Tandy School of Computer Science
Ph.D., The State University of New York-Buffalo
M.S., The State University of New York-Buffalo
B.A., The State University of New York-Buffalo
Intelligent Software Systems for Mining Non-coding DNA
The following may be selected publications rather than a comprehensive list.
H. Z. Girgis. Red: an intelligent, rapid, accurate tool for detecting repeats de-novo on the genomic scale. BMC Bioinformatics, 16(1):227, 2015.
H. Z. Girgis and S. Sheetlin. MsDetector: toward a standard computational tool for DNA microsatellites detection. Nucleic Acids Research, 41(1):e22, 2013.
A. Visel, L. Taher, H. Z. Girgis, M. J. Blow, J. A. Akiyama et al. A high-resolution enhancer atlas of the developing telencephalon. Cell, 152(4):895-908, 2013.
H. Z. Girgis and I. Ovcharenko. Predicting tissue specific cis-regulatory modules in the human genome using pairs of co-occurring motifs. BMC Bioinformatics, 13(1):25, 2012.
H. Z. Girgis, B. R. Mitchell, T. Dassopoulos, G. Mullin, and G. Hager. An intelligent system to detect Crohn’s disease inflammation in wireless capsule endoscopy videos. In Proceedings of the IEEE International Symposium on Biomedical Imaging, pages 1373–1376, 2010.
. Z. Girgis, J. J. Corso, and D. Fischer. On-line hierarchy of general linear models for selecting and ranking the best predicted protein structures. In Proceedings of the Annual International Conference of the IEEE Engineering in Medicine and Biology Society, pages 4949–4953, 2009.
K. Holler, J. Penne, A. Schneider, J. Jahn, H. Z. Girgis, J. Gutierrez, T. Wittenberg, and J. Hornegger. Suppression of shock based errors with gravity related endoscopic image rectification. In Proceedings of the Fifth Russian-Bavarian Conference on Biomedical Engineering, pages 43–47, 2009.
S. Seshamani, P. Rajan, R. Kumar, H. Z. Girgis, G. Mullin, T. Dassopoulos, and G. Hager. A meta registration framework for lesion matching. In Proceedings of the International Conference on Medical Image Computing and Computer Assisted Intervention, pages 582–589, 2009.
H. Z. Girgis and B. Jayaraman. JavaTA: a logic-based debugger for Java. In the Workshop on Logic-based Methods in Programming Environments, volume abs/cs/0701107, 2007.
H. Z. Girgis, B. Jayaraman, and P. Gestwicki. Visualizing errors in object oriented programs. In Proceedings Companion to the ACM SIGPLAN Conference on Object-oriented Programming, Systems, Languages, and Applications, pages 156–157, 2005.
CS 3863 Special Topics