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Hani Girgis, PhD

Hani Girgis, PhD
Assistant Professor of Computer Science
College of Engineering & Natural Sciences
Computer Science
Rayzor Hall


PhD – The State University of New York-Buffalo MS – The State University of New York-Buffalo BA – The State University of New York-Buffalo

Research Interests

Non-coding DNA
Intelligent Software Systems for Mining Non-coding DNA

Teaching Interests

Programming Languages
Machine Learning


Journal Articles

  • H. Z. Girgis. Red: an intelligent, rapid, accurate tool for detecting repeats de-novo on the genomic scale. BMC Bioinformatics, 16(1):227, 2015.

  • 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 S. Sheetlin. MsDetector: toward a standard computational tool for DNA microsatellites detection. Nucleic Acids Research, 41(1):e22, 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.

Conference Proceedings

  • 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.

  • 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, 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.

  • 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.

Courses Taught

  • Special Topics
  • Special Topics in Computer Science
  • Programming Languages and Structures