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·         Sondos Seif and Mohamed Abouelhoda. Practical Distributed Computation of Maximal Exact Matches in the Cloud. Accepted in the IEEE-EMBS International Conferences on Biomedical and Health Informatics , to appear in IEEE, 2014.

·         Anas Abu-Doleh, Kamer Kaya, Mohamed Abouelhoda, and  Umit V. Catalyurek.  Extracting Maximal Exact Matches on GPU. Proceedings of the Workshop on Multi-Threaded Architectures and Applications (MTAAP), to appear in IEEE, 2014.

·         Abdelhadi A, Kandil AH, Abouelhoda M. Cloud-based Parallel Suffix Array Construction Algorithm based on MPI.  Proceeding of MECBCME 2014, To appear in IEEExplore, 2014.

·         Maan H. Rachid, Qutaibah Malluhi, Mohamed Abouelhoda. A Space-Efficient Solution to Find the Maximum Overlap Using a Compressed Suffix Array. Proceeding of MECBCME 2014, To appear in IEEExplore, 2014

·         Amro Ahmed, Mohamed Abouelhoda, Ayman Khalifa, Ahmed Fahmy . Estimation of the myocardium rotation from standard cine magnetic resonance imaging sequences. ICASSP 2013.

·         Mohamed Abouelhoda, Sondos Seif. Efficient Distributed Computation of Maximal Exact Matches. Accepted at 19th EuroMPI 2012.

·         Enno Ohlebusch, Timo Beller and Mohamed Abouelhoda. Computing the Burrows-Wheeler Transform of a String and its Reverse. Combinatorial Pattern Matching, LNCS 7354, 243-256.

·         Mohamed Abouelhoda, Shady Alaa, Moustafa Ghanem. Tavaxy: Interoperability between Taverna and Galaxy. WANDS 2010. ACM SIGMOD, USA. 2010.

·         Mohamed Abouelhoda, Hisham Adel. Parallel Chaining Algorithms. 17th EuroMPI: Recent Advances in the Message Passing Interface, LNCS 6305 , 142-151, 2010.

·         Abdel-Rahman N. Zekri, Abeer A. Bahnassy, Mohamed Abouelhoda, Mohamed M Hafez, ,Zeinab K Hassan, Ahmed Ali, Dina H. ELdahshan. Global gene expression profiles of the Egyptian Hepatocellular carcinoma Associated with HCV-Genotype-4. 101st AACR, USA. 2010.

·         Mohamed, H. and  Abouelhoda, M. Parallel suffix sorting based on bucket pointer refinement.

·         5th Cairo International Biomedical Engineering Conference (CIBEC 2010),  IEEExplore, DOI: 10.1109/CIBEC.2010.5716066: 98 – 102, 2010.

·         Ali, A. and Gad, H. and Ghanem, M. and  Abouelhoda, M. EGEPT: Monitoring Middle East genomic data. 5th Cairo International Biomedical Engineering Conference (CIBEC2010), IEEExplore, DOI: 10.1109/CIBEC.2010.5716097, 133 – 137, 2010.

·         Hisham Mohamed and Mohamed Abouelhoda. WinBioinfTools: Bioinformatics Tools for Windows Cluster. IEEE International Conference on Cluster Computing CLUSTER’09, New Orleans, Louisiana, USA, September 2009.  IEEExplore, DPI:10.1109/CLUSTR.2009.5289141, 1 – 4, 2009.

·         Mohamed I. Abouelhoda, Robert Giegerich, Behshad Behzadi, Jean-Marc Steyaert. Alignment of Minisatellite Maps: A Minimum Spanning Tree Approach. Accepted at the Asian Pacific Bioinformatics Confernece, 2008.

·         Mohamed I. Abouelhoda.  Mapping cDNA Sequences to Multiple Genomes. Accepted at the 14th International Symposium on String Processing and Information Retrieval, 2008.

