Designing and Enhancing Software: A Bioinformatician's Life
John C. Obenauer, Ph.D.
A Member Since October 2004
As a bioinformatician, John Obenauer is never happier than when he is thinking about new ways to analyze and characterize biological data. In fact, in his free time, he scans the Internet for open source software to see what programs he can use or modify to better perform his job. He claims that “using information contained within scientific databases to derive medically important conclusions” is one of the most rewarding aspects of his job.
Dr. Obenauer is an associate research scientist at St. Jude Children’s Research Hospital in Memphis, Tennessee. St. Jude is a research hospital dedicated to treating catastrophic childhood diseases, such as leukemia, infant brain tumors, AIDS, and sickle-cell anemia. As a member of the Hartwell Center for Bioinformatics and Biotechnology, he is responsible for assisting faculty members with their bioinformatics research needs and particularly enjoys using computational methods to solve biomedical problems.
He has taken a lead role in assembling data from public sources for the Center’s gene annotation database, HCNetDat. He has developed a program to convert liquid chromatography/mass spectrometry (LC/MS) data to a 2D graphical image for peak processing using standard graphics software. Other work includes identifying genes likely to be translationally regulated by microRNAs and examining promoter regions of differentially regulated genes for single nucleotide polymorphisms (SNPs) that may disrupt transcription factor binding sites.
Dr. Obenauer’s Ph.D. is in Biochemistry from Brandeis University (Waltham, MA). During graduate school, he studied structural features of electron transfer proteins by nuclear magnetic resonance (NMR). Specifically, he was interested in characterizing adrenodoxin (a human iron-sulfur protein), as well as its bacterial homologs putidaredoxin and terpredoxin, because these proteins activate cytochrome P450 enzymes that are important in drug metabolism and steroid hormone biosynthesis. Even while performing his biochemical analyses, Dr. Obenauer was cultivating bioinformatics experience. He developed a semi-automated curve fitting tool using Visual Basic for Applications, Microsoft Excel and Mathcad; wrote programs for text processing of NMR chemical shift lists using Perl; and made a toolbar for Microsoft Word with buttons to convert DNA sequences to protein sequences, display the strand complementary to a DNA template, and calculate molecular weights.
Before his current position, he accepted a research scientist position at the Massachusetts Institute of Technology. Working in MIT's Center for Cancer Research, he developed software for predicting phosphoprotein interactions important in cancer biology, using data derived from oriented peptide library experiments. This program, called Scansite (scansite.mit.edu), is a web-accessible research tool written in C, Perl, PHP, and MySQL, and predicts which protein sequences bind to well-known domain types. As an affiliate of the MIT BioMicro Center, Dr. Obenauer assisted in the selection and setup of computational tools for analyzing DNA microarray data. This included adapting the open source BioArray Software Environment (BASE) database to work with the BioMicro Center's array fabrication equipment and data formats.
Interested in learning more about bioinformatics? Be sure to read these other articles posted on The Science Advisory Board members:
The Tools & Techniques of Drug Discovery: Bioinformatics
The Tools and Techniques of Protein Science: Protein Databases and Software
A Self-Made Bioinformatician Relies on His Molecular Biology and Genetics Roots
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