Curriculum Vitae

EDUCATION

Brigham Young University, UT

Ph.D. Student

Areas of Concentration: Evolution of codon bias, predictability of human DNA, Phylogenetic Analysis, Algorithm Design

 

Brigham Young University, UT

2015—present

Undergraduate

Areas of Concentration: Bioinformatics, Computer Science, Portuguese

Graduated Cum Laude with 3.91 G.P.A.  2010 – 2015

 

COMPUTER SKILLS

• Programming languages: Python, VBA, Java, C#, R, bash, C++, SQL, MATLAB, Julia

• Operating systems: MS Windows, Linux, Unix

• Applications: MS Office Suite, MS Visual Studio, Adobe Suite

• Concepts: Big Data Analysis, Machine Learning, Parallel Processing, Big O

 

GRANTS, AWARDS AND HONORS 

• Willi Hennig Society Founder’s Award ($2,800)

• BYU Research Presentation Award ($400)

• CREEDS travel grant (airfare + 2 weeks lodging in New York City + conference registration)

• Phi Kappa Phi Membership

• Golden Key Honour Society Membership

• Phi Eta Sigma Membership

• BYU Academic Full Tuition Scholarship

• Boy Scouts of America Eagle Scout

 

WORK EXPERIENCE

2015 – Present

Brigham Young University, Provo, UT

PhD student and Teaching Assistant in Biology Department

Analyze the evolution of codon usage bias across the Tree of Life

Assistant lecturer with dedicated lab office hours

 

2015 – 2016

Imagine Learning, Provo, UT

Data Analyst

Created reports that helped generate about $5 million in revenue

Brigham Young University, Provo, UT

 

2014 – 2015

Brigham Young University, Provo, UT

Research Assistant

Used a variety of bioinformatics tools to analyze DNA sequences

 

2014 – 2015

Brigham Young University, Provo, UT

Teaching Assistant – to Dr. Perry Ridge in “Intro to Bioinformatics”

Taught students needing help during office hours, passed off programming projects

 

2011 – 2013

The Church of Jesus Christ of Latter-day Saints, Ribeirão Preto, SP, Brazil

Missionary

Helped people with their physical and spiritual needs

 

PUBLICATIONS

Miller, J. B., Hippen, A. A., Wright, S. M., Morris, C. & Ridge, P. G. Human viruses have codon usage biases that match highly expressed proteins in the tissues they infect. Biomedical Genetics and Genomics 2, doi:10.15761/bgg.1000134 (2017).

• Pickett, B.D., J.B. Miller, and P.G. Ridge, Kmer-SSR: A Fast and Exhaustive SSR Search Algorithm. Bioinformatics, 2017.

Miller, J. B., Hippen, A. A., Belyeu, J. R., Whiting, M. F. & Ridge, P. G. Missing something? Codon aversion as a new character system in phylogenetics. Cladistics, doi:10.1111/cla.12183 (2017).

• Mark T.W. Ebbert, Mark E. Wadsworth, Lyndsay A. Staley, Kaitlyn L. Hoyt, Brandon D. Pickett, Justin B. Miller, John D. Duce, John S.K. Kauwe, Perry G. Ridge: Evaluating the necessity of PCR duplicate removal from next-generation sequencing data and a comparison of approaches. BMC Bioinformatics, July 2016

•Stewart G. Gardner, Justin B. Miller, Tanner Dean, Tanner Robinson, McCall Erickson, Perry Ridge, William R. McCleary: Genetic analysis, structural modeling and direct coupling analysis suggest a mechanism for phosphate signaling in E. coli. BMC Bioinformatics, 2014.

 

ORAL PRESENTATIONS

Justin B. Miller, Lauren M. McKinnon, Michael F. Whiting, Perry G. Ridge (2017). Codon Aversion Motifs: An alignment-free method to recover phylogenies. ISCB Rocky Mountain Bioinformatics Conference, Aspen/Snowmass, Colorado, USA.

Justin B. Miller, Ariel A. Hippen, Sage M. Wright, Caroline Morris, Perry G. Ridge (2016). Human-Infecting Viruses Mimic Host Codon Usage Biases. Biotechnology and Bioinformatics Symposium 2016, Brigham Young University, Provo, UT.

Justin B. Miller, Ariel A. Hippen, Jonathon R. Belyeu, Michael F. Whiting, Perry G. Ridge (2015). Missing something?: Codon non-usage as a character in phylogenetic inference in Tetrapods. Biotechnology and Bioinformatics Symposium 2015, Brigham Young University, Provo, UT.

 

POSTER PRESENTATIONS

Justin B. Miller, Lauren M. McKinnon, Michael F. Whiting, Perry G. Ridge (2017). Codon Aversion Motifs: An alignment-free method to recover phylogenies. ISCB Rocky Mountain Bioinformatics Conference, Aspen/Snowmass, Colorado, USA.

Justin B. Miller, Brandon D. Pickett, Perry G. Ridge (2017). JustOrthologs: A Fast, Accurate, and User-Friendly Ortholog-Identification Algorithm. ISMB/ECCB Intelligent Systems for Molecular Biology and Computational Biology Conference, Prague, Czech Republic.

