| 2013 | CPM | A Bit-Parallel, General Integer-Scoring Sequence Alignment Algorithm. | Gary Benson, Yzen Hernndez, Joshua Loving |
| 2013 | SISAP | Longest Common Subsequence in k Length Substrings. | Gary Benson, Avivit Levy, B. Riva Shalom |
| 2008 | SPIRE | Exact Distribution of a Spaced Seed Statistic for DNA Homology Detection. | Gary Benson, Denise Y. F. Mak |
| 2007 | APBC | All Hits All The Time: Parameter Free Calculation of Seed Sensitivity. | Denise Y. F. Mak, Gary Benson |
| 2006 | ICDM | Discovering Frequent Poly-Regions in DNA Sequences. | Panagiotis Papapetrou, Gary Benson, George Kollios |
| 2006 | ISMB | Indel seeds for homology search. | Denise Y. F. Mak, Yevgeniy Gelfand, Gary Benson |
| 2006 | SODA | Pattern matching with address errors: rearrangement distances. | Amihood Amir, Yonatan Aumann, Gary Benson, Avivit Levy, Ohad Lipsky, Ely Porat, Steven Skiena, Uzi Vishne |
| 2003 | WABI | Composition Alignment. | Gary Benson |
| 2002 | ECCB | A new distance measure for comparing sequence profiles based on path lengths along an entropy surface. | Gary Benson |
| 2001 | CPM | Tandem Cyclic Alignment. | Gary Benson |
| 1999 | ISMB | Reconstructing the Duplication History of a Tandem Repeat. | Gary Benson, Lan Dong |
| 1998 | RECOMB | An algorithm for finding tandem repeats of unspecified pattern size. | Gary Benson |
| 1997 | RECOMB | Sequence alignment with tandem duplication. | Gary Benson |
| 1997 | RECOMB | Pooling strategies for establishing physical genome maps using FISH. | Fengzhu Sun, Gary Benson, Norman Arnheim, Michael S. Waterman |
| 1994 | CPM | A Space Efficient Algorithm for Finding the Best Non-Overlapping Alignment Score. | Gary Benson |
| 1994 | ICALP | Optimal Two-Dimensional Compressed Matching. | Amihood Amir, Gary Benson, Martin Farach |
| 1994 | SODA | Let Sleeping Files Lie: Pattern Matching in Z-compressed Files. | Amihood Amir, Gary Benson, Martin Farach |
| 1993 | SPAA | Optimal Parallel Two Dimensional Pattern Matching. | Amihood Amir, Gary Benson, Martin Farach |
| 1992 | DCC | Efficient Two-Dimensional Compressed Matching. | Amihood Amir, Gary Benson |
| 1992 | SODA | Two-Dimensional Periodicity and Its Applications. | Amihood Amir, Gary Benson |
| 1992 | STOC | Alphabet Independent Two Dimensional Matching | Amihood Amir, Gary Benson, Martin Farach |