Publications

all Publications


Pasaribu, B., Acosta, K., Aylward, A., Liang, Y., Abramson, B.W., Colt, K., Hartwick, N.T., Shanklin, J., Michael, T.P., Lam, E. Genomics of turions from the Greater Duckweed reveal its pathways for dormancy and re-emergence strategy. (2023) New Phytologist. DOI: 10.1111/nph.18941

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Acosta, K., Sorrels, S., Chrisler, W., Huang, W., Gilbert, S., Brinkman, T., Michael, T.P., Lebeis, S.L., Lam, E. Optimization of Molecular Methods for Detecting Duckweed-Associated Bacteria. (2023) Plants. 12(4). DOI: 10.3390/plants12040872

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Silva, S.R., F O Miranda, V., Michael, T.P., Płachno, B.J., Matos, R.G., Adamec, L., L K Pond, S., Lucaci, A.G., Pinheiro, D.G., Varani, A.M. The phylogenomics and evolutionary dynamics of the organellar genomes in carnivorous Utricularia and Genlisea species (Lentibulariaceae). (2023) Mol Phylogenet Evol.:107711 DOI: 10.1016/j.ympev.2023.107711

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Michael, T.P. Time of Day Analysis over a Field Grown Developmental Time Course in Rice. (2022) Plants (Basel). 12(1). DOI: 10.3390/plants12010166

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Snoeck, S., Abramson, B.W., Garcia, A.G.K., Egan, A.N., Michael, T.P., Steinbrenner, A. Evolutionary gain and loss of a plant pattern-recognition receptor for HAMP recognition. (2022) Elife. 11. DOI: 10.7554/eLife.81050

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Minich, J.J., Härer, A., Vechinski, J., Frable, B.W., Skelton, Z.R., Kunselman, E., Shane, M.A., Perry, D.S., Gonzalez, A., McDonald, D., Knight, R., Michael, T.P., Allen, E.E. Host biology, ecology and the environment influence microbial biomass and diversity in 101 marine fish species. (2022) Nature Communications. 13(1):6978. DOI: 10.1038/s41467-022-34557-2

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Baggs, E.L., Tiersma, M.B., Abramson, B.W., Michael, T.P., Krasileva, K.V. Characterization of defense responses against bacterial pathogens in duckweeds lacking EDS1. (2022) New Phytol. DOI: 10.1111/nph.18453

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Low, Y.W., Rajaraman, S., Tomlin, C.M., Ahmad, J.A., Ardi, W.H., Armstrong, K., Athen, P., Berhaman, A., Bone, R.E., Cheek, M., Cho, N.R.W., Choo, L.M., Cowie, I.D., Crayn, D., Fleck, S.J., Ford, A.J., Forster, P.I., Girmansyah, D., Goyder, D.J., Gray, B., Heatubun, C.D., Ibrahim, A., Ibrahim, B., Jayasinghe, H.D., Kalat, M.A., Kathriarachchi, H.S., Kintamani, E., Koh, S.L., Lai, J.T.K., Lee, S.M.L., Leong, P.K.F., Lim, W.H., Lum, S.K.Y., Mahyuni, R., McDonald, W.J.F., Metali, F., Mustaqim, W.A., Naiki, A., Ngo, K.M., Niissalo, M., Ranasinghe, S., Repin, R., Rustiami, H., Simbiak, V.I., Sukri, R.S., Sunarti, S., Trethowan, L.A., Trias-Blasi, A., Vasconcelos, T.N.C., Wanma, J.F., Widodo, P., Wijesundara, D.S.A., Worboys, S., Yap, J.W., Yong, K.T., Khew, G.S.W., Salojärvi, J., Michael, T.P., Middleton, D.J., Burslem, D.F.R.P., Lindqvist, C., Lucas, E.J., Albert, V.A. Genomic insights into rapid speciation within the world’s largest tree genus Syzygium. (2022) Nature Communications. 13(1):5031. DOI: 10.1038/s41467-022-32637-x

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Michael, T.P. Core circadian clock and light signaling genes brought into genetic linkage across the green lineage. (2022) Plant Physiology. DOI: 10.1093/plphys/kiac276

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Zhang, T., Mudgett, M., Rambabu, R., Abramson, B., Dai, X., Michael, T.P., Zhao, Y. Retraction Note: Selective inheritance of target genes from only one parent of sexually reproduced F1 progeny in Arabidopsis. (2022) Nature Communications. 13(1):3270. DOI: 10.1038/s41467-022-31001-3


