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BCIT Citations Collection
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- Using EA to study the evolution of GRNs controlling biological development
- This chapter surveys recent developments in simulating the evolution of GRNs in developmental biology. Over the past two decades, computational biologists have developed a number of approaches to study how developmental GRNs evolve. This has led to a number of breakthroughs in understanding the mechanisms of how species maintain their body plans, and how they evolve or speciate in response to environmental perturbations. EA uses the general evolutionary processes of repeated mutation, reproduction and selection in optimization problems. The progress in computational biology described here has deepened and refined understanding of the biological principles underlying these processes. Our aim is for this chapter to provide some inspiration to computer scientists in EA to incorporate new biologically inspired techniques. We feel this offers a large potential for improving EA efficiency. In turn, computational biology could greatly benefit from EA research, for instance in multi-objective optimization, coding of multiscale problems, and efficiencies in solution techniques. Following a brief survey of the major trends in the computational biology approaches, we discuss the refinements these have made to understanding evolutionary mechanisms. In particular, we discuss the factors affecting GRN evolvability and robustness; the effect different genetic alteration mechanisms (e.g. types of mutation) have on evolutionary speed and robustness; the role of network growth; modelling co-evolution; modelling multi-factor control of gene expression; and applying these techniques to the evolution of GRNs controlling spatially-dependent gene expression (underlying embryonic tissue differentiation). We finish with a brief summary of how these might be incorporated into and improve EA searches., Book chapter, Published.
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- Using evolutionary computations to understand the design and evolution of gene and cell regulatory networks
- This paper surveys modeling approaches for studying the evolution of gene regulatory networks (GRNs). Modeling of the design or ‘wiring’ of GRNs has become increasingly common in developmental and medical biology, as a means of quantifying gene–gene interactions, the response to perturbations, and the overall dynamic motifs of networks. Drawing from developments in GRN ‘design’ modeling, a number of groups are now using simulations to study how GRNs evolve, both for comparative genomics and to uncover general principles of evolutionary processes. Such work can generally be termed evolution in silico. Complementary to these biologically-focused approaches, a now well-established field of computer science is Evolutionary Computations (ECs), in which highly efficient optimization techniques are inspired from evolutionary principles. In surveying biological simulation approaches, we discuss the considerations that must be taken with respect to: (a) the precision and completeness of the data (e.g. are the simulations for very close matches to anatomical data, or are they for more general exploration of evolutionary principles); (b) the level of detail to model (we proceed from ‘coarse-grained’ evolution of simple gene-gene interactions to ‘fine-grained’ evolution at the DNA sequence level); (c) to what degree is it important to include the genome’s cellular context; and (d) the efficiency of computation. With respect to the latter, we argue that developments in computer science EC offer the means to perform more complete simulation searches, and will lead to more comprehensive biological predictions., Peer-reviewed article, Published.
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- Using ranking functions to determine plausible action histories
- Proceedings of the Sixth Workshop on Nonmonotonic Reasoning, Action, and Change (NRAC-05), Edinburgh, Scotland, 2005. We use ranking functions to reason about belief change following an alternating sequence of actions and observations. At each instant, an agent assigns a plausibility value to every action and every state; the most plausible world histories are obtained by minimizing the sum of these values. Since plausibility is given a quantitative rank, an agent is able to compare the plausibility of actions and observations. This allows action occurrences to be postulated or refuted in response to new observations. We demonstrate that our formalism is a generalization of our previous work on the interaction of revision and update., Conference paper, Published.
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- Variable patterning in fruit fly embryos due to basins of attraction in underlying gene regulatory dynamics
- Proceedings of Previous work on a reaction-diffusion model of a 4-gene regulatory network governing insect segmentation characterized the dynamical basis of robustness to perturbations in this system [1,2]. Here, we computationally study system behavior near bifurcation points corresponding to weak-allele mutant embryos (i.e. with altered gene regulation). Our computations suggest that the variable expressivity and incomplete penetrance observed in some gene mutations may stem from response of the dynamical system to variable input (regulatory genes) near such bifurcation points., Peer-reviewed article, Published. Received: 14 April 2012; Accepted: 2 October 2012.
