Michael Berry

Professor

UT

Research

Professor Berry is the co-author and editor of two recent books published by SIAM (Society for Industrial and Applied Mathematics): "Understanding Search Engines: Mathematical Modeling and Text Retrieval, Second Edition" and "Computational Information Retrieval". A third edited volume entitled "A Survey of Text Mining" was published by Springer-Verlag in August of 2003. He has published over 75 refereed journal and conference publications.

He has organized numerous workshops on Text Mining and was Conference Co-Chair of the 2003 SIAM Third International Conference on Data Mining (May 1-3) in San Francisco, CA. He was also Program Co-Chair of the 2004 Co-Chair of the 2003 SIAM Fourth International Conference on Data Mining (April 22-24) in Orlando, FL. He is a member of SIAM, ACM, and the IEEE Computer Society and is on the editorial board of "Computing in Science and Engineering" and the "SIAM Journal of Scientific Computing".

Description of Research

His research interests include parallel and scientific computing, information retrieval, text mining, bioinformatics, and computational science. Current projects in bioinformatics include the Semantic Gene Organizer (SGO) in collaboration with Prof. Ramin Homayouni in the Department of Radiology, UT Health Sciences Center (Memphis), and computational approaches to whole genome phylogeny with Prof. Gary Stuart, Department of Life Sciences, Indiana State University. Professor Berry is currently supported by grants and contracts from the National Science Foundation, US Departments of Energy and Defense, and the National Institutes of Health.

Education

• PhD: Computer Science, University of Illinois at Urbana-Champaign
• MS: Applied Mathematics, North Carolina State University
• BS: Mathematics, University of Georgia

Publications

Classification of T Cell Movement Tracks Allows for Prediction of Cell Function , R.K. Kelemen, G.F. He, H.L. Woo, T. Lane, C. Rempe, J. Wang, I.A. Cockburn, R. Amino, V.V. Ganusov, and M.W. Berry, Int. J. Comput. Bio. and Drug Design 7(2-3):113-129, 2014.

PolyLens: Software for Map-based Visualization and Analysis of Genome-scale Polymorphism Data, G.W. Stuart, T. Gao, R. Pathan, and M.W. Berry, Int. J. Comput. Bio. and Drug Design 6(1):93-106, 2013. [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.

Text Mining: Applications and Theory, Michael W. Berry and Jacob Kogan (Eds.), Wiley, Chichester, UK, (2010), ISBN: 978-0-470-74982-1.

"Gene Set Cohesion Analysis Using Information in Medline Abstracts," L. Xu, N. Furlotte, E.O. George, K. Heinrich, M.W. Berry, and R. Homayouni, submitted to Genome Research, 2010.

Survey of Text Mining II: Clustering, Classification, and Retrieval, M.W. Berry and M. Castellanos (Eds.), Springer-Verlag, London, pp. 240, 2008, ISBN 978-1-84800-045-2.

"Gene Tree Labeling Using Nonnegative Matrix Factorization on Biomedical Literature," Kevin E. Heinrich, Michael W. Berry,and Ramin Homayouni, Journal of Computational Intelligence and Neuroscience 2008, Article ID  276535, 12 pp., 2008.

"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.

"Using a Literature-based NMF Model for Discovering Gene Functional Relationships," Elina Tjioe, Michael Berry, and Ramin 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.