Mueller, R. L. and Jockusch, E. L. 2018. Jumping genomic gigantism. Nature Ecology and Evolution 2: 1687-1688.
Mueller, R. L. 2017. piRNAs and evolutionary trajectories in genome size and content. Journal of Molecular Evolution 85(5-6): 169-171.
Chong, R. A. and Mueller, R. L. 2017. Polymorphic duplicate genes and persistent non-coding sequences reveal heterogeneous patterns of mitochondrial DNA loss in salamanders. BMC Genomics 18(1):992.
Staub, N. and Mueller, R. L. 2017. David Burton Wake: A Historical Perspective. Copeia 105(2): 415-426.
Madison-Villar, M. J., Sun, C., Lau, N. C., and Mueller, R. L. 2016. Small RNAs from a big genome: the piRNA pathway and transposable elements in the salamander species Desmognathus fuscus. Journal of Molecular Evolution 83:126-136.
Mohlhenrich, E. and Mueller, R. L. 2016. Genetic drift and mutational hazard in the evolution of salamander genomic gigantism. Evolution .
Recommended by Faculty of 1000: http://f1000.com/prime/726822561
Associated Evolution Digest: Salamanders’ slow slither into genomic gigantism http://onlinelibrary.wiley.com/wol1/doi/10.1111/evo.13112/full
Chen, X., Jiang, X., Gu, J., Xu, M., Wu, Y., Deng, Y., Zhang, C., Bonizzoni, M., Dermauw, W., Vontas, J., Armbruster, P., Huang, X., Yang, Y., Zhang, H., He, W., Peng, H., Liu, Y., Wu, K., Chen, J., Lirakis, M., Topalis, P., Van Leeuwen, T., Hall, A. B., Jiang, X., Thorpe, C., Mueller, R. L., Sun, C., Waterhouse, R. M., Yan, G., T, Z. J., Fang, X., and James, A. A. 2015. Genome sequence of the Asian Tiger mosquito, Aedes albopictus, reveals insights into its biology, genetics, and evolution. Proceedings of the National Academy of Sciences 112(44):E5907-E5915.
Sun, C., Feschotte, C., Wu, Z., and Mueller, R. L. 2015. DNA transposons have colonized the genome of the giant virus Pandoravirus salinus. BMC Biology: 13:38.
Mueller, R.L. 2015. Genome biology and the evolution of cell size diversity. In Heald, R., Hariharan, I., and Wake, D.B. (Eds.), Size Control in Biology, from Organelles to Organisms. Cold Spring Harbor Press. Free downloads of this chapter available at the following link:
Frahry, M.B., Sun, C., Chong, R.A. and Mueller, R.L. 2015. Low levels of retrotransposon deletion by ectopic recombination in the gigantic genomes of salamanders. Journal of Molecular Evolution 80(2):120-129.
Sun, C. and Mueller, R.L. 2014. Hellbender genome sequences shed light on genomic expansion at the base of crown salamanders. Genome Biology and Evolution 6(7): 1818-1829.
Sun, C., Wyngaard, G., Walton, D.B., Wichman, H.A., Mueller, R.L. 2014. Billions of basepairs of recently expanded, repetitive sequences are eliminated from the somatic genome during copepod development. BMC Genomics 15:186.
Chong, R.A. and Mueller, R.L. 2013. Evolution along the mutation gradient within the dynamic mitochondrial genome of salamanders. Genome Biology and Evolution 5(9):1652-60.
Warga, R., Mueller, R.L., Ho, R.K., and Kane, D.A. 2013. Zebrafish Tbx16 regulates intermediate mesoderm cell fate by attenuating Fgf activity. Developmental Biology 383(1):75-89.