Guedes Matos, R., Rodrigues da Silva, S., Jan Płachno, B., Adamec, L., Michael, T.P., de Mello Varani, A., Miranda, V.F.O. The complete mitochondrial genome of carnivorous Genlisea tuberosa (Lentibulariaceae): structure and evolutionary aspects. (2022) Gene.:146391 DOI: 10.1016/j.gene.2022.146391

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Sutton, G., Fogel, G.B., Abramson, B., Brinkac, L., Michael, T., Liu, E.S., Thomas, S. Horizontal transfer and evolution of wall teichoic acid gene cassettes in  . (2022) F1000Res. 10:354. DOI: 10.12688/f1000research.51874.1

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Kawash, J., Colt, K., Hartwick, N.T., Abramson, B.W., Vorsa, N., Polashock, J.J., Michael, T.P. Contrasting a reference cranberry genome to a crop wild relative provides insights into adaptation, domestication, and breeding. (2022) PLOS One. 17(3):e0264966. DOI: 10.1371/journal.pone.0264966

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Abramson, B.W., Novotny, M., Hartwick, N.T., Colt, K., Aevermann, B.D., Scheuermann, R.H., Michael, T.P. The genome and preliminary single-nuclei transcriptome of Lemna minuta reveals mechanisms of invasiveness. (2021) Plant Physiology. DOI: 10.1093/plphys/kiab564

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Lam, E., Michael, T.P. Wolffia, a minimalist plant and synthetic biology chassis. (2021) Trends in Plant Science. DOI: 10.1016/j.tplants.2021.11.014

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Wickell, D., Kuo, L.Y., Yang, H.P., Dhabalia Ashok, A., Irisarri, I., Dadras, A., de Vries, S., de Vries, J., Huang, Y.M., Li, Z., Barker, M.S., Hartwick, N.T., Michael, T.P., Li, F.W. Underwater CAM photosynthesis elucidated by Isoetes genome. (2021) Nature Communications. 12(1):6348. DOI: 10.1038/s41467-021-26644-7

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Naish, M., Alonge, M., Wlodzimierz, P., Tock, A.J., Abramson, B.W., Schmücker, A., Mandáková, T., Jamge, B., Lambing, C., Kuo, P., Yelina, N., Hartwick, N., Colt, K., Smith, L.M., Ton, J., Kakutani, T., Martienssen, R.A., Schneeberger, K., Lysak, M.A., Berger, F., Bousios, A., Michael, T.P., Schatz, M.C., Henderson, I.R. The genetic and epigenetic landscape of the centromeres. (2021) Science. 374(6569):eabi7489. DOI: 10.1126/science.abi7489


Mansfeld, B.N., Boyher, A., Berry, J.C., Wilson, M., Ou, S., Polydore, S., Michael, T.P., Fahlgren, N., Bart, R.S. Large structural variations in the haplotype-resolved African cassava genome. (2021) Plant Journal. DOI: 10.1111/tpj.15543

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Acosta, K., Appenroth, K.J., Borisjuk, L., Edelman, M., Heinig, U., Jansen, M.A.K., Oyama, T., Pasaribu, B., Schubert, I., Sorrels, S., Sree, K.S., Xu, S., Michael, T.P., Lam, E. Return of the Lemnaceae: Duckweed as a model plant system in the genomics and post-genomics era. (2021) Plant Cell. DOI: 10.1093/plcell/koab189

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Zhang, T., Mudgett, M., Rambabu, R., Abramson, B., Dai, X., Michael, T.P., Zhao, Y. Selective inheritance of target genes from only one parent of sexually reproduced F1 progeny in Arabidopsis. (2021) Nature Communications. 12(1):3854. DOI: 10.1038/s41467-021-24195-5

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Harkess, A., McLoughlin, F., Bilkey, N., Elliott, K., Emenecker, R., Mattoon, E., Miller, K., Czymmek, K., Vierstra, R.D., Meyers, B.C., Michael, T.P. Improved Spirodela polyrhiza genome and proteomic analyses reveal a conserved chromosomal structure with high abundance of chloroplastic proteins favoring energy production. (2021) J Exp Bot. 72(7):2491-2500. DOI: 10.1093/jxb/erab006

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Michael, T.P., Ernst, E., Hartwick, N., Chu, P., Bryant, D., Gilbert, S., Ortleb, S., Baggs, E.L., Sree, K.S., Appenroth, K.J., Fuchs, J., Jupe, F., Sandoval, J.P., Krasileva, K.V., Borisjuk, L., Mockler, T.C., Ecker, J., Martienssen, R.A., Lam, E. Genome and time-of-day transcriptome of link morphological minimization with gene loss and less growth control. (2020) Genome Research. DOI: 10.1101/gr.266429.120

