Publications for the McIntyre Lab (2005-2009)
Gonzalo, M., Holland, J. B., Vyn, T. J., and McIntyre, L. M. (2009) Direct Mapping Of Density Response In a Population of B73 x Mo17 Recombinant Inbred Lines of Maize (Zea Mays L.). Heredity in press.
Morse, A.M., Whetten, R., Dubos, C., Campbell, M.M. (2009) Post-translational modification of an R2R3-MYB transcription factor by a MAP Kinase during xylem development. New Phytologist. 183: 1001-1013.
Ramirez-Carvajal, G.A., Morse, A.M., Dervinis, C., Davis, J.M. (2009). The cytokinin type-B response regulator PtRR13 is a negative regulator of adventitious root development in Populus. Plant Physiology. 150:759-771.
Main, B.J., Bickel, R.D., McIntyre, L.M., Graze, R.M., Calabrase, P.P., Nuzhdin, S.V. (2009) Allele-specific expression assays using Solexa. BMC Genomics 10:422.
Telonis-Scott M., Hallas, R., McKechnie, S.W., Wee, C.W. and Hoffmann, A.A. (2009) Selection for cold resistance alters gene transcript levels in Drosophila melanogaster. Journal of Insect Physiology 55:549-555.
Graze, R.M., McIntyre, L.M., Main, B.J., Wayne, M.L., and Nuzhdin, S.V. (2009) Regulatory divergence in Drosophila melanogaster and D. simulans, a genome-wide analysis of allele-specific expression. Genetics 183: 547-561.
Nuzhdin, S.V., Brisson, J.A., Pickering, A., Wayne, M.L., Harshman, L. G., and McIntyre, L.M. (2009) Natural genetic variation in transcriptome reflects network structure inferred with major effect mutations: insulin TOR and associated phenotypes in Drosophila melanogaster. BMC Genomics 10:124.
Engelkes, T., Morrien, E., Verhoeven, K.J.F., Bezemer, T.M., Biere, A., Harvey, J.A., McIntyre, L.M., Tamis, W. L. M., and van der Putten, W. H. (2008) Successful range-expanding plants experience less above-ground and below-ground enemy impact. Nature 456:946-948.
Genissel, A., McIntyre, L.M. , Wayne, M.L., Nuzhdin, S.V. (2008) Cis and trans regulatory effects contribute to natural variation in transcriptome of Drosophila melanogaster. Molecular Biology and Evolution. 25: 101-110.
Kopp, A., Barmina, O., Hamilton, A. M., Higgins, L. A., McIntyre, L. M., and Jones, C. (2008) Evolution of gene expression in the Drosophila olfactory system. Molecular Biology and Evolution 25:1081-1092.
Telonis-Scott, M., Kopp, A., Wayne, M. L., Nuzhdin, S. V., McIntyre, L. M. (2008) Sex-specific Splicing in Drosophila: Widespread Occurrence, Tissue-specificity, and Evolutionary Conservation. Genetics 181:421-434.
Fung, R.W.M., Gonzalo, M., Fekete, C., Kovacs, L.G., He, Y., Marsh, E., McIntyre, L.M., Schachtman, D.P. Qin, W. (2008) Powdery Mildew Induces Defense-Oriented Reprogramming of the Transcriptome in a Susceptible but not in a Resistant Grapevine. Plant Physiology. 146: 236-249.
Fowler, V.G., Nelson, C.L., McIntyre L.M., Kreiswirth, B.N., Monk, A., Archer, G.L., Federspiel, J., Naidich, S., Remortel, B., Rude, T., Brown, P., Reller, L.B., Corey, G.R., Gill, S.R. (2007) Potential Associations between Hematogenous Complications and Bacterial Genotype in Staphylococcus aureus. Journal of Infectious Diseases 196:738-47.
