Sami Khuri's Publications |

N. Buduma, J. Balabanian, P. Dalvi, SK. Chia, A. Dhaliwal, D. Eliya, J. Boothby, S. Bros-Seemann, R. Kibler, S. Khuri and S. Veregge, Modulation of Phagocytosis in Tetrahymena thermophila by Histamine and the Antihistamine Diphenhydramine Acta Protozoologica , Krakow, Poland, 2013, Volume 52, Issue 4, pp. 317-323.

S. Khuri (editor) with M. Bursa and M. Renda, Information Technology in Bio- and Medical Informatics, Lecture Notes in Computer Science (LNCS) 6080, published by Springer-Verlag, Berlin, Germany, 2013. ISBN 978-3-642-40092-6.

S. Khuri (editor) with C. Böhm, L. Lhotska and M. Renda, Information Technology in Bio- and Medical Informatics, Lecture Notes in Computer Science (LNCS) 7451, published by Springer-Verlag, Berlin, Germany, 2012. ISBN 978-3-642-32394-2.

S. Khuri (editor) with C. Böhm, L. Lhotska and N. Pisanti, Information Technology in Bio- and Medical Informatics, Lecture Notes in Computer Science (LNCS) 6865, published by Springer-Verlag, Berlin, Germany, 2011. ISBN 978-3-642-23207-7.

S. Khuri (editor) with Lenka Lhotska and Nadia Pisanti, Information Technology in Bio- and Medical Informatics, Lecture Notes in Computer Science (LNCS) 6266, published by Springer-Verlag, Berlin, Germany, 2010. ISBN 978-3-642-23207-7.

G. Luque, E. Alba Torres and S. Khuri, Assembling DNA Fragments with a Distributed Genetic Algorithm, Parallel Computing for Bioinformatics and Computational Biology, Wiley-Interscience, New Jersey, 2006, Chapter 12, pp. 285-302.

S. Khuri, E. Alba, Sequential and Distributed Evolutionary Algorithms for Combinatorial Optimization Problems, Recent Advances in Intelligent Paradigms and Applications, Springer-Verlag, Berlin, 2002, Chapter 10, pp. 211-233.

E. Alba Torres, S. Khuri, Applying Evolutionary Algorithms to Combinatorial Optimization Problems (ps), Lecture Notes in Computer Science, vol. 2074, Part II, Springer-Verlag, Berlin, Heidelberg, 2001, pp. 689-700.

S. Khuri, A User-Centred Approach for Designing Algorithm Visualizations (pdf file) , special issue of Informatik/Informatique, No.2, April 2001, pp. 12-17.

S. Khuri, Un enfoque entrado en el usuario par diseñar, animaciones de algoritmos (in Spanish), NOVATICA/UPGRADE, No. 150, March/April 2001, pp. 16-20.

S. Khuri, S. Miryala, Genetic Algorithms for Solving Open Shop Scheduling Problems (ps file), Lecture Notes in Artificial Intelligence: Progress in Artificial Intelligence, Springer Verlag, Berlin, September 1999, pp. 357-369.

S. Khuri, Walsh Analysis, Walsh Transforms (ps, 120K) in Fundamental Concepts of Evolutionary Computation: Theoretical Foundations and Properties of Evolutionary Computation, Handbook of Evolutionary Computation; Oxford University Press, 1997, pp. B2.6:1-B2.6:5.

S. Khuri, Transform Methods: Haar Analysis, Haar Transforms (ps, 138K) in Fundamental Concepts of Evolutionary Computation: Theoretical Foundations and Properties of Evolutionary Computation, Handbook of Evolutionary Computation; Oxford University Press, 1997, pp. B2.6:5-B2.6:10.

T. Bäck, M. Schütz, S. Khuri, Comparative Study of a Penalty Function, a Repair Heuristic, and Stochastic Operators with the Set-Covering Problem (ps, 120K) Artificial Evolution: Lecture Notes in Computer Science, volume 1063, Springer Verlag, Berlin, pp. 320-332, 1995.

S. Khuri, T. Bäck, An Evolutionary Heuristic for the Minimum Vertex Cover Problem (ps, 142K),18.Deutsche Jahrestagung für Künstliche Intelligenz: Extended Abstracts, Gesellschaft für Informatik, Bonn, pp. 83-84, and Max-P lanck-Institut für Informatik Journal, MPI-I-94-241, August 1994, pp. 86-90.

