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Publications

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Journal Article
C. Doherty, Friesner, J., Gregory, B., Loraine, A., Megraw, M., Provart, N., R Slotkin, K., Town, C., Assmann, S. M., Axtell, M., Berardini, T., Chen, S., Gehan, M., Huala, E., Jaiswal, P., Larson, S., Li, S., May, S., Michael, T., Pires, C., Topp, C., Walley, J., and Wurtele, E., Arabidopsis bioinformatics resources: The current state, challenges, and priorities for the future, Plant Direct, vol. 3, no. 1, 2019.
C. Doherty, Friesner, J., Gregory, B., Loraine, A., Megraw, M., Provart, N., R Slotkin, K., Town, C., Assmann, S. M., Axtell, M., Berardini, T., Chen, S., Gehan, M., Huala, E., Jaiswal, P., Larson, S., Li, S., May, S., Michael, T., Pires, C., Topp, C., Walley, J., and Wurtele, E., Arabidopsis bioinformatics resources: The current state, challenges, and priorities for the future, Plant Direct, vol. 3, no. 1, 2019.
M. G. Ivanchenko, Zhu, J., Wang, B., Medvecká, E., Du, Y., Azzarello, E., Mancuso, S., Megraw, M., Filichkin, S., Dubrovsky, J. G., Friml, J., and Geisler, M., The cyclophilin A DIAGEOTROPICA gene affects auxin transport in both root and shoot to control lateral root formation., Development, vol. 142, no. 4, pp. 712-21, 2015.
H. Iizasa, Wulff, B. - E., Alla, N. R., Maragkakis, M., Megraw, M., Hatzigeorgiou, A., Iwakiri, D., Takada, K., Wiedmer, A., Showe, L., Lieberman, P., and Nishikura, K., Editing of Epstein-Barr virus-encoded BART6 microRNAs controls their dicer targeting and consequently affects viral latency., J Biol Chem, vol. 285, no. 43, pp. 33358-70, 2010.
H. Iizasa, Wulff, B. - E., Alla, N. R., Maragkakis, M., Megraw, M., Hatzigeorgiou, A., Iwakiri, D., Takada, K., Wiedmer, A., Showe, L., Lieberman, P., and Nishikura, K., Editing of Epstein-Barr virus-encoded BART6 microRNAs controls their dicer targeting and consequently affects viral latency., J Biol Chem, vol. 285, no. 43, pp. 33358-70, 2010.
L. Zhang, Volinia, S., Bonome, T., Calin, G. Adrian, Greshock, J., Yang, N., Liu, C. - G., Giannakakis, A., Alexiou, P., Hasegawa, K., Johnstone, C. N., Megraw, M. S., Adams, S., Lassus, H., Huang, J., Kaur, S., Liang, S., Sethupathy, P., Leminen, A., Simossis, V. A., Sandaltzopoulos, R., Naomoto, Y., Katsaros, D., Gimotty, P. A., DeMichele, A., Huang, Q., Bützow, R., Rustgi, A. K., Weber, B. L., Birrer, M. J., Hatzigeorgiou, A. G., Croce, C. M., and Coukos, G., Genomic and epigenetic alterations deregulate microRNA expression in human epithelial ovarian cancer., Proc Natl Acad Sci U S A, vol. 105, no. 19, pp. 7004-9, 2008.
L. Zhang, Huang, J., Yang, N., Greshock, J., Megraw, M. S., Giannakakis, A., Liang, S., Naylor, T. L., Barchetti, A., Ward, M. R., Yao, G., Medina, A., O'brien-Jenkins, A., Katsaros, D., Hatzigeorgiou, A., Gimotty, P. A., Weber, B. L., and Coukos, G., microRNAs exhibit high frequency genomic alterations in human cancer., Proc Natl Acad Sci U S A, vol. 103, no. 24, pp. 9136-41, 2006.
L. Zhang, Huang, J., Yang, N., Greshock, J., Megraw, M. S., Giannakakis, A., Liang, S., Naylor, T. L., Barchetti, A., Ward, M. R., Yao, G., Medina, A., O'brien-Jenkins, A., Katsaros, D., Hatzigeorgiou, A., Gimotty, P. A., Weber, B. L., and Coukos, G., microRNAs exhibit high frequency genomic alterations in human cancer., Proc Natl Acad Sci U S A, vol. 103, no. 24, pp. 9136-41, 2006.
