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 B. Kennedy, I. Lim, Gary Benson, J. Vincent, M. Ferenc, B. Heinrich, L.
Jarzylo, H.-Y. Man, and J. Deshler. 3'-UTR SIRF: A Database for Identifying Clusters of Short Interspersed Repeats in 3' Untranslated
Regions,, BMC Bioinformatics 2007, 8:274 doi:10.1186/1471-2105-8-274
J. Giordano, Y. Ge, Y. Gelfand, G. Benson, and P. Warburton. Evolutionary History of Mammalian Transposons Determined by Genome-wide Defragmentation, PLOS Computational
Biology, (doi:)
J. Laidlaw, Y. Gelfand, K.-W. Ng,
H. Garner, R. Ranganathan, G. Benson, and J. Fondon, III. Elevated Basal Slippage Mutation Rates among the Canidae, Journal of Heredity, (doi:10.1093/jhered/esm017), PLoS Comput Biol. 2007 July; 3(7): e137. doi: 10.1371/journal.pcbi.0030137
W.
Tembe, N. Zavaljevski, E. Bode, C. Chase, J. Geyer, L. Wasieloski, G. Benson and J.
Reifman. Oligonucleotide Fingerprint Identification for Microarray-Based Pathogen Diagnostic Assays, Bioinformatics 2007 23(1):5-13; doi:10.1093/bioinformatics/btl549.
D. Sokol, G. Benson, and J. Tojeira. Tandem Repeats over the Edit Distance, Proceedings of
the 5th European Conference on Computational Biology (ECCB 2006), Eilat, Israel,
Bioinformatics 23(2):e30-e35, 2007 (doi:10.1093/bioinformatics/btl309)
P. Papapetrou, G. Kollios, and
G. Benson. Discovering Frequent Poly-Regions in DNA Sequences, Proceedings of the IEEE ICDM 2006 Workshop on Data Mining
in Bioinformatics (DMB 2006), Hong Kong, China, pp 94-98, 2006.
(doi.ieeecomputersociety.org/10.1109/ICDMW.2006.63)
A. Amir, Y. Aumann, G. Benson,
A. Levy, O. Lipsky, E. Porat, S. Skiena, and U. Vishna. Pattern Matching with Address Errors: Rearrangement Distances, Proceedings of the 17th
Annual ACM-SIAM Symposium on Discrete Algorithms (SODA 2006), pp 1221-1226,
2006. (doi.acm.org/10.1145/1109557.1109692)
Denise Y.F. Mak, Gary Benson (2007) All hits all the time:
parameter free calculation of seed sensitivity, APBC 2007 conference in Hong Kong
Mak, D., Gelfand, Y., Benson, G. (2006) Indel seeds for homology search. Bioinformatics Jul. 15; 22(14):e341-9
Yevgeniy Gelfand, Alfredo Rodriguez and Gary Benson TRDB—The Tandem Repeats Database, Nucleic Acids Research, 2006, Vol. 00, Database issue D1-D8 doi:10.1093/nar/gkl1013 [Full Text]
Suyog Rao, Alfredo Rodriguez and G. Benson. Evaluating distance functions for clustering
tandem repeats
P. E. Warburton, J. Giordano, F. Cheung, Y. Gelfand and G. Benson. Inverted Repeat Structure of the Human Genome: The X-Chromosome Contains a Preponderance of Large, Highly Homologous Inverted Repeats That Contain Testes Genes , Genome Research, 14:1861-1869, 2004.
D. Ahlbrandt, G. Benson, W. Casey. Minimal Entropy Probability Paths Between Genome Families, Journal of Mathematical Biology, 48(5):563-90.
G. Benson. Composition Alignment, Proceedings of the Workshop on Algorithms in Bioinformatics 2003, Budapest, Hungary, September 2003.
F. Denoeud, G. Vergnaud and G. Benson. Predicting Human Minisatellite Polymorphism, Genome Research, 13(5):856-867, 2000.
G. Benson. A new distance measure for comparing sequence profiles based on path lengths along an entropy surface, Proceedings of the European Conference on Computational Biology 2002, Bioinformatics, 18: Supplement 2, S44-S52, 2002.
D. Marras, L. Bruggeman, N.
Tanji, M. Mansukhani, A. Cara, M. Ross, G. Benson, V. D'Agati, M.
Klotman, and P. Klotman. Evolution of HIV-1 quasispecies in kidney
epithelium in HIV-associated nephropathy, Nature Medicine, 8:522-526, 2002.
J. Walewski, J. Gutierrez, W. Branch-Elliman, D. Stump, T. Keller, A. Rodriguez,
G. Benson, and A. Branch. Mutation Master: Profiles of Substitutions
in Hepatitis C Virus RNA of the Core, Alternate Reading Frame and NS2
Coding Regions, RNA, 8:557-571, 2002.
G. Benson. Tandem Cyclic Alignment. Proceedings of the 12th Annual Symposium on Combinatorial Pattern
Matching (CPM 2001), LNCS, 2089:118-130,
2001.
P. Le Fleche, Y. Hauck, L. Onteniente, A. Prieur,
F. Denoeud, V. Ramisse, P. Sylvestre, G. Benson, F. Ramisse, G. Vergnaud. A Tandem Repeats Database for Bacterial Genomes: Application to the Genotyping of Yersinia pestis and
Bacillus anthracis. BioMed Central Microbiology 1:2-15,
2001.
G. Benson and L. Dong. Reconstructing the Duplication History of a Tandem Repeat.
Proceedings of the Seventh International Conference on Intelligent Systems for Molecular Biology
(ISMB-99), 44-53, 1999.
G. Benson. Tandem repeats finder -- a program to analyze DNA sequences. Nucleic Acids Research 27:573-580,
1999.
G. Benson. and X. Su. On the distribution of k-tuple matches for sequence homology: a constant time-exact
calculation of the variance. J. Comp. Biol., 5:87-100, 1998.
G. Benson. Sequence alignment with tandem duplication. J. Comp. Biol. 4:351-367, 1997.
G. Benson. A space-efficient algorithm for finding best scoring non-overlapping alignments. Theoretical Computer
Science 145:357-369, 1995.
G. Benson and M. Waterman. A method for fast database search for all k-nucleotide repeats. Nucleic Acids Research
22:4828-4836, 1994.
Sun, F., G. Benson, N. Arnheim, and M. Waterman. Pooling strategies for establishing physical genome maps using
FISH. J. Comp. Biol. 4(4):467-86, 1997.
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