Iowa State University

IaState

Ph.D. in bioinformatics

Doctor of Philosophy, Bioinformatics and computational biology
Iowa State University, 2014 (expected)
Wendell Miller Trust Fellow

Experience as a graduate research assistant: assemble and annotate genome of the social wasp Polistes dominulus; assist with data management and migration of a large comparative plant genomics database (PlantGDB); develop and participate in a course on NGS applications to genomics (including read processing, genome assembly, transcript assembly/mapping, and genome annotation); develop software for comparison of whole-genome annotations; identify transposable elements in various Gossypium (cotton) species; develop parallel software for short read error correction

Brigham Young University

BYU

B.S. in bioinformatics

Bachelor of Science, Bioinformatics, 2010
Minor in Mathematics
Minor in Computer science
3.53/4.00 GPA

University Honors
Honors thesis: PhyloProf: a software package for predicting gene function using phylogenetic profile analysis

Ph.D. candidate

GDCB Department, Iowa State

Dissertation: Next-generation innovations in gene and genome annotation
Committee: Volker Brendel (advisor), Amy Toth (co-advisor), Karin Dorman, Xiaoqui Huang, Jonathan Wendel

On 18 April 2012, I passed my preliminary qualification exams to become an official Ph.D. candidate!

Research technician

Genetics Lab, BYU

Research technician
Genetics Lab
Department of Plant and Wildlife Sciences
Brigham Young University

Experience: analysis of homoeologous gene expression (genes duplicated by polyploidy) in cotton with high-throughput sequencing technology; prototyping of an electronic sample submission system for on-site 454 sequencer; development of software for SNP analysis in polyploid organisms; assembly and mapping of high-throughput sequence data (454 and Illumina); configuration of a genome browser for transcriptome visualization

Research intern, UGA

Research intern
NSF REU: Fungal genomics and computational biology
Department of Genetics
University of Georgia

Experience: modeling and simulation of genetic networks in Neurospora crassa; study of biological clocks in fungi using basic experimental protocols (Northern blot, RNA extraction, gel electrophoresis, etc); introduction to systems biology and network modeling; introduction to high-performance computing; identification of genes involved with the biosynthesis of cell wall monosaccharides using phylogenenetic profile analysis

Teaching assistant

Biol 120 Honors
College of Life Sciences, BYU

Teaching assistant
Biol 120H: The Science of Biology (Honors)
College of Life Sciences
Brigham Young University

I was a TA for Dr. Craig Coleman's Honors Science of Biology class. The class focuses on the scientific process and the fundamentals of the biological sciences, with a heavy emphasis on writing. The (typically first-year) students were introduced to the major core disciplines within the life sciences, including biochemistry, cell biology, genetics, molecular biology, and evolutionary biology. Each unit included a computer-based experiment simulation, for which students then had to write a report in the form of a scientific paper. I tutored students, held comprehensive reviews for each exam, and graded reports and exams.

Missionary

South Africa Cape Town Mission
The Church of Jesus Christ of Latter-day Saints

Missionary
South Africa Cape Town Mission
The Church of Jesus Christ of Latter-day Saints

I took a 2-year academic deferral so that I could perform missionary service in South Africa. As a missionary, I devoted my time to teaching and serving in the community, working with local leaders and families. I held various leadership responsibilities during my mission, and at times was responsible for the activity of up to 11 other missionaries.

Research assistant

ARCLITE Lab
Center for Language Studies
Brigham Young University

Consultant

Institute for Defense Analyses
US Dept. of Defense

Research assistant
ARCLITE Lab
Center for Language Studies
Brigham Young University

Experience: develop applications and architectures to support development, delivery, and assessment of electronic learning resources and student performance; focus on technical best practices such as separation of content, presentation, and logic; work directly with subject matter experts and instructional designers to create instructional materials; evangelize the topics of openness, modularity, and interoperability in the learning community; served briefly as chair of the Architecture working group for LETSI (the International Federation for Learning, Education, and Training Systems Interoperability); provided consulting for the DOD Institute for Defense Analyses regarding e-learning technologies

HTML
PHP
MySQL
JavaScript

Web technologies

I gained my initial experience in web development and web programming through elective coursework and through my research at the ARCLITE Lab. Creating database-driven web resources was a very common task at ARCLITE, and I was typically responsible both for developing backends (PHP, MySQL, AJAX, etc) as well as frontend interfaces (HTML, CSS, JavaScript, etc). After building applications from scratch for several years, I gained experience with the Symfony PHP framework, an MVC-based web development framework.

Perl

An NSF internship at UGA provided my first exposure to Perl programming. Subsequent coursework and research have honed my Perl skills significantly. Perl, along with Linux command-line tools, is my primary toolkit for exploratory research and data processing. I have broad spectrum of experience, from piping together quick-and-dirty one-liners directly on the command to applying object-oriented principles when creating reusable modules.

Java

Most of my introductory CS courses as an undergraduate used Java as the language of instruction. While I do not code much in Java anymore, there is a lot I like about the language's syntax and structure.

C

As a graduate student I have taught myself to program in ANSI C. I still use Perl extensively in my research, but when it comes to software development, the performance of C is unmatched by almost any other language. In my current research, I make extensive use of the GenomeTools library, which provides a variety of data parsers, advanced data structures, and visualization tools.

C++
C#

My advanced CS courses as an undergraduate used C++ and C# as the languages of instruction. Aside from several significant programming projects, most of my experience with these languages has been recreational. This did, however, give me a good foundation for learning C, which is my primary language for software development.

Lab techniques

I majored in molecular biology before discovering bioinformatics, and accordingly I enrolled in coursework designed to provide exposure to the most common molecular lab techniques used in research. My internship at UGA provided additional exposure. I have experience with DNA / RNA extraction, PCR, gel electrophoresis, western / northern blot, bacterial transformation and cloning, and Sanger sequencing. Even after changing my major to bioinformatics, I entertained the possibility of doing wet lab and dry lab work concurrently, although as a graduate student I have been happy to do all of my work in silico.

HPC

Starting with my internship at UGA, I have used high-performance computing frequently in my research. I have experience with several job schedulers, including PBS, SGE, and Moab, and have used HPC resources to perform tasks ranging from an all-against-all BLAST of bacterial genomes to mapping NGS reads to a reference genome for subsequent RNA-seq analysis to whole-genome assembly to protein fold prediction. Graduate coursework has also provided me experience with parallel programming using both distributed-memory (MPI) and shared-memory (OpenMP) paradigms.


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