sequence Reconstruction: From Chemical Paleogenetics to Maximum Likelihood Algorithms and Beyond. J Mol Evol, 89(3), 157-164. Germany. 10.1007/s00239-021-09993-1

  • Goldman, A.D. & Liberles, D.A. (2021). The Journal of Molecular Evolution Turns 50. J Mol Evol, 89(3), 119-121. Germany. 10.1007/s00239-021-10000-w

  • Ritchie, A.M., Stark, T.L., & Liberles, D.A. (2021). Inferring the number and position of changes in selective regime in a non-equilibrium mutation-selection framework. BMC Ecol Evol, 21(1), 39. England. 10.1186/s12862-021-01770-4

  • Liberles, D.A. (2021). 2020 Zuckerkandl Prize. J Mol Evol, 89(1-2), 1. Germany. 10.1007/s00239-020-09990-w

  • Chi, P.B., Kosater, W.M., & Liberles, D.A. (2020). Detecting Signatures of Positive Selection against a Backdrop of Compensatory Processes. Mol Biol Evol, 37(11), 3353-3362. United States. 10.1093/molbev/msaa161

  • Wilson, A.E., Kosater, W.M., & Liberles, D.A. (2020). Evolutionary Processes and Biophysical Mechanisms: Revisiting Why Evolved Proteins Are Marginally Stable. J Mol Evol, 88(5), 415-417. Germany. 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.A., 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. J Mol Evol, 88(3), 211-226. Germany. 10.1007/s00239-020-09932-6

  • Liberles, D.A. (2020). 2019 Zuckerkandl Prize. J Mol Evol, 88(2), 121. Germany. 10.1007/s00239-019-09924-1

  • Northover, D.E., Shank, S.D., & Liberles, D.A. (2020). Characterizing lineage-specific evolution and the processes driving genomic diversification in chordates. BMC Evol Biol, 20(1), 24. England. 10.1186/s12862-020-1585-y