Boston University Department of Biology

Faculty Profiles

Current Research

Our research focuses on development of algorithms and software tools for the detection and analysis of novel patterns and repeats in DNA and RNA sequences. Our goal is to deliver tools that are effective, efficient, and easy to use. We have a number of ongoing collaborations. Please visit our research page for details on our most recent projects.

Courses Taught

• BE 768 Biological Database Systems
• BE 561 DNA and Protein Sequence Analysis
• CS 591 Pattern Matching and Pattern Detection Algorithms with Applications in Biological Sequence Analysis

Selected Publications

• Andken BB, Lim I, Benson G, Vincent JJ, Ferenc MT, Heinrich B, Jarzylo LA, Man HY, Deshler JO. (2007). 3 '-UTR SIRF: A database for identifying clusters of whort interspersed repeats in 3 ' untranslated regions. BMC Bioinformatics 8.
• Gelfand Y, Rodriguez A, Benson G. (2007). TRDB - The Tandem Repeats Database. Nucleic Acids Research 35, D80-D87.
• Giordano J, Ge YC, Gelfand Y, Abrusan G, Benson G, Warburton PE (2007). Evolutionary history of mammalian transposons determined by genome-wide defragmentation. PLoS Computational Biology 3, 1321-1334.
• Laidlaw J, Gelfand Y, Ng KW, Garner HR, Ranganathan R, Benson G, Fondon JW(2007). Elevated basal slippage mutation rates among the Canidae. Journal of Heredity 98, 452-460.
• Tembe W, Zavaljevski N, Bode E, Chase C, Geyer J, Wasieloski L, Benson G, Reifman J (2007). Oligonucleotide fingerprint identification for microarray-based pathogen diagnostic assays. Bioinformatics 23, 5-13.
• Mak D, Gelfand Y, Benson G (2006). Indel seeds for homology search. Bioinformatics 22, E341-E349.
• Benson G (2005). Tandem cyclic alignment. Discrete Applied Mathematics 146, 124-133.
• Warburton PE, Giordano J, Cheung F, Gelfand Y, Benson G (2004). 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.