S. Khuri, A. Batarekh, __A Binary Decision Algorithm__ Information
Sciences: An International Journal, vol. 53, number 3, February 1991, pp.
251-270.

A. Bortolazzo, N. Khuri and S. Khuri; Computational Modeling of Cryptic Splicing Events; accepted for presentation at the Great Lakes Bioinformatics Conference 2013, Pittsburgh, PA, May 14-16, 2013; and will be published in the Proceedings of the Great Lakes Bioinformatics Conference, 2013.

A. Bortolazzo and S. Khuri, Detecting Cryptic Splice Sites in Genes, presented at the 25th Annual CSU Biotechnology Symposium, Los Angeles, January 5-7, 2013; and published in the Proceedings of the 25th Annual CSU Biotechnology Symposium, 2013.

Y. Newton, N. Khuri and S. Khuri, Building Compound-Target Interaction Networks; presented at the 23rd Annual CSU Biotechnology Symposium, Los Angeles, January 7-8, 2011; and published in the Proceedings of the 23rd Annual CSU Biotechnology Symposium, 2011.

K. Karhu, S. Khuri, J. Tarhio, Identifying Human miRNA Targets with a Genetic Algorithm. International Symposium on Biocomputing, Calicut, Kerala, India, February 15-17, 2010; and published in the Proceedings of the International Symposium on Biocomputing, ACM Press, February 2010.

J. Makinen, S. Khuri, J. Tarhio, PMSGA: A Fast DNA Fragment Assembler. Bioinformatics 2010: International Conference on Bioinformatics, Valencia, Spain, January 20-23, 2010; and published in the Proceedings of Bioinformatics 2010: International Conference on Bioinformatics, January 2010, pp. 77-82.

S. Khuri, Introducing Bioinformatics Algorithms in Computer Science Courses. Workshop presented at the 40th ACM SIGCSE Technical Symposium and abstract published in the Proceeding of the 40th ACM SIGCSE Technical Symposium, ACM Press, March 2009.

W. Lee, N. Fong, M. Franco, R. Fowler, S. Khuri, Inferring Phylogenetic Relationships between Organisms for Y-Family Polymerases Using HMMER 2.0 and the Neighbor-Joining Method. Abstract published in the Proceedings of the IEEE Computer Society Bioinformatics Conference, Stanford University, August 2008.

W. Lee, N. Fong, M. Franco, S. Khuri, R. Fowler, Detection of Remote Protein Homology by Comparing Profile Hidden Markov Models for the Y-Family Polymerase Family. Abstract published in the Proceedings of the IEEE Computer Society Bioinformatics Conference, Stanford University, August 2008.

S. Khuri, A Bioinformatics Track in Computer Science. Proceedings of the 38th ACM SIGCSE Technical Symposium, ACM Press, March 2008.

S. Khuri, Introducing Bioinformatics Algorithms in Computer Science Courses. Workshop presented at the 39th ACM SIGCSE Technical Symposium and abstract published in the Proceeding of the 39th ACM SIGCSE Technical Symposium, ACM Press, March 2008.

C.C. Li and S. Khuri; Parallel Euler Algorithms for DNA Fragment Assembly, presented at the 20th Annual CSU Biotechnology Symposium, Oakland, January 11-13, 2008; and published in the Proceedings of the 20th Annual CSU Biotechnology Symposium, 2008.

K. Callenberg and S. Khuri; A Web-driven Database of Beta Globin Mutations leading to Beta Thalassemia, presented at the 20th Annual CSU Biotechnology Symposium, Oakland, January 11-13, 2008; and published in the Proceedings of the 20th Annual CSU Biotechnology Symposium, 2008.

E. Alba, G. Luque, S. Khuri, Assembling DNA Fragments with Parallel Algorithms. Proceedings of the IEEE Congress on Evolutionary Computation, Edinburgh, UK, September 2005, pp. 57-65.

C. Wilks, S. Khuri, A Fast Shotgun Assembling Heuristic. Proceedings of the 2005 IEEE Computational Systems Bioinformatics Conference, Stanford University, IEEE Computer Society, August 2005, pp. 122-23.

S. Khuri, L. Li, Assembling DNA Fragments Using Probes and Interprobe Distances. Proceedings of the 2005 International Conference on Research Trends in Science and Technology, Beirut, Lebanon, March 2005.

