Curriculum vitae

I am a Ph.D. candidate in the research groups of Volker Brendel (Indiana University) and Amy Toth (Iowa State University). My research interests are in data-intensive genome biology, with a particular focus on genome annotation and analysis of high-throughput sequence data. I am committed to open, transparent, reproducible research, and to observing established software engineering practices in tool development.

Education

2010 — 2015 Ph.D. in Bioinformatics and Computational Biology
Iowa State University
In residence at Indiana University since July 2012
2003 — 2010 B.S. in Bioinformatics (with minors in Mathematics and Computer Science)
Brigham Young University
University Honors

Scholarship

Publications
  • Duvick JP, Standage DS, Merchant N, Brendel VP (2015) xGDBvm: A Web GUI-driven workflow for annotating eukaryotic genomes in the cloud. Manuscript under review.
  • Standage DS, Brendel VP (2012) ParsEval: parallel comparison and analysis of gene structure annotations. BMC Bioinformatics, 13:187, doi:10.1186/1471-2105-13-187.
  • Doyle EL, Booher NJ, Standage DS, Voytas DF, Brendel VP, VanDyk JK, Bogdanove AJ (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.
Oral Presentations
  • Standage DS, Toth AL, Brendel VP. iLoci: scalable annotation for provisional genome assemblies. Presented at CSHL Biology and Genomics of Social Insects Meeting, May 2015. Manuscript in preparation.
  • Duvick JP, Denton JF, Standage DS, Merchant N, Brendel VP. xGDBvm: a virtual platform for annotating eukaryotic genomes. Invited talk given at PAG XXI, January 2013.
Posters
  • Standage DS, Berens AJ, Severin AJ, Glastad KM, Hunt BG, Weiner SA, Goodisman MAD, Brendel VP, Toth AL. Genome sequence and annotation of the primitively social paper wasp Polistes dominula. Presented at Notre Dame Arthropod Genomics Conference, June 2013. Manuscript in preparation.
  • Brendel VP, Standage DS. mRNAmarkup: quality control and annotation of de novo transcriptome assemblies. Presented at CSHL Genome Informatics meeting, November 2013. Manuscript in preparation.

Research Experience

Graduate Research Assistant, Computational Genome Science Lab, Indiana University, 2012 — present
  • Implement version control tools for genome annotations
  • Conduct comparative analysis of genome composition in social insects
  • Design new methods for organizing genomes to facilitate comparison and analysis between annotations, assemblies, and species
  • Investigate genome composition, differential expression, alternative splicing, and methylation in the paper wasp Polistes dominula
Graduate Research Assistant, BCB Graduate Program, Iowa State University, 2010 — 2012
  • Develop tools for comparing gene structure annotations
  • Implement parallel version of an NGS error correction program
  • Evaluate existing software tools for transposable element prediction
Undegraduate Research Assistant, Plant Genetics Lab, Brigham Young University, 2009 — 2010
  • Analyze expression of homoeologous genes in Gossypium (cotton)
  • Prototype sample submission system for on-site 454 sequencer
  • Develop tools for SNP analysis in polyploid organisms
Research Intern, Department of Genetics, University of Georgia, 2008
  • Investigate genes involved in biosynthesis of plant cell wall monosaccharides using phylogenetic profile analysis
  • Model gene regulatory networks in fungus Neurospora crassa
Undegraduate Research Assistant, Center for Language Studies, Brigham Young University, 2007 — 2010
  • Work with domain experts to produce responsive online learning materials
  • Research and prototype open, modular, and interoperable e-learning architectures

Professional Activities

Journal Review
  • Science, May 2013
  • Bioinformatics, April 2013
Open-source Science Software and Data
Community Training
  • 2014 course on Analyzing NGS Data, MSU; invited instructor
  • Software Carpentry certified instructor

Teaching

Computational Genome Science (Fall 2011, Spring 2013, Spring 2014, Spring 2015)

Graduate course covering the full range of computational genomics analysis: quality control, read mapping, expression profiling, genome assembly, transcript assembly, and annotation. The class provides brief exposure to relevant theory, but focuses primarily on installing and running software and (most importantly) critical analysis and biological interpretation of results. I helped develop the course in 2011, and since 2013 I have been the primary instructor.

Science of Biology, Honors (Spring 2007, Spring 2008)

As an undergraduate I was a teaching assistant for Prof. 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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