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Minich, J.J., Petrus, S., Michael, J.D., Michael, T.P., Knight, R., Allen, E.E. Temporal, Environmental, and Biological Drivers of the Mucosal Microbiome in a Wild Marine Fish, Scomber japonicus. (2020) mSphere. 5(3). DOI: 10.1128/mSphere.00401-20

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Liu, J., Seetharam, A.S., Chougule, K., Ou, S., Swentowsky, K.W., Gent, J.I., Llaca, V., Woodhouse, M.R., Manchanda, N., Presting, G.G., Kudrna, D.A., Alabady, M., Hirsch, C.N., Fengler, K.A., Ware, D., Michael, T.P., Hufford, M.B., Dawe, R.K. Gapless assembly of maize chromosomes using long-read technologies. (2020) Genome Biology. 21(1):121. DOI: 10.1186/s13059-020-02029-9

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Michael, T.P., VanBuren, R. Building near-complete plant genomes. (2020) Current Opinion in Plant Biology. 54:26-33. DOI: 10.1016/j.pbi.2019.12.009

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Poplawski, S.G., Garbett, K.A., McMahan, R.L., Kordasiewicz, H.B., Zhao, H., Kennedy, A.J., Goleva, S.B., Sanders, T.H., Motley, S.T., Swayze, E.E., Ecker, D.J., Sweatt, J.D., Michael, T.P., Greer, C.B. An Antisense Oligonucleotide Leads to Suppressed Transcription of Hdac2 and Long-Term Memory Enhancement. (2020) Mol Ther Nucleic Acids. 19:1399-1412. DOI: 10.1016/j.omtn.2020.01.027

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MacKinnon, K.J., Cole, B.J., Yu, C., Coomey, J.H., Hartwick, N.T., Remigereau, M.S., Duffy, T., Michael, T.P., Kay, S.A., Hazen, S.P. Changes in ambient temperature are the prevailing cue in determining Brachypodium distachyon diurnal gene regulation. (2020) New Phytol. DOI: 10.1111/nph.16507

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VanBuren, R., Man Wai, C., Wang, X., Pardo, J., Yocca, A.E., Wang, H., Chaluvadi, S.R., Han, G., Bryant, D., Edger, P.P., Messing, J., Sorrells, M.E., Mockler, T.C., Bennetzen, J.L., Michael, T.P. Exceptional subgenome stability and functional divergence in the allotetraploid Ethiopian cereal teff. (2020) Nature Communications. 11(1):884. DOI: 10.1038/s41467-020-14724-z

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Silva, S.R., Moraes, A.P., Penha, H.A., Julião, M.H.M., Domingues, D.S., Michael, T.P., Miranda, V.F.O., Varani, A.M. The Terrestrial Carnivorous Plant Sheds Light on Environmental and Life-Form Genome Plasticity. (2019) International Journal of Molecular Sciences. 21(1). DOI: 10.3390/ijms21010003

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Silva, S.R., Pinheiro, D.G., Penha, H.A., Płachno, B.J., Michael, T.P., Meer, E.J., Miranda, V.F.O., Varani, A.M. Intraspecific Variation within the Species Morphotypes Based on Chloroplast Genomes. (2019) International Journal of Molecular Sciences. 20(24). DOI: 10.3390/ijms20246130

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Chekan, J.R., McKinnie, S.M.K., Moore, M.L., Poplawski, S.G., Michael, T.P., Moore, B.S. Scalable Biosynthesis of the Seaweed Neurochemical, Kainic Acid. (2019) Angewandte Chemie. 58(25):8454-8457. DOI: 10.1002/anie.201902910

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Wai, C.M., Weise, S.E., Ozersky, P., Mockler, T.C., Michael, T.P., VanBuren, R. Time of day and network reprogramming during drought induced CAM photosynthesis in Sedum album. (2019) PLOS Genetics. 15(6):e1008209. DOI: 10.1371/journal.pgen.1008209

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Mower, J.P., Ma, P.F., Grewe, F., Taylor, A., Michael, T.P., VanBuren, R., Qiu, Y.L. Lycophyte plastid genomics: extreme variation in GC, gene and intron content and multiple inversions between a direct and inverted orientation of the rRNA repeat. (2019) New Phytol. 222(2):1061-1075. DOI: 10.1111/nph.15650

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Jupe, F., Rivkin, A.C., Michael, T.P., Zander, M., Motley, S.T., Sandoval, J.P., Slotkin, R.K., Chen, H., Castanon, R., Nery, J.R., Ecker, J.R. The complex architecture and epigenomic impact of plant T-DNA insertions. (2019) PLOS Genetics. 15(1):e1007819. DOI: 10.1371/journal.pgen.1007819

