B.S. — Biotechnology, University of Central Florida, 2012 - 2015 Distinctions: Summa Cum Laude, Top Honors, University Honors GPA: 4.0 / 4.0
Marine Biological Laboratory, Woods Hole, MA, 2016 Course: Computational Image Analysis in Cell and Developmental Biology
University of California San Francisco, San Francisco, CA, 2015 - Present PhD Candidate Principal Investigators: Andrew Brack & Wallace Marshall Thesis: Inferring stem cell state from cell behavior
Developed software tools to infer cell state from motility behaviors
Quantified state transition rates during muscle stem cell activation based on timelapse image data
Developed tools to apply deep convolutional neural networks to the analysis of cell motility
Developing an image based classification method for muscle stem cell subpopulation states
University of Central Florida, Orlando, FL, 2011 - 2015 Research and Mentoring Program Scholar, Burnett Research Scholar Principal Investigator: Kiminobu Sugaya, PhD
Characterized induced pluripotent reprogramming in mesenchymal stem cells using machine-learning based image analysis, investigated cell sorting applications
Examined the use of polarized optical torques to guide cell motility in collaboration with U. of Central Florida’s optics research center
Investigated a pathway for producing neuronal cells from adipose derived stem cells by modulation of Nanog. Published as a first-author paper, presented at Neuroscience 2013.
University of California San Francisco, San Francisco, CA, 2014 Summer Summer Research and Training Program, Amgen Scholar Principal Investigator: K. Mark Ansel, PhD
Investigated the role of microRNA-29 in the regulation of cytokine production in T-cells
Awarded the summer program’s competitive Outstanding Presentation Award
National Institute on Aging, Baltimore, MD, 2012 Summer Summer Fellow, Image Informatics and Computational Biology Unit Principal Investigator: Ilya G. Goldberg, PhD
Identified differential aging rates across the anatomy of C. elegans using machine learning based image classification
Investigated the relationship between cognitive and age related morphologies in the primate hippocampus
Python, Matlab, R
Deep learning with convolutional neural networks
Quantitative imaging, multivariate data analysis, machine learning
Object-oriented programming, VCS (git/svn), Test Driven Development
Jacob C. Kimmel, Amy Y. Chang, Andrew S. Brack, Wallace F. Marshall. Inferring cell state by quantitative motility analysis reveals a dynamic state system and broken detailed balance. 2017. bioRxiv 168534; doi: https://doi.org/10.1101/168534. (Submitted for publication).
Jacob C. Kimmel, Andrew S. Brack, and Wallace F. Marshall. 2017. Deep convolutional neural networks allow analysis of cell motility during stem cell differentiation and neoplastic transformation. bioRxiv. doi: https://doi.org/10.1101/159202. (Submitted for publication).
Colin Constant, Jacob C. Kimmel, Kiminobu Sugaya, Aristide Dogariu. Optically Controlled Subcellular Diffusion. Frontiers in Optics & Laser Science. 2015.
Jacob C. Kimmel, Kiminobu Sugaya. Nanog Overexpression Increases Neural Marker Expression in Adipose Derived Stem Cells. Recent Patents in Regenerative Medicine. 2014. 4(1):69-74.
Kimmel J, Chang A, Brack AS, Marshall WF. Inferring cell state from cell motility behavior. Selected oral presentation to the NSF Quantitative Cell Biology Network Workshop. Allen Institute for Cell Science, Seattle, WA. 2016.
Kimmel J, Willenberg BJ, Brown A, Sugaya K. Delivery of TGF-beta signaling factors by capillary alginate gel. U. of Central Florida, Showcase of Research Excellence. 2015.
Kimmel J, Kageyama R, Steiner D, Ansel KM. miR-29 Regulation of TNF-alpha production in T cells. University of California, San Francisco. 2014.
Kimmel J, Yuan B, Constant C, Dogariu D, Foroosh H, Sugaya K. Characterization of induced pluripotent reprogramming in mesenchymal stem cells by quantitative image analysis. U. of Central Florida, Showcase of Research Excellence. 2014.
Kimmel J, Sugaya K. Nanog overexpression improves neural transdifferentiation in adipose derived stem cells. Neuroscience 2013, San Diego, CA. 2013.
Kimmel J, Eckley DM, Colleta C, Long J, Orlov N, Rapp P, Goldberg IG. Do different tissues age at different rates?. National Institute on Aging, Baltimore, MD. 2012.