58. Arslan, A. N., He, D., He, Y., and Wu, X. (2015) "Pattern Matching With Wildcards and Length Constraints Using Maximum Network Flow", Journal of Discrete Algorithms, Vol. 35, pp. 9-16 DOI information: 10.1016/j.jda.2015.08.003

57. Arslan, A. N., George, B., and Stor, K. (2015) "New Algorithms for Pattern Matching with Wildcards and Length Constraints", Discrete Mathematics, Algorithms and Applications, Vol. 7, No. 3, doi: 101142/S1793830915500329

56. Arslan, A. N. (2015) "A Variant of Waring's Problem", Notes on Number Theory and Discrete Mathematics, Vol. 21, No. 3, 22-26

55. Arslan, A. N., Hempelmann, C. F., Attardo, S., Blount, G. P. and Sirakov, N. M. (2015) "Threat Assessment Using Visual Hierarchy and Conceptual Firearms Ontology",Optical Engineering, 54(5), 053109 (2015). doi:10.1117/1.OE.54.5.053109.

54. Arslan, A. N. (2015) "Fast Algorithms for Local Similarity Queries in Two Sequences",International Journal of Foundations of Computer Science, Vol. 26, No. 5 (2015) 625–642, DOI: 10.1142/S0129054115500355

53. Arslan, A. N., Hempelmann, C. F., Attardo, S., Blount, G. P., Sirakova, N. N. and Sirakov, N. M. (to appear) "Identification of Partially Occluded Firearms Through Partonomy", SPIE 2015

52. Arslan, A. N. (2015) "Expressing Integers as Sums of Many Distinct Primes", JP Journal of Algebra, Number Theory and Applications, 36(1), 1-15

51. Kandhare, P, Arslan, A. N., Sirakov, N. M. (2014) "Tracking Partially Occluded Objects with Centripetal Active Contour", International Workshop on Combinatorial Image Processing 2014 IWCIA, Bruno, Czech Republic, May 2014, Mathematics for Applications, ISSN 1805-3610, indexed by Zentralblatt and MathSciNet. Published by the Technical University of Brno (ISBN: 80-214-020-X), http://ma.fme.vutbr.cz/

50. Sakoglu, U., Arslan, A. N., Bohra, K., Flores, H. (2014) "In Search of Optimal Space-Filling Curves for 3-D to 1-D Mapping: Application to 3-D Brain MRI Data", In Proc. of the 6th International Conference on Bioinformatics and Computational Biology (BICoB), March 24 - 26, 2014 Las Vegas, Nevada

49. Hempelmann, C. F., Arslan, A. N., Attardo, S., Blount, G. P., and Sirakov, N. M. (2014) "Assessing the Threat of Firearms: New Threat Formula, Resources, and Ontological Linking Algorithms", In: Kadar, Ivan. Ed. Signal Processing, Sensor/Information Fusion, and Target Recognition XXIII, Proceedings of SPIE, Vol. 9091. Bellingham, WA: SPIE. 90910U1-12. doi: 10.1117/12.2050814

48. Wu, X., Zhu, X., He, Y., Arslan, A. N. (2013) "PMBC: Pattern mining from biological sequences with wildcard constraints", Comp. in Bio. and Med. 43(5): 481-492

47. Arslan, A. N., Hempelmann, C. F., Di Ferrante, C., Attardo, S., Sirakov, N. M. (2013) "From Shape to Threat: Exploiting the Convergence Between Visual and Conceptual Organization for Weapon Identification and Threat Assessment", In: Sadjadi, Firooz A. and Abhijit Mahalanobis. Eds. Automatic Target Recognition XXIII. Proceedings of SPIE 0277-768X, V. 8744. Bellingham, WA: SPIE. 87440P. pp. 1-15. doi:10.1117/12.2015591 (Winner of the Lockheed Martin Best Paper Award)

46. Arslan A. N., Sirakov, N. M., and Attardo, S. (2012) "Weapon Ontology Annotation Using Boundary Describing Sequences", In Proceedings of the2012 IEEE Southwest Symposium on Image Analysis and Interpretation, April 22-24, 2012, Santa Fe, New Mexico

45. Arslan, A. N. and Chidri, Arvind (2011) "A clustering-based matrix multiplication algorithm", In Proceedings of International Conference on Scientific Computing (CSC 2011), pp. 303-307

44. Arslan, A. N. and Chidri, Arvind (2010) "An efficient multiplication algorithm for thin matrices and for matrices with similar rows and columns", In Proceedings of International Conference on Scientific Computing (CSC 2010), pp. 147-152

43. Arslan, A. N (2010) "Heuristic algorithms for local sequence alignment with inversions and reversals", The 15th Anniversary Celebration, Transformative Systems Conference, SDPS 2010, Dallas, TX, June 6-11, 2010

42. Arslan, A. N. (2010) "A fast longest common subsequence algorithm for similar strings", The 4th International Conference on Language and Automata Theory and Applications (LATA 2010), Trier, Germany, May 24-28, 2010, Lecture Notes in Computer Science 6031, pp. 82-93

41. J. Zhang, G. Li, J. Y. Yang Editors, and A. Arslan et al. Associate Editors. (2009) "The Proceeding of the international conferences on bioinformatics, systems biology, and intelligent computing", IEEE Computer Society, ISBN 978-0-7695-3739-9

