Skip to main content
Skip to navigation

Todd Mockler

Adjunct Associate Professor of Biological Sciences
Associate Member, Donald Danforth Plant Science Center
PhD, 2002 UCLA

Office: 975 N. Warson Road St. Louis, MO
Phone: 314-587-1694
Additional: Website, Twitter
Headshot of Todd Mockler


Research summary

Application of computational bioinformatics and molecular genomics to plant genomes.

Research description

The Mockler lab is located at the Donald Danforth Plant Science Center in St. Louis, Missouri.

His lab applies cutting edge technology and pioneers new analytical techniques to better understand plant genomes. His lab has been a major proponent of Brachypodium distachyon as a model organism for studying major crops, since it is much more closely related to several essential grains such as rice and sorghum. In addition, his lab has also sequenced the genomes of a number of other commercially relevant crops and hope to promote a better future through a deeper scientific understanding of the organisms we so heavily rely upon.

Select Publications

Select Publications

Marinoni, D.T., Valentini, N., Portis, E., Acquadro, A., Beltramo, C., Mehlenbacher, S.A., Mockler, T.C., Rowley, E.R., Botta, R. High density SNP mapping and QTL analysis for time of leaf budburst in Corylus avellana L. (2018) PLoS ONE, 13 (4), art. no. e0195408, DOI: 10.1371/journal.pone.0195408

Jibran, R., Dzierzon, H., Bassil, N., Bushakra, J.M., Edger, P.P., Sullivan, S., Finn, C.E., Dossett, M., Vining, K.J., Vanburen, R., Mockler, T.C., Liachko, I., Davies, K.M., Foster, T.M., Chagné, D. Chromosome-scale scaffolding of the black raspberry (Rubus occidentalis L.) genome based on chromatin interaction data (2018) Horticulture Research, 5 (1), art. no. 8, DOI: 10.1038/s41438-017-0013-y

Vanburen, R., Wai, C.M., Ou, S., Pardo, J., Bryant, D., Jiang, N., Mockler, T.C., Edger, P., Michael, T.P. Extreme haplotype variation in the desiccation-tolerant clubmoss Selaginella lepidophylla (2018) Nature Communications, 9 (1), art. no. 2546, DOI: 10.1038/s41467-017-02546-5

Boyle, G., Richter, K., Priest, H.D., Traver, D., Mockler, T.C., Chang, J.T., Kay, S.A., Breton, G.Comparative analysis of vertebrate diurnal/circadian transcriptomes (2017) PLoS ONE, 12 (1), art. no. e0169923,

Michael, T.P., Bryant, D., Gutierrez, R., Borisjuk, N., Chu, P., Zhang, H., Xia, J., Zhou, J., Peng, H., El Baidouri, M., ten Hallers, B., Hastie, A.R., Liang, T., Acosta, K., Gilbert, S., McEntee, C., Jackson, S.A., Mockler, T.C., Zhang, W., Lam, E. Comprehensive definition of genome features in Spirodela polyrhiza by high-depth physical mapping and short-read DNA sequencing strategies (2017) Plant Journal, 89 (3), pp. 617-635.

Shakoor, N., Lee, S., Mockler, T.C. High throughput phenotyping to accelerate crop breeding and monitoring of diseases in the field (2017) Current Opinion in Plant Biology, 38, pp. 184-192.

Wai, C.M., VanBuren, R., Zhang, J., Huang, L., Miao, W., Edger, P.P., Yim, W.C., Priest, H.D., Meyers, B.C., Mockler, T., Smith, J.A.C., Cushman, J.C., Ming, R. Temporal and spatial transcriptomic and microRNA dynamics of CAM photosynthesis in pineapple (2017) Plant Journal, 92 (1), pp. 19-30.

VanBuren, R., Wai, C.M., Zhang, Q., Song, X., Edger, P.P., Bryant, D., Michael, T.P., Mockler, T.C., Bartels, D. Seed desiccation mechanisms co-opted for vegetative desiccation in the resurrection grass Oropetium thomaeum (2017) Plant Cell and Environment, 40 (10), pp. 2292-2306.

