User:Sameh

Research Interests:

Well, I am interested in the applications of computing in solving biology problems. More specifically, I am interested in building and using computer systems and other instruments to detect and visualize biological processes, signatures, cells, DNA, etc. I am also interested in developing algorithms and programs to help analyze and understand the detected/collected signals. Recently I have been working in the following areas:

• Signal processing and pattern classification techniques for DNA Sequencing.
• Numerical modeling of microchips.
• Scientific instrumentations and LIMS.
• DNA forensics.

You can reach me at samehd_at_gmaildotcom.

Publications:

Journal Papers:
1. S. El-Difrawy, A. Srivastava et al. “Numerical model for DNA loading in microdevices: Stacking and autogating effects”, Electrophoresis, 27, 3779-3787, 2006.
2. J. Ueberfeld, S. El-Difrawy et al. “Solid-Support Sample Loading for DNA Sequencing”, Analytical Chemistry, 78, 3632-3637, 2006.
3. N. Goedecke, B. McKenna, S. El-Difrawy et al. "Microdevice DNA Forensics by the Simple Tandem Repeat Method." Journal of Chromatography A In Press, Corrected Proof.
4. S. El-Difrawy, R. Lam et al. “High Throughput System for DNA Sequencing” Rev. Sci. Instruments, 76, 074301, 2005.
5. J. Aborn, S. El-Difrawy, et al. “A 768-Lane Microfabricated System for Genome-Scale DNA Sequencing”, Lab on a Chip, 5, 669-674. 2005.
6. N. Goedecke, B. McKenna, S. El-Difrawy, et al. “A High-Performance Multilane Microdevice System Designed for the DNA Forensics Laboratory”, Electrophoresis, 25, 1678–1686, 2004.
7. P. Boufounos, S. El-Difrawy and D. Ehrlich “Base Calling Using Hidden Markov Models”, Journal of the Franklin Institute, 341, 23-36, 2004.
8. M. Pereira, L. Andrade, S. El-Difrawy and E. Manolakos “Statistical Learning Formulation of the DNA Base Calling Problem and Its Solution Using a Bayesian EM Framework.” Discrete Applied Mathematics, 104, 229-258, 2000.
9. L. Koutny, D. Schmalzing, O. Salas-Solano, S. El-Difrawy, A. Adourian, S. Buonocore, K. Abbey, P. McEwan, P. Matsudaira and D. Ehrlich “Eight Hundred Base Sequencing in a Microfabricated Electrophoretic Device “ Analytical Chemistry, 72, 3388-3391, 2000.
10. D. Schmalzing, A. Belenky, M. Novotny, L. Koutny, O. Salas-Solano, S. El-Difrawy et al. “Microchip Electrophoresis: A Method for high-speed SNP Detection” Nucleic Acid Research, 28, No. 9 E43, 2000.

Conference Papers:
11. N. Goedecke, B. McKenna, S. El-Difrawy, et al “Quantification Of Simple Tandem Repeat Profiles For DNA Forensics”, MicroTas 2005, Boston, MA October 2005.
12. D. Ehrlich, S. El-Difrawy, N. Goedecke, et al “Status Of Genome-Center DNA Sequencing Technology On MEMS”, MicroTas 2005, Boston, MA. October 2005.
13. A. Selim, B. McKenna, S. El-Difrawy et al “Development of a Novel Cell-Scanning System (cell Track) for Expression Cloning of the Carboxyl-Terminal Parathyroid Hormone Receptor (CPTHR).” 27th ASMBR, Nashville, TN. September 2005.
14. M. Liu, S. El-Difrawy and D. Ehrlich “Allelic Ladder Identification In Forensic DNA Genotyping”, GENSIPS 04, Baltimore, MD, May 2004.
15. S. El-Difrawy, R. Lam and D. Ehrlich “Uniform Acquisition for High-Throughput DNA Sequencing“ Proc. of the IEEE 30th Annual Northeast Bioengineering Conference, Springfield, MA. April 2004.
16. S. El-Difrawy and D. Ehrlich “A Numerical Optimization Approach for Color Correction in Forensic DNA Genotyping”, Asilomar 2003, Asilomar, CA. November 2003.
17. S. El-Difrawy and E. Manolakos “An Analytical Solution to the Mobility Shifts Corrections Problem for DNA Chromatograms”, GENSIPS 02, Raleigh, NC. October 2002.
18. P. Boufounos, S. El-Difrawy and D. Ehrlich “Hidden Markov Models for DNA Sequencing”, GENSIPS 02, Raleigh, NC. October 2002.
19. D. Ehrlich, L. Carey, J. Chiou, S. Desmarais, S. El-Difrawy et al. “MEMS-based systems for DNA sequencing and forensics” Proceedings of IEEE Sensors, 1, 12-14 June 2002.

Other Publications:
20. D. Ehrlich, J. Aborn, S. El-Difrawy et al., “Microelectrophoresis Devices for DNA Sequencing”, in Encyclopedia of Genetics, Genomics, Proteomics and Bioinformatics, John Wiley & Sons, Sept 2005.
21. S. El-Difrawy “A Soft Computing Pattern Recognition System for Accurate DNA Base calling”, Ph.D Thesis, Northeastern University, Boston, June 2002.
22. S. El-Difrawy and S. Buus “Microprocessor Lab Manual”, Northeastern University 1996.

Presentations:
23. M. Liu, S. El-Difrawy, B. McKeena, D. Ehrlich and P. Matsudaira “Robust Algorithms for Forensic DNA Genotyping”, CSBI 2004 Symposium in Systems Biology, Cambridge, MA. January 2004.