Research Interests

My interests are evolutionarily broad and include animals, plants and fungi. A major focus of the lab is the genomic analysis of gene expression programs during plant gene expression programs, particularly during embryogenesis and seed development, and the underlying regulatory mechanisms required for the initiation and maintenance of these programs. This work has illustrated the combinatorial interactions of cis and trans -acting factors that result in specific gene regulatory events. We are also using genomics tools to study the interaction of the rice blast fungus, Magnaporthe grisea , with plant hosts; the circadian control of gene expression; and the development of the vertebrate retina. An additional focal area is the utilization of molecular and cellular approaches for crop improvement. As part of these research activities, we have developed or adapted high throughput genomics approaches to accelerate the gene discovery process and subsequent analysis of gene expression and function.

1. Bennett, LD, Beremand, P, Thomas, TL, Bell-Pedersen, D. Circadian activation of the mitogen-activated protein kinase MAK-1 facilitates rhythms in clock-controlled genes in Neurospora crassa. Eukaryot Cell. 2013;12 (1):59-69. doi: 10.1128/EC.00207-12. PubMed PMID:23125351 PubMed Central PMC3535850.
2. Alvarado, VY, Tag, A, Thomas, TL. A cis regulatory element in the TAPNAC promoter directs tapetal gene expression. Plant Mol Biol. 2011;75 (1-2):129-39. doi: 10.1007/s11103-010-9713-5. PubMed PMID:21107887 .
3. Karaganis, SP, Kumar, V, Beremand, PD, Bailey, MJ, Thomas, TL, Cassone, VM et al.. Circadian genomics of the chick pineal gland in vitro. BMC Genomics. 2008;9 :206. doi: 10.1186/1471-2164-9-206. PubMed PMID:18454867 PubMed Central PMC2405806.
4. Menger, GJ, Allen, GC, Neuendorff, N, Nahm, SS, Thomas, TL, Cassone, VM et al.. Circadian profiling of the transcriptome in NIH/3T3 fibroblasts: comparison with rhythmic gene expression in SCN2.2 cells and the rat SCN. Physiol Genomics. 2007;29 (3):280-9. doi: 10.1152/physiolgenomics.00199.2006. PubMed PMID:17284666 .
5. Holtman, CK, Chen, Y, Sandoval, P, Gonzales, A, Nalty, MS, Thomas, TL et al.. High-throughput functional analysis of the Synechococcus elongatus PCC 7942 genome. DNA Res. 2005;12 (2):103-15. doi: 10.1093/dnares/12.2.103. PubMed PMID:16303742 .
6. Gray, CA, Abbey, CA, Beremand, PD, Choi, Y, Farmer, JL, Adelson, DL et al.. Identification of endometrial genes regulated by early pregnancy, progesterone, and interferon tau in the ovine uterus. Biol Reprod. 2006;74 (2):383-94. doi: 10.1095/biolreprod.105.046656. PubMed PMID:16251498 .
7. Bell-Pedersen, D, Cassone, VM, Earnest, DJ, Golden, SS, Hardin, PE, Thomas, TL et al.. Circadian rhythms from multiple oscillators: lessons from diverse organisms. Nat Rev Genet. 2005;6 (7):544-56. doi: 10.1038/nrg1633. PubMed PMID:15951747 PubMed Central PMC2735866.
8. Bailey, MJ, Beremand, PD, Hammer, R, Reidel, E, Thomas, TL, Cassone, VM et al.. Transcriptional profiling of circadian patterns of mRNA expression in the chick retina. J Biol Chem. 2004;279 (50):52247-54. doi: 10.1074/jbc.M405679200. PubMed PMID:15448147 .
9. Bailey, MJ, Beremand, PD, Hammer, R, Bell-Pedersen, D, Thomas, TL, Cassone, VM et al.. Transcriptional profiling of the chick pineal gland, a photoreceptive circadian oscillator and pacemaker. Mol Endocrinol. 2003;17 (10):2084-95. doi: 10.1210/me.2003-0121. PubMed PMID:12881511 .
10. Kim, SY, Ma, J, Perret, P, Li, Z, Thomas, TL. Arabidopsis ABI5 subfamily members have distinct DNA-binding and transcriptional activities. Plant Physiol. 2002;130 (2):688-97. doi: 10.1104/pp.003566. PubMed PMID:12376636 PubMed Central PMC166598.