Begemann, M.B., Gray, B.N., January, E., Gordon, G.C., He, Y., Liu, H., Wu, X., Brutnell, T.P., Mockler, T.C., Oufattole, M. Precise insertion and guided editing of higher plant genomes using Cpf1 CRISPR nucleases (2017) Scientific Reports, 7 (1), art. no. 11606,

Greenham, K., Guadagno, C.R., Gehan, M.A., Mockler, T.C., Weinig, C., Ewers, B.E., McClung, C.R. Temporal network analysis identifies early physiological and transcriptomic indicators of mild drought in brassica rapa (2017) eLife, 6, art. no. e29655, . DOI: 10.7554/eLife.29655

Pengpumkiat S, Koesdjojo M, Rowley ER, Mockler TC, Remcho VT: Rapid synthesis of a long double-stranded oligonucleotide from a single-stranded nucleotide using magnetic beads and an oligo library. PLoS ONE 2016, 11(3).

Rhee SY, Parker JE, Mockler TC: A glimpse into the future of genome-enabled plant biology from the shores of Cold Spring Harbor. Genome Biology 2016, 17(1).

Wang L, Czedik-Eysenberg A, Mertz RA, Si Y, Tohge T, Nunes-Nesi A, Arrivault S, Dedow LK, Bryant DW, Zhou W et al: Comparative analyses of C4 and C3 photosynthesis in developing leaves of maize and rice. Nature Biotechnology 2016, 32(11):1158-1164.

Sebastian, J., Yee, M.-C., Viana, W.G., Rellán-Álvarez, R., Feldman, M., Priest, H.D., Trontin, C., Lee, T., Jiang, H., Baxter, I., Mockler, T.C., Hochholdinger, F., Brutnell, T.P., Dinneny, J.R. Grasses suppress shoot-borne roots to conserve water during drought (2016) Proceedings of the National Academy of Sciences of the United States of America, 113 (31), pp. 8861-8866.

VanBuren, R., Bryant, D., Bushakra, J.M., Vining, K.J., Edger, P.P., Rowley, E.R., Priest, H.D., Michael, T.P., Lyons, E., Filichkin, S.A., Dossett, M., Finn, C.E., Bassil, N.V., Mockler, T.C. The genome of black raspberry (Rubus occidentalis) (2016) Plant Journal, 87 (6), pp. 535-547.

Bushakra JM, Bryant DW, Dossett M, Vining KJ, VanBuren R, Gilmore BS, Lee J, Mockler TC, Finn CE, Bassil NV: A genetic linkage map of black raspberry (Rubus occidentalis) and the mapping of Ag <inf> 4</inf> conferring resistance to the aphid Amphorophora agathonica. Theoretical and Applied Genetics 2015, 128(8):1631-1646.

Carbonell A, Fahlgren N, Mitchell S, Cox KL, Reilly KC, Mockler TC, Carrington JC: Highly specific gene silencing in a monocot species by artificial microRNAs derived from chimeric miRNA precursors. Plant Journal 2015, 82(6):1061-1075.

Filichkin S, Priest HD, Megraw M, Mockler TC: Alternative splicing in plants: Directing traffic at the crossroads of adaptation and environmental stress. Current Opinion in Plant Biology 2015, 24:125-135.

Filichkin SA, Cumbie JS, Dharmawardhana P, Jaiswal P, Chang JH, Palusa SG, Reddy ASN, Megraw M, Mockler TC: Environmental stresses modulate abundance and timing of alternatively spliced circadian transcripts in Arabidopsis. Molecular Plant 2015, 8(2):207-227.

Gehan MA, Greenham K, Mockler TC, McClung CR: Transcriptional networks-crops, clocks, and abiotic stress. Current Opinion in Plant Biology 2015, 24:39-46.

Howe GT, Horvath DP, Dharmawardhana P, Priest HD, Mockler TC, Strauss SH: Extensive transcriptome changes during natural onset and release of vegetative bud dormancy in Populus. Frontiers in Plant Science 2015, 6(DEC).

Kim DM, Zhang H, Zhou H, Du T, Wu Q, Mockler TC, Berezin MY: Highly sensitive image-derived indices of water-stressed plants using hyperspectral imaging in SWIR and histogram analysis. Scientific Reports 2015, 5.