40. 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

39. Arslan, A. N. (2007) "Regular expression constrained sequence alignment", Journal of Discrete Algorithms, Elsevier, 5(4), 647-661

38. Arslan, A. N. (2007) "Sequence alignment guided by common motifs described by context free grammars", The 4th Biotechnology and Bioinformatics Symposium (BIOT) 2007, October 19-20, Colorado Springs, CO

37. Arslan, A. N. and Bizargity, P. (2007) "Phylogeny by top down clustering using a given multiple alignment", The Proceedings of the 7th IEEE Symposium on Bioinformatics and Biotechnology (BIBE 2007), Vol. II, pp. 809-814, Harvard Medical School, Boston, Massachusetts, October 14-17, 2007

36. 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 7th IEEE Symposium on Bioinformatics and Biotechnology (BIBE 2007), Vol. II, pp. 1199-1203, Harvard Medical School, Boston, Massachusetts, October 14-17, 2007

35. Arslan, A. N. (2007) "A largest common d-dimensional subsequence of two d-dimensional strings", The 16th 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

34. 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

33. A. N. Arslan and J. Nowak. "Efficient approximate dictionary look-up for words over small alphabets", Technical Report TUM-I0708, Technische Universität München, Institut für Informatik, January 2007 (http://www14.in.tum.de/personen/nowakj/)

32. 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

31. 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

30. 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

29. Arslan, A. N. and He, D. (2006) "An improved algorithm for the regular expression constrained multiple sequence alignment problem", The Proceedings of the 6th IEEE Symposium on Bioinformatics and Biotechnology (BIBE 2006), pp. 121-126, Washington, DC, October 16-18, 2006

28. Arslan, A. N. (2006) "An algorithm for string edit distance allowing substring reversals", The Proceedings of the 6th IEEE Symposium on Bioinformatics and Biotechnology (BIBE 2006), pp. 220-226, Washington, DC, October 16-18, 2006

27. 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

26. 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

25. 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

24. 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

23. 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 (see also http://www14.in.tum.de/personen/nowakj/ )

22. 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

21. He, D and Arslan, A. N. (2005) "A space-efficient algorithm for the pairwise sequence alignment algorithm", Genome Informatics,16(2): pp. 237-246

20. 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

19. 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

18. He, Dan and Arslan, A. N. (2005) "A parallel algorithm for the constrained multiple sequence alignment problem", Proc. IEEE the 5th Symposium on Bioinformatics and Biotechnology (BIBE'05), pp. 258-262, Minneapolis, Minnesota, October 19-21, 2005

17. 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

16. 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

15. 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

14. 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

13. 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

12. 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

11. 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

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

9. 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

8. 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, 9th International Symposium (SPIRE 2002), Lisbon, Portugal, September 11-13, 2002

7. Arslan, A. N. and Egecioglu, O. (2002) "Dictionary look-up within small edit distance", Lecture Notes in Computer Science 2387:127-136, 8th Annual International Computing and Combinatorics Conference (COCOON), Singapore, August 15-17, 2002

6. Arslan, A. N. and Egecioglu, O. (2002) "Algorithms For Local Alignment With Length Constraints", Proc. 5th Latin American Theoretical Informatics Symposium (LATIN 2002), LNCS 2286, pp. 38-51, Cancun, Mexico, April 2002

5. Arslan, A. N., Egecioglu, O. and Pevzner, P.A. (2001) "A new approach to sequence comparison: normalized sequence alignment", Bioinformatics 17:327-337

4. 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

3. Arslan, A. N. and Egecioglu, O. and Pevzner, P.A. (2001) "A new approach to sequence alignment: normalized sequence alignment", The Fifth Annual International Conference on Computational Molecular Biology (RECOMB 2001), pp. 2-11, Montreal, Canada,, April 22-25, 2001

2. 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

1. 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

58. Arslan, A. N., He, D., He, Y., and Wu, X. (2015) "Pattern Matching With Wildcards and Length Constraints Using Maximum Network Flow", Journal of Discrete Algorithms, Vol. 35, pp. 9-16 DOI information: 10.1016/j.jda.2015.08.003

57. Arslan, A. N., George, B., and Stor, K. (2015) "New Algorithms for Pattern Matching with Wildcards and Length Constraints", Discrete Mathematics, Algorithms and Applications, Vol. 7, No. 3, doi: 101142/S1793830915500329

56. Arslan, A. N. (2015) "A Variant of Waring's Problem", Notes on Number Theory and Discrete Mathematics, Vol. 21, No. 3, 22-26

55. Arslan, A. N., Hempelmann, C. F., Attardo, S., Blount, G. P. and Sirakov, N. M. (2015) "Threat Assessment Using Visual Hierarchy and Conceptual Firearms Ontology",Optical Engineering, 54(5), 053109 (2015). doi:10.1117/1.OE.54.5.053109.

