Maloof Lab:Publications

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Publications Maloof, J. N., Nozue, K., Mumbach, M. R., and Palmer, C. M. (2013). LeafJ: An ImageJ Plugin for Semi-automated Leaf Shape Measurement. JoVE. [1] Sharlach, M., Dahlbeck, D., Liu, L., Chiu, J., Jiménez-Gómez, J. M., Kimura, S., Koenig, D., Maloof, J. N., Sinha, N., Minsavage, G. V., et al. (2012). Fine genetic mapping of RXopJ4, a bacterial spot disease resistance locus from Solanum pennellii LA716. Theor Appl Genet.[2] Seymour, D. K., Filiault, D. L., Henry, I. M., Monson-Miller, J., Ravi, M., Pang, A., Comai, L., Chan, S. W. L., and Maloof, J. N. (2012). Rapid creation of Arabidopsis doubled haploid lines for quantitative trait locus mapping. Proc Natl Acad Sci USA 109, 4227–4232.[3] Filiault, D. L., and Maloof, J. N. (2012). A Genome-Wide Association Study Identifies Variants Underlying the Arabidopsis thaliana Shade Avoidance Response. PLoS Genet 8, e1002589.[4] Chitwood, D. H., Headland, L. R., Kumar, R., Peng, J., Maloof, J. N., and Sinha, N. R. (2012). The developmental trajectory of leaflet morphology in wild tomato species. Plant Physiol.[5] Kumar, R., Ichihashi, Y., Kimura, S., Chitwood, D. H., Headland, L. R., Peng, J., Maloof, J. N., and Sinha, N. R. (2012). A High-Throughput Method for Illumina RNA-Seq Library Preparation. Front Plant Sci 3, 202. [6] Chitwood, D. H., Headland, L. R., Filiault, D. L., Kumar, R., Jiménez-Gómez, J. M., Schrager, A. V., Park, D. S., Peng, J., Sinha, N. R., and Maloof, J. N. (2012). Native Environment Modulates Leaf Size and Response to Simulated Foliar Shade across Wild Tomato Species. PLoS ONE 7, e29570.[7] Jiménez-Gómez, J. M., Corwin, J. A., Joseph, B., Maloof, J. N., and Kliebenstein, D. J. (2011). Genomic analysis of QTLs and genes altering natural variation in stochastic noise. PLoS Genet 7, e1002295.[8] Holtan, H. E., Bandong, S., Marion, C. M., Adam, L., Tiwari, S., Shen, Y., Maloof, J. N., Maszle, D. R., Ohto, M.-A., Preuss, S., et al. (2011). BBX32, an Arabidopsis B-Box protein, functions in light signaling by suppressing HY5-regulated gene expression and interacting with STH2/BBX21. Plant Physiol 156, 2109–2123.[9] Arana, M. V., Marín-de la Rosa, N., Maloof, J. N., Blázquez, M. A., and Alabadí, D. (2011). Circadian oscillation of gibberellin signaling in Arabidopsis. Proc Natl Acad Sci USA 108, 9292–9297.[10] Stewart, J. L., Maloof, J. N., and Nemhauser, J. L. (2011). PIF genes mediate the effect of sucrose on seedling growth dynamics. PLoS ONE 6, e19894. [11] Kerwin, R. E., Jimenez-Gomez, J. M., Fulop, D., Harmer, S. L., Maloof, J. N. & Kliebenstein, D. J. Network Quantitative Trait Loci Mapping of Circadian Clock Outputs Identifies Metabolic Pathway-to-Clock Linkages in Arabidopsis. Plant Cell 23, 471-485 (2011). [12] Chang, C. S., Maloof, J. N. & Wu, S. H. COP1-mediated degradation of BBX22/LZF1 optimizes seedling development in Arabidopsis. Plant Physiol (2011). [13] Nozue, K., Harmer, S. L. & Maloof, J. N. Genomic analysis of circadian clock-, light-, and growth-correlated genes reveals PIF5 as a modulator of auxin signaling in Arabidopsis. Plant Physiol (2011). [14] Kim, K., Shin, J., Lee, S. H., Kweon, H. S., Maloof, J. N. & Choi, G. Phytochromes inhibit hypocotyl negative gravitropism by regulating the development of endodermal amyloplasts through phytochrome-interacting factors. Proc Natl Acad Sci U S A 108, 1729-1734 (2011). [15] Maloof, J. N. Recent advances in regulation of flowering. F1000 Biol Rep 2, (2010). [16] Brock, M. T., Dechaine, J. M., Iniguez-Luy, F. L., Maloof, J. N., Stinchcombe, J. R. & Weinig, C. Floral Genetic Architecture: An Examination of QTL Architecture Underlying Floral (Co)Variation Across Environments. Genetics 