Lee I, Mockler TC: Editorial overview: Genome studies and molecular genetics: Data-driven approaches to genotype-to-phenotype studies in crops. Current Opinion in Plant Biology 2015, 24:4-6.

Ming R, VanBuren R, Wai CM, Tang H, Schatz MC, Bowers JE, Lyons E, Wang ML, Chen J, Biggers E et al: The pineapple genome and the evolution of CAM photosynthesis. Nature Genetics 2015, 47(12):1435-1442.

Vanburen R, Bryant D, Edger PP, Tang H, Burgess D, Challabathula D, Spittle K, Hall R, Gu J, Lyons E et al: Single-molecule sequencing of the desiccation-tolerant grass Oropetium thomaeum. Nature 2015, 527(7579):508-511.

Vragović K, Selaa A, Friedlander-Shani L, Fridman Y, Hacham Y, Holland N, Bartom E, Mockler TC, Savaldi-Goldstein S: Translatome analyses capture of opposing tissuespecific brassinosteroid signals orchestrating root meristem differentiation. Proceedings of the National Academy of Sciences of the United States of America 2015, 112(3):923-928.

Bassil N, Gilmore B, Hummer K, Dossett M, Mockler T, Filichkin S, Peterson M, Finn CE, Lee J, Fernandez G et al: Genetic and developing genomic resources in black raspberry. In: Acta Horticulturae. vol. 1048; 2014: 19-24.

Fox SE, Christie MR, Marine M, Priest HD, Mockler TC, Blouin MS: Sequencing and characterization of the anadromous steelhead (Oncorhynchus mykiss) transcriptome. Marine Genomics 2014, 15:13-15.

Gordon SP, Priest H, Des Marais DL, Schackwitz W, Figueroa M, Martin J, Bragg JN, Tyler L, Lee CR, Bryant D et al: Genome diversity in Brachypodium distachyon: Deep sequencing of highly diverse inbred lines. Plant Journal 2014, 79(3):361-374.

Jung HS, Mockler TC: A new alternative in plant retrograde signaling. Genome Biology 2014, 15(5).

Priest HD, Fox SE, Rowley ER, Murray JR, Michael TP, Mockler TC: Analysis of global gene expression in Brachypodium distachyon reveals extensive network plasticity in response to abiotic stress. PLoS ONE 2014, 9(1).

Rowley ER, Bryant DW, Fox SE, Givan SA, Mehlenbacher SA, Mockler TC: Genome sequencing and resource development for European hazelnut. In: Acta Horticulturae. vol. 1052; 2014: 75-78.

Wang W, Haberer G, Gundlach H, Gläßer C, Nussbaumer T, Luo MC, Lomsadze A, Borodovsky M, Kerstetter RA, Shanklin J et al: The Spirodela polyrhiza genome reveals insights into its neotenous reduction fast growth and aquatic lifestyle. Nature Communications 2014, 5.

Ibarra-Laclette E, Lyons E, Hernández-Guzmán G, Pérez-Torres CA, Carretero-Paulet L, Chang TH, Lan T, Welch AJ, Juárez MJA, Simpson J et al: Architecture and evolution of a minute plant genome. Nature 2013, 498(7452):94-98.

Jeong DH, Schmidt SA, Rymarquis LA, Park S, Ganssmann M, German MA, Accerbi M, Zhai J, Fahlgren N, Fox SE et al: Parallel analysis of rna ends enhances global investigation of micrornas and target rnas of brachypodium distachyon. Genome Biology 2013, 14(12).

Jung HS, Crisp PA, Estavillo GM, Cole B, Hong F, Mockler TC, Pogson BJ, Chory J: Subset of heat-shock transcription factors required for the early response of Arabidopsis to excess light. Proceedings of the National Academy of Sciences of the United States of America 2013, 110(35):14474-14479.

Ming R, VanBuren R, Liu Y, Yang M, Han Y, Li LT, Zhang Q, Kim MJ, Schatz MC, Campbell M et al: Genome of the long-living sacred lotus (Nelumbo nucifera Gaertn.). Genome Biology 2013, 14(5).

