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.

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.  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.

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.

M.  Ansariola, Megraw, M., and Koslicki, D., ?IndeCut evaluates performance of network motif discovery algorithms?, Bioinformatics, vol. 34, no. 9, pp. 1514-1521, 2018.

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.

S. A.  Filichkin and Megraw, M., ?DNase I SIM: A Simplified In-Nucleus Method for DNase I Hypersensitive Site Sequencing?, in Methods Mol Biol, vol. 1629, 2017, pp. 141-154.

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.

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.

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.

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.

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.

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.

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.

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, 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.  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.

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, 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.

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. 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.

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.

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.

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.

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.  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.