Maloof Lab Publications

  • Ranjan A, Budke JM, Rowland SD, Chitwood DH, Kumar R, et al. (2016). eQTL Regulating Transcript Levels Associated with Diverse Biological Processes in Tomato. Plant Physiol 172(1): 328-40. PubMed Plant Physiol PDF

  • Fulop D, Ranjan A, Ofner I, Covington MF, Chitwood DH, et al. (2016). A New Advanced Backcross Tomato Population Enables High Resolution Leaf QTL Mapping and Gene Identification. G3 (Bethesda). PubMed G3 (Bethesda)

  • Carriedo LG, Maloof JN, Brady SM (2016). Molecular control of crop shade avoidance. Curr Opin Plant Biol 30: 151-8. PubMed PDF

  • Brock MT, Lucas LK, Anderson NA, Rubin MJ, Markelz RJ, et al. (2016). Genetic architecture, biochemical underpinnings and ecological impact of floral UV patterning. Mol Ecol 25(5): 1122-40. PubMed Mol Ecol

  • Müller NA, Wijnen CL, Srinivasan A, Ryngajllo M, Ofner I, et al. (2016). Domestication selected for deceleration of the circadian clock in cultivated tomato. Nat Genet 48(1): 89-93. PubMed Nat Genet PDF

  • Nguyen TT, Slaughter DC, Max N, Maloof JN, Sinha N (2015). Structured Light-Based 3D Reconstruction System for Plants. Sensors (Basel) 15(8): 18587-612. PubMed Sensors (Basel) PDF

  • Brady SM, Burow M, Busch W, Carlborg Ö, Denby KJ, et al. (2015). Reassess the t Test: Interact with All Your Data via ANOVA. Plant Cell. PubMed Plant Cell PDF

  • Baker RL, Leong WF, Brock MT, Markelz RJ, Covington MF, et al. (2015). Modeling development and quantitative trait mapping reveal independent genetic modules for leaf size and shape. New Phytol. PubMed New Phytol PDF

  • Nozue K, Tat AV, Kumar Devisetty U, Robinson M, Mumbach MR, et al. (2015). Shade avoidance components and pathways in adult plants revealed by phenotypic profiling. PLoS Genet 11(4): e1004953. PubMed PLoS Genet PDF

  • Chitwood DH, Kumar R, Ranjan A, Pelletier JM, Townsley BT, et al. (2015). Light-Induced Indeterminacy Alters Shade-Avoiding Tomato Leaf Morphology. Plant Physiol 169(3): 2030-47. PubMed Plant Physiol

  • Rellán-Álvarez R, Lobet G, Lindner H, Pradier PL, Sebastian J, et al. (2015). GLO-Roots: an imaging platform enabling multidimensional characterization of soil-grown root systems. Elife 4. PubMed Elife

  • Bolger A, Scossa F, Bolger ME, Lanz C, Maumus F, et al. (2014). The genome of the stress-tolerant wild tomato species Solanum pennellii. Nat Genet 46(9): 1034-8. PubMed Nat Genet

  • Chitwood DH, Ranjan A, Kumar R, Ichihashi Y, Zumstein K, et al. (2014). Resolving distinct genetic regulators of tomato leaf shape within a heteroblastic and ontogenetic context. Plant Cell 26(9): 3616-29. PubMed Plant Cell

  • Devisetty UK, Covington MF, Tat AV, Lekkala S, Maloof JN (2014). Polymorphism identification and improved genome annotation of Brassica rapa through Deep RNA sequencing. G3 (Bethesda) 4(11): 2065-78. PubMed G3 (Bethesda) PDF

  • Ichihashi Y, Aguilar-Martínez JA, Farhi M, Chitwood DH, Kumar R, et al. (2014). Evolutionary developmental transcriptomics reveals a gene network module regulating interspecific diversity in plant leaf shape. Proc Natl Acad Sci U S A 111(25): E2616-21. PubMed Proc Natl Acad Sci U S A

  • Fitz Gerald JN, Carlson AL, Smith E, Maloof JN, Weigel D, et al. (2014). New Arabidopsis advanced intercross recombinant inbred lines reveal female control of nonrandom mating. Plant Physiol 165(1): 175-85. PubMed Plant Physiol

  • Chitwood DH, Ranjan A, Martinez CC, Headland LR, Thiem T, et al. (2014). A modern ampelography: a genetic basis for leaf shape and venation patterning in grape. Plant Physiol 164(1): 259-72. PubMed Plant Physiol PDF

  • Koenig D, Jiménez-Gómez JM, Kimura S, Fulop D, Chitwood DH, et al. (2013). Comparative transcriptomics reveals patterns of selection in domesticated and wild tomato. Proc Natl Acad Sci U S A 110(28): E2655-62. PubMed Proc Natl Acad Sci U S A PDF

