| 2018 | CIBCB | RNA secondary structure graphical rendering library. | Keith A. Monschke, Abdullah N. Arslan |
| 2017 | IWCIA | Shape Matching for Rigid Objects by Aligning Sequences Based on Boundary Change Points. | Abdullah N. Arslan, Nikolay Metodiev Sirakov |
| 2010 | LATA | A Fast Longest Common Subsequence Algorithm for Similar Strings. | Abdullah N. Arslan |
| 2007 | BIBE | Phylogeny By Top Down Clustering Using a Given Multiple Alignment. | Abdullah N. Arslan, Peyman Bizargity |
| 2007 | BIBE | Iterative Refinement of Repeat Sequence Specification Using Constrained Pattern Matching. | Dan He, Abdullah N. Arslan, Yu He, Xindong Wu |
| 2007 | FCT | A Largest Common d-Dimensional Subsequence of Two d-Dimensional Strings. | Abdullah N. Arslan |
| 2007 | IRI | Mining Frequent Patterns with Wildcards from Biological Sequences. | Yu He, Xindong Wu, Xingquan Zhu, Abdullah N. Arslan |
| 2006 | BIBE | An algorithm for string edit distance allowing substring reversals. | Abdullah N. Arslan |
| 2006 | BIBE | An improved algorithm for the regular expression constrained multiple sequence alignment problem. | Abdullah N. Arslan, Dan He |
| 2006 | CSR | Fast Motif Search in Protein Sequence Databases. | Elena Zheleva, Abdullah N. Arslan |
| 2006 | LATIN | Efficient Approximate Dictionary Look-Up for Long Words over Small Alphabets. | Abdullah N. Arslan |
| 2005 | BIBE | A Parallel Algorithm for the Constrained Multiple Sequence Alignment Problem. | Dan He, Abdullah N. Arslan |
| 2005 | CIBCB | Multiple Sequence Alignment Containing a Sequence of Regular Expressions. | Abdullah N. Arslan |
| 2005 | CPM | Regular Expression Constrained Sequence Alignment. | Abdullah N. Arslan |
| 2002 | COCOON | Dictionary Look-Up within Small Edit Distance. | Abdullah N. Arslan, mer Egecioglu |
| 2002 | LATIN | Algorithms for Local Alignment with Length Constraints. | Abdullah N. Arslan, mer Egecioglu |
| 2002 | SPIRE | Efficient Computation of Long Similar Subsequences. | Abdullah N. Arslan, mer Egecioglu |
| 2001 | COCOON | An Improved Upper Bound on the Size of Planar Convex-Hulls. | Abdullah N. Arslan, mer Egecioglu |
| 2001 | RECOMB | A new approach to sequence comparison: normalized sequence alignment. | Abdullah N. Arslan, mer Egecioglu, Pavel A. Pevzner |
| 1999 | SPIRE | An Efficient Uniform-Cost Normalized Edit Distance Algorithm. | Abdullah N. Arslan, mer Egecioglu |