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
Honors thesis: PhyloProf: a software package for predicting gene function
using phylogenetic profile analysis
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.
- 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.
- 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.
Daniel S. Standage
2128 Molecular Biology Building
Iowa State University
Ames, IA 50010