  • Chitwood DH, Kumar R, Headland LR, Ranjan A, Covington MF, et al. (2013). A quantitative genetic basis for leaf morphology in a set of precisely defined tomato introgression lines. Plant Cell 25(7): 2465-81. PubMed Plant Cell PDF

  • Chitwood DH, Maloof JN, Sinha NR (2013). Dynamic transcriptomic profiles between tomato and a wild relative reflect distinct developmental architectures. Plant Physiol 162(2): 537-52. PubMed Plant Physiol

  • Ron M, Dorrity MW, de Lucas M, Toal T, Hernandez RI, et al. (2013). Identification of novel loci regulating interspecific variation in root morphology and cellular development in tomato. Plant Physiol 162(2): 755-68. PubMed Plant Physiol

  • Sharlach M, Dahlbeck D, Liu L, Chiu J, Jiménez-Gómez JM, et al. (2013). Fine genetic mapping of RXopJ4, a bacterial spot disease resistance locus from Solanum pennellii LA716. Theor Appl Genet 126(3): 601-9. PubMed Theor Appl Genet

  • Maloof JN, Nozue K, Mumbach MR, Palmer CM (2013). LeafJ: an ImageJ plugin for semi-automated leaf shape measurement. J Vis Exp. PubMed J Vis Exp

  • Seymour DK, Filiault DL, Henry IM, Monson-Miller J, Ravi M, et al. (2012). Rapid creation of Arabidopsis doubled haploid lines for quantitative trait locus mapping. Proc Natl Acad Sci U S A 109(11): 4227-32. PubMed Proc Natl Acad Sci U S A

  • Chitwood DH, Headland LR, Kumar R, Peng J, Maloof JN, et al. (2012). The developmental trajectory of leaflet morphology in wild tomato species. Plant Physiol 158(3): 1230-40. PubMed Plant Physiol

  • Chitwood DH, Headland LR, Filiault DL, Kumar R, Jiménez-Gómez JM, et al. (2012). Native environment modulates leaf size and response to simulated foliar shade across wild tomato species. PLoS One 7(1): e29570. PubMed PLoS One PDF

  • Filiault DL, Maloof JN (2012). A genome-wide association study identifies variants underlying the Arabidopsis thaliana shade avoidance response. PLoS Genet 8(3): e1002589. PubMed PLoS Genet

  • Kumar R, Ichihashi Y, Kimura S, Chitwood DH, Headland LR, et al. (2012). A High-Throughput Method for Illumina RNA-Seq Library Preparation. Front Plant Sci 3: 202. PubMed Front Plant Sci

  • Jimenez-Gomez JM, Corwin JA, Joseph B, Maloof JN, Kliebenstein DJ (2011). Genomic analysis of QTLs and genes altering natural variation in stochastic noise. PLoS Genet 7(9): e1002295. PubMed PLoS Genet

  • Holtan HE, Bandong S, Marion CM, Adam L, Tiwari 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(4): 2109-23. PubMed Plant Physiol

  • Arana MV, Marín-de la Rosa N, Maloof JN, Blázquez MA, Alabadí D (2011). Circadian oscillation of gibberellin signaling in Arabidopsis. Proc Natl Acad Sci U S A 108(22): 9292-7. PubMed Proc Natl Acad Sci U S A

  • Chang CS, Maloof JN, Wu SH (2011). COP1-mediated degradation of BBX22/LZF1 optimizes seedling development in Arabidopsis. Plant Physiol 156(1): 228-39. PubMed Plant Physiol

  • Nozue K, Harmer SL, Maloof JN (2011). Genomic analysis of circadian clock-, light-, and growth-correlated genes reveals PHYTOCHROME-INTERACTING FACTOR5 as a modulator of auxin signaling in Arabidopsis. Plant Physiol 156(1): 357-72. PubMed Plant Physiol

  • Kerwin RE, Jimenez-Gomez JM, Fulop D, Harmer SL, Maloof JN, et al. (2011). Network quantitative trait loci mapping of circadian clock outputs identifies metabolic pathway-to-clock linkages in Arabidopsis. Plant Cell 23(2): 471-85. PubMed Plant Cell

  • Kim K, Shin J, Lee SH, Kweon HS, Maloof JN, et al. (2011). Phytochromes inhibit hypocotyl negative gravitropism by regulating the development of endodermal amyloplasts through phytochrome-interacting factors. Proc Natl Acad Sci U S A 108(4): 1729-34. PubMed Proc Natl Acad Sci U S A

