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.
  
  
• Text Mining: Applications and Theory, M.W Berry and J. Kogan (Eds.), Wiley, West Sussex, 2010, ISBN: 978-0-470074982-1, 224p.
  
  
• High-Performance Scientific Computing, M.W. Berry, K.A. Gallivan, E. Gallopoulos, A. Grama, B. Philippe, Y. Saad, and F. Saied (Eds.) Springer, London, 2012, ISBN: 978-1-4471-2436-81, 346p.
  
  

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]
  
  
• Bioinformatic Analysis Reveals cRel as a Putative Regulator of a Subset of Interferon Stimulated Genes, L. Wei, L. Xu, K. Heinrich, M.W. Berry, R. Homayouni, and L.M. Pfeffer, Journal of Interferon & Cytokine Research 28(9):541-552, 2008. [DOI Link]
  
  
• Using a Literature-based NMF Model for Discovering Gene Functional Relationship, E. Tjioe, M.W. Berry, and R.Homayouni, Proceedings of the First Workshop on Data Mining in Functional Genomics, IEEE International Conference on Bioinformatics and Biomedicine, Philadelphia, PA, Nov. 3-5, (2008), pp. 185-192. [DOI Link]
  
  
• Discovering Gene Functional Relationships Using FAUN (Feature Annotation Using Nonnegative matrix factorization), Elina Tjioe, Michael W. Berry, and Ramin Homayouni, BMC Bioinformatics 2010 11(Suppl 6):S14. [DOI Link]
  
  
• Functional Cohesion of Gene Sets Determined by Latent Semantic Indexing of PubMed Abstracts, L. Xu, N. Furlotte, E.O. George, K. Heinrich, M.W. Berry, and R. Homayouni, PLoS ONE 6(4):e18851, 2011. [DOI Link]
  
  
• Latent Semantic Indexing of PubMed abstracts for identification of transcription factor candidates from microarray derived gene sets, S. Roy, K. Heinrich, V. Phan, M.W. Berry, and R. Homayouni, BMC Bioinformatics 12(Suppl 10):S19, 2011.