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- Variation of select flavonols and chlorogenic acid content of elderberry collected throughout the Eastern United States
- American elderberries are commonly collected from wild plants for use as food and medicinal products. The degree of phytochemical variation among wild populations has not been established and might affect the overall quality of elderberry dietary supplements. The three major flavonols identified in elderberries are rutin, quercetin and isoquercetin. Variation in the flavonols and chlorogenic acid was determined for 107 collections of elderberries from throughout the eastern United States using an optimized high performance liquid chromatography with ultraviolet detection method. The mean content was 71.9 mg per 100 g fresh weight with variation ranging from 7.0 to 209.7 mg per 100 g fresh weight within the collected population. Elderberries collected from southeastern regions had significantly higher contents in comparison with those in more northern regions. The variability of the individual flavonol and chlorogenic acid profiles of the berries was complex and likely influenced by multiple factors. Several outliers were identified based on unique phytochemical profiles in comparison with average populations. This is the first study to determine the inherent variability of American elderberries from wild collections and can be used to identify potential new cultivars that may produce fruits of unique or high-quality phytochemical content for the food and dietary supplement industries., Peer-reviewed article, Published. Received 16 April 2015; Revised 29 October 2015; Accepted 20 December 2015; Available online 23 December 2015.
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- Variations in the hygrothermal properties of several wood-based building products
- Proceedings of Second International Building Physics Conference: 14 September 2003, Leuven, Belgium. A systematic investigation of the hygrothermal properties of a number of oriented strand boards, plywood products, wood fibreboards and composite wood sidings has resulted in new information on the variations of thermal conductivity, water vapour permeability, moisture diffusivity, sorption- desorption-suction isotherms, water absorption coefficient and air permeability of these classes of products in North America. The experimental and analytical procedures used in the investigation are all based eitheron International Standards or on well-documented and peer-reviewed approaches. This paper presents the description of the products in each category and detailed information on the range of properties. The details include, density and temperature dependences of thermal conductivity,dependence of vapour resistance factor on relative humidity, dependence of moisture diffusivity on moisture concentration, equilibrium moisture content for the full range of relative humidity, variations in the water absorption coefficients and dependence of air permeability on pressure difference., Conference paper, Published. A version of this document is published in: Research in Building Physics, Leuven, Belgium, Sept. 14-18, 2003, pp. 35-42.
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- Verification and validation
- The hygrothermal performance of building envelope systems is dictated by their responses to combined heat, air and moisture fluctuations produced by exterior and interior conditions. Research has focused on both laboratory experimentation and modeling of envelope systems by computer programs (hygrothermal tools). Experimental studies played a crucial role in the development of hygrothermal tools, and continue to offer useful information for their improvement. To be used with confidence, however, hygrothermal tools must be verified and, if possible, validated. To date, no comprehensive schemes for benchmarking hygrothermal tools exist as, for example, exist for energy simulation tools. Three comparisons are typically used to show the practical merits of simulation tools: inter-model, analytical, and empirical. This paper demonstrates how confidence in a 1-dimensional hygrothermal simulation tool can be built by such comparisons, and proposes them as the basis for a verification and validation methodology., Research report, Published.
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- Which foot? A comparative effectiveness study of subject-generated ankle kinetics as a measure of prosthetic foot function across a range of K levels
- This double-blind randomized controlled trial offers evidence that flexible energy storage return (ESR) feet produce lower peak moments during walking and are preferred by trans-tibial amputees., Research report, Published.
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- Women in a male-dominated field
- Proceedings of AERA 2019 Conference in Toronto, ON from April 5th to 9th, 2019., Peer reviewed, Accepted for publication., Conference paper