Publications

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2006
P. Sethupathy, Megraw, M., and Hatzigeorgiou, A. G., “A guide through present computational approaches for the identification of mammalian microRNA targets.”, Nat Methods, vol. 3, no. 11, pp. 881-6, 2006.
M. Megraw, Baev, V., Rusinov, V., Jensen, S. T., Kalantidis, K., and Hatzigeorgiou, A. G., “MicroRNA promoter element discovery in Arabidopsis.”, RNA, vol. 12, no. 9, pp. 1612-9, 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.
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.
2007
M. Megraw, Sethupathy, P., Corda, B., and Hatzigeorgiou, A. G., “miRGen: a database for the study of animal microRNA genomic organization and function.”, Nucleic Acids Res, vol. 35, no. Database issue, pp. D149-55, 2007.
2008
Y. Kawahara, Megraw, M., Kreider, E., Iizasa, H., Valente, L., Hatzigeorgiou, A. G., and Nishikura, K., “Frequency and fate of microRNA editing in human brain.”, Nucleic Acids Res, vol. 36, no. 16, pp. 5270-80, 2008.
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.
2009
M. Megraw, Pereira, F., Jensen, S. T., Ohler, U., and Hatzigeorgiou, A. G., “A transcription factor affinity-based code for mammalian transcription initiation.”, Genome Res, vol. 19, no. 4, pp. 644-56, 2009.
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.
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.
M. Megraw and Hatzigeorgiou, A. G., “MicroRNA promoter analysis.”, Methods Mol Biol, vol. 592, pp. 149-61, 2010.
P. Alexiou, Vergoulis, T., Gleditzsch, M., Prekas, G., Dalamagas, T., Megraw, M., Grosse, I., Sellis, T., and Hatzigeorgiou, A. G., “miRGen 2.0: a database of microRNA genomic information and regulation.”, Nucleic Acids Res, vol. 38, no. Database issue, pp. D137-41, 2010.
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.
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.
2012
J. J. Petricka, Schauer, M. A., Megraw, M., Breakfield, N. W., J Thompson, W., Georgiev, S., Soderblom, E. J., Ohler, U., Moseley, M. Arthur, Grossniklaus, U., and Benfey, P. N., “The protein expression landscape of the Arabidopsis root.”, Proc Natl Acad Sci U S A, vol. 109, no. 18, pp. 6811-8, 2012.
J. J. Petricka, Schauer, M. A., Megraw, M., Breakfield, N. W., J Thompson, W., Georgiev, S., Soderblom, E. J., Ohler, U., Moseley, M. Arthur, Grossniklaus, U., and Benfey, P. N., “The protein expression landscape of the Arabidopsis root.”, Proc Natl Acad Sci U S A, vol. 109, no. 18, pp. 6811-8, 2012.
2013
M. Megraw, Mukherjee, S., and Ohler, U., “Sustained-input switches for transcription factors and microRNAs are central building blocks of eukaryotic gene circuits.”, Genome Biol, vol. 14, no. 8, p. R85, 2013.
M. Megraw, Mukherjee, S., and Ohler, U., “Sustained-input switches for transcription factors and microRNAs are central building blocks of eukaryotic gene circuits.”, Genome Biol, vol. 14, no. 8, p. R85, 2013.
2014
S. Gouthu, O'Neil, S. T., Di, Y., Ansarolia, M., Megraw, M., and Deluc, L. G., “A comparative study of ripening among berries of the grape cluster reveals an altered transcriptional programme and enhanced ripening rate in delayed berries.”, J Exp Bot, vol. 65, no. 20, pp. 5889-902, 2014.
S. A. Filichkin, Cumbie, J. S., J Dharmawadhana, P., Jaiswal, P., Chang, J. H., Palusa, S. G., Reddy, A. S. N., Megraw, M., and Mockler, T. C., “Environmental Stresses Modulate Abundance and Timing of Alternatively Spliced Circadian Transcripts in Arabidopsis.”, Mol Plant, 2014.
S. A. Filichkin, Cumbie, J. S., J Dharmawadhana, P., Jaiswal, P., Chang, J. H., Palusa, S. G., Reddy, A. S. N., Megraw, M., and Mockler, T. C., “Environmental Stresses Modulate Abundance and Timing of Alternatively Spliced Circadian Transcripts in Arabidopsis.”, Mol Plant, 2014.
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.
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.
2015
S. Filichkin, Priest, H. D., Megraw, M., and Mockler, T. C., “Alternative splicing in plants: directing traffic at the crossroads of adaptation and environmental stress.”, Curr Opin Plant Biol, vol. 24, pp. 125-35, 2015.
S. Filichkin, Priest, H. D., Megraw, M., and Mockler, T. C., “Alternative splicing in plants: directing traffic at the crossroads of adaptation and environmental stress.”, Curr Opin Plant Biol, vol. 24, pp. 125-35, 2015.

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