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ABOUT SCOTT RONQUIST
I am a Bioinformatics PhD Candidate at the University of Michigan (advisor, Indika Rajapakse). I received my BSE in Chemical Engineering at the University of Michigan in 2014. My research interests are in cellular reprogramming, dynamical nuclear image analysis, and applying engineering concepts to understand biological networks.
LinkedIn: https://www.linkedin.com/in/scott-ronquist/
github: https://github.com/scotronq
RESEARCH PROJECTS
4DNvestigator
Problem: The combined analysis of genome structure and function over time is referred to as the 4D Nucleome (4DN). 4DN analysis is necessary to fully understand how a cell operates, but analysis tools are currently underdeveloped.
Goal: Create a 4DN analysis toolbox to provide future researchers with the methods and software necessary to easily comprehend these data
Novelty: Automated analysis of time series Hi-C and RNA-seq data
Impact: 4DN analysis ease of use
MYOD1-mediated fibroblast to muscle cell analysis
Problem: Genome structure and function changes during myogenesis and cellular reprogramming are not well understood
Goal: Improve our understanding of cellular reprogramming through collection and analysis of time series chromatin form and function data
Novelty: Times series data collection and network centrality analysis on coupled form and function data
Impact: Better understanding of cellular reprogramming; tissue regeneration and network control
Algorithm for Cellular Reprogramming
Problem: Determination of transcription factors that can be used for cellular reprogramming is time consuming and inefficient
Goal: Predict transcription factors that can be used to reprogram cells
Novelty: Control theory concepts on time series gene expression data
Impact: Tissue regeneration; cancer cell treatment
Dynamical Nuclear Imaging
Problem: Nucleus image analysis is time consuming, subjective, and often performed on static, unnatural images
Goal: Introduce new methods for the automated analysis of nucleus images
Novelty: Canonical framework detection for time series images, image object recognition techniques tailored for nucleus images
Impact: Automated objective analysis of nucleus images; biopsy analysis
PUBLICATIONS
Braun, R., Ronquist, S.*, …, Rajapakse, I., Ried, T. Single chromosome aneuploidy induces genome-wide perturbation of nuclear organization and gene expression. Neoplasia, 21(4), 401-412
Liu, S., Chen, H., Ronquist, S.*, … & Rajapakse, I. (2018). Genome Architecture Mediates Transcriptional Control of Human Myogenic Reprogramming. iScience 6, 232-246
Ronquist, S., Patterson, G., Brown, M., Chen, H., Bloch, A., Muir, L., ... & Rajapakse, I. (2017). Algorithm for Cellular Reprogramming. Proceedings in the National Academy of Sciences, 114(45), 11832-11837.
Ronquist, S., Meixner, W., Rajapakse, I., & Snyder, J. (2017). Insight into dynamic genome imaging: Canonical framework identification and high-throughput analysis. Methods.
Chen, H., Comment, N., Chen, J., Ronquist, S., Hero, A., Ried, T., & Rajapakse, I. (2015). Chromosome conformation of human fibroblasts grown in 3-dimensional spheroids. Nucleus, 6(1), 55-65.
Chen, H., Chen, J., Muir, L. A., Ronquist, S., Meixner, W., Ljungman, M., ... & Rajapakse, I. (2015). Functional organization of the human 4D Nucleome. Proceedings of the National Academy of Sciences, 112(26), 8002-8007.
SUBMISSIONS
Ronquist, S., Liu, S., Perlman, M., Rajapakse, I. 4DNvestigator: a toolbox for the analysis of time series Hi-C and RNA-seq data
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