User:Sameh

Research Interests:

Well, I am interested in using computers to solve biology problems. Either by building Computer systems and other instruments for detecting and visualizing biological processes, signatures, cells or DNA, etc. or designing algorithms and programs to help analyize 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.

Publications:

Journal Papers:
1. J. Ueberfeld, S. El-Difrawy et al. “Solid-Support Sample Loading for DNA Sequencing”, submitted.
2. S. El-Difrawy, A. Srivastava et al. “Understanding DNA Loading in Micordevices Using Numerical Models”, in preparation.
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.<cr> 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.