Trabucco GM, Matos DA, Lee SJ, Saathoff AJ, Priest HD, Mockler TC, Sarath G, Hazen SP: Functional characterization of cinnamyl alcohol dehydrogenase and caffeic acid O-methyltransferase in Brachypodium distachyon. BMC Biotechnology 2013, 13.

Vining K, Pomraning KR, Wilhelm LJ, Ma C, Pellegrini M, Di Y, Mockler TC, Freitag M, Strauss SH: Methylome reorganization during in vitro dedifferentiation and regeneration of Populus trichocarpa. BMC Plant Biology 2013, 13(1).

Slavov GT, Difazio SP, Martin J, Schackwitz W, Muchero W, Rodgers-Melnick E, Lipphardt MF, Pennacchio CP, Hellsten U, Pennacchio LA et al: Genome resequencing reveals multiscale geographic structure and extensive linkage disequilibrium in the forest tree Populus trichocarpa. New Phytologist 2012, 196(3):713-725.

Li C, Rudi H, Stockinger EJ, Cheng H, Cao M, Fox SE, Mockler TC, Westereng B, Fjellheim S, Rognli OA et al: Comparative analyses reveal potential uses of Brachypodium distachyon as a model for cold stress responses in temperate grasses. BMC Plant Biology 2012, 12.

Pandelova I, Figueroa M, Wilhelm LJ, Manning VA, Mankaney AN, Mockler TC, Ciuffetti LM: Host-selective toxins of pyrenophora tritici-repentis induce common responses associated with host susceptibility. PLoS ONE 2012, 7(7).

Filichkin SA, Mockler TC: Unproductive alternative splicing and nonsense mRNAs: A widespread phenomenon among plant circadian clock genes. Biology Direct 2012, 7.

Verde I, Bassil N, Scalabrin S, Gilmore B, Lawley CT, Gasic K, Micheletti D, Rosyara UR, Cattonaro F, Vendramin E et al: Development and evaluation of a 9k snp array for peach by internationally coordinated snp detection and validation in breeding germplasm. PLoS ONE 2012, 7(4).

Wang Y, Zeng X, Iyer NJ, Bryant DW, Mockler TC, Mahalingam R: Exploring the switchgrass transcriptome using second-generation sequencing technology. PLoS ONE 2012, 7(3).

Chagné D, Crowhurst RN, Troggio M, Davey MW, Gilmore B, Lawley C, Vanderzande S, Hellens RP, Kumar S, Cestaro A et al: Genome-wide SNP detection, validation, and development of an 8K SNP array for apple. PLoS ONE 2012, 7(2).

Vining KJ, Pomraning KR, Wilhelm LJ, Priest HD, Pellegrini M, Mockler TC, Freitag M, Strauss SH: Dynamic DNA cytosine methylation in the Populus trichocarpa genome: Tissue-level variation and relationship to gene expression. BMC Genomics 2012, 13(1).

Rowley ER, Fox SE, Bryant DW, Sullivan CM, Priest HD, Givan SA, Mehlenbacher SA, Mockler TC: Assembly and characterization of the European hazelnut 'Jefferson' transcriptome. Crop Science 2012, 52(6):2679-2686.

Peace C, Bassil N, Main D, Ficklin S, Rosyara UR, Stegmeir T, Sebolt A, Gilmore B, Lawley C, Mockler TC et al: Development and Evaluation of a Genome-Wide 6K SNP Array for Diploid Sweet Cherry and Tetraploid Sour Cherry. PLoS ONE 2012, 7(12).

Bryant DW, Priest HD, Mockler TC: Detection and quantification of alternative splicing variants using RNA-seq. In: Methods in Molecular Biology. vol. 883; 2012: 97-110.

Bryant DW, Mockler TC: De novo short-read assembly. In: Bioinformatics for High Throughput Sequencing. 2012: 85-105.

Honors & Awards

Selected honors and awards

Virgil Distinguished Investigator 2012

Oregon State University Promising Scholar Award 2010

Phi Kappa Phi Engineering Scholar Award 2009