54. Arslan, A. N. (2015) "Fast Algorithms for Local Similarity Queries in Two Sequences",International Journal of Foundations of Computer Science, Vol. 26, No. 5 (2015) 625–642, DOI: 10.1142/S0129054115500355

52. Arslan, A. N. (2015) "Expressing Integers as Sums of Many Distinct Primes", JP Journal of Algebra, Number Theory and Applications, 36(1), 1-15

51. Kandhare, P, Arslan, A. N., Sirakov, N. M. (2014) "Tracking Partially Occluded Objects with Centripetal Active Contour", International Workshop on Combinatorial Image Processing 2014 IWCIA, Bruno, Czech Republic, May 2014, Mathematics for Applications, ISSN 1805-3610, indexed by Zentralblatt and MathSciNet. Published by the Technical University of Brno (ISBN: 80-214-020-X), http://ma.fme.vutbr.cz/

48. Wu, X., Zhu, X., He, Y., Arslan, A. N. (2013) "PMBC: Pattern mining from biological sequences with wildcard constraints", Comp. in Bio. and Med. 43(5): 481-492

45. Arslan, A. N. and Chidri, Arvind (2011) "A clustering-based matrix multiplication algorithm", In Proceedings of International Conference on Scientific Computing (CSC 2011), pp. 303-307

44. Arslan, A. N. and Chidri, Arvind (2010) "An efficient multiplication algorithm for thin matrices and for matrices with similar rows and columns", In Proceedings of International Conference on Scientific Computing (CSC 2010), pp. 147-152

43. Arslan, A. N (2010) "Heuristic algorithms for local sequence alignment with inversions and reversals", The 15th Anniversary Celebration, Transformative Systems Conference, SDPS 2010, Dallas, TX, June 6-11, 2010

42. Arslan, A. N. (2010) "A fast longest common subsequence algorithm for similar strings", The 4th International Conference on Language and Automata Theory and Applications (LATA 2010), Trier, Germany, May 24-28, 2010, Lecture Notes in Computer Science 6031, pp. 82-93

40. 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

39. Arslan, A. N. (2007) "Regular expression constrained sequence alignment", Journal of Discrete Algorithms, Elsevier, 5(4), 647-661

38. Arslan, A. N. (2007) "Sequence alignment guided by common motifs described by context free grammars", The 4th Biotechnology and Bioinformatics Symposium (BIOT) 2007, October 19-20, Colorado Springs, CO

37. Arslan, A. N. and Bizargity, P. (2007) "Phylogeny by top down clustering using a given multiple alignment", The Proceedings of the 7th IEEE Symposium on Bioinformatics and Biotechnology (BIBE 2007), Vol. II, pp. 809-814, Harvard Medical School, Boston, Massachusetts, October 14-17, 2007

36. 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 7th IEEE Symposium on Bioinformatics and Biotechnology (BIBE 2007), Vol. II, pp. 1199-1203, Harvard Medical School, Boston, Massachusetts, October 14-17, 2007

35. Arslan, A. N. (2007) "A largest common d-dimensional subsequence of two d-dimensional strings", The 16th 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

34. 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

32. 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

31. 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

30. 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

29. Arslan, A. N. and He, D. (2006) "An improved algorithm for the regular expression constrained multiple sequence alignment problem", The Proceedings of the 6th IEEE Symposium on Bioinformatics and Biotechnology (BIBE 2006), pp. 121-126, Washington, DC, October 16-18, 2006

28. Arslan, A. N. (2006) "An algorithm for string edit distance allowing substring reversals", The Proceedings of the 6th IEEE Symposium on Bioinformatics and Biotechnology (BIBE 2006), pp. 220-226, Washington, DC, October 16-18, 2006

27. 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

26. 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

25. 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

24. 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

23. 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 (see also http://www14.in.tum.de/personen/nowakj/ )

22. 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

21. He, D and Arslan, A. N. (2005) "A space-efficient algorithm for the pairwise sequence alignment algorithm", Genome Informatics,16(2): pp. 237-246

20. 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

19. 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

18. He, Dan and Arslan, A. N. (2005) "A parallel algorithm for the constrained multiple sequence alignment problem", Proc. IEEE the 5th Symposium on Bioinformatics and Biotechnology (BIBE'05), pp. 258-262, Minneapolis, Minnesota, October 19-21, 2005

17. 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

16. 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

15. 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

14. 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

13. 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

9. 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

8. 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, 9th International Symposium (SPIRE 2002), Lisbon, Portugal, September 11-13, 2002

7. Arslan, A. N. and Egecioglu, O. (2002) "Dictionary look-up within small edit distance", Lecture Notes in Computer Science 2387:127-136, 8th Annual International Computing and Combinatorics Conference (COCOON), Singapore, August 15-17, 2002

6. Arslan, A. N. and Egecioglu, O. (2002) "Algorithms For Local Alignment With Length Constraints", Proc. 5th Latin American Theoretical Informatics Symposium (LATIN 2002), LNCS 2286, pp. 38-51, Cancun, Mexico, April 2002

5. Arslan, A. N., Egecioglu, O. and Pevzner, P.A. (2001) "A new approach to sequence comparison: normalized sequence alignment", Bioinformatics 17:327-337

4. 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

3. Arslan, A. N. and Egecioglu, O. and Pevzner, P.A. (2001) "A new approach to sequence alignment: normalized sequence alignment", The Fifth Annual International Conference on Computational Molecular Biology (RECOMB 2001), pp. 2-11, Montreal, Canada,, April 22-25, 2001