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Hoang, P.N.T., Michael, T.P., Gilbert, S., Chu, P., Motley, S.T., Appenroth, K.J., Schubert, I., Lam, E. Generating a high-confidence reference genome map of the Greater Duckweed by integration of cytogenomic, optical mapping, and Oxford Nanopore technologies. (2018) Plant Journal. 96(3):670-684. DOI: 10.1111/tpj.14049

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Chu, P., Wilson, G.M., Michael, T.P., Vaiciunas, J., Honig, J., Lam, E. Sequence-guided approach to genotyping plant clones and species using polymorphic NB-ARC-related genes. (2018) Plant Molecular Biology. 98(3):219-231. DOI: 10.1007/s11103-018-0774-1

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Michael, T.P., Jupe, F., Bemm, F., Motley, S.T., Sandoval, J.P., Lanz, C., Loudet, O., Weigel, D., Ecker, J.R. High contiguity Arabidopsis thaliana genome assembly with a single nanopore flow cell. (2018) Nature Communications. 9(1):541. DOI: 10.1038/s41467-018-03016-2

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Minich, J.J., Morris, M.M., Brown, M., Doane, M., Edwards, M.S., Michael, T.P., Dinsdale, E.A. Elevated temperature drives kelp microbiome dysbiosis, while elevated carbon dioxide induces water microbiome disruption. (2018) PLOS One. 13(2):e0192772. DOI: 10.1371/journal.pone.0192772

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Aranguren-Díaz, Y.C., Varani, A.M., Michael, T.P., Miranda, V.F.O. Development of microsatellite markers for the carnivorous plant Genlisea aurea (Lentibulariaceae) using genomics data of NGS. (2018) Mol. Biol. Rep. 45(1):57-61. DOI: 10.1007/s11033-017-4140-1

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Silva, S.R., Michael, T.P., Meer, E.J., Pinheiro, D.G., Varani, A.M., Miranda, V.F.O. Comparative genomic analysis of Genlisea (corkscrew plants-Lentibulariaceae) chloroplast genomes reveals an increasing loss of the ndh genes. (2018) PLOS One. 13(1):e0190321. DOI: 10.1371/journal.pone.0190321

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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):13. DOI: 10.1038/s41467-017-02546-5

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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 & Environment. 40(10):2292-2306. DOI: 10.1111/pce.13027

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Silva, S.R., Alvarenga, D.O., Aranguren, Y., Penha, H.A., Fernandes, C.C., Pinheiro, D.G., Oliveira, M.T., Michael, T.P., Miranda, V.F.O., Varani, A.M. The mitochondrial genome of the terrestrial carnivorous plant Utricularia reniformis (Lentibulariaceae): Structure, comparative analysis and evolutionary landmarks. (2017) PLOS One. 12(7):e0180484. DOI: 10.1371/journal.pone.0180484

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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):617-635. DOI: 10.1111/tpj.13400

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Silva, S.R., Diaz, Y.C., Penha, H.A., Pinheiro, D.G., Fernandes, C.C., Miranda, V.F., Michael, T.P., Varani, A.M. The Chloroplast Genome of Utricularia reniformis Sheds Light on the Evolution of the ndh Gene Complex of Terrestrial Carnivorous Plants from the Lentibulariaceae Family. (2016) PLOS One. 11(10):e0165176. DOI: 10.1371/journal.pone.0165176

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Kennedy, A.J., Rahn, E.J., Paulukaitis, B.S., Savell, K.E., Kordasiewicz, H.B., Wang, J., Lewis, J.W., Posey, J., Strange, S.K., Guzman-Karlsson, M.C., Phillips, S.E., Decker, K., Motley, S.T., Swayze, E.E., Ecker, D.J., Michael, T.P., Day, J.J., Sweatt, J.D. Tcf4 Regulates Synaptic Plasticity, DNA Methylation, and Memory Function. (2016) Cell Reports. 16(10):2666-2685. DOI: 10.1016/j.celrep.2016.08.004

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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):535-47. DOI: 10.1111/tpj.13215

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VanBuren, R., Bryant, D., Edger, P.P., Tang, H., Burgess, D., Challabathula, D., Spittle, K., Hall, R., Gu, J., Lyons, E., Freeling, M., Bartels, D., Ten Hallers, B., Hastie, A., Michael, T.P., Mockler, T.C. Single-molecule sequencing of the desiccation-tolerant grass Oropetium thomaeum. (2015) Nature. 527(7579):508-11. DOI: 10.1038/nature15714

