Daniel S. Standage

Education

Ph.D. in Bioinformatics and Computational Biology
Iowa State University, 2014 (expected)

B.S. in Bioinformatics, Minor in Mathematics, Minor in Computer Science
Brigham Young University, April 2010
3.53/4.00 GPA
University Honors
Honors thesis: PhyloProf: a software package for predicting gene function using phylogenetic profile analysis

Research

I am a graduate student in the research groups of Volker Brendel and Amy Toth at 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.

Recent innovations in sequencing technology have elevated the rate of genome sequencing to a staggering level, and the community is struggling to meet the corresponding demand for whole-genome gene annotations. Focusing instead on high-quality annotation of an individual gene of interest in a scaled-up comparative context (that is, the gene and all its homologs in all available related genomes) provides a novel way of leveraging the full scale of available genomic data. This paradigm is well-suited for the analytical approach employed by many biologists that focus their research projects on a single gene or small group of genes. My research interest is developing a framework that facilitates annotation and subsequent large-scale comparative analysis of individual genes of interest. Recent developments in the social insect community (a BGI initiative to sequence 100 social insect genomes within the next two years) and within the broader arthropod community (the i5k initiative to sequence 5000 insect and insect-related genomes within the next five years) provide an unprecedented opportunity to develop and apply this framework.

Publications

• Daniel S. Standage and Volker P. Brendel (2012) ParsEval: parallel comparison and analysis of gene structure annotations. BMC Bioinformatics, 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.

Posters

• R. Taylor Raborn, Krishnakumar Sridharan, Daniel S. Standage, John M. Logsdon Jr., and Volker Brendel (2012) Comparative genome-wide analysis of transcription initiation and promoter architecture in eukaryotes. 20th Annual International Conference on Intelligent Systems for Molecular Biology.
• Daniel S. Standage and Volker P. Brendel (2011) ParsEval: parallel comparison and analysis of gene structure annotations. Genome Informatics Conference, Cold Spring Harbor Laboratory.
• Daniel S. Standage, Mark J. Clement, and Keith A. Crandall (2010). PhyloProf: a software package for predicting gene function using phylogenetic profile analysis, Honors Symposium, Brigham Young University.
• Daniel S. Standage, Lex Flagel, Kara Grupp, Jonathan F. Wendel, and Joshua A. Udall (2010). Measuring Gene Expression in Tetraploid Cotton with Illumina Sequencing, International Plant and Animal Genome Conference.
• Marcus M. Soliai, David D. Elzinga, Daniel S. Standage, Scott M. Yourstone, Joshua A. Udall, Susan E. Meyer, and Craig E. Coleman (2010). Whole Genome Sequencing and SNP Genotyping of the Black Fingers of Death, International Plant and Animal Genome Conference.
• Daniel S. Standage, Phuongan Dam, Maor Bar-Peled, and Ying Xu (2008). Functional Assignment of Genes Using Phylogenetic Profile Analysis, NSF REU, Fungal Genomics and Computational Biology, University of Georgia.

Social

• StackExchange
• BioStar
• Mendeley
• BitBucket