·         Mohamed Abouelhoda, Ayat Dawood. Fine Tuning the Enhanced Suffix Array, In proceedings of the 4th Cairo International Biomedical Engineering Conference. IEEExplore, DOI : 10.1109/CIBEC.2008.4786040, 1-4, 2008.

·         Mahmoud Mohamed, Mohamed Abouelhoda, Ahmed Kandil, Ahmed Elbialy. Constructing Suffix Array During Decompression, In proceedings of the 4th Cairo International Biomedical Engineering Conference. IEEExplore, DOI: 10.1109/CIBEC.2008.4786040, 1-4, 2008.

·         Asem Othman, Alfons Martin, Dennis Butterstein, Mohamed Abouelhoda. VisCHAINER: Visualizing Genome Comparisons. In proceedings of the 4th Cairo International Biomedical Engineering Conference. IEEExplore DOI : 10.1109/CIBEC.2008.4786040, 1-4, 2008.

·         Mohamed Abouelhoda, CoCoNUT: A software system for comparative genomics. In proceedings of the 5th Annual Meeting African Society of Human Genetics, 2007, Cairo, Egypt.

·         Mohamed I. Abouelhoda, Stefan Kurtz, Enno Ohlebusch. CoCoNUT: A Software System for Comparative Genomics. Genome Informatics, UK, 2008. (extended abstract)

·         Mohamed I. Abouelhoda, A Chaining Algorithm for Mapping a cDNA Sequence to Multiple Genomic Sequences. Cairo International Biomedical Engineering Conference, 2006.

·         Christian Wawra, Mohamed I. Abouelhoda, Enno Ohlebusch. Efficient Mapping of Large cDNA/EST Databases to Genomes: A Comparison of two Different Strategies. Proceedings of the German Conference on Bioinformatics, pages 29-43, LNI 73, GI, 2005.

·         Enno Ohlebusch, Mohamed I. Abouelhoda, Kathrin Hockel, Jan Stallkamp. The Median Problem for the Reversal Distance in Circular Bacterial Genomes. Proceedings of the 16th Annual Symposium on Combinatorial Pattern Matching. LNCS 3537, pages 101-176 2005.

·         Mohamed I. Abouelhoda, Enno Ohlebusch. CHAINER: Software for Comparing Genomes. Short paper at ISMB/ECCB 2004 (12th International Conference on Intelligent Systems for Molecular Biology/3rd European Conference on Computational Biology)

·         Mohamed I. Abouelhoda, Enno Ohlebusch. A Local Chaining Algorithm and its Applications in Comparative Genomics. Proceedings of the 3rd Workshop on Algorithms in Bioinformatics, pages 1-16, LNBI 2812, 2003. © Springer-Verlag

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·         Mohamed I. Abouelhoda, Enno Ohlebusch. Multiple Genome Alignment: Chaining Algorithms Revisited. Proceedings of the 14th Annual Symposium on Combinatorial Pattern Matching, pages 1-16, LNCS 2676, 2003. © Springer-Verlag

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·         Mohamed I. Abouelhoda, Stefan Kurtz, Enno Ohlebusch. The Enhanced Suffix Array and its Applications to Genome Analysis. Proceedings of the 2nd Workshop on Algorithms in Bioinformatics, pages 449-463, LNCS 2452, 2002. © Springer-Verlag

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·         Mohamed I. Abouelhoda, Enno Ohlebusch, Stefan Kurtz. Optimal Exact String Matching Based on Suffix Arrays. Proceedings of the 9th International Symposium on String Processing and Information Retrieval, pages 31-43, LNCS 2476, 2002. © Springer-Verlag

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·         Mohamed I. Abouelhoda, Bassel Tawfik. A Prim-based Heuristic for Obstacle Avoiding Rectilinear Steiner Minimal Tree. 1st Cologne-Twente Workshop on Graphs and Combinatorial Optimization, 2001.