S. Khuri, Introduction to Bioinformatics, workshop given at the 2005 International Conference on Research Trends in Science and Technology, Lebanese American University, Byblos, Lebanon, March 2005; and abstract published in the Proceedings of the 2005 International Conference on Research Trends in Science and Technology, Beirut, Lebanon, March 2005.

L. Li, S. Khuri, A Comparison of DNA Fragment Assembly Algorithms (pdf file). Proceedings of the 2004 International Conference on Mathematics and Engineering Techniques in Medicine and Biological Sciences, Las Vegas, June 2004, pp. 329-335.

C. Yang, S. Khuri, PTC: An Interactive Tool for Phylogenetic Tree Construction (pdf file). Proceedings of the IEEE Computer Society Bioinformatics Conference, Stanford Univeristy, August 2003, pp. 476-7.

Y. Jing, S. Khuri, Exact and Heuristic Algorithms for the DNA Fragment Assembly Problem. Proceedings of the IEEE Computer Society Bioinformatics Conference, Stanford University, August 2003, pp. 581-2.

S. Khuri, K. Holzapfel, EVEGA: An educational visualization environment for graph algorithms (ps file), Proceedings of the 6th Annual Conference on Innovation and Technology in Computer Science Education, Canterbury, UK, June 2001.

S. Khuri, Designing Effective Algorithm Visualizations (ps file), Proceedings of the First Program Visualization Workshop, Porvoo, Finland, 2001, pp. 1-12.

E. Alba Torres, S. Khuri, Applying Evolutionary Algorithms to Combinatorial Optimization Problems. Proceedings of the International Conference on Computational Science - Part II, Springer-Verlag, 2001.

S. Khuri, H. Hsu, Interactive Packages for Learning Image Compression Algorithms (ps file), Proceedings of the 5th Annual Conference on Innovation and Technology in Computer Science Education, July, 2000, pp. 73-76. RLE, Quadtree and JPEG packages are available here.

S. Khuri, T. Naps, Interacting with Java-Based Algorithm Visualizations. Workshop at the 5th Annual Conference on Innovation and Technology in Computer Science Education}, Finland and abstract published in the Proceedings of ITiCSE'2000, ACM Press, July 2000.

S. Khuri, T. Walters, Y. Sugono, A Grouping Genetic Algorithm for Coloring the Edges of Graphs (ps file), Proceedings of the 2000 ACM Symposium on Applied Computing, Evolutionary Computation and Optimization Track, March 2000, Volume 1, pp. 422-427.

S. Khuri, H.Hsu, Tools for Visualizing Text Compression Algorithms (ps.gz), Proceedings of the 2000 ACM Symposium on Applied Computing, Special Track on Computer Uses in Education, March 2000, Volume 1, pp. 119-123. LZ and AHuffman packages are available here.

S. Khuri, Lossless and Lossy Data Compression. Workshop given at the 30th ACM SIGCSE Technical Symposium, and abstract published in the Proceedings of the 30th SIGCSE Technical Symposium on Computer Science Education, ACM Press, 1999.

S. Khuri, H. Hsu, Visualizing the CPU Scheduler and Page Replacement Algorithms (pdf file), Proceedings of the 30th SIGCSE Technical Symposium, March 1999, pp. 227-231. The MLFQ and PAGE packages are available here.

R. Jiménez-Peris, S. Khuri, M. Patiño-Martínez, Adding Breadth to CS1 and CS2 Courses Through Visual and Interactive Programming Projects (pdf, 617K), Proceedings of the 30th SIGCSE Technical Symposium, March 1999, pp. 252-256.

S. Khuri, M. Moh, F. Chung, Code Assignments in CDMA Networks: Distributed Algorithms and Genetic Algorithm Heuristics (ps, 182K) Proceedings of the IEEE Singapore International Conference on Networks (SICON), Singapore, July 1998, pp. 91-105.

S. Khuri, Y.Sugono, Animating Parsing Algorithms (ps.Z, 201K) Proceedings of the 29th SIGCSE Technical Symposium, ACM Press, NY, 1998, pp. 232-236.

S. Khuri, Applying Genetic Algorithms to Scheduling Problems (abstract), Proceedings of the Sixth INFORMS Computer Science and Operations Research: Recent Advances in the Inter face, 1998.

