Butte Lab Researchers Present at Biocomputing Symposium

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by Shauna Kanel

Two researchers from the Butte lab were invited to present their papers at the 2008 Pacific Symposium on Biocomputing, which was held Jan. 4-8 in Hawaii.

Bioinformatics programmer Joel Dudley and graduate student David Chen had their papers accepted to different sessions in the symposium. It is rare for two researchers from the same lab to be asked to present papers at this conference.

Dudley’s paper, presented in a session on translating biology, focused on automatically text mining the free-text description of experiments in the NCBI Gene Expression Omnibus for human disease-related experiments measuring both disease and “normal control” states.

Using automated text mining that employs Natural Language Processing, Dudley was able to identify a significant number of experiments with data from both states, representing diseases accounting for 30% of all human disease-related mortality in the United States.

“This work demonstrates that we now have the necessary tools and methods to initiate large-scale translational bioinformatics inquiry across the broad spectrum of high-impact human disease,” Dudley says.

These techniques will give translational bioinformaticians the tools to amass electronic clinical data and gene measurements with which they can analyze human disease research. This will reveal targets for novel therapeutics and diagnostic tools.

The next step will be to develop a means by which experiments without free-text annotation can be automatically evaluated.

Chen’s paper was presented in a session co-chaired by his principal investigator Atul Butte, and so was chosen by a sub-committee to ensure fair review. It represents part of his graduate research which aims to link clinical phenotypes to discover genes related to certain human diseases. He is a student in Stanford’s Biomedical Informatics Training program.

In order to prove this concept, Chen looked at electronic medical record data of patients from age 0-17 with certain diseases to find gene expression measurements that would highlight genes involved with human maturation and aging.

In looking at more than 5,000 genes, Chen found several biomarker candidates for aging, confirming several genes previously believed to be involved in aging. He also discovered that absolute lymphocyte count is a significant marker of maturation, and speculates that the rate of absolute lymphocyte change is representative of disease-specific rates of aging.

Chen hopes to expand the study to include a wider age range and larger electronic data set to find candidate genes linked to human disease.

Dudley’s paper can be found here: Integrative Genomic Analysis through Text Mining
Chen’s paper can be found here: Genetic Markers of Maturation
Pacific Symposium on Biocomputing

last updated: 4 February, 2008