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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.\par \par 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.\par \par 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.\par \par 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.\par \par 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.\par \par }