Research Interests

My first love in biology was development (thanks to Kaye Edwards at Haverford) and that is what I pursued for my PhD with Cynthia Kenyon.  As I finished my PhD I became fascinated by trying to understand how organisms modify their development in response to the environment.  Thankfully fellow graduate student Lee Honigberg dropped a paper on my desk reviewing plant response to their light environment and I was hooked.  I went to Joanne Chory's and Detlef Weigel's labs at The Salk and started a program on the quantitative genetics of plant light responses.

I am still fascinated by light regulated development and shade avoidance.  Over time I have also become more generally interested in how plants respond to their environment and how these responses evolve to allow plants to adapt to different habitats.

I have always also loved computer programming and am excited to be participating in the application of computational techniques in biology.

Personal Interests

Outside of lab, I enjoy the abundant produce at the Davis Farmer's Market, cooking, eating, sharing wine with friends, cycling, hiking, backcountry skiing, and trips to San Francisco for great restaurants, jazz, and theater.


Degree Field Institution Year(s) Advisor
Ph.D. Development and Genetics U. C. S. F. 1990 - 1998 Cynthia Kenyon
B.A. Biology Haverford College 1985 - 1989 Kaye Edwards


Position Field Institution Year(s) Advisor
Professor Plant Biology University of California, Davis 2012 - Present
Associate Professor Plant Biology University of California, Davis 2009 - 2012
Assistant Professor Plant Biology University of California, Davis 2002 - 2009
Postdoctoral Researcher Plant Genetics The Salk Institute for Biological Studies 1998 - 2002 Detlef Weigel and Joanne Chory


  • Cobo-Simón I, Maloof JN, Li R, Amini H, Méndez-Cea B, et al. (2023). Contrasting transcriptomic patterns reveal a genomic basis for drought resilience in the relict fir Abies pinsapo Boiss. Tree Physiol 43(2): 315-334. PubMed

  • Davis JT, Li R, Kim S, Michelmore R, Kim S, et al. (2023). Whole genome sequence of synthetically derived Brassica napus inbred cultivar Da-Ae. G3 (Bethesda). PubMed PDF

  • Creux NM, Brown EA, Garner AG, Saeed S, Scher CL, et al. (2021). Flower orientation influences floral temperature, pollinator visits and plant fitness. New Phytol. PubMed

  • Li C, Nozue K, Maloof JN (2020). MYCs and PIFs Act Independently in Arabidopsis Growth Regulation. G3 (Bethesda) 10(5): 1797-1807. PubMed PDF

  • Karunanithi PS, Berrios DI, Wang S, Davis J, Shen T, et al. (2020). The foxtail millet (Setaria italica) terpene synthase gene family. Plant J 103(2): 781-800. PubMed PDF

  • Rowland SD, Zumstein K, Nakayama H, Cheng Z, Flores AM, et al. (2020). Leaf shape is a predictor of fruit quality and cultivar performance in tomato. New Phytol 226(3): 851-865. PubMed PDF

  • Baker RL, Leong WF, Brock MT, Rubin MJ, Markelz RJC, et al. (2019). Integrating transcriptomic network reconstruction and eQTL analyses reveals mechanistic connections between genomic architecture and Brassica rapa development. PLoS Genet 15(9): e1008367. PubMed PLoS Genet PDF

  • Nohales MA, Liu W, Duffy T, Nozue K, Sawa M, et al. (2019). Multi-level Modulation of Light Signaling by GIGANTEA Regulates Both the Output and Pace of the Circadian Clock. Dev Cell 49(6): 840-851.e8. PubMed Dev Cell

  • Amini H, Naghavi MR, Shen T, Wang Y, Nasiri J, et al. (2019). Tissue-Specific Transcriptome Analysis Reveals Candidate Genes for Terpenoid and Phenylpropanoid Metabolism in the Medicinal Plant <i>Ferula assafoetida</i>. G3 (Bethesda) 9(3): 807-816. PubMed G3 (Bethesda) PDF

  • Markelz RJC, Covington MF, Brock MT, Devisetty UK, Kliebenstein DJ, et al. (2017). Using RNA-Seq for Genomic Scaffold Placement, Correcting Assemblies, and Genetic Map Creation in a Common Brassica rapa Mapping Population. G3 (Bethesda) 7(7): 2259-2270. PubMed G3 (Bethesda)

  • 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

  • Müller-Moulé P, Nozue K, Pytlak ML, Palmer CM, Covington MF, et al. (2016). YUCCA auxin biosynthetic genes are required for Arabidopsis shade avoidance. PeerJ 4: e2574. PubMed PeerJ 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

  • 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

  • Borevitz JO, Maloof JN, Lutes J, Dabi T, Redfern JL, et al. (2002). Quantitative trait loci controlling light and hormone response in two accessions of Arabidopsis thaliana. Genetics 160(2): 683-96. PubMed

  • Nordborg M, Borevitz JO, Bergelson J, Berry CC, Chory J, et al. (2002). The extent of linkage disequilibrium in Arabidopsis thaliana. Nat Genet 30(2): 190-3. PubMed Nat Genet

  • Friedrichsen DM, Nemhauser J, Muramitsu T, Maloof JN, Alonso J, et al. (2002). Three redundant brassinosteroid early response genes encode putative bHLH transcription factors required for normal growth. Genetics 162(3): 1445-56. PubMed

  • Maloof JN, Borevitz JO, Dabi T, Lutes J, Nehring RB, et al. (2001). Natural variation in light sensitivity of Arabidopsis. Nat Genet 29(4): 441-6. PubMed Nat Genet

  • Maloof JN, Borevitz JO, Weigel D, Chory J (2000). Natural variation in phytochrome signaling. Semin Cell Dev Biol 11(6): 523-30. PubMed

  • Schlesinger A, Shelton CA, Maloof JN, Meneghini M, Bowerman B (1999). Wnt pathway components orient a mitotic spindle in the early Caenorhabditis elegans embryo without requiring gene transcription in the responding cell. Genes Dev 13(15): 2028-38. PubMed

  • Hunter CP, Harris JM, Maloof JN, Kenyon C (1999). Hox gene expression in a single Caenorhabditis elegans cell is regulated by a caudal homolog and intercellular signals that inhibit wnt signaling. Development 126(4): 805-14. PubMed

  • Maloof JN, Whangbo J, Harris JM, Jongeward GD, Kenyon C (1999). A Wnt signaling pathway controls hox gene expression and neuroblast migration in C. elegans. Development 126(1): 37-49. PubMed

  • Eisenmann DM, Maloof JN, Simske JS, Kenyon C, Kim SK (1998). The beta-catenin homolog BAR-1 and LET-60 Ras coordinately regulate the Hox gene lin-39 during Caenorhabditis elegans vulval development. Development 125(18): 3667-80. PubMed

  • Maloof JN, Kenyon C (1998). The Hox gene lin-39 is required during C. elegans vulval induction to select the outcome of Ras signaling. Development 125(2): 181-90. PubMed

  • Kenyon CJ, Austin J, Costa M, Cowing DW, Harris JM, et al. (1997). The dance of the Hox genes: patterning the anteroposterior body axis of Caenorhabditis elegans. Cold Spring Harb Symp Quant Biol 62: 293-305. PubMed

  • Chavez RA, Maloof J, Beeson D, Newsom-Davis J, Hall ZW (1992). Subunit folding and alpha delta heterodimer formation in the assembly of the nicotinic acetylcholine receptor. Comparison of the mouse and human alpha subunits. J Biol Chem 267(32): 23028-34. PubMed