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The Center for Informatics Science (CIS)

About CIS

The Center for Informatics Science (CIS) was founded by late Dr. Moustafa Mahmoud Ghanem in 2008 and is dedicated to applied informatics research focusing on the research and development of novel computing methods and algorithms for processing, management and interpretation of scientific information.

Mission and Vision

The CIS vision is to be the leading center for informatics science benefiting Egypt and the region by advocating excellence in goal-oriented applied informatics research. Our mission is to conduct research and development of novel technologies for the management and interpretation of scientific information. The center strives to promote high-quality interdisciplinary collaborative research and to work closely with local and worldwide partners to address contemporary and future critical challenges in a number of areas of national importance to Egypt and impact on the Egyptian society.

Research Groups and Topics


Works on developing efficient algorithmic methods for sequence data manipulation with a focus on comparative genomics, as well as on developing new software tools for the integration, processing and analysis of large-scale biological data sets. Recent algorithmic work has included development of novel methods for efficient representation and analysis of genomic sequences and representation and analysis of mini-satellite data. Recent applied research projects include the design and implementation of NUBIOS, the first bioinformatics server in Egypt providing web-based access to both commonly used bioinformatics tools and proprietary ones developed by the group. It also included the design and implementation of cancer bioinformatics data mart and tools for the management, integration, and interpretation of Bladder and Ovarian Cancer data, and the design and implementation of a Buffalo Genome Analysis Portal.

Computer Vision

Focuses on the development of efficient algorithms and techniques for effective multimedia description and analysis. Recent work has included developing novel methods for content-based description and analysis of image and video data sets. Recent applications have covered automated Human Action and Activity Recognition, Object & Scene Detection and Tracking, Video Registration, Categorization, and Retrieval, and Facial Recognition Systems.

Data and Text Mining

Covers machine learning theory and algorithms as well as the development and use of novel data mining and text mining tools and applications. Recent theoretical machine learning work has covered the development of multiple classifier algorithms and time series analysis algorithms. Recent data mining work has covered the development and applications of classification and clustering methods for biomedical imaging data, and the classification and analysis of audio recordings and streaming data.  Recent text mining work has covered the development of key-phrase extraction algorithms and tools, automatic sentiment analysis of text documents as well as ontology and concept extraction from text documents.

Distributed and Peer-to-Peer Systems

Focuses on the development of efficient peer-to-peer algorithms, architectures and applications. Algorithmic work covers the construction and maintenance of dynamic overlay networks as well as efficient search and look-up techniques. Architecture work covers the design and implementation of efficient distributed and peer-to-peer storage systems. Application work covers content-piracy detection systems, video broadcasting, e-voting systems and systems for measurement, modeling and analysis of internet traffic behavior.

High-Performance and Cloud Computing

Focuses on the development and application of service-based and cloud-based middleware and applications for scientific applications. Recent research has included design and implementation of workflow programming models and systems for large-scale data and application integration, the development of efficient parallel data analysis algorithms on a variety of architectures (including the IBM Blue Gene and work station clusters), and the development of efficient cloud-based middleware to support bioinformatics and multimedia applications.

Information Security

Focuses on the development of novel algorithms and tools for risk analysis and intrusion detection in computer systems. Recent work has covered wireless networks and cloud-based systems.

Medical Imaging and Image Processing

Focuses on theoretical and applied research for developing efficient algorithms and techniques for fast image processing and analysis to support diagnosis and analysis of medical images. Recent work has covered two main tracks: analysis of magnetic resonance images of the heart; and the analysis of retinal images. Examples in cardiac applications have included segmentation of CINE SSFP MR Images,  and SENC MRI Images, analysis of Perfusion MRI Images, Tagging MR Images, analysis of T2* MR Images, and Regional Function Evaluation from CINE SSFP MR Images. Examples of retinal disease have included development of algorithms for segmentation and analysis of the Optic Disc, of Diabetic Macular Edema, and of Choroidal Neovascularization.

Multimedia Systems

Focuses on the development and application of interactive multimedia techniques and algorithms for education including gaming technology, virtual worlds, simulations and virtual labs. One objective of the research is to introduce the concept of a Generic Virtual Lab (GVL) that enables teachers to create labs and experiments in different fields and subjects with game-like features to ease the way of education. The second objective is to create this virtual lab in an adaptable form that enables students and teachers to interactively communicate through deployment on a cloud computing architecture.

Ubiquitous and Visual Computing Systems

Focuses on applied research integrating a number of technologies that facilitate ubiquitous intelligent environments in a range of applications including physical security, proactive healthcare delivery, traffic management, and environmental monitoring. The core research issues addresses the informatics challenges in large-scale wireless sensor networks, embedded systems, computer vision, computer graphics and machine intelligence. The Group's outputs include smart traffic cameras with innovative algorithms for vehicle detection and classification in intelligent transportation systems, visual sensor devices for human motion analysis in surveillance applications, and tools for managing large wireless sensor network deployment and visualization/analysis of collected data.