J. Friesner, Assmann, S. M., Bastow, R., Bailey-Serres, J., Beynon, J., Brendel, V., C. Buell, R., Bucksch, A., Busch, W., Demura, T., Dinneny, J. R., Doherty, C. J., Eveland, A. L., Falter-Braun, P., Gehan, M. A., Gonzales, M., Grotewold, E., Gutierrez, R., Kramer, U., Krouk, G., Ma, S., Markelz, R. J. Cody, Megraw, M., Meyers, B. C., Murray, J. A. H., Provart, N. J., Rhee, S., Smith, R., Spalding, E. P., Taylor, C., Teal, T. K., Tor, ii, K. U., Town, C., Vaughn, M., Vierstra, R., Ware, D., Wilkins, O., Williams, C., and Brady, S. M., The Next Generation of Training for Arabidopsis Researchers: Bioinformatics and Quantitative Biology, Plant Physiology, vol. 175, pp. 1499-1509, 2017.
J. Friesner, Assmann, S. M., Bastow, R., Bailey-Serres, J., Beynon, J., Brendel, V., C. Buell, R., Bucksch, A., Busch, W., Demura, T., Dinneny, J. R., Doherty, C. J., Eveland, A. L., Falter-Braun, P., Gehan, M. A., Gonzales, M., Grotewold, E., Gutierrez, R., Kramer, U., Krouk, G., Ma, S., Markelz, R. J. Cody, Megraw, M., Meyers, B. C., Murray, J. A. H., Provart, N. J., Rhee, S., Smith, R., Spalding, E. P., Taylor, C., Teal, T. K., Tor, ii, K. U., Town, C., Vaughn, M., Vierstra, R., Ware, D., Wilkins, O., Williams, C., and Brady, S. M., The Next Generation of Training for Arabidopsis Researchers: Bioinformatics and Quantitative Biology, Plant Physiology, vol. 175, pp. 1499-1509, 2017.
J. Friesner, Assmann, S. M., Bastow, R., Bailey-Serres, J., Beynon, J., Brendel, V., C. Buell, R., Bucksch, A., Busch, W., Demura, T., Dinneny, J. R., Doherty, C. J., Eveland, A. L., Falter-Braun, P., Gehan, M. A., Gonzales, M., Grotewold, E., Gutierrez, R., Kramer, U., Krouk, G., Ma, S., Markelz, R. J. Cody, Megraw, M., Meyers, B. C., Murray, J. A. H., Provart, N. J., Rhee, S., Smith, R., Spalding, E. P., Taylor, C., Teal, T. K., Tor, ii, K. U., Town, C., Vaughn, M., Vierstra, R., Ware, D., Wilkins, O., Williams, C., and Brady, S. M., The Next Generation of Training for Arabidopsis Researchers: Bioinformatics and Quantitative Biology, Plant Physiology, vol. 175, pp. 1499-1509, 2017.
T. Morton, Petricka, J., Corcoran, D. L., Li, S., Winter, C. M., Carda, A., Benfey, P. N., Ohler, U., and Megraw, M., Paired-end analysis of transcription start sites in Arabidopsis reveals plant-specific promoter signatures., Plant Cell, vol. 26, no. 7, pp. 2746-60, 2014.
S. M. Brady, Zhang, L., Megraw, M., Martinez, N. J., Jiang, E., Yi, C. S., Liu, W., Zeng, A., Taylor-Teeples, M., Kim, D., Ahnert, S., Ohler, U., Ware, D., Walhout, A. J. M., and Benfey, P. N., A stele-enriched gene regulatory network in the Arabidopsis root., Mol Syst Biol, vol. 7, p. 459, 2011.
S. M. Brady, Zhang, L., Megraw, M., Martinez, N. J., Jiang, E., Yi, C. S., Liu, W., Zeng, A., Taylor-Teeples, M., Kim, D., Ahnert, S., Ohler, U., Ware, D., Walhout, A. J. M., and Benfey, P. N., A stele-enriched gene regulatory network in the Arabidopsis root., Mol Syst Biol, vol. 7, p. 459, 2011.
T. Morton, Wong, W. - K., and Megraw, M., TIPR: transcription initiation pattern recognition on a genome scale., Bioinformatics, vol. 31, no. 23, pp. 3725-32, 2015.