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Journal Papers

     

Investigation of the Legionella pneumophila population structure by analysis of tandem repeat copy number and internal sequence variation, P. Visca, S. DArezzo, F. Ramisse, Y. Gelfand, G. Benson, G. Vergnaud, N. Fry, and C. Pourcel, Microbiology, in press, 2011. PMID: 21622529.

Mining Poly-regions in DNA, P. Papapetrou, G. Benson, G. Kollios, International Journal of Data Mining and Bioinformatics, in press, 2011.

Targeted analysis of glycomics liquid chromatography/mass spectrometry data, J. Dreyfus, C. Jacobs, Y. Gindin, G. Benson, G. O. Staples and J. Zaia, Analytical and Bioanalytical Chemistry, 399(2):727-35, 2011. doi: 10.1007/s00216-010-4235-1; PMID: 20953780.

The distribution of inverted repeat sequences in the Saccharomyces cerevisiae genome, E. M. Straw- bridge, G. Benson, Y. Gelfand, and C. J. Benham, Curr Genet. 56(4):321-40, 2010. doi: 10.1007/s00294-010-0302-6; PMID: 20446088. PMCID: PMC2908449.

Mutations in the Hepatitis C Virus Core Gene Are Associated with Advanced Liver Disease and Hepatocellular Carcinoma, S. Fishman, S. Factor, C. Balestrieri, X. Fan, A. DiBisceglie, S. Desai, G. Benson, and A. Branch, Clinical Cancer Research, 15:3205-3213, 2009. doi: 10.1158/1078-0432.CCR-08-2418; PMID: 19383824.

All Hits All The Time: Parameter Free Calculation of Spaced Seed Sensitivity, D.Y.F. Mak and G. Benson, Bioinformatics, 25(3):302-308, 2009. doi: 10.1093/bioinformatics/btn643; PMID: 19095701.

Pattern matching with address errors: Rearrangement distances,” A. Amir, Y. Aumann, G. Benson, A. Levy, O. Lipsky, E. Porat, S. Skiena and U. Vishne, J. Comput. Syst. Sci., J. Comput. Syst. Sci., 75(6): 359-370, 2009. doi: 10.1016/j.jcss.2009.03.001;

3'-UTR SIRF: A Database for Identifying Clusters of Short Interspersed Repeats in 3' Untranslated Regions, B. Kennedy, I. Lim, G. Benson, J. Vincent, M. Ferenc, B. Heinrich, L. Jarzylo, H.-Y. Man, and J. Deshler, BMC Bioinformatics, 8:274, 2007. doi:10.1186/1471-2105-8-274; PMID: 17663765; PMCID: PMC1973087.

Evolutionary History of Mammalian Transposons Determined by Genome-wide Defragmentation, J. Giordano, Y. Ge, Y. Gelfand, G. Benson, and P. Warburton, PLOS Computational Biology, 3(7):e137, 2007. doi:10.1371/journal.pcbi.0030137; PMID:17630829; PMCID:PMC1914374.

Elevated Basal Slippage Mutation Rates among the Canidae, J. Laidlaw, Y. Gelfand, K.-W. Ng, H. Garner, R. Ranganathan, G. Benson, and J. Fondon, III , Journal of Heredity, 98(5):452-460, 2007. doi:10.1093/jhered/esm017; PMID:17437958.

TRDB -- The Tandem Repeats Database, Y. Gelfand, A. Rodriguez and G. Benson, Nucleic Acids Research, 2006, 35(Database issue):D80-87, 2006. doi:10.1093/nar/gkl1013; PMID:17175540; PMCID:PMC1781109.

Oligonucleotide Fingerprint Identification for Microarray-Based Pathogen Diagnostic Assays, Tembe, N. Zavaljevski, E. Bode, C. Chase, J. Geyer, L. Wasieloski, G. Benson and J. Reifman, Bioinformatics, 23(1):5-13, 2007. doi:10.1093/bioinformatics/btl549. PMID:17068088;

Tandem Cyclic Alignment, G. Benson, Discrete Applied Mathematics, 146:124-133, 2006. doi:10.1016/j.dam.2004.04.009.

