Faculty Profiles

Gary Benson

Gary Benson

Associate Professor of Biology and Computer Science Program in Bioinformatics

PhD, University of Maryland, 1992
Areas of Interest: algorithm development for DNA sequence analysis
(617) 358-2965

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

  • Benson G, Hernandez Y, Loving J (2013) A Bit-Parallel, General Integer-Scoring Sequence Alignment Algorithm. 24th Annual Symposium on Combinatorial Pattern Matching (CPM- 2013), Lecture Notes in Computer Science, 7922:50-61, Bad Herrenalb, Germany (doi: 10.1007/978-3-642-38905-4 7).
  • Visca P, DArezzo S, Ramisse F, Gelfand Y, Benson G, Vergnaud G, Fry N, Pourcel C (2011) Investigation of the population structure of Legionella pneumophila by analysis of tandem repeat copy number and internal sequence variation, Microbiology, 157:2582-94 (doi:10.1099/mic.0.047258-0; PMID:21622529).
  • Mak DY, Benson G (2009) All Hits All The Time: Parameter Free Calculation of Spaced Seed Sensitivity, Bioinformatics, 25(3):302-308 (doi:10.1093/bioinformatics/btn643; PMID:19095701).
  • Benson G, Mak DY (2008) Exact Distribution of a Spaced Seed Statistic for DNA Homology Detection, Proceedings of the 15th String Processing and Information Retrieval Symposium (SPIRE 2008), Melbourne, Australia, November 2008.
  • 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.
  • Mak D, Gelfand Y, Benson G (2006) Indel seeds for homology search. Bioinformatics 22, E341-E349.