Donald A. Stewart

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Massively parallel sequencing instruments enable rapid and inexpensive DNA sequence data production. Because these instruments are new, their data require characterization with respect to accuracy and utility. To address this, we sequenced a Caernohabditis elegans N2 Bristol strain isolate using the Solexa Sequence Analyzer, and compared the reads to the(More)
Previously reported applications of the 454 Life Sciences pyrosequencing technology have relied on deep sequence coverage for accurate polymorphism discovery because of frequent insertion and deletion sequence errors. Here we report a new base calling program, Pyrobayes, for pyrosequencing reads. Pyrobayes permits accurate single-nucleotide polymorphism(More)
—Electroporation has been widely used to manipulate cells and tissues, but quantitative understanding of electrical behavior in cell membranes has not been achieved. According to the transient aqueous pore hypothesis, pore creation and expansion is a nonlinear, hysteretic process. Different membrane sites respond locally to their own transmembrane voltage(More)
BACKGROUND Investigation of bioheat transfer problems requires the evaluation of temporal and spatial distributions of temperature. This class of problems has been traditionally addressed using the Pennes bioheat equation. Transport of heat by conduction, and by temperature-dependent, spatially heterogeneous blood perfusion is modeled here using a transport(More)
The frequency and time domain transmembrane voltage responses of a cylindrical cell in an external electric field are calculated using a transport lattice, which allows solution of a variety of biologically relevant transport problems with complex cell geometry and field interactions. Here we demonstrate the method for a cylindrical membrane geometry and(More)
Cells exposed to electric fields are often confined to a small volume within a solid tissue or within or near a device. Here we report on an approach to describing the frequency and time domain electrical responses of a spatially confined spherical cell by using a transport lattice system model. Two cases are considered: (1) a uniform applied field created(More)
Conditions that stimulate action potentials in one or more nerves is of widespread interest. Axon and nerve models are usually based on two dimensional pre-specified lumped equivalents that assume where currents will flow. In contrast, here we illustrate creation of three dimensional (3D) system models with a transport lattice of interconnected local models(More)
Massively parallel sequencing instruments enable rapid and inexpensive DNA sequence data production. Because these instruments are new, their data require characterization with respect to accuracy and utility. To address this, we sequenced a Caernohabditis elegans N2 Bristol strain isolate using the Solexa Sequence Analyzer, and compared the reads to the(More)
The MIT Faculty has made this article openly available. Please share how this access benefits you. Your story matters. Abstract Background: Investigation of bioheat transfer problems requires the evaluation of temporal and spatial distributions of temperature. This class of problems has been traditionally addressed using the Pennes bioheat equation.(More)
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