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.
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., Dharmawardhana, 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, vol. 8, no. 2, pp. 207-27, 2015.
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., Dharmawardhana, 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, vol. 8, no. 2, pp. 207-27, 2015.
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, 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, 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.
J. S. Cumbie, Filichkin, S. A., and Megraw, M., “Improved DNase-seq protocol facilitates high resolution mapping of DNase I hypersensitive sites in roots in Arabidopsis thaliana.”, Plant Methods, vol. 11, p. 42, 2015.
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.
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.
J. S. Cumbie, Ivanchenko, M. G., and Megraw, M., “NanoCAGE-XL and CapFilter: an approach to genome wide identification of high confidence transcription start sites.”, BMC Genomics, vol. 16, p. 597, 2015.
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.
M. Megraw, Cumbie, J. S., Ivanchenko, M. G., and Filichkin, S. A., “Small Genetic Circuits and MicroRNAs: Big Players in Polymerase II Transcriptional Control in Plants.”, Plant Cell, vol. 28, no. 2, pp. 286-303, 2016.