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· Maan H. Rachid, Qutaibah Malluhi and Mohamed Abouelhoda. Using the Sadakane Compressed Suffix Tree to Solve the All-Pairs Suffix Prefix Problem. To appear in BioMed Research International, 2014. 
· Mohamed Abouelhoda, Shady Issa, and Moustafa Ghanem . Towards Scalable and Cost-aware BioinformaticsWorkflow Execution in the Cloud - Recent Advances to the Tavaxy Workflow System. Accepted for publication in Fundamenta Informatica.
· Enno Ohlebusch, Timo Beller, Mohamed Ibrahim Abouelhoda. Computing the Burrows-Wheeler Transform of a String and its Reverse in Parallel. Journal of Discrete Algorithms, to appear.
· Shadi A. Issa, Romeo Kienzler, Mohamed El-Kalioby, Peter J. Tonellato, Dennis Wall, Rémy Bruggmann, and Mohamed Abouelhoda. Streaming Support for Data Intensive Cloud-Based Sequence Analysis. BioMed Research International. 2013;2013:791051, 2013
· Mohamed I. Abouelhoda, Shady Alaa Isaa, Moustafa Ghane. Tavaxy: Integrating Taverna and Galaxy Workflows with Cloud Computing support. BMC Bioinformatics 13:77, 2012.
· Mohamed Elkalioby, Mohamed Abouelhoda, Peter Tonellato, Dennis Wall, Jan Krueger, Alenandre Sczyrba, Robert Giegerich. Personalized Cloud-based Bioinformatics Services for Research and Education. BMC Bioinformatics 2012, 13(Suppl 17):S22.
· Mostafa M Abbas, Mohamed Abouelhoda, Hazem Bahig. A Hybrid Method for Solving the Planted Motif Problem. BMC Bioinformatics 2012, 13(Suppl 17):S10.
· Zekri AR, Hassan ZK, Bahnassy AA, Sherif GM, ELdahshan D, Abouelhoda M, Ali A, Hafez MM. Molecular prognostic profile of Egyptian HCC cases infected with hepatitis C virus. Asian Pac J Cancer Prev. 2012;13(11):5433-8, 2012.
· Mohamed I. Abouelhoda, Mohamed El-Kalioby, Robert Giegerich, WAMI: Web Server for the Analysis of Minisatellite Maps. BMC Evolutionary Biology. 2010.
· Mohamed Abouelhoda and Mostafa Ghanem. Bioinformatics at Nile University: Perspectives for Egypt and the whole Region. EMBnet Journal, Vol 15 No. 4. 2010. (Invited Presentation Paper).
· Mohamed I. Abouelhoda, Robert Giegerich, Behshad Behzadi, Jean-Marc Steyaert. Alignment of Ministellite Maps based on Run Length Encoding Sequences. Journal of Bioinformatics and Computational Biology. 7(2) , Pages:287-308, 2009.
· Martin Bader, Mohamed I. Abouelhoda, Enno Ohlebusch. A fast algorithm for the multiple genome rearrangement problem with weighted reversals and transpositions. BMC Bioinformatics, 9:516, 2008.
· Abouelhoda, M.I., Kurtz, S., Ohlebusch, E. CoCoNUT: An efficient system for the comparison and analysis of genomes. BMC Bioinformatics, 9:476, 2008.
· Enno Ohlebusch, Mohamed I. Abouelhoda, Kathrin Hockel. A linear time algorithm for the inversion median problem in circular bacterial genomes. Journal of Discrete Algorithms, Volume 5 ,  Issue 4, December 2007
· Mohamed I. Abouelhoda, Enno Ohlebusch. Chaining Algorithms for Multiple Genome Comparison. Journal of Discrete Algorithms, 3:321-341, 2005.
· Mohamed I. Abouelhoda, Stefan Kurtz, Enno Ohlebusch. Replacing Suffix Trees with Enhanced Suffix Arrays. Journal of Discrete Algorithms, 2(1):53-86, 2004.