Gary Benson

Gary Benson, Yozen Hernandez, Joshua Loving: A Bit-Parallel, General Integer-Scoring Sequence Alignment Algorithm. CPM 2013: 50-61

Panagiotis Papapetrou, Gary Benson, George Kollios: Mining poly-regions in DNA. IJDMB 6(4): 406-428 (2012)

Gary Benson: Editorial. Nucleic Acids Research 40(Web-Server-Issue): 1-2 (2012)

Gary Benson: Editorial. Nucleic Acids Research 38(Web-Server-Issue): 1-2 (2010)

Denise Y. F. Mak, Gary Benson: All hits all the time: parameter-free calculation of spaced seed sensitivity. Bioinformatics 25(3): 302-308 (2009)

Amihood Amir, Yonatan Aumann, Gary Benson, Avivit Levy, Ohad Lipsky, Ely Porat, Steven Skiena, Uzi Vishne: Pattern matching with address errors: Rearrangement distances. J. Comput. Syst. Sci. 75(6): 359-370 (2009)

Gary Benson: Nucleic Acids Research annual Web Server Issue in 2009. Nucleic Acids Research 37(Web-Server-Issue): 1-2 (2009)

Denise Y. F. Mak, Gary Benson: Consensus RNA Secondary Structure Prediction by Ranking k-Length Stems. BIOCOMP 2009: 521-527

Gary Benson: Editorial. Nucleic Acids Research 36(Web-Server-Issue): 1 (2008)

Gary Benson, Denise Y. F. Mak: Exact Distribution of a Spaced Seed Statistic for DNA Homology Detection. SPIRE 2008: 282-293

Waibhav Tembe, Nela Zavaljevski, Elizabeth A. Bode, Catherine Chase, Jeanne Geyer, Leonard P. Wasieloski, Gary Benson, Jaques Reifman: Oligonucleotide fingerprint identification for microarray-based pathogen diagnostic assays. Bioinformatics 23(1): 5-13 (2007)

Dina Sokol, Gary Benson, Justin Tojeira: Tandem repeats over the edit distance. Bioinformatics 23(2): 30-35 (2007)

Benjamin B. Andken, In Lim, Gary Benson, John J. Vincent, Matthew T. Ferenc, Bianca Heinrich, Larissa A. Jarzylo, Heng-Ye Man, James O. Deshler: 3'-UTR SIRF: A database for identifying clusters of short interspersed repeats in 3' untranslated regions. BMC Bioinformatics 8 (2007)

Yevgeniy Gelfand, Alfredo Rodriguez, Gary Benson: TRDB - The Tandem Repeats Database. Nucleic Acids Research 35(Database-Issue): 80-87 (2007)

Gary Benson: Editorial. Nucleic Acids Research 35(Web-Server-Issue): 1 (2007)

Joti Giordano, Yongchao Ge, Yevgeniy Gelfand, György Abrusán, Gary Benson, Peter E. Warburton: Evolutionary History of Mammalian Transposons Determined by Genome-Wide Defragmentation. PLoS Computational Biology 3(7) (2007)

Denise Y. F. Mak, Gary Benson: All Hits All The Time: Parameter Free Calculation of Seed Sensitivity. APBC 2007: 327-340

Panagiotis Papapetrou, Gary Benson, George Kollios: Discovering Frequent Poly-Regions in DNA Sequences. ICDM Workshops 2006: 94-98

Denise Y. F. Mak, Yevgeniy Gelfand, Gary Benson: Indel seeds for homology search. ISMB (Supplement of Bioinformatics) 2006: 341-349

Amihood Amir, Yonatan Aumann, Gary Benson, Avivit Levy, Ohad Lipsky, Ely Porat, Steven Skiena, Uzi Vishne: Pattern matching with address errors: rearrangement distances. SODA 2006: 1221-1229

Gary Benson: Tandem cyclic alignment. Discrete Applied Mathematics 146(2): 124-133 (2005)

Gary Benson: Composition Alignment. WABI 2003: 447-461

Gary Benson, Roderic D. M. Page (Eds.): Algorithms in Bioinformatics, Third International Workshop, WABI 2003, Budapest, Hungary, September 15-20, 2003, Proceedings. Lecture Notes in Computer Science 2812, Springer 2003, isbn 3-540-20076-2

Gary Benson: A new distance measure for comparing sequence profiles based on path lengths along an entropy surface. ECCB 2002: 44-53

Gary Benson: Tandem Cyclic Alignment. CPM 2001: 118-130

Gary Benson, Lan Dong: Reconstructing the Duplication History of a Tandem Repeat. ISMB 1999: 44-53

Amihood Amir, Gary Benson, Martin Farach: Optimal Parallel Two Dimensional Text Searching on a CREW PRAM. Inf. Comput. 144(1): 1-17 (1998)

Gary Benson, X. Su: On the Distribution of K-tuple Matches for Sequence Homology: A Constant Time Exact Calculation of the Variance. Journal of Computational Biology 5(1): 87-100 (1998)

Amihood Amir, Gary Benson: Two-Dimensional Periodicity in Rectangular Arrays. SIAM J. Comput. 27(1): 90-106 (1998)

Gary Benson: An algorithm for finding tandem repeats of unspecified pattern size. RECOMB 1998: 20-29

Amihood Amir, Gary Benson, Martin Farach: Optimal Two-Dimensional Compressed Matching. J. Algorithms 24(2): 354-379 (1997)

Gary Benson: Sequence Alignment with Tandem Duplication. Journal of Computational Biology 4(3): 351-367 (1997)

Fengzhu Sun, Gary Benson, Norman Arnheim, Michael S. Waterman: Pooling Strategies for Establishing Physical Genome Maps Using FISH. Journal of Computational Biology 4(4): 467-486 (1997)

Gary Benson: Sequence alignment with tandem duplication. RECOMB 1997: 27-36

Fengzhu Sun, Gary Benson, Norman Arnheim, Michael S. Waterman: Pooling strategies for establishing physical genome maps using FISH. RECOMB 1997: 294-299

Amihood Amir, Gary Benson, Martin Farach: Let Sleeping Files Lie: Pattern Matching in Z-Compressed Files. J. Comput. Syst. Sci. 52(2): 299-307 (1996)

Gary Benson: A Space Efficient Algorithm for Finding the Best Nonoverlapping Alignment Score. Theor. Comput. Sci. 145(1&2): 357-369 (1995)

Amihood Amir, Gary Benson, Martin Farach: An Alphabet Independent Approach to Two-Dimensional Pattern Matching. SIAM J. Comput. 23(2): 313-323 (1994)

Gary Benson: A Space Efficient Algorithm for Finding the Best Non-Overlapping Alignment Score. CPM 1994: 1-14

Amihood Amir, Gary Benson, Martin Farach: Optimal Two-Dimensional Compressed Matching. ICALP 1994: 215-226

Amihood Amir, Gary Benson, Martin Farach: Let Sleeping Files Lie: Pattern Matching in Z-compressed Files. SODA 1994: 705-714

Amihood Amir, Gary Benson, Martin Farach: Optimal Parallel Two Dimensional Pattern Matching. SPAA 1993: 79-85

Amihood Amir, Gary Benson: Efficient Two-Dimensional Compressed Matching. Data Compression Conference 1992: 279-288

Amihood Amir, Gary Benson: Two-Dimensional Periodicity and Its Applications. SODA 1992: 440-452

Amihood Amir, Gary Benson, Martin Farach: Alphabet Independent Two Dimensional Matching. STOC 1992: 59-68