Inverted Repeat Structure of the Human Genome: The X-Chromosome Contains a Preponderance of Large, Highly Homologous Inverted Repeats That Contain Testes Genes, P. E. Warburton, J. Giordano, F. Cheung, Y. Gelfand and G. Benson, Genome Research, 14:1861-1869, 2004. doi:10.1101/gr.2542904; PMID:15466286; PMCID:PMC524409.

Minimal Entropy Probability Paths Between Genome Families, C. Ahlbrandt and G. Benson and W. Casey, Journal of Mathematical Biology, 48(5):563-590, 2004. doi:10.1007/s00285-003-0248-0; PMID:15133624.

Predicting Human Minisatellite Polymorphism, F. Denoeud, G. Vergnaud and G. Benson. , Genome Research, 13(5):856-867, 2000. doi:10.1101/gr.574403; PMID:12695323; PMCID:PMC430879.

Replication and compartmentalization of HIV-1 in kidney epithelium of patients with HIV-associated nephropathyauthor={D. Marras, L. Bruggeman, F. Gao, N. Tanji, M. Mansukhani, A. Cara, M. Ross, G. Gusella, G. Benson, V. D'Agati, B. Hahn, M. Klotman, and P. Klotman, Nature Medicine, 8(5):522-526, 2002. doi:10.1038/nm0502-522; PMID:11984599

Mutation Master: Profiles of Substitutions in Hepatitis C Virus RNA of the Core, Alternate Reading Frame and NS2 Coding Regions, J. Walewski, J. Gutierrez, W. Branch-Elliman, D. Stump, T. Keller, A. Rodriguez, G. Benson, and A. Branch., RNA, 8:557-571, 2002. doi:10+1017+S1355838202029023; PMID:12022223; PMCID:PMC1370277.

A Tandem Repeats Database for Bacterial Genomes: Application to the Genotyping of Yersinia pestis and Bacillus anthracis, P. Le Fleche, Y. Hauck, L. Onteniente, A. Prieur, F. Denoeud, V. Ramisse, P. Sylvestre, G. Benson, F. Ramisse, G. Vergnaud. BioMed Central Microbiology 1:2-15, 2001. PMID:11299044; PMCID:PMC31411.

Tandem repeats finder -- a program to analyze DNA sequences, G. Benson, Nucleic Acids Research 27:573-580, 1999. PMID:9862982; PMCID:PMC148217.

On the distribution of k-tuple matches for sequence homology: a constant time-exact calculation of the variance, G. Benson and X. Su. J. Comp. Biol., 5:87-100, 1998. PMID:9541873.

Two-dimensional periodicity in rectangular arrays, A. Amir and G. Benson, Siam J. of Computing, 27:90-106, 1998. doi:10.1137/S0097539795298321.

Optimal parallel two dimensional text searching on a CREW PRAM, A. Amir, G. Benson, and M. Farach-Colton, Information and Computation, 144:1-17, 1998. doi:10.1006/inco.1998.2705.

Sequence alignment with tandem duplication, G. Benson, J. Comp. Biol., 4:351-367, 1997. PMID:9278065.

Pooling strategies for establishing physical genome maps using FISH, Sun, F., G. Benson, N. Arnheim, and M. Waterman, J. Comp. Biol., 4(4):467-86, 1997. PMID:9385540.

Optimal two-dimensional compressed matching, A. Amir, G. Benson, and M. Farach-Colton, J. of Algorithms, 24:354-379, 1997.

Let sleeping files lie: Pattern matching in Z-compressed files, Amir, A., G . Benson, and M.. Farach, J. Computer and Systems Sciences, 52:299-307, 1996.

A space-efficient algorithm for finding best scoring non-overlapping alignments, G. Benson, Theoretical Computer Science, 145:357-369, 1995.

A method for fast database search for all k-nucleotide repeats, G. Benson and M. Waterman, Nucleic Acids Research, 22:4828-4836, 1994. PMID:7984436; PMCID:PMC308537.

An alphabet independent approach to two dimensional matching, A. Amir, G. Benson, and M. Farach, SIAM J. Computing, 23:313-323, 1994.