186, 1451-1465 (2010). [17] Brock, M. T., Maloof, J. N. & Weinig, C. Genes underlying quantitative variation in ecologically important traits: PIF4 (phytochrome interacting factor 4) is associated with variation in internode length, flowering time, and fruit set in Arabidopsis thaliana. Mol Ecol 19, 1187-1199 (2010). [18] Jiménez-Gómez, J. M., Wallace, A. D. & Maloof, J. N. Network analysis identifies ELF3 as a QTL for the shade avoidance response in Arabidopsis. PLoS Genet 6, (2010). [19] Jimenez-Gomez, J. M. & Maloof, J. N. Sequence diversity in three tomato species: SNPs, markers, and molecular evolution. BMC Plant Biol 9, 85 (2009). [20] Jiménez-Gómez, J. M. & Maloof, J. N. Plant research accelerates along the (bio)informatics superhighway: symposium on plant sensing, response and adaptation to the environment. EMBO Rep 10, 568-572 (2009). [21] Schwartz, C., Balasubramanian, S., Warthmann, N., Michael, T. P., Lempe, J., Sureshkumar, S., Kobayashi, Y., Maloof, J. N., Borevitz, J. O., Chory, J. & Weigel, D. Cis-regulatory Changes at FLOWERING LOCUS T Mediate Natural Variation in Flowering Responses of Arabidopsis thaliana. Genetics 183, 723-32, 1SI-7SI (2009). [22] Balasubramanian, S., Schwartz, C., Singh, A., Warthmann, N., Kim, M. C., Maloof, J. N., Loudet, O., Trainer, G. T., Dabi, T., Borevitz, J. O., Chory, J. & Weigel, D. QTL Mapping in New Arabidopsis thaliana Advanced Intercross-Recombinant Inbred Lines. PLoS ONE 4, e4318 (2009). [23] Covington, M. F., Maloof, J. N., Straume, M., Kay, S. A. & Harmer, S. L. Global transcriptome analysis reveals circadian regulation of key pathways in plant growth and development. Genome Biol 9, R130 (2008). [24] Filiault, D. L., Wessinger, C. A., Dinneny, J. R., Lutes, J., Borevitz, J. O., Weigel, D., Chory, J. & Maloof, J. N. Amino acid polymorphisms in Arabidopsis phytochrome B cause differential responses to light. Proc Natl Acad Sci U S A 105, 3157-3162 (2008). [25] Weinig, C., Johnston, J. A., Willis, C. G. & Maloof, J. N. Antagonistic multilevel selection on size and architecture in variable density settings. Evolution 61, 58-67 (2007). [26] Nozue, K., Covington, M. F., Duek, P. D., Lorrain, S., Fankhauser, C., Harmer, S. L. & Maloof, J. N. Rhythmic growth explained by coincidence between internal and external cues. Nature 448, 358-361 (2007). [27] Maloof, J. N. Small but not forgotten. Heredity 96, 1-2 (2006). [28] Balasubramanian, S., Sureshkumar, S., Agrawal, M., Michael, T. P., Wessinger, C., Maloof, J. N., Clark, R., Warthmann, N., Chory, J. & Weigel, D. The PHYTOCHROME C photoreceptor gene mediates natural variation in flowering and growth responses of Arabidopsis thaliana. Nat Genet 38, 711-715 (2006). [29] Nozue, K. & Maloof, J. N. Diurnal regulation of plant growth. Plant Cell Environ 29, 396-408 (2006). Lu, L., Lee, Y. R., Pan, R., Maloof, J. N. & Liu, B. An internal motor kinesin is associated with the Golgi apparatus and plays a role in trichome morphogenesis in Arabidopsis. Mol Biol Cell 16, 811-823 (2005). [30] Maloof, J. N. Plant development: slowing root growth naturally. Curr Biol 14, R395-R396 (2004). [31] Wolyn, D. J., Borevitz, J. O., Loudet, O., Schwartz, C., Maloof, J., Ecker, J. R., Berry, C. C. & Chory, J. Light-response quantitative trait loci identified with composite interval and eXtreme array mapping in Arabidopsis thaliana. Genetics 167, 907-917 (2004). [32] Maloof, J. N. Genomic approaches to analyzing natural variation in Arabidopsis thaliana. Curr Opin Genet Dev 13, 576-582 (2003). Maloof, J. N. QTL for plant growth and morphology. Curr Opin Plant Biol 6, 85-90 (2003). Nemhauser, J. L., Maloof, J. N. & Chory, J. Building integrated models of plant growth and development. Plant Physiol 132, 436-439 (2003). [33]