Gary Benson

Publication Activity (10 Years)

Years Active: 1992-2017
Publications (10 Years): 5

Top Topics

Sequence Alignment

Top Venues

Nucleic Acids Res.

Theor. Comput. Sci.

Publications

Joshua Loving, John P. Scaduto, Gary Benson
An SIMD Algorithm for Wraparound Tandem Alignment. ISBRA (2017)
Gary Benson
Editorial: Nucleic Acids Research annual Web Server Issue in 2016. Nucleic Acids Res. 44 (Webserver-Issue) (2016)
Gary Benson, Martin Farach-Colton, Moshe Lewenstein, Ely Porat
Special issue in honor of the 60th birthday of Amihood Amir. Theor. Comput. Sci. 638 (2016)
Gary Benson, Avivit Levy, S. Maimoni, D. Noifeld, B. Riva Shalom
LCSk: A refined similarity measure. Theor. Comput. Sci. 638 (2016)
Gary Benson
Editorial: Nucleic Acids Research annual Web Server Issue in 2015. Nucleic Acids Res. 43 (Webserver-Issue) (2015)
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
Clinical PathoScope: rapid alignment and filtration for accurate pathogen identification in clinical samples using unassembled sequencing data. BMC Bioinform. 15 (2014)
Joshua Loving, Yözen Hernández, Gary Benson
BitPAl: a bit-parallel, general integer-scoring sequence alignment algorithm. Bioinform. 30 (22) (2014)
Gary Benson, Avivit Levy, B. Riva Shalom
Longest Common Subsequence in k-length substrings. CoRR (2014)
Gary Benson
annual Web Server Issue in 2014. Nucleic Acids Res. 42 (Webserver-Issue) (2014)
Gary Benson, Avivit Levy, B. Riva Shalom
Longest Common Subsequence in k Length Substrings. SISAP (2013)
Gary Benson
Editorial. Nucleic Acids Res. 41 (Webserver-Issue) (2013)
Gary Benson, Yözen Hernández, Joshua Loving
A Bit-Parallel, General Integer-Scoring Sequence Alignment Algorithm. CPM (2013)
Panagiotis Papapetrou, Gary Benson, George Kollios
Mining poly-regions in DNA. Int. J. Data Min. Bioinform. 6 (4) (2012)
Gary Benson
Editorial. Nucleic Acids Res. 40 (Web-Server-Issue) (2012)
Gary Benson
Editorial. Nucleic Acids Res. 38 (Web-Server-Issue) (2010)
Denise Y. F. Mak, Gary Benson
All hits all the time: parameter-free calculation of spaced seed sensitivity. Bioinform. 25 (3) (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) (2009)
Gary Benson
annual Web Server Issue in 2009. Nucleic Acids Res. 37 (Web-Server-Issue) (2009)
Denise Y. F. Mak, Gary Benson
Consensus RNA Secondary Structure Prediction by Ranking k-Length Stems. BIOCOMP (2009)
Gary Benson, Denise Y. F. Mak
Exact Distribution of a Spaced Seed Statistic for DNA Homology Detection. SPIRE (2008)
Gary Benson
Editorial. Nucleic Acids Res. 36 (Web-Server-Issue) (2008)
Joti Giordano, Yongchao Ge, Yevgeniy Gelfand, György Abrusán, Gary Benson, Peter E. Warburton
Evolutionary History of Mammalian Transposons Determined by Genome-Wide Defragmentation. PLoS Comput. Biol. 3 (7) (2007)
Gary Benson
Editorial. Nucleic Acids Res. 35 (Web-Server-Issue) (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 Bioinform. 8 (2007)
Yevgeniy Gelfand, Alfredo Rodriguez, Gary Benson
TRDB - The Tandem Repeats Database. Nucleic Acids Res. 35 (Database-Issue) (2007)
Dina Sokol, Gary Benson, Justin Tojeira
Tandem repeats over the edit distance. Bioinform. 23 (2) (2007)
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. Bioinform. 23 (1) (2007)
Denise Y. F. Mak, Gary Benson
All Hits All The Time: Parameter Free Calculation of Seed Sensitivity. APBC (2007)
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)
Denise Y. F. Mak, Yevgeniy Gelfand, Gary Benson
Indel seeds for homology search. ISMB (Supplement of Bioinformatics) (2006)
Panagiotis Papapetrou, Gary Benson, George Kollios
Discovering Frequent Poly-Regions in DNA Sequences. ICDM Workshops (2006)
Gary Benson
Tandem cyclic alignment. Discret. Appl. Math. 146 (2) (2005)
Gary Benson
Composition Alignment. WABI (2003)
Gary Benson
A new distance measure for comparing sequence profiles based on path lengths along an entropy surface. ECCB (2002)
Gary Benson
Tandem Cyclic Alignment. CPM (2001)
Gary Benson, Lan Dong
Reconstructing the Duplication History of a Tandem Repeat. ISMB (1999)
Gary Benson, X. Su
On the Distribution of K-tuple Matches for Sequence Homology: A Constant Time Exact Calculation of the Variance. J. Comput. Biol. 5 (1) (1998)
Gary Benson
An algorithm for finding tandem repeats of unspecified pattern size. RECOMB (1998)
Amihood Amir, Gary Benson
Two-Dimensional Periodicity in Rectangular Arrays. SIAM J. Comput. 27 (1) (1998)
Amihood Amir, Gary Benson, Martin Farach
Optimal Parallel Two Dimensional Text Searching on a CREW PRAM. Inf. Comput. 144 (1) (1998)
Gary Benson
Sequence Alignment with Tandem Duplication. J. Comput. Biol. 4 (3) (1997)
Gary Benson
Sequence alignment with tandem duplication. RECOMB (1997)
Fengzhu Sun, Gary Benson, Norman Arnheim, Michael S. Waterman
Pooling Strategies for Establishing Physical Genome Maps Using FISH. J. Comput. Biol. 4 (4) (1997)
Amihood Amir, Gary Benson, Martin Farach
Optimal Two-Dimensional Compressed Matching. J. Algorithms 24 (2) (1997)
Fengzhu Sun, Gary Benson, Norman Arnheim, Michael S. Waterman
Pooling strategies for establishing physical genome maps using FISH. RECOMB (1997)
Amihood Amir, Gary Benson, Martin Farach
Let Sleeping Files Lie: Pattern Matching in Z-Compressed Files. J. Comput. Syst. Sci. 52 (2) (1996)
Gary Benson
A Space Efficient Algorithm for Finding the Best Nonoverlapping Alignment Score. Theor. Comput. Sci. 145 (1&2) (1995)
Amihood Amir, Gary Benson, Martin Farach
An Alphabet Independent Approach to Two-Dimensional Pattern Matching. SIAM J. Comput. 23 (2) (1994)
Amihood Amir, Gary Benson, Martin Farach
Optimal Two-Dimensional Compressed Matching. ICALP (1994)
Amihood Amir, Gary Benson, Martin Farach
Let Sleeping Files Lie: Pattern Matching in Z-compressed Files. SODA (1994)
Gary Benson
A Space Efficient Algorithm for Finding the Best Non-Overlapping Alignment Score. CPM (1994)
Amihood Amir, Gary Benson, Martin Farach
Optimal Parallel Two Dimensional Pattern Matching. SPAA (1993)
Amihood Amir, Gary Benson, Martin Farach
Alphabet Independent Two Dimensional Matching STOC (1992)
Amihood Amir, Gary Benson
Two-Dimensional Periodicity and Its Applications. SODA (1992)
Amihood Amir, Gary Benson
Efficient Two-Dimensional Compressed Matching. Data Compression Conference (1992)