all Publications

Schley, R.J., Pennington, R.T., Twyford, A.D., Dexter, K.G., Kidner, C., Michael, T.P., ., ., ., ., ., . The genome sequence of Benth. (2024) Wellcome Open Res. 9:607. DOI: 10.12688/wellcomeopenres.23146.1

Schley, R.J., Pennington, R.T., Twyford, A.D., Dexter, K.G., Kidner, C., Michael, T.P., ., ., ., . The genome sequence of (Sw.) Willd. (2024) Wellcome Open Res. 9:567. DOI: 10.12688/wellcomeopenres.23057.1

Mudgett, M., Abramson, B., Dai, X., Kang, R., Young, E., Michael, T., Zhao, Y. Gene targeting in Arabidopsis through one-armed homology-directed repair. (2024) Plant & Cell Physiology. DOI: 10.1093/pcp/pcae117

Kitony, J.K., Colt, K., Abramson, B.W., Hartwick, N.T., Petrus, S., Konozy, E.H.E., Karimi, N., Yant, L., Michael, T.P. Chromosome-level baobab genome illuminates its evolutionary trajectory and environmental adaptation. (2024) Nature Communications. 15(1):8833. DOI: 10.1038/s41467-024-53157-w

Baeza, J.A., Minish, J.J., Michael, T.P. Assembly of Mitochondrial Genomes Using Nanopore Long-Read Technology in Three Sea Chubs (Teleostei: Kyphosidae). (2024) Mol Ecol Resour.:e14034 DOI: 10.1111/1755-0998.14034

Longo, G.C., Minich, J.J., Allsing, N., James, K., Adams-Herrmann, E.S., Larson, W., Hartwick, N., Duong, T., Muhling, B., Michael, T.P., Craig, M.T. Crossing the Pacific: Genomics Reveals the Presence of Japanese Sardine (Sardinops melanosticta) in the California Current Large Marine Ecosystem. (2024) Mol Ecol.:e17561 DOI: 10.1111/mec.17561

Denyer, T., Wu, P.J., Colt, K., Abramson, B., Pang, Z., Solansky, P., Mamerto, A., Nobori, T., Ecker, J., Lam, E., Michael, T.P., Timmermans, M.C. Streamlined spatial and environmental expression signatures characterize the minimalist duckweed . (2024) Genome Research. DOI: 10.1101/gr.279091.124

Tomlin, C.M., Rajaraman, S., Sebesta, J.T., Scheen, A.C., Bendiksby, M., Low, Y.W., Salojärvi, J., Michael, T.P., Albert, V.A., Lindqvist, C. Allopolyploid origin and diversification of the Hawaiian endemic mints. (2024) Nature Communications. 15(1):3109. DOI: 10.1038/s41467-024-47247-y

Harkess, A., Bewick, A.J., Lu, Z., Fourounjian, P., Michael, T.P., Schmitz, R.J., Meyers, B.C. Unusual predominance of maintenance DNA methylation in Spirodela polyrhiza. (2024) G3. DOI: 10.1093/g3journal/jkae004

Minich, J.J., Moore, M.L., Allsing, N.A., Aylward, A., Murray, E.R., Tran, L., Michael, T.P. Generating high-quality plant and fish reference genomes from field-collected specimens by optimizing preservation. (2023) Communications Biology. 6(1):1246. DOI: 10.1038/s42003-023-05615-2

Steele, T.S., Burkhardt, I., Moore, M.L., de Rond, T., Bone, H.K., Barry, K., Bunting, V.M., Grimwood, J., Handley, L.H., Rajasekar, S., Talag, J., Michael, T.P., Moore, B.S. Biosynthesis of Haloterpenoids in Red Algae via Microbial-like Type I Terpene Synthases. (2023) ACS Chemical Biology. DOI: 10.1021/acschembio.3c00627

Saul, F., Scharmann, M., Wakatake, T., Rajaraman, S., Marques, A., Freund, M., Bringmann, G., Channon, L., Becker, D., Carroll, E., Low, Y.W., Lindqvist, C., Gilbert, K.J., Renner, T., Masuda, S., Richter, M., Vogg, G., Shirasu, K., Michael, T.P., Hedrich, R., Albert, V.A., Fukushima, K. Subgenome dominance shapes novel gene evolution in the decaploid pitcher plant Nepenthes gracilis. (2023) Nature Plants. DOI: 10.1038/s41477-023-01562-2

Aylward, A.J., Petrus, S., Mamerto, A., Hartwick, N.T., Michael, T.P. PanKmer: k-mer based and reference-free pangenome analysis. (2023) Bioinformatics . DOI: 10.1093/bioinformatics/btad621

Stack, G.M., Cala, A.R., Quade, M.A., Toth, J.A., Monserrate, L.A., Wilkerson, D.G., Carlson, C.H., Mamerto, A., Michael, T.P., Crawford, S., Smart, C., Smart, L.B. Genetic mapping, identification, and characterization of a candidate susceptibility gene for powdery mildew in L. (2023) Molecular Plant-Microbe Interactions. DOI: 10.1094/MPMI-04-23-0043-R

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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