publications

papers revised

or

under preparation

PR7.	Arslan, A. N. A fast algorithm for finding a longest common subsequence of two similar strings. This algorithm uses a smart data structure and runs fast to find a longest common subsequence of two given strings. This algorithm is provably faster than existing solutions when the given strings are “relatively similar”.
PR6.	Arslan, A. N. Reordered suffix trees for fast approximate look-up. This paper studies functions which can be used to reorder suffix trees to reduce tree-height such that look-up problems with certain proximity measures can be answered fast.
PR5.	Arslan, A. N. Multi-item multi-vendor cost optimization for a single buyer. Formulated a new computational problem, which has potential applications on on-line shopping.
PR4.	Arslan, A. N. Fast algorithms for sequence alignment with inversions. This paper presents new algorithms (based on very effective heuristics) for the sequence alignment problem in which inversions (block reversals after possibly performing other operations at the character level). This problem was introduced by Schöniger and Waterman in 1992, and studied also by others. The algorithms presented in this paper are much faster than existing algorithms for this problem.
PR3.	Arslan, A. N. , George, B., and Stor, K. Algorithms for pattern matching with wildcards and length constraints. Betsy George is a Math MS and Kirsten Stor is a Math PhD student. This paper presents new algorithms for a pattern matching problem
PR2.	Arslan, A. N., He, D., and DeHaas D. Improved algorithms for regular expression constrained multiple sequence alignment problems. This paper presents results of parallel algorithms developed and implemented by the authors for the regular expression constrained multiple sequence alignment problem.
PR1.	Arslan, A. N. and Nowak, J. Efficient approximate dictionary look-up for long words over small alphabets. This paper is revised (extended with implementations and test results) for resubmission for possible publication in Pattern Recognition.

book chapters

BC2.

Arslan, A. N. (2008) Guided Sequence Alignment. Encyclopedia of Data Warehousing and Mining - 2nd Edition, Edited by John Wang, Professor, Department of Management & Information Science, Montclair State University, scheduled for publication by IGI Global (Formerly “Idea Group Inc.”), Hershey, PA, USA, in August 2008 (a peer-reviewed chapter)

BC1.

Arslan, A. N. and Egecioglu, O. (2007) Chapter 76. Dynamic and fractional programming approximation algorithms for local alignment with constraints. Handbook of Approximation Algorithms and Metaheuristics, Edited by: Teofilo F. Gonzalez, Chapman & Hall/CRC in the Computer & Information Science Series, Volume 13, ISBN: 9781584885504

journal papers

J11.	Arslan, A. N. (2008) An algorithm with linear expected running time for string editing with substitutions and substring reversals. Information Processing Letters, 106(5):213-218 (available online: 10.1016/j.ipl.2007.11.017 )
J10.	Arslan, A. N. (2007) Regular expression constrained sequence alignment. Journal of Discrete Algorithms, Elsevier, 5(4), 647-661 (available online: http://dx.doi.org/10.1016/j.jda.2007.01.003 ), ( the formulation of sequence alignment presented in this paper was adopted in the alignment tool RE-MuSiC as reported in an article in Nucleic Acids Research in 2007)
J9.	He, D., Arslan, A. N., and Ling, A. C. H. (2006) A fast algorithm for the constrained multiple sequence alignment problem. Acta Cybernetica, 17: 701-717
J8.	Chen, G., Wu, X., Zhu, X., Arslan, A. N., and He, Yu. (2006) Efficient string matching with wildcards and length constraints. Knowledge and Information Systems, 10(4):399-419 (available online DOI: 10.1007/s10115-006-0016-8)
J7.	He, D and Arslan, A. N. (2005) A space-efficient algorithm for the pairwise sequence alignment algorithm. Genome Informatics, 16(2): pp. 237–246
J6.	Arslan, A. N. and Egecioglu, O. (2005) Algorithms for the constrained longest common subsequence problems. International Journal of Foundations of Computer Science, (16)6:1099-1111, December 2005
J5.	Arslan, A. N. and Egecioglu, O. (2004) Dynamic programming based approximation algorithms for sequence alignment with constraints. INFORMS Journal on Computing, Special issue on Computational Molecular Biology/Bioinformatics, Vol. 16, No. 4, pp. 441-458
J4.	Arslan, A. N. and Egecioglu, O. (2004) Dictionary look-up within small edit distance. International Journal of Foundations of Computer Science, Vol. 15, No 1, pp. 57-71, February 2004
J3.	Arslan, A. N. and Egecioglu, O. (2002) Approximation algorithms for local alignment with length constraints. International Journal of Foundations of Computer Science 13:751-567
J2.	Arslan, A. N., Egecioglu, O. and Pevzner, P.A. (2001) A new approach to sequence comparison: normalized sequence alignment. Bioinformatics 17:327-337 (the paper proposed using length-normalized scores for eliminating mosaic and shadow effects (some undesired anomalies) that arise when the common notion of sequence similarity is used. This fractional programming algorithm is strikingly fast although the optimization problem solved is complex)
J1.	Arslan, A. N. and Egecioglu, O. (2000) Efficient algorithms for normalized edit distance. Journal of Discrete Algorithms (Special Issue on Matching Patterns) 1(1):3-20