2. 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

1. 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

58. Arslan, A. N., He, D., He, Y., and Wu, X. (2015) "Pattern Matching With Wildcards and Length Constraints Using Maximum Network Flow", Journal of Discrete Algorithms, Vol. 35, pp. 9-16 DOI information: 10.1016/j.jda.2015.08.003

57. Arslan, A. N., George, B., and Stor, K. (2015) "New Algorithms for Pattern Matching with Wildcards and Length Constraints", Discrete Mathematics, Algorithms and Applications, Vol. 7, No. 3, doi: 101142/S1793830915500329

56. Arslan, A. N. (2015) "A Variant of Waring's Problem", Notes on Number Theory and Discrete Mathematics, Vol. 21, No. 3, 22-26

55. Arslan, A. N., Hempelmann, C. F., Attardo, S., Blount, G. P. and Sirakov, N. M. (2015) "Threat Assessment Using Visual Hierarchy and Conceptual Firearms Ontology",Optical Engineering, 54(5), 053109 (2015). doi:10.1117/1.OE.54.5.053109.

54. Arslan, A. N. (2015) "Fast Algorithms for Local Similarity Queries in Two Sequences",International Journal of Foundations of Computer Science, Vol. 26, No. 5 (2015) 625–642, DOI: 10.1142/S0129054115500355

53. Arslan, A. N., Hempelmann, C. F., Attardo, S., Blount, G. P., Sirakova, N. N. and Sirakov, N. M. (to appear) "Identification of Partially Occluded Firearms Through Partonomy", SPIE 2015

52. Arslan, A. N. (2015) "Expressing Integers as Sums of Many Distinct Primes", JP Journal of Algebra, Number Theory and Applications, 36(1), 1-15

51. Kandhare, P, Arslan, A. N., Sirakov, N. M. (2014) "Tracking Partially Occluded Objects with Centripetal Active Contour", International Workshop on Combinatorial Image Processing 2014 IWCIA, Bruno, Czech Republic, May 2014, Mathematics for Applications, ISSN 1805-3610, indexed by Zentralblatt and MathSciNet. Published by the Technical University of Brno (ISBN: 80-214-020-X), http://ma.fme.vutbr.cz/

48. Wu, X., Zhu, X., He, Y., Arslan, A. N. (2013) "PMBC: Pattern mining from biological sequences with wildcard constraints", Comp. in Bio. and Med. 43(5): 481-492

40. 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

39. Arslan, A. N. (2007) "Regular expression constrained sequence alignment", Journal of Discrete Algorithms, Elsevier, 5(4), 647-661

32. 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

31. 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

21. He, D and Arslan, A. N. (2005) "A space-efficient algorithm for the pairwise sequence alignment algorithm", Genome Informatics,16(2): pp. 237-246

20. 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

15. 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

14. 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

9. 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

5. Arslan, A. N., Egecioglu, O. and Pevzner, P.A. (2001) "A new approach to sequence comparison: normalized sequence alignment", Bioinformatics 17:327-337

2. 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

53. Arslan, A. N., Hempelmann, C. F., Attardo, S., Blount, G. P., Sirakova, N. N. and Sirakov, N. M. (to appear) "Identification of Partially Occluded Firearms Through Partonomy", SPIE 2015

51. Kandhare, P, Arslan, A. N., Sirakov, N. M. (2014) "Tracking Partially Occluded Objects with Centripetal Active Contour", International Workshop on Combinatorial Image Processing 2014 IWCIA, Bruno, Czech Republic, May 2014, Mathematics for Applications, ISSN 1805-3610, indexed by Zentralblatt and MathSciNet. Published by the Technical University of Brno (ISBN: 80-214-020-X), http://ma.fme.vutbr.cz/

50. Sakoglu, U., Arslan, A. N., Bohra, K., Flores, H. (2014) "In Search of Optimal Space-Filling Curves for 3-D to 1-D Mapping: Application to 3-D Brain MRI Data", In Proc. of the 6th International Conference on Bioinformatics and Computational Biology (BICoB), March 24 - 26, 2014 Las Vegas, Nevada

49. Hempelmann, C. F., Arslan, A. N., Attardo, S., Blount, G. P., and Sirakov, N. M. (2014) "Assessing the Threat of Firearms: New Threat Formula, Resources, and Ontological Linking Algorithms", In: Kadar, Ivan. Ed. Signal Processing, Sensor/Information Fusion, and Target Recognition XXIII, Proceedings of SPIE, Vol. 9091. Bellingham, WA: SPIE. 90910U1-12. doi: 10.1117/12.2050814

47. Arslan, A. N., Hempelmann, C. F., Di Ferrante, C., Attardo, S., Sirakov, N. M. (2013) "From Shape to Threat: Exploiting the Convergence Between Visual and Conceptual Organization for Weapon Identification and Threat Assessment", In: Sadjadi, Firooz A. and Abhijit Mahalanobis. Eds. Automatic Target Recognition XXIII. Proceedings of SPIE 0277-768X, V. 8744. Bellingham, WA: SPIE. 87440P. pp. 1-15. doi:10.1117/12.2015591 (Winner of the Lockheed Martin Best Paper Award)

46. Arslan A. N., Sirakov, N. M., and Attardo, S. (2012) "Weapon Ontology Annotation Using Boundary Describing Sequences", In Proceedings of the2012 IEEE Southwest Symposium on Image Analysis and Interpretation, April 22-24, 2012, Santa Fe, New Mexico