Selected Publications

  • N. El Gayar, Josef Kittler, Fabio Roli (Eds.).“Multiple Classifier Systems, 9th International Workshop”. MCS 2010, Cairo, Egypt, April 7-9, 2010. Proceedings. Lecture Notes in Computer Science LNCS 5997, Springer 2010.
  • Mohamed I. Abouelhoda, Moustafa Ghanem. “String Mining in Bioinformatics”. In M. M. Gaber (Editor)Scientific Data Mining and Knowledge Discovery, Springer, 2009.
  • N. Azam, V. Curcin, L. Guo, M. Ghanem. “Towards Automatic Service Composition within ARGUGRID”.In K. Ragab, A. Hassanien, T. Helmy (Editors) Developing Advanced Web Services through P2P Computing and Autonomous Agents: Trends and Innovation, IG-Global, 2010.
  • M. I. Abouelhoda, M. El-Kalioby, R.Giegerich. “WAMI: Web Server for the Analysis of Minisatellite Maps”. BMC Evolutionary Biology, 2010.
  • R. Maged and M. ElHelw. “Interactive 3D Visualization for Wireless Sensor Networks”. The Visual Computer, Springer, 2010.
  • G. Korosoglou, S. Lehrke, A. Wochele, B. Hoerig, D. Lossnitzer, H. Steen, E. Giannitsis, N. F. Osman, H. A. Katus. “Strain-Encoded CMR for the Detection of Inducible Ischemia during Intermediate Stress”. J Am CollCardiolImg, 2010; 3:361-371.
  • M. Abouelhoda and M. Ghanem. “Bioinformatics at Nile University: Perspectives for Egypt and the whole Region”.EMBnet Journal, vol 15, no. 4. 2010.
  • Mahfouz, A. S Fahmy. “Fast localization of the optic disc using projection of the image features”. IEEE Trans on Image Processing, vol. 19, no. 12, 2010.
  • N. El Gayar, M. Saleh,  A. Zakhary, H. Abdel Aziz, A. Atiya, H. El-Shishiny. “An Integrated Framework for Advanced Hotel Revenue “. International Journal of Contemporary Hotel Management, 2020 Vision for the Hospitality Industry special issue,vol. 23, issue 1, 2011.
  • Shosha, A. Kamel, M. Allam. “Model Consistency Checker Using Object State Machine”. International Journal of Software Engineering.
  • M. Abouelhoda, Shady Alaa, Moustafa Ghanem. “Tavaxy: Interoperability between Taverna and Galaxy”. WANDS 2010. ACM SIGMOD, USA. 2010.
  • M. ElSayed, A. Alsebai, A. Salaheldin, N. El Gayar, M. ElHelw. “Body and Visual Sensor Fusion for Motion Analysis in Ubiquitous Healthcare Systems, 7th International Conference on  Body Sensor Networks (BSN 2010) June 7 - 9, Biopolis, Singapore, 2010.
  • M. Naeil, M. M. Abdelwahab, W. B. Mikhael. “Human Action recognition employing PCA and VQ in the spatio-temporal domain“. In Proceedings of the 8th International IEEE-NEWCAS Conference, Montreal, Canada, June 2010.
  • K Rabieh, M.Azer, “Combating Sybil Attacks in Vehicular Ad Hoc Networks”, The Third International Conference on Wireless & Mobile Networks (WiMo-2011), Ankara Turkey, June 2011.
  • Owhofasa O. Agbedia, Mohamed Ibrahim, Yasir J. Sepah, Millena Bittencourt, Eman Magdy, Raafay Sophie, Anam Akhlaq, Hong T. Liu, Ahmed S. Fahmy, Quan D. Nguyen, “Quantitative Assessment of Diabetic Macular Edema using Digital Subtraction of Early and Late Acquisitions of Fluorescein Angiograms,” Annual meeting Assoc. for Research in Vision and Ophthalmology (ARVO), Florida, USA, 2012.
  • Mona Ragab, Ahmed S. Fahmy, “Evaluation of the cardiac function from tagged magnetic resonance images,” Int. Conf. Imaging and Signal Processing in Healthcare and Technology (ISPHT), Baltimore, USA, 2012.
  • Ayman Khalifa, Lamees Nasser, Ahmed S. Fahmy, “Motion tracking of the right ventricle from magnetic resonance tagged images,” Computer Assisted Radiology and Surgery (CARS), Italy, 2012.
  • Eman Marzaban, Ahmed S. Fahmy, “Comparison between Horn-Schunck and Lucas-Kanade methods for myocardium segmentation in short axis cardiac CineMR images,” Computer Assisted Radiology and Surgery (CARS), Italy, 2012.
  • Karim Mansour, Wael Farag, Mohamed ElHelw, “AiroDiag: A Sophisticated Tool that Diagnoses and Updates Vehicles Software over Air”, IEEE International Electric Vehicle Conference, South Carolina, U.S., 2012.
  • Heba Ezzat, Souraya Ezzat, Samhaa R. El-Beltagy, and Moustafa M. Ghanem. "TopicAnalyzer: A System for Unsupervised Multi-Label Arabic Topic Categorization ". Proceedings of the International Conference on Innovations and Information Technology (IIT2012). Al Ain-UAE, March, 2012.



Industry and Academic Collaborations


  • Cairo University
  • Johns Hopkins University
  • National Cancer Institute
  • Ain Shams University
  • Harvard University
  • Imperial College London
  • University of ULM
  • Heidelberg Hospital University
  • Inotek Systems
  • Diagnosoft
  • IBM
  • Orange Labs
  • Microsoft
  • Valeo
  • Vodafone
  • Philips


CIS Faculty

  • Dr. Ahmed Samir Fahmy
  • Dr. Marianne Azer
  • Dr. Mohamed Abouelhoda
  • Dr. Mohamed ElHelw (Director)
  • Dr. Nashwa Abdelbaky
  • Dr. Sameh El-Ansary
  • Dr. Samhaa El-Beltagy



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