peer-reviewed conference papers

C24.	Arslan, A. N. (2007) Sequence alignment guided by common motifs described by context free grammars (The 4^th Biotechnology and Bioinformatics Symposium (BIOT) 2007), October 19-20, Colorado Springs, CO
C23.	Arslan, A. N. and Bizargity, P. (2007) Phylogeny by top down clustering using a given multiple alignment. The Proceedings of the 7^thIEEE Symposium on Bioinformatics and Biotechnology (BIBE 2007), Vol. II, pp. 809-814, Harvard Medical School, Boston, Massachusetts, October 14-17, 2007
C22.	He, D., Arslan, A. N., He, Y. and Wu, X. (2007) Iterative refinement of repeat sequence specification using constrained pattern matching. The Proceedings of the 7^thIEEE Symposium on Bioinformatics and Biotechnology (BIBE 2007), Vol. II, pp. 1199-1203, Harvard Medical School, Boston, Massachusetts, October 14-17, 2007
C21.	Arslan, A. N. (2007) A largest common d-dimensional subsequence of two d-dimensional strings. The 16^th International Symposium on Fundamentals of Computation Theory (FCT 2007), Budapest, Hungary, August 2007, Lecture Notes in Computer Science (LNCS) 4639, Erzsebet Csuhaj-Varju, Zoltan Esik (Eds.), Springer, pp. 40-51
C20.	He, Y., Wu, X., Zhu, X. and Arslan, A. N. (2007) Mining Frequent Patterns with Wildcards from Biological Sequences. Proc. of the IEEE International Conference on Information Reuse and Integration (IEEE IRI-07), pp. 329-334, Las Vegas, August 13-15, 2007
C19.	Arslan, A. N. (2006) An algorithm with linear expected running time for string editing with substitutions and substring reversals. The Proceedings of the Biotechnology and Bioinformatics Symposium (BIOT-2006), pp. 90-96, Provo, Utah, October 20-21, 2006
C18.	Arslan, A. N. and He, D. (2006) An improved algorithm for the regular expression constrained multiple sequence alignment problem. The Proceedings of the 6^thIEEE Symposium on Bioinformatics and Biotechnology (BIBE 2006), pp. 121-126, Washington, DC, October 16-18, 2006
C17.	Arslan, A. N. (2006) An algorithm for string edit distance allowing substring reversals. The Proceedings of the 6^th IEEE Symposium on Bioinformatics and Biotechnology (BIBE 2006), pp. 220-226, Washington, DC, October 16-18, 2006
C16.	He, D. and Arslan, A. N. (2006) FastPCMSA: An Improved Parallel Algorithm for the constrained multiple sequence alignment problem. FCS'06 - The 2006 International Conference on Foundations of Computer Science, pp. 88-94, Monte Carlo Resort, Las Vegas, Nevada, June 26-29, 2006
C15.	He, D. and Arslan, A. N. (2006) Space-efficient algorithms for the constrained multiple sequence alignment problem. BIOCOMP'06- The 2006 International Conference on Bioinformatics & Computational Biology, pp. 10-16, Monte Carlo Resort, Las Vegas, Nevada, June 26-29, 2006
C14.	He, D. and Arslan, A. N. (2006) A* algorithms for the constrained multiple sequence alignment problem. ICAI'06 - The 2006 International Conference on Artificial Intelligence, pp. 465-479, Las Vegas, Nevada, June 26-29, 2006
C13.	Zheleva, E. and Arslan, A. N. (2006) Fast motif search in protein sequence databases. International Computer Science Symposium in Russia (CSR 2006), Lecture Notes in Computer Science 3967, pp. 670-681, St.Petersburg, Russia, June 8-12, 2006
C12.	Arslan, A. N. (2006) Efficient approximate dictionary look-up for long words over small alphabets. Lecture Notes in Computer Science 3887, pp. 118-129, Latin American Theoretical Informatics LATIN’06, Valdivia, Chile, March 20-24, 2006
