John Yin
Principal Investigator, Vilas Distinguished Achievement Professor
How can we translate human physiology into models that are computable?
In our cross-disciplinary study of the lower urinary tract, we reviewed the literature, highlighting how fluid flows and bio-mechanical signals share information with the nervous system. Our current efforts are advancing hybrid mechanistic-neural network models, informed by experimental rat data. The greatest gap in our understanding in the interface of the bladder-and-urethra with the nervous
How does the timing of virus infection depend on their host?
To address this question, consider the delay time that describes how long it will take, following the start of infection, for virus progeny to be released from infected cells (left). Analysis of such growth curves for more than 100 viruses indicate delay times from less than 100 to more than 10,000 minutes or about 1
Heterogeneity in the production of virus particles by individual infected cells
Different cells from the same environment produce a wide range of virus particles from less than 100 (curve B3) to nearly 10,000 (curve C7 and A3); experiments are for vesicular stomatitis virus (VSV) infections of BHK21 host cells. For details see Timm and Yin (2012).
Computational modeling of virus growth in cells
When a virus infects a living cell, how long before virus progeny are released, and how many particles will be made? One may build a model for infection by writing equations that describe each of the essential steps: entry, transcription, translation, genome replication, particle assembly and release from the cell. Experimental data are used to
Patterns of infection interference
In the absence of interfering particles, virus infections spread uniformly to greater radii (far left, red protein expression linked to virus growth). When interfering particles are present, infection is limited (only patchy red). Green protein expression is driven by interfering particles, and yellow reflects a balance of co-infection (virus and interfering particles). For details, see
Fluid flow enhances the spread of virus infection
In the absence of flow regions of cell infection are localized (white points). But in the presence of outward radial flows, regions of infection are spread in the direction of flow (white comets). Culture wells are 35mm in diameter. Details are Zhu et al. 2007. How do spontaneous fluid flows arise in culture wells? Evaporation
Drying process could be key step in the development of life
https://engineering.wisc.edu/news/drying-process-could-be-key-step-in-the-development-of-life/
Astrovirology: how viruses enhance our understanding of life in the Universe
Viruses are ubiquitous replicators of molecular information and agents of community change. They potently affect life on Earth, and they may play a critical role in human spaceflight, for life-detection missions to other planetary bodies and in planetary protection. Read more...
Opening: Post-doctoral Research Associate
Post-doctoral Research Associate Wisconsin Institute for Discovery, Chemical and Biological Engineering University of Wisconsin-Madison The Yin Lab at the University of Wisconsin-Madison (wid.wisc.edu) has an immediate opening at the postdoctoral level to pursue projects in computational biology at the interface between mechanistic modeling and machine learning. NIH and NSF funded projects span diverse application areas