CV

Education

Louisiana State University

• Ph.D. in Biological Sciences (2019) Dissertation: Model Scaling from Protein Subnetworks to Populations in Mathematical Biology
• M. Stat. in Applied Statistics (2019) Thesis: Bayesian Estimate of the Parameters of a Stochastic Differential Model of HIV Incidence in the United States
• M.S. in Cell Biology 2015 *Thesis: Mathematical Model of the Split Firefly Luciferase Assay *
• B.S. in Biological Sciences 2013
• B.A. in Philosophy 2013 Thesis: Empathy, Altruism, and Prosocial Behavior in Humans and Primates

Appointments

• Teaching Assistant 2013 - 2018

BIOL 1208 Introductory Biology Lab I & BIOL 1209 Lab II
BIOL 1005 Introductory Biology Lab for Non Majors
Duties: Development of teaching materials and in-class activities, quiz and exam writing, leading student experiments in inquiry-based lab setting

• Plantae Fellow 2017 – 2018

Duties: Development of materials for Plantae, particularly Big data and Computational Infrastructure network

• Guest Instructor Fall 2017

  BIOL 7800 Mathematical Modeling LSU

• Research Assistant Summer 2017

  Mathematics 										                                LSU
  

• Research Assistant Spring & Summer 2017

  Biological Sciences						                        			    LSU
  

• Supplemental Instruction Leader Fall 2012

  Biology 1001 						                                        Center for Academic Success, LSU
  

• Undergraduate Researcher Aug 2010 – Jan 2012

  Environmental Engineering 								                      LSU
  

Publications

Increased phosphate transport of Arabidopsis thaliana Pht1;1 by site-directed mutagenesis of tyrosine 312 may be attributed to the disruption of homomeric interactions

Fontenot, E. B., Ditusa, S. F., Kato, N., Olivier, D. M., Dale, R., Lin, W. Y., Chiou, T. J., Macnaughtan, M. A., Smith, A. P. (2015). Increased phosphate transport of Arabidopsis thaliana Pht1;1 by site-directed mutagenesis of tyrosine 312 may be attributed to the disruption of homomeric interactions. Plant Cell Environ 38(10): 2012-2022.

Functional Conservation in the SIAMESE-RELATED Family of Cyclin-Dependent Kinase Inhibitors in Land Plants.

Kumar, N., Harashima, H., Kalve, S., Bramsiepe, J., Wang, K., Sizani, B. L., Bertrand, L. L., Johnson, M. C., Faulk, C., Dale, R., Simmons, L. A., Churchman, M. L., Sugimoto, K., Kato, N., Dasanayake, M., Beemster, G., Schnittger, A., Larkin, J. C. (2015). Functional Conservation in the SIAMESE-RELATED Family of Cyclin-Dependent Kinase Inhibitors in Land Plants. Plant Cell 27(11): 3065-3080.

Brauer, E. K., Ahsan, N., Dale, R., Kato, N., Coluccio, A. E., Piñeros, M. A., Kochian, L. V., Thelen, J. J., Popescu, S. C. (2016). The Raf-like kinase ILK1 and the high affinity K+ transporter HAK5 are required for Innate Immunity and Abiotic Stress Response. Plant Physiology. pp.00035.2016. http://dx.doi.org/10.1104/pp.16.00035

Brauer, E. K., Ahsan, N., Dale, R., Kato, N., Coluccio, A. E., Piñeros, M. A., Kochian, L. V., Thelen, J. J., Popescu, S. C. (2016). The Raf-like kinase ILK1 and the high affinity K+ transporter HAK5 are required for Innate Immunity and Abiotic Stress Response. Plant Physiology. pp.00035.2016. http://dx.doi.org/10.1104/pp.16.00035

Mathematical Model of the Firefly Luciferase Complementation Assay Reveals a Non-Linear Relationship between the Detected Luminescence and the Affinity of the Protein Pair Being Analyzed