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Michael, T.P., VanBuren, R. Progress, challenges and the future of crop genomes. (2015) Current Opinion in Plant Biology. 24:71-81. DOI: 10.1016/j.pbi.2015.02.002

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Fleischmann, A., Michael, T.P., Rivadavia, F., Sousa, A., Wang, W., Temsch, E.M., Greilhuber, J., Müller, K.F., Heubl, G. Evolution of genome size and chromosome number in the carnivorous plant genus Genlisea (Lentibulariaceae), with a new estimate of the minimum genome size in angiosperms. (2014) Ann. Bot. 114(8):1651-63. DOI: 10.1093/aob/mcu189

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Michael, T.P. Plant genome size variation: bloating and purging DNA. (2014) Briefings in Functional Genomics. 13(4):308-17. DOI: 10.1093/bfgp/elu005

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Priest, H.D., Fox, S.E., Rowley, E.R., Murray, J.R., Michael, T.P., Mockler, T.C. Analysis of global gene expression in Brachypodium distachyon reveals extensive network plasticity in response to abiotic stress. (2014) PLOS One. 9(1):e87499. DOI: 10.1371/journal.pone.0087499

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Ibarra-Laclette, E., Lyons, E., Hernández-Guzmán, G., Pérez-Torres, C.A., Carretero-Paulet, L., Chang, T.H., Lan, T., Welch, A.J., Juárez, M.J., Simpson, J., Fernández-Cortés, A., Arteaga-Vázquez, M., Góngora-Castillo, E., Acevedo-Hernández, G., Schuster, S.C., Himmelbauer, H., Minoche, A.E., Xu, S., Lynch, M., Oropeza-Aburto, A., Cervantes-Pérez, S.A., de Jesús Ortega-Estrada, M., Cervantes-Luevano, J.I., Michael, T.P., Mockler, T., Bryant, D., Herrera-Estrella, A., Albert, V.A., Herrera-Estrella, L. Architecture and evolution of a minute plant genome. (2013) Nature. 498(7452):94-8. DOI: 10.1038/nature12132

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Ming, R., VanBuren, R., Liu, Y., Yang, M., Han, Y., Li, L.T., Zhang, Q., Kim, M.J., Schatz, M.C., Campbell, M., Li, J., Bowers, J.E., Tang, H., Lyons, E., Ferguson, A.A., Narzisi, G., Nelson, D.R., Blaby-Haas, C.E., Gschwend, A.R., Jiao, Y., Der, J.P., Zeng, F., Han, J., Min, X.J., Hudson, K.A., Singh, R., Grennan, A.K., Karpowicz, S.J., Watling, J.R., Ito, K., Robinson, S.A., Hudson, M.E., Yu, Q., Mockler, T.C., Carroll, A., Zheng, Y., Sunkar, R., Jia, R., Chen, N., Arro, J., Wai, C.M., Wafula, E., Spence, A., Han, Y., Xu, L., Zhang, J., Peery, R., Haus, M.J., Xiong, W., Walsh, J.A., Wu, J., Wang, M.L., Zhu, Y.J., Paull, R.E., Britt, A.B., Du, C., Downie, S.R., Schuler, M.A., Michael, T.P., Long, S.P., Ort, D.R., Schopf, J.W., Gang, D.R., Jiang, N., Yandell, M., dePamphilis, C.W., Merchant, S.S., Paterson, A.H., Buchanan, B.B., Li, S., Shen-Miller, J. Genome of the long-living sacred lotus (Nelumbo nucifera Gaertn.). (2013) Genome Biology. 14(5):R41. DOI: 10.1186/gb-2013-14-5-r41

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Luo, C., Sidote, D.J., Zhang, Y., Kerstetter, R.A., Michael, T.P., Lam, E. Integrative analysis of chromatin states in Arabidopsis identified potential regulatory mechanisms for natural antisense transcript production. (2013) Plant Journal. 73(1):77-90. DOI: 10.1111/tpj.12017

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Michael, T.P., Alba, R. The tomato genome fleshed out. (2012) Nature Biotechnology. 30(8):765-7. DOI: 10.1038/nbt.2319


Filichkin, S.A., Breton, G., Priest, H.D., Dharmawardhana, P., Jaiswal, P., Fox, S.E., Michael, T.P., Chory, J., Kay, S.A., Mockler, T.C. Global profiling of rice and poplar transcriptomes highlights key conserved circadian-controlled pathways and cis-regulatory modules. (2011) PLOS One. 6(6):e16907. DOI: 10.1371/journal.pone.0016907