C11.	Singh, D. R. , Arslan, A. N, and Wu, X. (2006) Using an extended suffix tree to speed-up sequence alignment. IADIS International Conference on Applied Computing, pp. 655-660, San Sebastian, Spain, February 25-28, 2006
C10.	Arslan, A. N. (2005) Multiple sequence alignment containing a sequence of regular expressions, Proc. IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology (CIBCB’05), pp. 230-236, La Jolla, November 14-15, 2005
C9.	He, Dan and Arslan, A. N. (2005) A parallel algorithm for the constrained multiple sequence alignment problem, Proc. IEEE the 5^th Symposium on Bioinformatics and Biotechnology (BIBE’05), pp. 258-262, Minneapolis, Minnesota, October 19-21, 2005
C8.	Arslan, A. N. (2005) Regular expression constrained sequence alignment, Lecture Notes in Computer Science 3537, pp. 322-333, Combinatorial Pattern Matching (CPM), Jeju Island, Korea, June 19-22, 2005
C7.	He, Dan and Arslan, A. N. (2005) A fast algorithm for the constrained multiple sequence problem. Proceedings. 11th International Conference on Automata and Formal Languages (AFL 2005), Zoltan Esik, Zoltan Fulop (Eds.) Institute of Informatics, University of Szeged, pp. 131-143, Dobogoko, Hungary, May 17-20, 2005
C6.	Arslan, A. N. and Egecioglu, O. (2004) Algorithms for the constrained longest common subsequence problems, Proceedings of the Prague Stringology Conference 2004, pp. 24-32, Edited by Milan Simanec and Jan Holub, Prague, Czech Republic, August 30-September 1, 2004
C5.	Arslan, A. N. and Egecioglu, O. (2002) Efficient computation of long similar subsequences. Lecture Notes in Computer Science 2476:77-90, String Processing and Information Retrieval, 9^th International Symposium (SPIRE 2002), Lisbon, Portugal, September 11-13, 2002
C4.	Arslan, A. N. and Egecioglu, O. (2002) Dictionary look-up within small edit distance. Lecture Notes in Computer Science 2387:127-136, 8^th Annual International Computing and Combinatorics Conference (COCOON), Singapore, August 15-17, 2002
C3.	Arslan, A. N. and Egecioglu, O. (2001) An improved upper bound on the size of planar convex-hulls. Lecture Notes in Computer Science 2108:111-120, COCOON, Guilin, China, August 20-23, 2001
C2.	Arslan, A. N. and Egecioglu, O. and Pevzner, P.A. (2001) A new approach to sequence alignment. The Fifth Annual International Conference on Computational Molecular Biology (RECOMB 2001), pp. 2-11, Montreal, Canada,, April 22-25, 2001
C1.	Arslan, A. N. and Egecioglu, O. (1999) An efficient uniform-cost normalized edit distance algorithm. IEEE Computer Society 6th International Symposium on String Processing and Information Retrieval (SPIRE 1999), pp. 8-15, Cancun, Mexico, September 22-24, 1999

other publications

O3.

Arslan, A. N. (2004) Algorithmic methods in bioinformatics, Biyoinformatik-II (Bioinformatics Graduate Summer School II, Sile/Turkey), pp. 1-11, August,2004 (Editors: Azmi Telefoncu, Fikrettin Sahin, Ali Kilinc), ISBN=975-483-637-X

O2.

Arslan, A. N. (2004) Sequence alignment, Biyoinformatik-II (Bioinformatics Graduate Summer School II, Sile/Turkey), pp. 101-114, August,2004 (Editors: Azmi Telefoncu, Fikrettin Sahin, Ali Kilinc), ISBN=975-483-637-X

O1.

Arslan, A. N. (2002) Algorithms for string similarity with constraints. Ph.D. Thesis at University of California, Santa Barbara. Published by UMI, Ann Arbor