Hi, I'm Matthew Eavenson. I recently defended my dissertation successfully under the advisement of Professor Krys Kochut. My research interests include the Semantic Web, Information Management, Data Visualization and Analysis, Information Integration, Databases, Bioinformatics, Data Mining, Web Applications, Knowledge Representation, and Information Retrieval. I have worked with the fine folks at the National Center for Biomedical Glycomics over the past few years developing visualization and curation tools for biomolecular pathways.
A major challenge of modern biological science is to analyze and interpret the huge amount of data that is routinely collected by high-throughput techniques, as in proteomics or glycomics analysis. Due to the complexity of biological systems, it is not sufficient to simply facilitate access to raw data; it is necessary to present such data in the context of what is known about the biological system being studied. One approach to address this requirement is to present experiment data (such as proteomics or transcriptomics data) in the context of a metabolic or signaling pathway in a process called "data overlaying". In the domain of glycobiology (the study of complex carbohydrates and their functional roles in living organisms), such a contextual illustration of data is complicated by the fact that the pathways involved in glycan biosynthesis are extremely complex.
GlycoBrowser is currently an early prototype, but should be available shortly after GlycoVault is finished.
Deciding whether glycans (compound sugar molecules) are structurally valid is a tedious, labor-intensive process. Utilizing a structure-matching algorithm guided by a canonical tree composed of a superset of biologically valid structures, the process of verifying the biosynthetic correctness of glycans can become considerably easier and less error-prone. Qrator is an application that uses a combination of external references, user annotations, and canonical trees to assist biologists in making informed decisions while curating glycans. Verification is a two-stage process, as a glycan is first reviewed when matched against a canonical tree, and then re-reviewed when a curator makes a final determination of whether a structure is correct. We hope this application will help to prevent human error in the curation process.
Qrator is currently available to the glycobiology community at Google Code.
Glycan biosynthesis is the process by which glycans are built inside cells. Information about this process is available from several Web accessible databases, published papers, and experimental data produced by glycobiologists. The principal purpose of GlycoVault is to support the research of glycobiologists in collecting and analyzing data about glycans, such as the changes in their abundance level over a cell's life cycle, as well as their correlation with gene expression levels for proteins that serve as enzymes in the biosynthetic process. Experiment protocols and other information related to the data collection process is also managed.
GlycoVault is currently still in development.
- Matthew Eavenson, Maciej Janik, Shravya Nimmagadda, John A. Miller, Krys J. Kochut, and William S. York. GlycoBrowser: A Tool for Contextual Visualization of Biological Data and Pathways Using Ontologies, In Fourth International Symposium on Bioinformatics Research and Applications (ISBRA), pp. 305-316. Springer Berlin Heidelberg, 2008.
- Shravya Nimmagadda, Amrita Basu, Matthew Eavenson, Jun Han, Maciej Janik, Rajesh Narra, Kishore Nimmagadda, Arpan Sharma, Krys J. Kochut, John A. Miller, and William S. York GlycoVault: A Bioinformatics Infrastructure for Glycan Pathway Visualization, Analysis and Modeling, In Fifth International Conference on Information Technology: New Generations (ITNG), pp. 692-697. IEEE, 2008.
- Boanerges Aleman-Meza, Phillip Burns, Matthew Eavenson, Devanand Palaniswami, and Amit Sheth. An Ontological Approach to the Document Access Problem of Insider Threat, In IEEE Intl. Conference on Intelligence and Security Informatics (ISI), pp. 486-491. Springer Berlin Heidelberg, 2005.
- Matthew Eavenson, Krys J. Kochut, John A. Miller, René Ranzinger, Michael Tiemeyer, Kazuhiro Aoki, and William S. York, Qrator: A Web-based Curation Tool for Glycan Structures, Glycobiology 25, no. 1 (2015): 66-73.
- Boanerges Aleman-Meza, Amit Sheth, Devanand Palaniswami, Matthew Eavenson, and I. Budak Arpinar. Semantic analytics in intelligence: Applying semantic association discovery to determine relevance of heterogeneous documents, In Advanced Topics in Database Research, pp. 401-419. Idea Group Publishing, 2006.