Conference Papers

     

A Bit-Parallel, General Integer-Scoring Sequence Alignment Algorithm, G. Benson, Y. Hernandez and J. Loving.

Consensus RNA Secondary Structure Prediction by Ranking k-Length Stems, D.Y.F. Mak and G. Benson, Proceedings of the 2009 International Conference on Bioinformatics and Computational Biology (BIOCOMP'09), Las Vegas, Nevada, July 2009.

Exact Distribution of a Spaced Seed Statistic for DNA Homology Detection, G. Benson and D.Y.F. Mak, Proceedings of the 15th String Processing and Information Retrieval Symposium (SPIRE 2008), Melbourne, Australia, November 2008.

Exact Distribution of a Spaced Seed Statistic for applications in DNA Repeat Detection, G. Benson and D.Y.F. Mak, Proceedings of the 2008 International Workshop on Applied Probability {(IWAP 2008), Compiè gne, France, July 2008.

All hits all the time: parameter free calculation of seed sensitivity D. Y. F. Mak and G. Benson, Proceedings of the Fifth Asia-Pacific Bioinformatics Conference (APBC 2007), pp. 327-340, Hong Kong, China, January 2007.

Tandem Repeats over the Edit Distance, D. Sokol, G. Benson, and J. Tojeira, Proceedings of the 5th European Conference on Computational Biology (ECCB 2006), Eilat, Israel, Bioinformatics 23(2):e30-e35, 2007. doi:10.1093/bioinformatics/btl309.

Discovering Frequent Poly-Regions in DNA Sequences, P. Papapetrou, G. Kollios, and G. Benson, Proceedings of the IEEE ICDM 2006 Workshop on Data Mining in Bioinformatics (DMB 2006), pp. 94-98, Hong Kong, China, 2006. doi:10.1109/ICDMW.2006.63

Indel seeds for homology search, D. Mak, Y. Gelfand and G. Benson, Proceedings of the 14th annual International Conference on Intelligent Systems for Molecular Biology (ISMB 2006), Fortaleza, Brazil, Bioinformatics Jul. 15; 22(14):e341-9, 2006. doi:10.1093/bioinformatics/btl263; PMID:16873491.

Pattern Matching with Address Errors: Rearrangement Distances, A. Amir, Y. Aumann, G. Benson, A. Levy, O. Lipsky, E. Porat, S. Skiena, and U. Vishna, Proceedings of the 17th Annual ACM-SIAM Symposium on Discrete Algorithms (SODA 2006), pp 1221-1226, 2006. doi.acm.org/10.1145/1109557.1109692.

Evaluating distance functions for clustering tandem repeats, S. Rao, A. Rodriguez and G. Benson, Proceedings of the 5th International Workshop on Bioinformatics and Systems Biology, Berlin, Germany, August 2005.

Composition Alignment, G. Benson, Proceedings of the Workshop on Algorithms in Bioinformatics Budapest, Hungary, Lecture Notes in Bioinformatics 2812:447-461, September 2003.

A new distance measure for comparing sequence profiles based on path lengths along an entropy surface, G. Benson, Proceedings of the European Conference on Computational Biology (ECCB 2002), Saarbrucken, Germany, Bioinformatics, 18(Supplement 2):S44-S52, October 2002. PMID:12385982.

Tandem cyclic alignment, G. Benson, Proceedings, 12th Annual Symposium on Combinatorial Pattern Matching (CPM 2001), Jerusalem, Israel, Lecture Notes in Computer Science, 2089:118-130, July 2001.

Reconstructing the Duplication History of a Tandem Repeat, G. Benson and L. Dong, Proceedings of the Seventh International Conference on Intelligent Systems for Molecular Biology (ISMB-99), 44-53, 1999.

An algorithm for finding tandem repeats of unspecified pattern size, G. Benson, Proceedings of the Second International Conference on Computational Molecular Biology, RECOMB 98, pp. 20-29, 1998.

Sequence Alignment with Tandem Duplication, G. Benson, Proceedings of the First Annual International Conference on Computational Molecular Biology, RECOMB 97, Santa Fe, New Mexico, January 1997.

 

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New Vntrseek 1.05 version is now available for download.
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  Page last updated:11/29/12