45. Arslan, A. N. and Chidri, Arvind (2011) "A clustering-based matrix multiplication algorithm", In Proceedings of International Conference on Scientific Computing (CSC 2011), pp. 303-307

44. Arslan, A. N. and Chidri, Arvind (2010) "An efficient multiplication algorithm for thin matrices and for matrices with similar rows and columns", In Proceedings of International Conference on Scientific Computing (CSC 2010), pp. 147-152

43. Arslan, A. N (2010) "Heuristic algorithms for local sequence alignment with inversions and reversals", The 15th Anniversary Celebration, Transformative Systems Conference, SDPS 2010, Dallas, TX, June 6-11, 2010

42. Arslan, A. N. (2010) "A fast longest common subsequence algorithm for similar strings", The 4th International Conference on Language and Automata Theory and Applications (LATA 2010), Trier, Germany, May 24-28, 2010, Lecture Notes in Computer Science 6031, pp. 82-93

38. Arslan, A. N. (2007) "Sequence alignment guided by common motifs described by context free grammars", The 4th Biotechnology and Bioinformatics Symposium (BIOT) 2007, October 19-20, Colorado Springs, CO

37. Arslan, A. N. and Bizargity, P. (2007) "Phylogeny by top down clustering using a given multiple alignment", The Proceedings of the 7th IEEE Symposium on Bioinformatics and Biotechnology (BIBE 2007), Vol. II, pp. 809-814, Harvard Medical School, Boston, Massachusetts, October 14-17, 2007

36. 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 7th IEEE Symposium on Bioinformatics and Biotechnology (BIBE 2007), Vol. II, pp. 1199-1203, Harvard Medical School, Boston, Massachusetts, October 14-17, 2007

35. Arslan, A. N. (2007) "A largest common d-dimensional subsequence of two d-dimensional strings", The 16th 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

34. 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

30. 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

29. Arslan, A. N. and He, D. (2006) "An improved algorithm for the regular expression constrained multiple sequence alignment problem", The Proceedings of the 6th IEEE Symposium on Bioinformatics and Biotechnology (BIBE 2006), pp. 121-126, Washington, DC, October 16-18, 2006

28. Arslan, A. N. (2006) "An algorithm for string edit distance allowing substring reversals", The Proceedings of the 6th IEEE Symposium on Bioinformatics and Biotechnology (BIBE 2006), pp. 220-226, Washington, DC, October 16-18, 2006

27. 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

26. 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

25. 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

24. 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

23. 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 (see also http://www14.in.tum.de/personen/nowakj/ )

22. 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

19. 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

18. He, Dan and Arslan, A. N. (2005) "A parallel algorithm for the constrained multiple sequence alignment problem", Proc. IEEE the 5th Symposium on Bioinformatics and Biotechnology (BIBE'05), pp. 258-262, Minneapolis, Minnesota, October 19-21, 2005

17. 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

16. 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

13. 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

8. 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, 9th International Symposium (SPIRE 2002), Lisbon, Portugal, September 11-13, 2002

7. Arslan, A. N. and Egecioglu, O. (2002) "Dictionary look-up within small edit distance", Lecture Notes in Computer Science 2387:127-136, 8th Annual International Computing and Combinatorics Conference (COCOON), Singapore, August 15-17, 2002

6. Arslan, A. N. and Egecioglu, O. (2002) "Algorithms For Local Alignment With Length Constraints", Proc. 5th Latin American Theoretical Informatics Symposium (LATIN 2002), LNCS 2286, pp. 38-51, Cancun, Mexico, April 2002

4. 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

3. Arslan, A. N. and Egecioglu, O. and Pevzner, P.A. (2001) "A new approach to sequence alignment: normalized sequence alignment", The Fifth Annual International Conference on Computational Molecular Biology (RECOMB 2001), pp. 2-11, Montreal, Canada,, April 22-25, 2001

1. 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

58. Arslan, A. N., He, D., He, Y., and Wu, X. (2015) "Pattern Matching With Wildcards and Length Constraints Using Maximum Network Flow", Journal of Discrete Algorithms, Vol. 35, pp. 9-16 DOI information: 10.1016/j.jda.2015.08.003

57. Arslan, A. N., George, B., and Stor, K. (2015) "New Algorithms for Pattern Matching with Wildcards and Length Constraints", Discrete Mathematics, Algorithms and Applications, Vol. 7, No. 3, doi: 101142/S1793830915500329

54. Arslan, A. N. (2015) "Fast Algorithms for Local Similarity Queries in Two Sequences",International Journal of Foundations of Computer Science, Vol. 26, No. 5 (2015) 625–642, DOI: 10.1142/S0129054115500355

50. Sakoglu, U., Arslan, A. N., Bohra, K., Flores, H. (2014) "In Search of Optimal Space-Filling Curves for 3-D to 1-D Mapping: Application to 3-D Brain MRI Data", In Proc. of the 6th International Conference on Bioinformatics and Computational Biology (BICoB), March 24 - 26, 2014 Las Vegas, Nevada

48. Wu, X., Zhu, X., He, Y., Arslan, A. N. (2013) "PMBC: Pattern mining from biological sequences with wildcard constraints", Comp. in Bio. and Med. 43(5): 481-492