Dale, R., Ohmuro-Matsuyama, Y., Ueda, H., Kato, N. (2016). Mathematical Model of the Firefly Luciferase Complementation Assay Reveals a Non-Linear Relationship between the Detected Luminescence and the Affinity of the Protein Pair Being Analyzed. PLoS ONE 11(2): e0148256. http://dx.doi.org/10.1371/journal.pone.0148256

Truly quantitative analysis of the firefly luciferase complementation assay

Dale, R., Kato, N. (2016). Truly quantitative analysis of the firefly luciferase complementation assay. Current Plant Biology 5(2016): 57-64.

Estimating epidemiological parameters of a stochastic differential model of HIV dynamics in the United States using a hierarchical Bayesian model.

Dale, R., Guo, B. (2017) Estimating epidemiological parameters of a stochastic differential model of HIV dynamics in the United States using a hierarchical Bayesian model. PLoS ONE. (preprint: https://doi.org/10.1101/219832)

Posterior Estimates of Dynamic Constants in HIV Transmission Modeling.

Chen, Y.C., Dale, R., He, Hongyu, Le, Quoc-Anh T. (2017) Posterior Estimates of Dynamic Constants in HIV Transmission Modeling. Computational and Mathematical Methods in Medicine.

Talks & Presentations

Posterior Estimates of Dynamic Constants in HIV Transmission Modeling

February 01, 2017

Talk at Scientific Computing Across Louisiana 2017, New Orleans, Louisiana

Posterior Estimates of Dynamic Constants in HIV Transmission Modeling

May 01, 2017

Talk at LSU Boyd Adventures in Research: A Pathway to Biomedical Research, Baton Rouge, Louisiana, USA

“Bayesian Estimate of the Parameters of a Stochastic Differential Model of HIV Incidence in the United States “

July 01, 2017

Talk at Annual Meeting of the Society for Mathematical Biology , Salt Lake City, UT, USA

“Is the HIV epidemic over? Bayesian methodology to estimate epidemiological parameters for a system of stochastic differential equations “

August 01, 2017

Talk at University of Louisiana Lafayette Graduate Symposium, Lafayette, Louisiana

“Bayesian Estimate of the Parameters of a Stochastic Differential Model of HIV Incidence in the United States “

October 01, 2017

Talk at Emory University Stat Fest , Atlanta, Georgia

Bayesian Estimate of the Parameters of a Stochastic Differential Model of HIV Incidence in the United States

December 01, 2017

Talk at Objective Bayes Workshop , Austin, TX

“Bayesian Estimate of the Parameters of a Stochastic Differential Model of HIV Incidence in the United States “

January 01, 2018

Talk at International Conference on Health Policy and Statistics 2018 , Charleston, North Carolina, USA

Improved Mathematical Model Enhances Understanding of Endoreplication in Arabidopsis Trichomes with 4D Visualization

February 01, 2018

Talk at American Association for the Advancement of Science Annual Meeting 2018, Austin, TX, USA

Rabbit and the Hare: Modeling Evolution in Yeast

February 01, 2018

Talk at Probability Meets Biology 2019, Bath, UK

Generation of nonlinear-differential-equations system from a model of Boolean relationships in Arabidopsis salt stress network

February 01, 2018

Talk at European Student Coucil Symposium 2018, Athens, Greece, EU

“Hierarchical modeling of HIV prevention “

February 01, 2018

Talk at Scientific Computing Across Louisiana 2018, Baton Rouge, Louisiana

Studying the effect of pre-exposure prophylaxis on the dynamics of different populations susceptible to HIV

February 01, 2018

Talk at Society for Mathematical Biology 2018, Sydney, AU

Improved Mathematical Model Enhances Understanding of Endoreplication in Arabidopsis Trichomes with 4D Visualization