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Lutz, K.A., Wang, W., Zdepski, A., Michael, T.P. Isolation and analysis of high quality nuclear DNA with reduced organellar DNA for plant genome sequencing and resequencing. (2011) BMC Biotechnol. 11:54. DOI: 10.1186/1472-6750-11-54

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Banks, J.A., Nishiyama, T., Hasebe, M., Bowman, J.L., Gribskov, M., dePamphilis, C., Albert, V.A., Aono, N., Aoyama, T., Ambrose, B.A., Ashton, N.W., Axtell, M.J., Barker, E., Barker, M.S., Bennetzen, J.L., Bonawitz, N.D., Chapple, C., Cheng, C., Correa, L.G., Dacre, M., DeBarry, J., Dreyer, I., Elias, M., Engstrom, E.M., Estelle, M., Feng, L., Finet, C., Floyd, S.K., Frommer, W.B., Fujita, T., Gramzow, L., Gutensohn, M., Harholt, J., Hattori, M., Heyl, A., Hirai, T., Hiwatashi, Y., Ishikawa, M., Iwata, M., Karol, K.G., Koehler, B., Kolukisaoglu, U., Kubo, M., Kurata, T., Lalonde, S., Li, K., Li, Y., Litt, A., Lyons, E., Manning, G., Maruyama, T., Michael, T.P., Mikami, K., Miyazaki, S., Morinaga, S., Murata, T., Mueller-Roeber, B., Nelson, D.R., Obara, M., Oguri, Y., Olmstead, R.G., Onodera, N., Petersen, B.L., Pils, B., Prigge, M., Rensing, S.A., Riaño-Pachón, D.M., Roberts, A.W., Sato, Y., Scheller, H.V., Schulz, B., Schulz, C., Shakirov, E.V., Shibagaki, N., Shinohara, N., Shippen, D.E., Sørensen, I., Sotooka, R., Sugimoto, N., Sugita, M., Sumikawa, N., Tanurdzic, M., Theissen, G., Ulvskov, P., Wakazuki, S., Weng, J.K., Willats, W.W., Wipf, D., Wolf, P.G., Yang, L., Zimmer, A.D., Zhu, Q., Mitros, T., Hellsten, U., Loqué, D., Otillar, R., Salamov, A., Schmutz, J., Shapiro, H., Lindquist, E., Lucas, S., Rokhsar, D., Grigoriev, I.V. The Selaginella genome identifies genetic changes associated with the evolution of vascular plants. (2011) Science. 332(6032):960-3. DOI: 10.1126/science.1203810

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Shulaev, V., Sargent, D.J., Crowhurst, R.N., Mockler, T.C., Folkerts, O., Delcher, A.L., Jaiswal, P., Mockaitis, K., Liston, A., Mane, S.P., Burns, P., Davis, T.M., Slovin, J.P., Bassil, N., Hellens, R.P., Evans, C., Harkins, T., Kodira, C., Desany, B., Crasta, O.R., Jensen, R.V., Allan, A.C., Michael, T.P., Setubal, J.C., Celton, J.M., Rees, D.J., Williams, K.P., Holt, S.H., Ruiz Rojas, J.J., Chatterjee, M., Liu, B., Silva, H., Meisel, L., Adato, A., Filichkin, S.A., Troggio, M., Viola, R., Ashman, T.L., Wang, H., Dharmawardhana, P., Elser, J., Raja, R., Priest, H.D., Bryant, D.W., Fox, S.E., Givan, S.A., Wilhelm, L.J., Naithani, S., Christoffels, A., Salama, D.Y., Carter, J., Lopez Girona, E., Zdepski, A., Wang, W., Kerstetter, R.A., Schwab, W., Korban, S.S., Davik, J., Monfort, A., Denoyes-Rothan, B., Arus, P., Mittler, R., Flinn, B., Aharoni, A., Bennetzen, J.L., Salzberg, S.L., Dickerman, A.W., Velasco, R., Borodovsky, M., Veilleux, R.E., Folta, K.M. The genome of woodland strawberry (Fragaria vesca). (2011) Nature Genetics. 43(2):109-16. DOI: 10.1038/ng.740

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Hong, S., Song, H.R., Lutz, K., Kerstetter, R.A., Michael, T.P., McClung, C.R. Type II protein arginine methyltransferase 5 (PRMT5) is required for circadian period determination in Arabidopsis thaliana. (2010) Proceedings of the National Academy of Sciences of the United States of America. 107(49):21211-6. DOI: 10.1073/pnas.1011987107