Parrie, L.M., Renfrew, E.M., Mueller, R.L., Garrity, D.M. 2013. Zebrafish tbx5 paralogs demonstrate independent essential requirements in cardiac and pectoral fin development. Developmental Dynamics 242(5):485-502. pdf
Chong, R.A. and Mueller, R.L. 2013. Low metabolic rates in salamanders are correlated with weak selective constraints on mitochondrial genes. Evolution 67(3):894-899. pdf
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Sun, C., Lopez Arriaza, J., Mueller, R.L. 2012. DNA loss is slow in the gigantic genomes of salamanders. Genome Biology Evolution 4(12):1340-1348. link
Recommended by Faculty of 1000: http://f1000.com/prime/718020336
Sun, C., Shepard, D. B., Chong, R. A., Lopez Arriaza, J.R., Hall, K., Castoe, T., Feschotte, C., Pollock, D., and Mueller, R. L. 2012. LTR retrotransposons contribute to genomic gigantism in plethodontid salamanders. Genome Biology Evolution 4(2):168-183. pdf
Mueller, R. L., Huang, C., Ho, R. K. 2010. Spatio-temporal regulation of Wnt and retinoic acid signaling by tbx16/spadetail during zebrafish mesoderm differentiation. BMC Genomics 11:492. pdf
Schwartz, R.S. and Mueller, R.L. 2010. Variation in DNA substitution rates among lineages erroneously inferred from simulated clock-like data. PLoS ONE 5(3): e9649. link
Schwartz, R.S. and Mueller, R.L. 2010. Limited effects of among lineage rate variation on the phylogenetic performance of molecular markers. Molecular Phylogenetics and Evolution 54(3): 849 – 856. link
Schwartz, R.S. and Mueller, R.L. 2010. Branch length estimation and divergence dating: estimates of erroneouslyror in Bayesian and maximum likelihood frameworks. BMC Evolutionary Biology 10:5. link
Kuchta, S. R., Parks, D., Mueller, R. L., Wake, D. B. 2009. Closing the ring: Historical biogeography of the salamander ring species Ensatina eschscholtzii. Journal of Biogeography 36: 992-995. pdf (Issue cover, below)
Ebert, A.M., McAnelly, C.A., Mueller, R. L., Horne, W. A., Garrity, D. M. 2008. Genomic organization, expression and phylogenetic analysis of Ca2+ channel B4 (CACNB4) genes in thirteen vertebrate species. Physiological Genomics 35: 133-144. pdf
Ebert, A. M., McAnelly, C. A., Srinivasan, A., Mueller, R. L., Garrity, D. B., Garrity, D. M. 2008. The calcium channel B2 (CACNB2) subunit repertoire in teleosts. BMC Molecular Biology 9:38. pdf
Mueller, R. L., Gregory, T. R., Gregory, S. M., Hsieh, A., Boore, J. L. 2008. Genome size, cell size, and the evolution of enucleated red blood cells in attenuate salamanders. Zoology 111: 218-230. pdf
Hurley, I. A.,* Mueller, R. L.,* Dunn, K. A.,* Schmidt, E. J., Friedman, M., Ho, R. K., Prince, V. E., Yang, Z., Thomas, M. G., Coates, M. I. 2007. A new time-scale for ray-finned fish evolution. Proceedings of the Royal Society B 274: 489-498. pdf *authors contributed equally (Issue cover, below)
Mueller, R. L. 2006. Evolutionary rates, divergence dates, and the performance of mitochondrial genes in Bayesian phylogenetic analysis. Systematic Biology 55(2): 289-300 (Winner of 2006 Systematic Biology Publisher’s Award). pdf
Mueller, R. L. and Boore, J. L. 2005. Molecular mechanisms of extensive mitochondrial gene rearrangement in plethodontid salamanders. Molecular Biology and Evolution 22(10): 2104-2112. pdf
Bonnet, R. M., Mueller, R. L., Wake, D. B. 2005. Why should reacquisition of larval stages by desmognathine salamanders surprise us? Herpetological Review 36(2): 112-113. pdf
Mueller, R. L., Macey, J. R., Jaekel, M., Wake, D. B., Boore, J. L. 2004. Morphological homoplasy, life history evolution, and historical biogeography of plethodontid salamanders inferred from complete mitochondrial genomes. Proceedings of the National Academy of Sciences 101(38): 13820-13825. pdf
Tsai, T., Fulton, L., Mueller, R. L., Smith, B. J., Gonzalez, G., O’Brien, J. M. 2004. Rapid identification of germline mutations in retinoblastoma by protein truncation testing. Archives of Ophthalmology 122: 239-248. pdf
Mueller, R. L. 2000. Who needs a nucleus? Red blood cells in the genus Batrachoseps. American Zoologist 40(6): 1142.
Autumn, K., Jindrich, D., DeNardo, D., Mueller, R.L. 1999. Locomotor performance at low temperature and the evolution of nocturnality in geckos. Evolution 53(2): 580-599. pdf
Murray, T. G., Cicciarelli, N., O’Brien, J. M., Hernandez, E., Mueller, R. L., Smith, B. J., Feuer, W. 1997. Subconjunctival carboplatin therapy and cryotherapy in the treatment of transgenic murine retinoblastoma. Archives of Ophthalmology 115(10): 1286-1290.
Mueller, R. L., Gordon, K. B., Smith, B. J., O’Brien, J. M. 1997. Genetic markers for second tumor susceptibility in retinoblastoma. Investigative Ophthalmology & Visual Science 38(4):S795.
