I am a graduate student in the research groups of Volker Brendel (Indiana University) and Amy Toth (Iowa State University). My general research interests are in genome informatics, with a particular focus on genome annotation and analysis of high-throughput sequence data.
Ph.D. in Bioinformatics and Computational Biology
Iowa State University, August 2010 - present
In residence at Indiana University since July 2012
B.S. in Bioinformatics (with minors in Mathematics and Computer Science)
Brigham Young University, August 2003 - April 2010
In the space of just a few years, genome sequencing has progressed from a multi-million-dollar venture to a routine experimental procedure compatible with even modest research budgets. However, raw genome sequence itself is of little value until it can be accurately assembled, and assembled genome sequences are of little value without reliable annotation. Tools for assembling and annotating genomes are struggling to keep pace with advances in sequencing technology, as is the expertise needed to interpret assemblies and annotations at the genome scale. My research expertise and interests involve leveraging genome-scale sequence data, annotations, and cyberinfrastructure to address fundamental questions in genome biology. I am committed to open, transparent, reproducible research, and to observing established software engineering practices in tool development.
- Daniel S. Standage and Volker P. Brendel (2012) ParsEval: parallel comparison and analysis of gene structure annotations. BMC Bioinformatics, 13:187, doi:10.1186/1471-2105-13-187.
- Erin L. Doyle, Nicholas J. Booher, Daniel S. Standage, Daniel F. Voytas, Volker P. Brendel, John K. VanDyk, Adam J. Bogdanove (2012) TAL Effector-Nucleotide Targeter (TALE-NT) 2.0: Tools for TAL effector design and target prediction. Nucleic Acids Research, 40 (W1): W117-W122, doi:10.1093/nar/gks608.
Computational Genome Science (Fall 2011, Spring 2013, Spring 2014)
I helped develop this course with Volker Brendel at Iowa State University in 2011, and participated in the course both as a student and a teaching assistant. The course covers the full range of computational genomics analysis, from quality control to de novo assembly to read mapping (and related applications) to annotation and visualization. The class provides brief exposure to relevant theory, but focuses primarily on installing and running software and (most importantly) critically evaluating the results of an analysis. For the 2013 and 2014 offerings of the course at Indiana University I am the primary instructor.
Science of Biology, Honors (Spring 2007, Spring 2008)
As an undergraduate I was a teaching assistant for Craig Coleman's Biol 120H class. This class provided a comprehensive introduction to the biological sciences, with modules for biochemistry, molecular biology, genetics, cell biology, and evolution. The course focused on learning the scientific method with computer-based experiment simulations, and had a heavy emphasis on writing.
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