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Atwell, S., Huang, Y.S., Vilhjálmsson, B.J., Willems, G., Horton, M., Li, Y., Meng, D., Platt, A., Tarone, A.M., Hu, T.T., Jiang, R., Muliyati, N.W., Zhang, X., Amer, M.A., Baxter, I., Brachi, B., Chory, J., Dean, C., Debieu, M., de Meaux, J., Ecker, J.R., Faure, N., Kniskern, J.M., Jones, J.D., Michael, T., Nemri, A., Roux, F., Salt, D.E., Tang, C., Todesco, M., Traw, M.B., Weigel, D., Marjoram, P., Borevitz, J.O., Bergelson, J., Nordborg, M. Genome-wide association study of 107 phenotypes in Arabidopsis thaliana inbred lines. (2010) Nature. 465(7298):627-31. DOI: 10.1038/nature08800

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Albert, V.A., Jobson, R.W., Michael, T.P., Taylor, D.J. The carnivorous bladderwort (Utricularia, Lentibulariaceae): a system inflates. (2010) J. Exp. Bot. 61(1):5-9. DOI: 10.1093/jxb/erp349

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Dayarian, A., Michael, T.P., Sengupta, A.M. SOPRA: Scaffolding algorithm for paired reads via statistical optimization. (2010) BMC Bioinformatics. 11:345. DOI: 10.1186/1471-2105-11-345

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Sasson, A., Michael, T.P. Filtering error from SOLiD Output. (2010) Bioinformatics . 26(6):849-50. DOI: 10.1093/bioinformatics/btq045

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Garvin, D.F., McKenzie, N., Vogel, J.P., Mockler, T.C., Blankenheim, Z.J., Wright, J., Cheema, J.J., Dicks, J., Huo, N., Hayden, D.M., Gu, Y., Tobias, C., Chang, J.H., Chu, A., Trick, M., Michael, T.P., Bevan, M.W., Snape, J.W. An SSR-based genetic linkage map of the model grass Brachypodium distachyon. (2010) Genome. 53(1):1-13. DOI: 10.1139/g09-079

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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. (2009) Genetics. 183(2):723-32, 1SI-7SI. DOI: 10.1534/genetics.109.104984

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Pan, Y., Michael, T.P., Hudson, M.E., Kay, S.A., Chory, J., Schuler, M.A. Cytochrome P450 monooxygenases as reporters for circadian-regulated pathways. (2009) Plant Physiology. 150(2):858-78. DOI: 10.1104/pp.108.130757

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Zdepski, A., Wang, W., Priest, H.D., Ali, F., Alam, M., Mockler, T.C., Michael, T.P. Conserved Daily Transcriptional Programs in Carica papaya. (2008) Tropical Plant Biology. 1(3-4):236-245. DOI: 10.1007/s12042-008-9020-3

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Loudet, O., Michael, T.P., Burger, B.T., Le Metté, C., Mockler, T.C., Weigel, D., Chory, J. A zinc knuckle protein that negatively controls morning-specific growth in Arabidopsis thaliana. (2008) Proceedings of the National Academy of Sciences of the United States of America. 105(44):17193-8. DOI: 10.1073/pnas.0807264105

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Michael, T.P., Breton, G., Hazen, S.P., Priest, H., Mockler, T.C., Kay, S.A., Chory, J. A morning-specific phytohormone gene expression program underlying rhythmic plant growth. (2008) PLOS Biology. 6(9):e225. DOI: 10.1371/journal.pbio.0060225

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Ming, R., Hou, S., Feng, Y., Yu, Q., Dionne-Laporte, A., Saw, J.H., Senin, P., Wang, W., Ly, B.V., Lewis, K.L., Salzberg, S.L., Feng, L., Jones, M.R., Skelton, R.L., Murray, J.E., Chen, C., Qian, W., Shen, J., Du, P., Eustice, M., Tong, E., Tang, H., Lyons, E., Paull, R.E., Michael, T.P., Wall, K., Rice, D.W., Albert, H., Wang, M.L., Zhu, Y.J., Schatz, M., Nagarajan, N., Acob, R.A., Guan, P., Blas, A., Wai, C.M., Ackerman, C.M., Ren, Y., Liu, C., Wang, J., Wang, J., Na, J.K., Shakirov, E.V., Haas, B., Thimmapuram, J., Nelson, D., Wang, X., Bowers, J.E., Gschwend, A.R., Delcher, A.L., Singh, R., Suzuki, J.Y., Tripathi, S., Neupane, K., Wei, H., Irikura, B., Paidi, M., Jiang, N., Zhang, W., Presting, G., Windsor, A., Navajas-Pérez, R., Torres, M.J., Feltus, F.A., Porter, B., Li, Y., Burroughs, A.M., Luo, M.C., Liu, L., Christopher, D.A., Mount, S.M., Moore, P.H., Sugimura, T., Jiang, J., Schuler, M.A., Friedman, V., Mitchell-Olds, T., Shippen, D.E., dePamphilis, C.W., Palmer, J.D., Freeling, M., Paterson, A.H., Gonsalves, D., Wang, L., Alam, M. The draft genome of the transgenic tropical fruit tree papaya (Carica papaya Linnaeus). (2008) Nature. 452(7190):991-6. DOI: 10.1038/nature06856