Gonzalo, M., Vyn,T., Holland, J.B., McIntyre, L.M. (2007) Mapping reciprocal effects and interactions with plant density stress in Zae mays L. Heredity 99:14-30.Slotte, T., Holm, K., McIntyre, L.M., Lagercrantz, U., Lascoux, M. (2007) Differential expression of genes important for adaptation in Capsella bursa-pastoris/ (Brassicaceae). Plant Physiology. 145:160-173.
Wayne, M.L., Telonis-Scott, M., Bono, L.M., Harshman, L., Artyom, K., Nuzhdin, S.V., McIntyre, L.M. (2007) Simpler mode of inheritance of transcriptional variation in male Drosophila melanogaster. Proceedings of the National Academy of Sciences of the United States of America. 104:18577-18582.
Gonzalo, M., Vyn, T.J., Holland, J.B., McIntyre, L.M. (2006) Mapping density response in maize: a direct approach for testing genotype and treatment interactions. Genetics. 173: 331-48.
McIntyre, L.M., Bono, L.M., Genissel, A., Westerman, R., Junk, D., Telonis-Scott, M., Harshman, L., Wayne, M.L., Kopp, A., Nuzhdin, S.V. (2006) Sex Specific expression of alternative transcripts in Drosophila. Genome Biology 7: R79.
Pienaar, J. & Greeff, J. M. (2006) Adaptive non-Fisherian sex ratios in a patchily distributed population with out-breeding. Evolutionary Ecology 20: 431-445.
Spurlock, D.M., McDaneld, T.G. and McIntyre, L.M. (2006) Changes in skeletal muscle gene expression following clenbuterol administration. BMC Genetics 7: 320.
Slotte, T., McIntyre, L.M. (2006) Quantitative Comparison of Image Analysis Software. DNA Array Image Analysis. DNA Press.
Subramanyam, S., Sardesai, N., Puthoff, D.P., Meyer, J.M., Gonzalo, M., Williams, C.E. (2006) Expression of two defense-response genes, Hfr-1 and Wci-1, under biotic and abiotic stresses in wheat. Plant Science 170: 90-103.
Telonis-Scott, M., Guthridge K.M., and Hoffmann, A.A. (2006). A new set of laboratory selected Drosophila melanogaster lines for the analysis of desiccation resistance: response to selection, physiology and correlated responses. Journal of Experimental Biology 209: 1837-1837.
Verhoeven, K.J., Jannink, J.L., McIntyre, L.M. (2006) Using mating designs to uncover QTL and the genetic architecture of complex traits. Heredity. 96: 139-49.
Barmina, O., Gonzalo, M., McIntyre, L.M., Kopp A (2005) Sex- and segment-specific modulation of gene expression profiles in Drosophila. Dev Biol. 288: 528-44.
Coffman, C.J., Doerge, R.W., Simonsen, K.L., Nichols, K.M,, Duarte, C.K., Wolfinger, R.D., McIntyre, L.M. (2005) Model selection in binary trait locus mapping. Genetics. 170: 1281-97.
Coffman, C.J., Wayne, M.L., Nuzhdin, S.V., Higgins, L.A., McIntyre, L.M. (2005) Identification of co-regulated transcripts affecting male body size in Drosophila. Genome Biol. 6: R53.
Hammes, U.Z., Schachtman, D.P., Berg, R.H., Nielsen, E., Koch, W., McIntyre, L.M., Taylor, C.G. (2005) Nematode-induced changes of transporter gene expression in Arabidopsis roots. Mol Plant Microbe Interact. 18: 1247-57.
Hoffmann, A.A., Hallas, R., Anderson, A.R. and Telonis-Scott, M. (2005). Evidence for a robust sex-specific trade-off between cold resistance and starvation resistance in Drosophila melanogaster. Journal of Evolutionary Biology 18: 804-810.
Telonis-Scott, M., McIntyre, L.M., Wayne, M.L. (2005) Genetic architecture of two fitness-related traits in Drosophila melanogaster: ovariole number and thorax length. Genetica. 125: 211-22.
Verhoeven, K., Simonsen, K., McIntyre, L.M. (2005) Implementing false discovery rate control: increasing your power. Oikos 108: 643-647.