Publications

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Author [ Title(Asc)] Type Year
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T
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.
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.
S
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.
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.
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.
P
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.
S. Ha, Dimitrova, E., Hoops, S., Altarawy, D., Ansariola, M., Deb, D., Glazebrook, J., Hillmer, R., Shahin, H., Katagiri, F., McDowell, J., Megraw, M., Setubal, J., Tyler, B. M., and Laubenbacher, R., “PlantSimLab-a modeling and simulation web tool for plant biologists”, BMC Bioinformatics, vol. 20, no. 1, pp. 1-11, 2019.
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.
N
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. 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.
M. G. Ivanchenko and Megraw, M., “NanoCAGE-XL: An Approach to High-Confidence Transcription Start Site Sequencing”, Methods in Molecular Biology, vol. 1830, pp. 225-237, 2018.
M
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.
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.
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, 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.
M. Megraw and Hatzigeorgiou, A. G., “MicroRNA promoter analysis.”, Methods Mol Biol, vol. 592, pp. 149-61, 2010.
V. N. Fraser, Philmus, B., and Megraw, M., “Metabolomics analysis reveals both plant variety and choice of hormone treatment modulate vinca alkaloid production in Catharanthus roseus”, Plant Direct, vol. 4, no. 9, 2020.
I
M. Ansariola, Megraw, M., and Koslicki, D., “IndeCut evaluates performance of network motif discovery algorithms”, Bioinformatics, vol. 34, no. 9, pp. 1514-1521, 2018.
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.
S. A. Filichkin, Ansariola, M., Fraser, V. N., and Megraw, M., “Identification of transcription factors from NF-Y, NAC, and SPL families responding to osmotic stress in multiple tomato varieties”, Plant Science, vol. 274, pp. 441-450, 2018.
G
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.
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.
F
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.
E
E. E. Sparks, Drapek, C., Gaudinier, A., Li, S., Ansariola, M., Shen, N., Hennacy, J. H., Zhang, J., Turco, G., Petricka, J. J., Foret, J., Hartemink, A. J., Gordan, R., Megraw, M., Brady, S. M., and Benfey, P. N., “Establishment of Expression in the SHORTROOT-SCARECROW Transcriptional Cascade through Opposing Activities of Both Activators and Repressors”, Dev Cell, vol. 39, pp. 585-596, 2016.
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.

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