S. Khuri, T. Chiu, Heuristic Algorithms for the Terminal Assignment Problem (ps, 160K) Proceedings of the 1997 ACM Symposium on Applied Computing, ACM Press, 1997, pp. 247-251.

S. Khuri, Computing with Haar Functions (ps, 150K) Proceedings of the 1997 ACM Symposium on Applied Computing, ACM Press, 1997, pp. 223-227.

S. Khuri, F. Stern, T. Chiu, Randomness of Finite Strings: A Reconstructive Approach (ps, 145K) Proceedings of the 1997 ACM Symposium on Applied Computing, ACM Press, 1997, pp. 527-531.

S. Khuri, J. Bergin, K. Brodlie, S. Rodger, M. Goldweber, R. Jiménez-Peris, M. Patiño-Martínez, M. McNally, T. Naps, and J. Wilson, An Overview of Visualization: its Use and Design (pdf file) ACM SIGCSE Bulletin, volume 28, ACM Press, 1996, pp. 192-200.

S. Khuri, J. Williams, Neuralis: A Neural Network Package (PDF, 423K) ACM SIGCSE Bulletin, volume 28, ACM Press, 1996, pp. 25-27.

S. Khuri, __An Evolutionary Heuristic for solving problems in Coding
Theory__ Proceedings of the Third European Conference on Artificial Life:
Abstracts Book, 1995, p. 90.

S. Khuri, M. Shütz, J. Heikötter, Evolutionary Heuristics for the Bin Packing Problem (ps, 142K), Proceedings of the ICANNGA, Springer-Verlag, Vienna, 1994, pp. 285-288.

T. Bäck, S. Khuri, An Evolutionary Heuristic for the Maximum Independent Set Problem (ps, 222K), Proceedings of the IEEE World Congress on Computational Intelligence, IEEE Service Center, Piscataway, N. J., vol. 2, pp. 531-535.

S. Khuri, Intractability: A Geometric Representation (PDF, 377K) Bulletin of the ACM/SIGCSE, vol. 26, number 1, March 1994, pp. 228-232.

S. Khuri, J. Williams, Understanding the Bottom-Up SLR Parser (PDF, 489K) Bulletin of the ACM/SIGCSE, vol. 26, number 1, March 1994, pp. 339-343.

S. Khuri, T. Bäck, J. Heikötter, The Zero/One Multiple Knapsack Problem and Genetic Algorithms (ps, 181K) Proceedings of the 1994 ACM Symposium on Applied Computing, 1994, pp. 188-193.

S. Khuri, Walsh and Haar Functions in Genetic Algorithms (ps, 154K) Proceedings of the 1994 ACM Symposium on Applied Computing", 1994, pp. 201-205.

S. Khuri, T. Bäck, J. Heikötter, An Evolutionary Approach to Combinatorial Optimization Problems (ps, 260K), Proceedings of the 22nd Annual ACM Computer Science Conference, ACM Press, NY, 1994, pp. 66-73.

S. Khuri, A. Batarekh, __Genetic Algorithms and Discrete Optimization__
Proceedings of the International Conference on Operations Research, 1990.

S. Khuri, A. Batarekh, __Heuristics for the Integer Knapsack Problem__
Proceedings of the Xth International Computer Science Conference, 1990,
pp. 161-172.

S. Khuri, A. Batarekh, __The Harmonium and Decision Problems__ Proceedings
of the IJCNN, vol. II, 1990, pp. 179-184.

S. Khuri, M. Hoang, __Genetic Heuristics in Optimization Problems__
Proceedings of the ACM CSC, 1990, p. 447.

S. Khuri, __Informatic Crossover in Genetic Algorithms__ International
Symposium on Information Theory Abstract of Papers, 1990, p. 62.

S. Khuri, __Optimal and Near-Optimal Space Efficient Decision Diagram
Algorithms__ Proceedings of the ACM CSC, 1989, p. 467.

S. Khuri, C. Hartmann, P. Varshney, __Applying Information Theory to
the Construction of Decision Diagrams__ ISIT Abstract of Papers, 1988,
p. 132.

S. Khuri, Counting Nodes in Binary Trees (pdf file) Bulletin of the ACM/SIGCSE, vol. 18, number 1, February 1986. pp. 182-185.