Efficient Two-Dimensional Compressed Matching. - Amihood Amir; Gary Benson (Data Compression Conference, 1992)

Two-Dimensional Periodicity and Its Applications. - Amihood Amir; Gary Benson (SODA, 1992)

Alphabet Independent Two Dimensional Matching - Amihood Amir; Gary Benson; Martin Farach (STOC, 1992)

Optimal Parallel Two Dimensional Pattern Matching. - Amihood Amir; Gary Benson; Martin Farach (SPAA, 1993)

A Space Efficient Algorithm for Finding the Best Non-Overlapping Alignment Score. - Gary Benson (CPM, 1994)

An Alphabet Independent Approach to Two-Dimensional Pattern Matching. - Amihood Amir; Gary Benson; Martin Farach (SIAM J. Comput., 1994)

A Space Efficient Algorithm for Finding the Best Nonoverlapping Alignment Score. - Gary Benson (Theor. Comput. Sci., 1995)

Let Sleeping Files Lie: Pattern Matching in Z-Compressed Files. - Amihood Amir; Gary Benson; Martin Farach (J. Comput. Syst. Sci., 1996)

Optimal Two-Dimensional Compressed Matching. - Amihood Amir; Gary Benson; Martin Farach (J. Algorithms, 1997)

Sequence Alignment with Tandem Duplication. - Gary Benson (J. Comput. Biol., 1997)

Pooling Strategies for Establishing Physical Genome Maps Using FISH. - Fengzhu Sun; Gary Benson; Norman Arnheim; Michael S. Waterman (J. Comput. Biol., 1997)

An algorithm for finding tandem repeats of unspecified pattern size. - Gary Benson (RECOMB, 1998)

Optimal Parallel Two Dimensional Text Searching on a CREW PRAM. - Amihood Amir; Gary Benson; Martin Farach (Inf. Comput., 1998)

On the Distribution of K-tuple Matches for Sequence Homology: A Constant Time Exact Calculation of the Variance. - Gary Benson; X. Su (J. Comput. Biol., 1998)

Two-Dimensional Periodicity in Rectangular Arrays. - Amihood Amir; Gary Benson (SIAM J. Comput., 1998)

Reconstructing the Duplication History of a Tandem Repeat. - Gary Benson; Lan Dong (ISMB, 1999)

A new distance measure for comparing sequence profiles based on path lengths along an entropy surface. - Gary Benson (ECCB, 2002)

Composition Alignment. - Gary Benson (WABI, 2003)

Tandem cyclic alignment. - Gary Benson (Discret. Appl. Math., 2005)

Discovering Frequent Poly-Regions in DNA Sequences. - Panagiotis Papapetrou; Gary Benson; George Kollios (ICDM Workshops, 2006)

Indel seeds for homology search. - Denise Y. F. Mak; Yevgeniy Gelfand; Gary Benson (ISMB (Supplement of Bioinformatics), 2006)

All Hits All The Time: Parameter Free Calculation of Seed Sensitivity. - Denise Y. F. Mak; Gary Benson (APBC, 2007)

Tandem repeats over the edit distance. - Dina Sokol; Gary Benson; Justin Tojeira (Bioinform., 2007)

Oligonucleotide fingerprint identification for microarray-based pathogen diagnostic assays. - Waibhav Tembe; Nela Zavaljevski; Elizabeth A. Bode; Catherine Chase; Jeanne Geyer; Leonard P. Wasieloski; Gary Benson; Jaques Reifman (Bioinform., 2007)

3'-UTR SIRF: A database for identifying clusters of short interspersed repeats in 3' untranslated regions. - Benjamin B. Andken; In Lim; Gary Benson; John J. Vincent; Matthew T. Ferenc; Bianca Heinrich; Larissa A. Jarzylo; Heng-Ye Man; James O. Deshler (BMC Bioinform., 2007)

TRDB - The Tandem Repeats Database. - Yevgeniy Gelfand; Alfredo Rodriguez; Gary Benson (Nucleic Acids Res., 2007)

Evolutionary History of Mammalian Transposons Determined by Genome-Wide Defragmentation. - Joti Giordano; Yongchao Ge; Yevgeniy Gelfand; György Abrusán; Gary Benson; Peter E. Warburton (PLoS Comput. Biol., 2007)

Exact Distribution of a Spaced Seed Statistic for DNA Homology Detection. - Gary Benson; Denise Y. F. Mak (SPIRE, 2008)

Editorial. - Gary Benson (Nucleic Acids Res., 2008)

Consensus RNA Secondary Structure Prediction by Ranking k-Length Stems. - Denise Y. F. Mak; Gary Benson (BIOCOMP, 2009)

All hits all the time: parameter-free calculation of spaced seed sensitivity. - Denise Y. F. Mak; Gary Benson (Bioinform., 2009)

Pattern matching with address errors: Rearrangement distances. - Amihood Amir; Yonatan Aumann; Gary Benson; Avivit Levy; Ohad Lipsky; Ely Porat; Steven Skiena; Uzi Vishne (J. Comput. Syst. Sci., 2009)

Nucleic Acids Research annual Web Server Issue in 2009. - Gary Benson (Nucleic Acids Res., 2009)

Mining poly-regions in DNA. - Panagiotis Papapetrou; Gary Benson; George Kollios (Int. J. Data Min. Bioinform., 2012)

A Bit-Parallel, General Integer-Scoring Sequence Alignment Algorithm. - Gary Benson; Yözen Hernández; Joshua Loving (CPM, 2013)

Longest Common Subsequence in k Length Substrings. - Gary Benson; Avivit Levy; B. Riva Shalom (SISAP, 2013)

BitPAl: a bit-parallel, general integer-scoring sequence alignment algorithm. - Joshua Loving; Yözen Hernández; Gary Benson (Bioinform., 2014)

Clinical PathoScope: rapid alignment and filtration for accurate pathogen identification in clinical samples using unassembled sequencing data. - Allyson L. Byrd; Joseph F. Perez-Rogers; Solaiappan Manimaran; Eduardo Castro-Nallar; Ian Toma; Tim McCaffrey; Marc Siegel; Gary Benson; Keith A. Crandall; William Johnson (BMC Bioinform., 2014)

Editorial: Nucleic Acids Research annual Web Server Issue in 2014. - Gary Benson (Nucleic Acids Res., 2014)

Editorial: Nucleic Acids Research annual Web Server Issue in 2015. - Gary Benson (Nucleic Acids Res., 2015)

Editorial: Nucleic Acids Research annual Web Server Issue in 2016. - Gary Benson (Nucleic Acids Res., 2016)

Special issue in honor of the 60th birthday of Amihood Amir. - Gary Benson; Martin Farach-Colton; Moshe Lewenstein; Ely Porat (Theor. Comput. Sci., 2016)

LCSk: A refined similarity measure. - Gary Benson; Avivit Levy; S. Maimoni; D. Noifeld; B. Riva Shalom (Theor. Comput. Sci., 2016)

An SIMD Algorithm for Wraparound Tandem Alignment. - Joshua Loving; John P. Scaduto; Gary Benson (ISBRA, 2017)