43. Arslan, A. N (2010) "Heuristic algorithms for local sequence alignment with inversions and reversals", The 15th Anniversary Celebration, Transformative Systems Conference, SDPS 2010, Dallas, TX, June 6-11, 2010

42. Arslan, A. N. (2010) "A fast longest common subsequence algorithm for similar strings", The 4th International Conference on Language and Automata Theory and Applications (LATA 2010), Trier, Germany, May 24-28, 2010, Lecture Notes in Computer Science 6031, pp. 82-93

41. J. Zhang, G. Li, J. Y. Yang Editors, and A. Arslan et al. Associate Editors. (2009) "The Proceeding of the international conferences on bioinformatics, systems biology, and intelligent computing", IEEE Computer Society, ISBN 978-0-7695-3739-9

40. 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

39. Arslan, A. N. (2007) "Regular expression constrained sequence alignment", Journal of Discrete Algorithms, Elsevier, 5(4), 647-661

38. Arslan, A. N. (2007) "Sequence alignment guided by common motifs described by context free grammars", The 4th Biotechnology and Bioinformatics Symposium (BIOT) 2007, October 19-20, Colorado Springs, CO

37. Arslan, A. N. and Bizargity, P. (2007) "Phylogeny by top down clustering using a given multiple alignment", The Proceedings of the 7th IEEE Symposium on Bioinformatics and Biotechnology (BIBE 2007), Vol. II, pp. 809-814, Harvard Medical School, Boston, Massachusetts, October 14-17, 2007

36. 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 7th IEEE Symposium on Bioinformatics and Biotechnology (BIBE 2007), Vol. II, pp. 1199-1203, Harvard Medical School, Boston, Massachusetts, October 14-17, 2007

34. 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

32. 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

31. 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

30. 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

29. Arslan, A. N. and He, D. (2006) "An improved algorithm for the regular expression constrained multiple sequence alignment problem", The Proceedings of the 6th IEEE Symposium on Bioinformatics and Biotechnology (BIBE 2006), pp. 121-126, Washington, DC, October 16-18, 2006

28. Arslan, A. N. (2006) "An algorithm for string edit distance allowing substring reversals", The Proceedings of the 6th IEEE Symposium on Bioinformatics and Biotechnology (BIBE 2006), pp. 220-226, Washington, DC, October 16-18, 2006

27. 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

26. 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

25. 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

24. 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

22. 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

21. He, D and Arslan, A. N. (2005) "A space-efficient algorithm for the pairwise sequence alignment algorithm", Genome Informatics,16(2): pp. 237-246

20. 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

19. 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

18. He, Dan and Arslan, A. N. (2005) "A parallel algorithm for the constrained multiple sequence alignment problem", Proc. IEEE the 5th Symposium on Bioinformatics and Biotechnology (BIBE'05), pp. 258-262, Minneapolis, Minnesota, October 19-21, 2005

17. 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

16. 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

15. 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

13. 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

12. 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

11. 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

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

9. 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

8. 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, 9th International Symposium (SPIRE 2002), Lisbon, Portugal, September 11-13, 2002

6. Arslan, A. N. and Egecioglu, O. (2002) "Algorithms For Local Alignment With Length Constraints", Proc. 5th Latin American Theoretical Informatics Symposium (LATIN 2002), LNCS 2286, pp. 38-51, Cancun, Mexico, April 2002

5. Arslan, A. N., Egecioglu, O. and Pevzner, P.A. (2001) "A new approach to sequence comparison: normalized sequence alignment", Bioinformatics 17:327-337

3. Arslan, A. N. and Egecioglu, O. and Pevzner, P.A. (2001) "A new approach to sequence alignment: normalized sequence alignment", The Fifth Annual International Conference on Computational Molecular Biology (RECOMB 2001), pp. 2-11, Montreal, Canada,, April 22-25, 2001

2. 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

1. 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

55. Arslan, A. N., Hempelmann, C. F., Attardo, S., Blount, G. P. and Sirakov, N. M. (2015) "Threat Assessment Using Visual Hierarchy and Conceptual Firearms Ontology",Optical Engineering, 54(5), 053109 (2015). doi:10.1117/1.OE.54.5.053109.

53. Arslan, A. N., Hempelmann, C. F., Attardo, S., Blount, G. P., Sirakova, N. N. and Sirakov, N. M. (to appear) "Identification of Partially Occluded Firearms Through Partonomy", SPIE 2015

49. Hempelmann, C. F., Arslan, A. N., Attardo, S., Blount, G. P., and Sirakov, N. M. (2014) "Assessing the Threat of Firearms: New Threat Formula, Resources, and Ontological Linking Algorithms", In: Kadar, Ivan. Ed. Signal Processing, Sensor/Information Fusion, and Target Recognition XXIII, Proceedings of SPIE, Vol. 9091. Bellingham, WA: SPIE. 90910U1-12. doi: 10.1117/12.2050814

