Publications -- Bioinformatics

Books:

• Templates for the Solution of Linear Systems: Building Blocks for Iterative Methods, SIAM Publication, Philadelphia, 1994, ISBN: 0-89871-328-5.
  
  
• Understanding Search Engines: Mathematical Modeling and Text Retrieval by M.W. Berry and M. Browne, SIAM Book Series: Software, Environments, and Tools, Second Edition (May 2005), ISBN: 0-89871-581-4.
  
  
• Computational Information Retrieval, Proceedings of CIR'00, SIAM Proceedings in Applied Mathematics, M. Berry (Ed.), SIAM, Philadelphia, 2001, ISBN: 0-89871-500-8, 185 p.
  
  
• Survey of Text Mining: Clustering, Classification, and Retrieval, M. Berry (Ed.), Springer-Verlag, New York, 2003, ISBN: 0-387-95563-1, 270 p.
  
  
• Lecture Notes in Data Mining, M.W. Berry and M. Browne (Eds.), World Scientific, Singapore, 2006, ISBN: 981-256-802-6, 230p; Scientia (Fall 2007)
  
  
• Survey of Text Mining II: Clustering, Classification, and Retrieval, M.W Berry and M. Castellanos (Eds.), Springer, London, 2008, ISBN: 978-1-84800-045-2, 240 p.
  
  

Recent publications:

Bioinformatics

• (PDF) -- A Comprehensive Whole Genome Bacterial Phylogeny Using Correlated Peptide Motifs Defined in a High Dimensional Vector Space, G.W. Stuart and M.W. Berry, J. of Bioinformatics and Computational Biology 1(3), 2003, pp. 475-493.
  
  
• (PDF) -- An SVD-based Comparison of Nine Whole Eukaryotic Genomes Supports a Coelomate rather than Ecdysozoan Lineage, G.W. Stuart and M.W. Berry, BMC Bioinformatics 5(204), 2004.
  
  
• (PDF) -- Gene Clustering by Latent Semantic Indexing of MEDLINE Abstracts, R. Homayouni, K. Heinrich, L. Wei, and M.W. Berry, Bioinformatics 21(1), 2005, pp. 104-115.
  
  
• (PDF) -- Gene Tree Labeling Using Nonnegative Matrix Factorization on Biomedical Literature, K.E. Heinrich, M.W. Berry, and R. Homayouni, Computational Intelligence and Neuroscience Vol. 2008, Article ID 276535, 2008, 12 pages. [DOI Link]