  • Stewart JL, Maloof JN, Nemhauser JL (2011). PIF genes mediate the effect of sucrose on seedling growth dynamics. PLoS One 6(5): e19894. PubMed PLoS One

  • Jiménez-Gómez JM, Wallace AD, Maloof JN (2010). Network analysis identifies ELF3 as a QTL for the shade avoidance response in Arabidopsis. PLoS Genet 6(9): e1001100. PubMed PLoS Genet

  • Brock MT, Maloof JN, Weinig C (2010). 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(6): 1187-99. PubMed Mol Ecol

  • Brock MT, Dechaine JM, Iniguez-Luy FL, Maloof JN, Stinchcombe JR, et al. (2010). Floral genetic architecture: an examination of QTL architecture underlying floral (co)variation across environments. Genetics 186(4): 1451-65. PubMed Genetics

  • Maloof JN (2010). Recent advances in regulation of flowering. F1000 Biol Rep 2. PubMed F1000 Biol Rep

  • Jiménez-Gómez JM, Maloof JN (2009). Plant research accelerates along the (bio)informatics superhighway: symposium on plant sensing, response and adaptation to the environment. EMBO Rep 10(6): 568-72. PubMed EMBO Rep

  • Schwartz C, Balasubramanian S, Warthmann N, Michael TP, Lempe J, et al. (2009). Cis-regulatory changes at FLOWERING LOCUS T mediate natural variation in flowering responses of Arabidopsis thaliana. Genetics 183(2): 723-32, 1SI-7SI. PubMed Genetics

  • Balasubramanian S, Schwartz C, Singh A, Warthmann N, Kim MC, et al. (2009). QTL mapping in new Arabidopsis thaliana advanced intercross-recombinant inbred lines. PLoS One 4(2): e4318. PubMed PLoS One

  • Jiménez-Gómez JM, Maloof JN (2009). Sequence diversity in three tomato species: SNPs, markers, and molecular evolution. BMC Plant Biol 9: 85. PubMed BMC Plant Biol

  • Filiault DL, Wessinger CA, Dinneny JR, Lutes J, Borevitz JO, et al. (2008). Amino acid polymorphisms in Arabidopsis phytochrome B cause differential responses to light. Proc Natl Acad Sci U S A 105(8): 3157-62. PubMed Proc Natl Acad Sci U S A

  • Covington MF, Maloof JN, Straume M, Kay SA, Harmer SL (2008). Global transcriptome analysis reveals circadian regulation of key pathways in plant growth and development. Genome Biol 9(8): R130. PubMed Genome Biol PDF

  • Nozue K, Covington MF, Duek PD, Lorrain S, Fankhauser C, et al. (2007). Rhythmic growth explained by coincidence between internal and external cues. Nature 448(7151): 358-61. PubMed Nature PDF

  • Weinig C, Johnston JA, Willis CG, Maloof JN (2007). Antagonistic multilevel selection on size and architecture in variable density settings. Evolution 61(1): 58-67. PubMed Evolution

  • Bush SM, Krysan PJ (2007). Mutational evidence that the Arabidopsis MAP kinase MPK6 is involved in anther, inflorescence, and embryo development. J Exp Bot 58(8): 2181-91. PubMed J Exp Bot

  • Balasubramanian S, Sureshkumar S, Agrawal M, Michael TP, Wessinger C, et al. (2006). The PHYTOCHROME C photoreceptor gene mediates natural variation in flowering and growth responses of Arabidopsis thaliana. Nat Genet 38(6): 711-5. PubMed Nat Genet

  • Nozue K, Maloof JN (2006). Diurnal regulation of plant growth. Plant Cell Environ 29(3): 396-408. PubMed

  • Maloof JN (2006). Small but not forgotten. Heredity (Edinb) 96(1): 1-2. PubMed Heredity (Edinb)

  • Lu L, Lee YR, Pan R, Maloof JN, Liu B (2005). An internal motor kinesin is associated with the Golgi apparatus and plays a role in trichome morphogenesis in Arabidopsis. Mol Biol Cell 16(2): 811-23. PubMed Mol Biol Cell

  • Maloof JN (2004). Plant development: slowing root growth naturally. Curr Biol 14(10): R395-6. PubMed

  • Nemhauser JL, Maloof JN, Chory J (2003). Building integrated models of plant growth and development. Plant Physiol 132(2): 436-9. PubMed Plant Physiol

  • Maloof JN (2003). QTL for plant growth and morphology. Curr Opin Plant Biol 6(1): 85-90. PubMed

  • Maloof JN (2003). Genomic approaches to analyzing natural variation in Arabidopsis thaliana. Curr Opin Genet Dev 13(6): 576-82. PubMed