47. Arslan, A. N., Hempelmann, C. F., Di Ferrante, C., Attardo, S., Sirakov, N. M. (2013) "From Shape to Threat: Exploiting the Convergence Between Visual and Conceptual Organization for Weapon Identification and Threat Assessment", In: Sadjadi, Firooz A. and Abhijit Mahalanobis. Eds. Automatic Target Recognition XXIII. Proceedings of SPIE 0277-768X, V. 8744. Bellingham, WA: SPIE. 87440P. pp. 1-15. doi:10.1117/12.2015591 (Winner of the Lockheed Martin Best Paper Award)

46. Arslan A. N., Sirakov, N. M., and Attardo, S. (2012) "Weapon Ontology Annotation Using Boundary Describing Sequences", In Proceedings of the2012 IEEE Southwest Symposium on Image Analysis and Interpretation, April 22-24, 2012, Santa Fe, New Mexico

56. Arslan, A. N. (2015) "A Variant of Waring's Problem", Notes on Number Theory and Discrete Mathematics, Vol. 21, No. 3, 22-26

52. Arslan, A. N. (2015) "Expressing Integers as Sums of Many Distinct Primes", JP Journal of Algebra, Number Theory and Applications, 36(1), 1-15

45. Arslan, A. N. and Chidri, Arvind (2011) "A clustering-based matrix multiplication algorithm", In Proceedings of International Conference on Scientific Computing (CSC 2011), pp. 303-307

44. Arslan, A. N. and Chidri, Arvind (2010) "An efficient multiplication algorithm for thin matrices and for matrices with similar rows and columns", In Proceedings of International Conference on Scientific Computing (CSC 2010), pp. 147-152

4. 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

58. Arslan, A. N., He, D., He, Y., and Wu, X. (2015) "Pattern Matching With Wildcards and Length Constraints Using Maximum Network Flow", Journal of Discrete Algorithms, Vol. 35, pp. 9-16 DOI information: 10.1016/j.jda.2015.08.003

57. Arslan, A. N., George, B., and Stor, K. (2015) "New Algorithms for Pattern Matching with Wildcards and Length Constraints", Discrete Mathematics, Algorithms and Applications, Vol. 7, No. 3, doi: 101142/S1793830915500329

56. Arslan, A. N. (2015) "A Variant of Waring's Problem", Notes on Number Theory and Discrete Mathematics, Vol. 21, No. 3, 22-26

55. Arslan, A. N., Hempelmann, C. F., Attardo, S., Blount, G. P. and Sirakov, N. M. (2015) "Threat Assessment Using Visual Hierarchy and Conceptual Firearms Ontology",Optical Engineering, 54(5), 053109 (2015). doi:10.1117/1.OE.54.5.053109.

54. Arslan, A. N. (2015) "Fast Algorithms for Local Similarity Queries in Two Sequences",International Journal of Foundations of Computer Science, Vol. 26, No. 5 (2015) 625–642, DOI: 10.1142/S0129054115500355

53. Arslan, A. N., Hempelmann, C. F., Attardo, S., Blount, G. P., Sirakova, N. N. and Sirakov, N. M. (to appear) "Identification of Partially Occluded Firearms Through Partonomy", SPIE 2015

52. Arslan, A. N. (2015) "Expressing Integers as Sums of Many Distinct Primes", JP Journal of Algebra, Number Theory and Applications, 36(1), 1-15

51. Kandhare, P, Arslan, A. N., Sirakov, N. M. (2014) "Tracking Partially Occluded Objects with Centripetal Active Contour", International Workshop on Combinatorial Image Processing 2014 IWCIA, Bruno, Czech Republic, May 2014, Mathematics for Applications, ISSN 1805-3610, indexed by Zentralblatt and MathSciNet. Published by the Technical University of Brno (ISBN: 80-214-020-X), http://ma.fme.vutbr.cz/

50. Sakoglu, U., Arslan, A. N., Bohra, K., Flores, H. (2014) "In Search of Optimal Space-Filling Curves for 3-D to 1-D Mapping: Application to 3-D Brain MRI Data", In Proc. of the 6th International Conference on Bioinformatics and Computational Biology (BICoB), March 24 - 26, 2014 Las Vegas, Nevada

49. Hempelmann, C. F., Arslan, A. N., Attardo, S., Blount, G. P., and Sirakov, N. M. (2014) "Assessing the Threat of Firearms: New Threat Formula, Resources, and Ontological Linking Algorithms", In: Kadar, Ivan. Ed. Signal Processing, Sensor/Information Fusion, and Target Recognition XXIII, Proceedings of SPIE, Vol. 9091. Bellingham, WA: SPIE. 90910U1-12. doi: 10.1117/12.2050814

48. Wu, X., Zhu, X., He, Y., Arslan, A. N. (2013) "PMBC: Pattern mining from biological sequences with wildcard constraints", Comp. in Bio. and Med. 43(5): 481-492

47. Arslan, A. N., Hempelmann, C. F., Di Ferrante, C., Attardo, S., Sirakov, N. M. (2013) "From Shape to Threat: Exploiting the Convergence Between Visual and Conceptual Organization for Weapon Identification and Threat Assessment", In: Sadjadi, Firooz A. and Abhijit Mahalanobis. Eds. Automatic Target Recognition XXIII. Proceedings of SPIE 0277-768X, V. 8744. Bellingham, WA: SPIE. 87440P. pp. 1-15. doi:10.1117/12.2015591 (Winner of the Lockheed Martin Best Paper Award)

