Publications

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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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.