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Michael, T.P., Mockler, T.C., Breton, G., McEntee, C., Byer, A., Trout, J.D., Hazen, S.P., Shen, R., Priest, H.D., Sullivan, C.M., Givan, S.A., Yanovsky, M., Hong, F., Kay, S.A., Chory, J. Network discovery pipeline elucidates conserved time-of-day-specific cis-regulatory modules. (2008) PLOS Genetics. 4(2):e14. DOI: 10.1371/journal.pgen.0040014

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Michael, T.P., Park, S., Kim, T.S., Booth, J., Byer, A., Sun, Q., Chory, J., Lee, K. Simple sequence repeats provide a substrate for phenotypic variation in the Neurospora crassa circadian clock. (2007) PLOS One. 2(8):e795. DOI: 10.1371/journal.pone.0000795

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Borevitz, J.O., Hazen, S.P., Michael, T.P., Morris, G.P., Baxter, I.R., Hu, T.T., Chen, H., Werner, J.D., Nordborg, M., Salt, D.E., Kay, S.A., Chory, J., Weigel, D., Jones, J.D., Ecker, J.R. Genome-wide patterns of single-feature polymorphism in Arabidopsis thaliana. (2007) Proceedings of the National Academy of Sciences of the United States of America. 104(29):12057-62. DOI: 10.1073/pnas.0705323104

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Mockler, T.C., Michael, T.P., Priest, H.D., Shen, R., Sullivan, C.M., Givan, S.A., McEntee, C., Kay, S.A., Chory, J. The DIURNAL project: DIURNAL and circadian expression profiling, model-based pattern matching, and promoter analysis. (2007) Cold Spring Harbor Symposia on Quantitative Biology. 72:353-63. DOI: 10.1101/sqb.2007.72.006

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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. (2006) Nature Genetics. 38(6):711-5. DOI: 10.1038/ng1818

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Mockler, T.C., Yu, X., Shalitin, D., Parikh, D., Michael, T.P., Liou, J., Huang, J., Smith, Z., Alonso, J.M., Ecker, J.R., Chory, J., Lin, C. Regulation of flowering time in Arabidopsis by K homology domain proteins. (2004) Proceedings of the National Academy of Sciences of the United States of America. 101(34):12759-64. DOI: 10.1073/pnas.0404552101

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Michael, T.P., Salomé, P.A., Yu, H.J., Spencer, T.R., Sharp, E.L., McPeek, M.A., Alonso, J.M., Ecker, J.R., McClung, C.R. Enhanced fitness conferred by naturally occurring variation in the circadian clock. (2003) Science. 302(5647):1049-53. DOI: 10.1126/science.1082971

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Michael, T.P., McClung, C.R. Enhancer trapping reveals widespread circadian clock transcriptional control in Arabidopsis. (2003) Plant Physiology. 132(2):629-39. DOI: 10.1104/pp.021006

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Michael, T.P., Salome, P.A., McClung, C.R. Two Arabidopsis circadian oscillators can be distinguished by differential temperature sensitivity. (2003) Proceedings of the National Academy of Sciences of the United States of America. 100(11):6878-83. DOI: 10.1073/pnas.1131995100

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Michael, T.P., McClung, C.R. Phase-specific circadian clock regulatory elements in Arabidopsis. (2002) Plant Physiology. 130(2):627-38. DOI: 10.1104/pp.004929

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Salomé, P.A., Michael, T.P., Kearns, E.V., Fett-Neto, A.G., Sharrock, R.A., McClung, C.R. The out of phase 1 mutant defines a role for PHYB in circadian phase control in Arabidopsis. (2002) Plant Physiology. 129(4):1674-85. DOI: 10.1104/pp.003418

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McClung, C.R., Salomé, P.A., Michael, T.P. The Arabidopsis circadian system. (2002) Arabidopsis Book. 1:e0044. DOI: 10.1199/tab.0044

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