Current Research and Projects
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Indigene I am working with faculty and researchers in Indiana University's Biology and Informatics departments to develop new methods in combining many low-resolution data sources to create new genetic pathways. We are developing an information system that has provoked research in database management, effective data integration techniques, and visualization of massive network data. Link to research group's home page Link to a Poster that was Presented at the iConference in 2005 |
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Data Integration As an extension of the Indigene project, I research new and effective ways to integrate genomic and proteomic data to be more informative to biological researchers. The focus of my work is in Drosophila. The data sources that I am exploring include microarray, yeast-2-hybrid, genetic interaction, phenotypic annotation, and transcription factor binding sites. |
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Inauthentic Paper Detector This project is intended for detecting whether a technical document is human written and authentic or not. Predictions may work for documents intended for entertainment (novels, news articles etc.). The main purpose of this research is to detect whether a technical document conforms to the statistical standards of an expository text. You can easily take a human written technical document and add some nonsense text somewhere in the middle, or paste a document generated by an automatic paper generator. We are trying to detect new, machine written texts that are simply generated not to have any meaning, yet appear to have meaning on the surface. Check out the Website Paper accepted at SIAM Data Mining 2006 |
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CATPA I work as an adviser in helping to develop a Java based research tool for Molecular Biologists. The tool allows a user to input protein and DNA sequences, annotate, curate, manipulate, and statistically analyze these sequences. Link to CATPA Link to Tech Report |
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DGRC Research Associate I am a research associate for the Drosophila Genomics Resource Center (DGRC), which is with the Center for Genomics and Bioinformatics (CGB) at Indiana University. I am part of the group that manufactures, tests, and supplies microarrays to the Drosophila community. I work mainly on the computer side of things, which consists of data quality control and developing and writing applications for data maintenance and analysis. In the recent past, I was also involved in the fabrication of microarrays and have done RNA extraction and performed hybridization experiments. One project I completed at the DGRC was to re-annotate the entire Transcriptome microarray that the DGRC manufactures. You can read about it here. I also helped write a basic hybridization analysis application for R. You can read about that here. Link to the DGRC's website Link to the CGB's website |
Previous Research and Projects
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Master's Capstone Project (BioKnOT: Biological Knowledge through Ontologies and TFIDF): I worked on a web-based text retrieval system that would allow users to accumulate the most timely, meaning up- to-date, and most important, meaning relevance to one's search, articles within their search criteria. This would involve pulling journal articles off the web and then, based on term frequency and citation information, construct a hierarchical time based graph. From this graph, we can then find the most timely and relevant articles to the user's search. Link to BioKnOT paper |
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Daphnia PhyloBlast I advised two undergraduate Informatics capstone projects dealing with Daphnia Genomics. The first group developed a web service that will allow users to submit a ribosomal gene and the program will create a phylogenetic tree from known Daphnia species and the submitted sequence. The second group developed a new technique to detect Transposable elements in the Daphnia genome, along with a web interface to visualize the TEs locations on the genome. Link to the Daphnia Genomics Consortium website |
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