Jarad Niemi

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An increasingly common component of studies in synthetic and systems biology is analysis of dynamics of gene expression at the single-cell level, a context that is heavily dependent on the use of time-lapse movies. Extracting quantitative data on the single-cell temporal dynamics from such movies remains a major challenge. Here, we describe novel methods(More)
A prerequisite for the mechanistic simulation of a biochemical system is detailed knowledge of its kinetic parameters. Despite recent experimental advances, the estimation of unknown parameter values from observed data is still a bottleneck for obtaining accurate simulation results. Many methods exist for parameter estimation in deterministic biochemical(More)
Advances in biology and engineering have enabled the reprogramming of cells with well-defined functions, leading to the emergence of synthetic biology. Early successes in this nascent field suggest its potential to impact diverse areas. Here, we examine the feasibility of engineering circuits for cell-based computation. We illustrate the basic concepts by(More)
Syndromic surveillance has, so far, considered only simple models for Bayesian inference. This paper details the methodology for a serious, scalable solution to the problem of combining symptom data from a network of U.S. hospitals for early detection of disease outbreaks. The approach requires high-end Bayesian modeling and significant computation, but the(More)
We explore how the big-three computing paradigms—symmetric multi-processor (SMP), graphical processing units (GPUs), and cluster computing—can together be brought to bear on large-data Gaussian processes (GP) regression problems via a careful implementation of a newly developed local approximation scheme. Our methodological contribution focuses primarily on(More)
A goal of systems biology is to understand the dynamics of intracellu-lar systems. Stochastic chemical kinetic models are often utilized to accurately capture the stochastic nature of these systems due to low numbers of molecules. Collecting system data allows for estimation of stochastic chemical kinetic rate parameters. We describe a well-known, but(More)
Management policies for disease outbreaks balance the expected morbidity and mortality costs versus the cost of intervention policies. We present a methodology for dynamic determination of optimal policies in a stochastic compartmental model with parameter uncertainty. Our approach is to first carry out sequential Bayesian estimation of outbreak parameters(More)
Phylogenetic trees are widely used visual representations in the biological sciences and the most important visual representations in evolutionary biology. Therefore, phylogenetic trees have also become an important component of biology education. We sought to characterize reasoning used by introductory biology students in interpreting taxa relatedness on(More)
reproduction in any medium, provided the original work is properly cited. Objective Develop fast sequential Bayesian inference for disease outbreak counts. Introduction Development of effective policy interventions to stem disease outbreaks requires knowledge of the current state of affairs, e.g. how many individuals are currently infected, a strain's(More)