Department of Integrative Biology

J. Joyner-Matos, Hicks, K. A., Cousins, D., Keller, M., Denver, D. R., Baer, C. F., and Estes, S., “Evolution of a Higher Intracellular Oxidizing Environment in Caenorhabditis elegans under Relaxed Selection”, Plos One, vol. 8, p. 6, 2013.

K. A. Hicks, Denver, D. R., and Estes, S., “Natural variation in Caenorhabditis briggsae mitochondrial form and function suggests a novel model of organelle dynamics”, Mitochondrion, vol. 13, pp. 44-51, 2013.

K. A. Hicks, Howe, D. K., Leung, A., Denver, D. R., and Estes, S., “In Vivo Quantification Reveals Extensive Natural Variation in Mitochondrial Form and Function in Caenorhabditis briggsae”, Plos One, vol. 7, p. 13, 2012.

K. A. Clark, Howe, D. K., Gafner, K., Kusuma, D., Ping, S., Estes, S., and Denver, D. R., “Selfish Little Circles: Transmission Bias and Evolution of Large Deletion-Bearing Mitochondrial DNA in Caenorhabditis briggsae Nematodes”, Plos One, vol. 7, p. 8, 2012.

I. Zasada, Peetz, A., Smythe, A., Howe, D., Cheam, D., and Denver, D. R., “USING MITOGENOMIC AND NUCLEAR RIBOSOMAL SEQUENCE DATA TO INVESTIGATE THE PHYLOGENY OF XIPHINEMA AMERICANUM POPULATIONS FROM THE UNITED STATES”, Journal of Nematology, vol. 44, pp. 500-500, 2012.

D. R. Denver, Wilhelm, L. J., Howe, D. K., Gafner, K., Dolan, P. C., and Baer, C. F., “Variation in Base-Substitution Mutation in Experimental and Natural Lineages of Caenorhabditis Nematodes”, Genome Biology and Evolution, vol. 4, pp. 513-522, 2012.

M. Blaxter and Denver, D. R., “The worm in the world and the world in the worm”, Bmc Biology, vol. 10, p. 3, 2012.

W. H. Pope, Jacobs-Sera, D., Russell, D. A., Peebles, C. L., Al-Atrache, Z., Alcoser, T. A., Alexander, L. M., Alfano, M. B., Alford, S. T., Amy, N. E., Anderson, M. D., Anderson, A. G., Ang, A. A. S., Ares, M., Barber, A. J., Barker, L. P., Barrett, J. M., Barshop, W. D., Bauerle, C. M., Bayles, I. M., Belfield, K. L., Best, A. A., Borjon, A., Bowman, C. A., Boyer, C. A., Bradley, K. W., Bradley, V. A., Broadway, L. N., Budwal, K., Busby, K. N., Campbell, I. W., Campbell, A. M., Carey, A., Caruso, S. M., Chew, R. D., Cockburn, C. L., Cohen, L. B., Corajod, J. M., Cresawn, S. G., Davis, K. R., Deng, L. S., Denver, D. R., Dixon, B. R., Ekram, S., Elgin, S. C. R., Engelsen, A. E., English, B. E. V., Erb, M. L., Estrada, C., Filliger, L. Z., Findley, A. M., Forbes, L., Forsyth, M. H., Fox, T. M., Fritz, M. J., Garcia, R., George, Z. D., Georges, A. E., Gissendanner, C. R., Goff, S., Goldstein, R., Gordon, K. C., Green, R. D., Guerra, S. L., Guiney-Olsen, K. R., Guiza, B. G., Haghighat, L., Hagopian, G. V., Harmon, C. J., Harmson, J. S., Hartzog, G. A., Harvey, S. E., He, S. P., He, K. J., Healy, K. E., Higinbotham, E. R., Hildebrandt, E. N., Ho, J. H., Hogan, G. M., Hohenstein, V. G., Holz, N. A., Huang, V. J., Hufford, E. L., Hynes, P. M., Jackson, A. S., Jansen, E. C., Jarvik, J., Jasinto, P. G., Jordan, T. C., Kasza, T., Katelyn, M. A., Kelsey, J. S., Kerrigan, L. A., Khaw, D., Kim, J., Knutter, J. Z., Ko, C. C., Larkin, G. V., Laroche, J. R., Latif, A., and Jo, Y. S., “Expanding the Diversity of Mycobacteriophages: Insights into Genome Architecture and Evolution”, Plos One, vol. 6, p. 20, 2011.

S. Estes, Phillips, P. C., and Denver, D. R., “FITNESS RECOVERY AND COMPENSATORY EVOLUTION IN NATURAL MUTANT LINES OF C. ELEGANS”, Evolution, vol. 65, pp. 2335-2344, 2011.

