Publications

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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.
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.
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.
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.
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.
2016
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.
2017
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.
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.
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.
2018
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.
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.
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.
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. 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.

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