• Stewart Morley, Justin Miller, Perry Ridge, Brent Nielson (2017). Assembling the Arabidopsis Mitochondrial DNA Replisome. 28th International Conference on Arabidopsis Research, St. Louis, MO.

• Mark Wadsworth, Justin Miller, Michael Cormier, Sage Wright, Perry G. Ridge (2016). Determining the Effects Variants have on Gene Splicing. Biotechnology and Bioinformatics Symposium, Brigham Young University, Provo, UT.

Justin B. Miller, Brandon D. Pickett, Perry G. Ridge (2016). JustOrthologs: A Fast, Accurate, and User-Friendly Ortholog-Identification Algorithm. American Society of Human Genetics (ASHG). Vancouver, BC, Canada.

• Brandon D. Pickett, Justin B. Miller, Perry G. Ridge (2016). Efficient, Accurate, and Complete Identification of Simple Sequence Repeats in Genomic Sequences. American Society of Human Genetics (ASHG). Vancouver, BC, Canada.

Justin B. Miller, Brandon D. Pickett, Perry G. Ridge (2016). JustOrthologs: A Fast, Accurate, and User-Friendly Ortholog-Identification Algorithm. LDS Life Science Symposium, Thanksgiving Point, UT.

• Brandon D. Pickett, Justin B. Miller, Perry G. Ridge (2016). Efficient, Accurate, and Complete Identification of Simple Sequence Repeats in Genomic Sequences. LDS Life Science Symposium, Thanksgiving Point, UT.

Justin B. Miller, Ariel A. Hippen, Jonathon R. Belyeu, Michael F. Whiting, Perry G. Ridge (2016). Missing Something?: Codon Aversion as a New Character System in Phylogenetics. Community Research Education and Engagement for Data Science at Icahn School of Medicine, New York City, NY.

Justin Miller, Ariel Hippen, Andy Himebaugh, Ryan Miller, Caroline Morris, Perry Ridge (2015). Viral Codon Bias Mimics Human Host Proteins. Biotechnology and Bioinformatics Symposium 2015, Brigham Young University, Provo, UT.

Justin B. Miller, John D. Duce, Perry G. Ridge (2014). The Alignable Portion. Biotechnology and Bioinformatics Symposium 2014, Brigham Young University, Provo, UT.

Justin B. Miller, Kaitlyn L. Hoyt, Jordon B. Richie, Artem V. Golotin (2014). Assembling a Chromosome from Overlap Regions. Biotechnology and Bioinformatics Symposium 2014, Brigham Young University, Provo, UT.

• Mark E. Wadsworth, Brandon D. Pickett, Justin B. Miller, John D. Duce, Ronald G. Munger, Christopher D. Corcoran, JoAnn T. Tschanz, Maria C. Norton, John S.K. Kauwe, Karl V. Voelkerding, Perry G. Ridge (2014). The Variant Characterization of 211 Whole Genome Sequences: The Cache County Study on Memory Health and Aging. Biotechnology and Bioinformatics Symposium 2014, Brigham Young University, Provo, UT.

• Mark E. Wadsworth, Brandon D. Pickett, Justin B. Miller, John D. Duce, Ronald G. Munger, Christopher D. Corcoran, JoAnn T. Tschanz, Maria C. Norton, John S.K. Kauwe, Karl V. Voelkerding, Perry G. Ridge (2014). The Variant Characterization of 211 Whole Genome Sequences: The Cache County Study on Memory Health and Aging. The American Society of Human Genetics 2014, San Diego, CA.

 

REFEREE/REVIEWER

• BMC Bioinformatics / BMC Genomics (December 2016)

• BMC Bioinformatics / BMC Genomics (December 2015)

 

TRAINING/CONFERENCES

ISCB Rocky Mountain Bioinformatics Conference in Aspen/Snowmass, Colorado (December, 2017)

• ISMB/ECCB Intelligent Systems for Molecular Biology and Computational Biology in Prague, Czech Republic (July, 2017)

• Biotechnology and Bioinformatics Symposium at Brigham Young University in Provo, Utah (December, 2016)

• LDS Life Science Symposium at Thanksgiving Point, Utah (July 2016)

• I was accepted to and participated in an extensive two week bioinformatics training program for the Community Research Education and     Engagement for Data Science at Icahn School of Medicine at Mount Sinai in New York City, New York (June 2016).

• Biotechnology and Bioinformatics Symposium at Brigham Young University in Provo, Utah (December, 2015)

• Biotechnology and Bioinformatics Symposium at Brigham Young University in Provo, Utah (December, 2014)

 

LANGUAGES

• English – native language

• Portuguese – 2 years living in Brazil. ACTFL certified; Advanced Proficiency

 

COMMUNITY OUTREACH

• Science fair judge at Wasatch Elementary School (November, 2017)

• Science fair judge at Westridge Elementary School (November, 2017)

• Boy Scout leader (2016-present)

 

 

 

 

 

 

 

 

 

 

 

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