May 01, 2018

Talk at Sigma Xi Student Research Showcase, Online

Scientific Outreach & Service to the Community

• Journal Reviewer, Heliyon (2018)
• Guest editor, What we’re reading. Collection of recent research on mathematical modeling in plant biology. https://plantae.org/what-were-reading-january-19th/ (2018)
• Plantae Fellow: scientific outreach with a focus on mathematical plant biology https://community.plantae.org/user/ReneeDale (2017-2018)
• Website Development: Volunteered to assist in web development for interdisciplinary collaborative website compmodelmatch.org. Current version: https://rdale1.shinyapps.io/compmodelmatch/ (2017)
• Academic blogging detailing computational procedures to help beginners in computational biology and the general computing public (iambecomecomputational.com) (2017)
• Academic Twitter devoted to scientific breakthroughs, opportunities for graduate students, computational methodologies, and mental health related information (@b10_m0del1ng) (2017)

Education & Mentoring Activities

• Volunteer statistical consultant with Statistics Without Borders (2018)
• Developed web application for undergraduate introductory biology students to enhance their understanding of traditionally difficult concepts, such as membrane potential. Current version: https://rdale1.shinyapps.io/wischu_biol2018/ (2017). The app will allow the instructor access to student activities when using the illustrations and answering questions.
• Developed web application on Ecological Inference to include RxC analysis for assisting laywers to determine possible cases of gerrymandering using district data (2017). Currently the code is private and still under development.
• CIRTL Scholar: The LSU Center for the Integration of Research, Teaching, and Learning (CIRTL) provides this certificate to graduate students who study STEM education, design and carry out an experiment, and present or publish their findings. I took discipline-based education resource (DBER) courses, independently studied the literature, designed and carried out an experiment while guest instructor with BIOL 7800, and analyzed the data. I am currently writing up the results.
• Curriculum Development: BIOL 7800 Mathematical Modeling in Cellular Biology with Dr. Kato at LSU (2017). I assisted in conceptual course material development (differential equations, cell biology) and was completely responsible for the technical, programming materials for the course. My lecture materials are available at iambecomecomputational.com and my code examples at https://github.com/rdale1/Matlab-Programming-Examples
• Curriculum Development: Helped develop a new coursework for use at LSU course BIOL 1005 Laboratory for non-science majors (2016). To help the students come up with independent research topics, I suggested the inclusion of a proposal presentation prior to their writeup.
• Mentor: Association for Women in Math Mentor Network (2017)
• Mentor: MentorNet (2017)
• Judge: Louisiana Science and Engineering Fair (LSEF) for middle and high school students (2014 – present)
• Mentor: Assisted local middle school students with their science fair projects (2014)

Computational Skills

• Computing languages Python, Matlab, Mathematica, R, Java, Comsol, C++, JMP, SAS, Spark

• Mathematical techniques
  Ordinary differential equations, stochastic differential equations, differential algebraic equations, mixed differential equations; Multivariate calculus, linear algebra

• Computational techniques
  Flux balance analysis, flux variability analysis; Global and local optimization; Parameter estimation, kinetic modeling, population modeling, protein-protein interaction modeling, gene expression and control modeling; Algorithm development and design;

• Statistical techniques Bayesian statistics, Data mining, linear and nonlinear regression, parameter selection, categorization, clustering

• Big Data-related skills Statistical techniques; Parallel computing (Matlab, R); GPU computing (CUDA in Matlab, R); Data sorting and large data set manipulation; Graphics (heat map, contour map, 3D graphics, 2D and 3D animation); Data mining; Matrix manipulation, High Performance Computing (Matlab); Database handling (Matlab, Python, Spark)

• Engineering-related skills Linux; Raspberry Pi setup and extension; RPi programming (including motors, automatic imaging); COMSOL microfluidic device design and fluids simulation

• Application development Graphical user interface design and implementation (Matlab, R), web application development (R Shiny); Virtual machines

• Other skills Latex, vector graphics in Latex;