Title: "Bibliomics, Literature Mining, and Biomarker Discovery"

Speaker: Matthew Palakal, Associate Dean for Research and Graduate Program in the School of Informatics and Professor of Computer Science in the School of Science at Indiana University Purdue University, Indianapolis

Place: HORT 117; September 29, 2009, Tuesday, 4:30pm


Bibliomics has an important role in Systems Biology research along with the other "omics" such as genomics, transcriptomics, proteomics, metabolomics, etc. Biological literature databases continue to grow rapidly with vital information that is important for conducting sound biomedical research. As data and information space continue to grow exponentially, the need for rapidly surveying the published literature, synthesizing, and discovering the embedded "knowledge" is becoming critical to allow the researchers to conduct "informed" work, avoid repetition, and generate new hypotheses. Knowledge, in this case, is defined as one-to-many and many-to-many relationships among biological entities such as gene, protein, drug, disease, etc. In this talk, we present a literature mining system called BioMAP. The BioMAP tool can carry out large-scale biomedical literature mining that could enhance the ability of biological researchers to formulate methods for the analysis of biological data such as identifying biological pathways and provide support for disease target and new biomarker discovery. Results from a large-scale literature mining on documents related to colon rectal cancer will be presented to illustrate that novel pathways and biomarkers can be found if exhaustive mining is used instead of relying on limited manually curated literature documents.

Associated Reading:

M. Palakal, T. Sebastian and D. L. Stocum. Discovering implicit protein-protein interactions in the Cell Cycle using bioinformatics approaches, Journal of Biomedical Science, 15(3): 317-331, 2008.

Click here for a full schedule of BIOINFORMATICS SEMINARS, past and present.