Scott Allen Funkhouser

Updated November 2018

Education

2013-2019

PhD, Genetics and Quantitative Biology; Michigan State University

2007-2011

BSc, Biochemistry; University of Washington

2005-2007

Valedictorian; Graham-Kapowsin HS

Research Positions

2014 - Present

Graduate Research Assistant; Mentor: Catherine Ernst PhD; Michigan State University

Estimating the genetic architectures of RNA editing and of complex traits among heterogenous populations.

2012 - 2013

Research Scientist I; Mentor: Mary Philip MD PhD; University of Washington

Investigated the role of a heme exporter, FLVCR, in the development of T lymphocytes.

2010 - 2011

Undergraduate Research Assistant; Mentor: Chris Hague PhD; University of Washington

Studied novel binding partners to pertinent G-Protein coupled receptors.

Awards, Grants, Scholarships

2018 NSIF Graduate Student Award

• $500 Prize for graduate work “Statistical methods to estimate breed composition and detect GxE interactions”.

USDA Pre-doctoral Fellowship

• 2017 - 2019 • $95,000

ISAG Travel Award

• $2,000 to attend the 2016 ISAG Conference in Salt Lake City, UT

2016 NSIF Graduate Student Travel Award

• $500 to attend 2016 NSIF meeting in Raleigh, NC

Fred and Lucille Stamper Academic College Scholarship

• 2007 - 2011 • $16,256

Memberships

ASHG Trainee Member

• 2018 - Present

GSA Trainee Member

• 2018 - Present

ASAS PhD Student Member

• 2015 – Present

Genetics Student Organization Officer

• 2017 - 2018: Genetics representative for Dean’s student council
• 2016 - 2017: President
• 2014 - 2015: Second-year Representative
• 2015 - 2016: Third-year Representative and Social Chair

Selected Graduate Coursework

• Molecular Biology (BMB 801)
• Eukaryotic Molecular Genetics (MMG 835)
• R Programming for Quantitative Genetics (ANS 824)
• Advanced Statistics for Biologists (STT 814)
• Intro to Statistical Genetics (STT 855)
• Bayesian Inference using MCMC (FW 849)

Teaching and Coordinating

• Co-organizer for the 2017 MSU Genetics Mini-symposium on Impact and Applications of Genome Editing Technologies (2017)
• Teaching assistant for Zoology 341: Fundamentals of Genetics in Fall of 2014

Skills

Each section listed in order from most skilled to least skilled

General programming

• The R language
• C++
• Bash
• Fortran
• Python
• Java

Web design

• Markdown
• HTML
• CSS
• Javascript

Bioinformatics

• Bowtie
• Tophat
• Picard
• SAMTools
• bcftools
• Variant Effect Predictor
• UCSC Genome Browser

General software development

• Git
• Github
• R Studio
• GNU Make

R software development:

• devtools
• roxygen
• testthat

Literate programming

• knitr
• Rmarkdown
• Shiny

Molecular biology

• Flow cytometry
• immunostaining
• qPCR
• PCR
• molecular cloning and techniques therein
• cell culture

Publications

1. Funkhouser SA, Steibel JP, Bates RO, Raney NE, Schenk D, Ernst CW. Evidence for transcriptome-wide RNA editing among Sus scrofa PRE-1 SINE elements. BMC Genomics. 2017;18: 360. doi:10.1186/s12864-017-3766-7
2. Funkhouser SA, Bates RO, Ernst CW, Newcom D, Steibel JP. Estimation of genome-wide and locus-specific breed composition in pigs. Trans Anim Sci. 2017; doi: 10.2527/tas2016.0003
3. Zhao D, Hamilton JP, Hardigan M, Yin D, He T, Vaillancourt B, Reynoso M, Funkhouser SA et al. Analysis of ribosome-associated mRNAs in rice reveals the importance of transcript size and GC content in translation. G3 (Bethesda). 2016;7: 203–219. doi:10.1534/g3.116.036020
4. Philip M, Funkhouser SA, Chiu EY, Phelps SR, Delrow JJ, Cox J, et al. Heme Exporter FLVCR Is Required for T Cell Development and Peripheral Survival. J Immunol. 2015; doi:10.4049/jimmunol.1402172

Pending Publications

1. Funkhouser SA, de los Campos G. Applying local Bayesian regressions to decipher sex-specific genetic architectures.
2. Funkhouser SA, Steibel JP, Bates RO, Raney NE, Sargolzaei M, Ernst CW. Utility of the Affymetrix Axiom Porcine Genotyping Array for genome-wide studies.

Meeting Presentations and Posters

• Funkhouser SA (2018) Statistical methods to estimate breed composition and detect GxE interactions. Oral presentation presented at the 2018 NSIF Meeting as the recipient of the 2018 NSIF Graduate Student Award.
• Funkhouser SA, de los Campos G. (2018) Deciphering sex-specific genetic architectures using Bayesian methods. Poster presented at the 2018 American Society of Human Genetics Annual Meeting.
• Funkhouser SA, de los Campos G. (2018) Mapping sex differences using local Bayesian regessions. Oral presentation given at the 2018 MSU Institute for Quantitative Health Sciences Retreat.
• Funkhouser SA, de los Campos G. (2018) Deciphering sex-specific genetic architectures using Bayesian methods. Poster presented at the 2018 GSA Population, Evolution, and Quantitative Genetics Conference.
• Funkhouser SA, Steibel JP, Bates RO, Raney NE, Ernst CW. (2017) Evidence for transcriptome-wide RNA editing among Sus scrofa PRE-1 SINE elements. Poster presented at the 2017 Gordon Conference on RNA Editing.
• Funkhosuer SA, Bates RO, CW Ernst, Newcom D, Steibel JP. (2016) Estimation of the composition of four U.S. swine breeds using genomic data. ePoster presented at the 2016 ASDA/AAS Joint Annual Meeting.
• Funkhouser SA, Steibel JP, Bates RO, Raney NE, Ernst CW. (2016) RNA editing in swine is associated with PRE-1 retrotransposons. ePoster presented at the 2016 International Society for Animal Genetics Conference.
• Funkhouser SA, Steibel JP, Bates RO, Raney NE, Ernst CW. (2015) Evidence of RNA editing in pig longissimus dorsi muscle. Oral presentation given at the American Dairy Science / American Society of Animal Science Midwest Conference.

scottafunkhouser.com • 474 S. Shaw Lane, Room 1205 - East Lansing, Michigan, USA