S. Estes, Coleman-Hulbert, A. L., Hicks, K. A., de Haan, G., Martha, S. R., Knapp, J. B., Smith, S. W., Stein, K. C., and Denver, D. R., “Natural variation in life history and aging phenotypes is associated with mitochondrial DNA deletion frequency in Caenorhabditis briggsae”, Bmc Evolutionary Biology, vol. 11, p. 8, 2011.

D. R. Denver, Clark, K. A., and Raboin, M. J., “Reproductive mode evolution in nematodes: Insights from molecular phylogenies and recently discovered species”, Molecular Phylogenetics and Evolution, vol. 61, pp. 584-592, 2011.

M. J. Raboin, Timko, A. F., Howe, D. K., Felix, M. A., and Denver, D. R., “Evolution of Caenorhabditis Mitochondrial Genome Pseudogenes and Caenorhabditis briggsae Natural Isolates”, Molecular Biology and Evolution, vol. 27, pp. 1087-1096, 2010.

D. K. Howe, Baer, C. F., and Denver, D. R., “High Rate of Large Deletions in Caenorhabditis briggsae Mitochondrial Genome Mutation Processes”, Genome Biology and Evolution, vol. 2, pp. 29-38, 2010.

D. R. Denver, Howe, D. K., Wilhelm, L. J., Palmer, C. A., Anderson, J. L., Stein, K. C., Phillips, P. C., and Estes, S., “Selective sweeps and parallel mutation in the adaptive recovery from deleterious mutation in Caenorhabditis elegans”, Genome Research, vol. 20, pp. 1663-1671, 2010.

C. F. Baer and Denver, D. R., “Spontaneous Mutations Decrease Sensitivity of Gene Expression to Random Environmental Variation in Caenorhabditis elegans”, Plos One, vol. 5, p. 4, 2010.

D. R. Denver, Dolan, P. C., Wilhelm, L. J., Sung, W., Lucas-Lledo, J. I., Howe, D. K., Lewis, S. C., Okamoto, K., Thomas, W. K., Lynch, M., and Baer, C. F., “A genome-wide view of Caenorhabditis elegans base-substitution mutation processes”, Proceedings of the National Academy of Sciences of the United States of America, vol. 106, pp. 16310-16314, 2009.

S. Subramanian, Denver, D. R., Millar, C. D., Heupink, T., Aschrafi, A., Emslie, S. D., Baroni, C., and Lambert, D. M., “High mitogenomic evolutionary rates and time dependency”, Trends in Genetics, vol. 25, pp. 482-486, 2009.

S. C. Lewis, Dyal, L. A., Hilburn, C. F., Weitz, S., Liau, W. S., LaMunyon, C. W., and Denver, D. R., “Molecular evolution in Panagrolaimus nematodes: origins of parthenogenesis, hermaphroditism and the Antarctic species P-davidi”, Bmc Evolutionary Biology, vol. 9, p. 13, 2009.

D. K. Howe and Denver, D. R., “Muller's Ratchet and compensatory mutation in Caenorhabditis briggsae mitochondrial genome evolution”, Bmc Evolutionary Biology, vol. 8, p. 13, 2008.

I. K. Jordan, Katz, L. S., Denver, D. R., and Streelman, J. T., “Natural selection governs local, but not global, evolutionary gene coexpression networks in Caenorhabditis elegans”, Bmc Systems Biology, vol. 2, p. 11, 2008.

P. C. Dolan and Denver, D. R., “TileQC: A system for tile-based quality control of Solexa data”, Bmc Bioinformatics, vol. 9, p. 10, 2008.

K. L. Vergin, Tripp, H. J., Wilhelm, L. J., Denver, D. R., Rappe, M. S., and Giovannoni, S. J., “High intraspecific recombination rate in a native population of Candidatus Pelagibacter ubique (SAR11)”, Environmental Microbiology, vol. 9, pp. 2430-2440, 2007.

C. F. Baer, Miyamoto, M. M., and Denver, D. R., “Mutation rate variation in multicellular eukaryotes: causes and consequences”, Nature Reviews Genetics, vol. 8, pp. 619-631, 2007.

S. C. Lewis and Denver, D. R., “Panagrolaimus mitochondrial genome evolution: Impact of reproductive mode”, Journal of Nematology, vol. 39, pp. 83-83, 2007.

C. F. Baer, Miyamoto, M. M., and Denver, D. R., “Reply to: Mutation rate variation in eukaryotes: evolutionary implications of site-specific mechanisms”, Nature Reviews Genetics, vol. 8, p. 1, 2007.