46. Arslan A. N., Sirakov, N. M., and Attardo, S. (2012) "Weapon Ontology Annotation Using Boundary Describing Sequences", In Proceedings of the2012 IEEE Southwest Symposium on Image Analysis and Interpretation, April 22-24, 2012, Santa Fe, New Mexico

45. Arslan, A. N. and Chidri, Arvind (2011) "A clustering-based matrix multiplication algorithm", In Proceedings of International Conference on Scientific Computing (CSC 2011), pp. 303-307

44. Arslan, A. N. and Chidri, Arvind (2010) "An efficient multiplication algorithm for thin matrices and for matrices with similar rows and columns", In Proceedings of International Conference on Scientific Computing (CSC 2010), pp. 147-152

43. Arslan, A. N (2010) "Heuristic algorithms for local sequence alignment with inversions and reversals", The 15th Anniversary Celebration, Transformative Systems Conference, SDPS 2010, Dallas, TX, June 6-11, 2010

42. Arslan, A. N. (2010) "A fast longest common subsequence algorithm for similar strings", The 4th International Conference on Language and Automata Theory and Applications (LATA 2010), Trier, Germany, May 24-28, 2010, Lecture Notes in Computer Science 6031, pp. 82-93

41. J. Zhang, G. Li, J. Y. Yang Editors, and A. Arslan et al. Associate Editors. (2009) "The Proceeding of the international conferences on bioinformatics, systems biology, and intelligent computing", IEEE Computer Society, ISBN 978-0-7695-3739-9

40. 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

39. Arslan, A. N. (2007) "Regular expression constrained sequence alignment", Journal of Discrete Algorithms, Elsevier, 5(4), 647-661

38. Arslan, A. N. (2007) "Sequence alignment guided by common motifs described by context free grammars", The 4th Biotechnology and Bioinformatics Symposium (BIOT) 2007, October 19-20, Colorado Springs, CO

37. Arslan, A. N. and Bizargity, P. (2007) "Phylogeny by top down clustering using a given multiple alignment", The Proceedings of the 7th IEEE Symposium on Bioinformatics and Biotechnology (BIBE 2007), Vol. II, pp. 809-814, Harvard Medical School, Boston, Massachusetts, October 14-17, 2007

36. 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 7th IEEE Symposium on Bioinformatics and Biotechnology (BIBE 2007), Vol. II, pp. 1199-1203, Harvard Medical School, Boston, Massachusetts, October 14-17, 2007

35. Arslan, A. N. (2007) "A largest common d-dimensional subsequence of two d-dimensional strings", The 16th 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

34. 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

33. A. N. Arslan and J. Nowak. "Efficient approximate dictionary look-up for words over small alphabets", Technical Report TUM-I0708, Technische Universität München, Institut für Informatik, January 2007 (http://www14.in.tum.de/personen/nowakj/)

32. 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

31. 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

30. 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

29. Arslan, A. N. and He, D. (2006) "An improved algorithm for the regular expression constrained multiple sequence alignment problem", The Proceedings of the 6th IEEE Symposium on Bioinformatics and Biotechnology (BIBE 2006), pp. 121-126, Washington, DC, October 16-18, 2006

28. Arslan, A. N. (2006) "An algorithm for string edit distance allowing substring reversals", The Proceedings of the 6th IEEE Symposium on Bioinformatics and Biotechnology (BIBE 2006), pp. 220-226, Washington, DC, October 16-18, 2006

27. 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

26. 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

25. 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

24. 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

23. 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 (see also http://www14.in.tum.de/personen/nowakj/ )

22. 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

21. He, D and Arslan, A. N. (2005) "A space-efficient algorithm for the pairwise sequence alignment algorithm", Genome Informatics,16(2): pp. 237-246

20. 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

19. 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

18. He, Dan and Arslan, A. N. (2005) "A parallel algorithm for the constrained multiple sequence alignment problem", Proc. IEEE the 5th Symposium on Bioinformatics and Biotechnology (BIBE'05), pp. 258-262, Minneapolis, Minnesota, October 19-21, 2005

17. 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

16. 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

15. 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

14. 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

13. 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

12. 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

11. 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

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

9. 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

8. 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, 9th International Symposium (SPIRE 2002), Lisbon, Portugal, September 11-13, 2002

7. Arslan, A. N. and Egecioglu, O. (2002) "Dictionary look-up within small edit distance", Lecture Notes in Computer Science 2387:127-136, 8th Annual International Computing and Combinatorics Conference (COCOON), Singapore, August 15-17, 2002

6. Arslan, A. N. and Egecioglu, O. (2002) "Algorithms For Local Alignment With Length Constraints", Proc. 5th Latin American Theoretical Informatics Symposium (LATIN 2002), LNCS 2286, pp. 38-51, Cancun, Mexico, April 2002

5. Arslan, A. N., Egecioglu, O. and Pevzner, P.A. (2001) "A new approach to sequence comparison: normalized sequence alignment", Bioinformatics 17:327-337

4. 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

3. Arslan, A. N. and Egecioglu, O. and Pevzner, P.A. (2001) "A new approach to sequence alignment: normalized sequence alignment", The Fifth Annual International Conference on Computational Molecular Biology (RECOMB 2001), pp. 2-11, Montreal, Canada,, April 22-25, 2001

2. 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

1. 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