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In this paper, we introduce overview visualization tools for large-scale multiple genome alignment data. Genome alignment visualization and, more generally, sequence alignment visualization are an important tool for understanding genomic sequence data. As sequencing techniques improve and more data become available, greater demand is being placed on(More)
There is substantial evidence implicating mitochondrial dysfunction and free radical generation as major mechanisms of neuronal death in neurodegenerative diseases. The major free radical scavenging enzyme in mitochondria is manganese superoxide dismutase (SOD2). In the present study we investigated the susceptibility of mice with a partial deficiency of(More)
Visualizations often seek to aid viewers in assessing the big picture in the data, that is, to make judgments about aggregate properties of the data. In this paper, we present an empirical study of a representative aggregate judgment task: finding regions of maximum average in a series. We show how a theory of perceptual averaging suggests a visual design(More)
Many visualization tasks require the viewer to make judgments about aggregate properties of data. Recent work has shown that viewers can perform such tasks effectively, for example to efficiently compare the maximums or means over ranges of data. However, this work also shows that such effectiveness depends on the designs of the displays. In this paper, we(More)
Many bioinformatics applications construct classifiers that are validated in experiments that compare their results to known ground truth over a corpus. In this paper, we introduce an approach for exploring the results of such classifier validation experiments, focusing on classifiers for regions of molecular surfaces. We provide a tool that allows for(More)
Our visual system can extract statistical properties of large collections of objects. Most studies of this ability focus on mean value judgments across a constrained set of dimensions 1-3. We explore how two visual representations of a set, line height and color, influence viewers' abilities to visually extract different properties from the set. Experiment(More)
In this position paper, we enumerate two approaches to the evaluation of visualizations which are associated with two approaches to knowledge formation in science: reductionism, which holds that the understanding of complex phenomena is based on the understanding of simpler components; and holism, which states that complex phenomena have characteristics(More)
Many bioinformatics applications utilize machine learning techniques to create models for predicting which parts of proteins will bind to targets. Understanding the results of these protein surface binding classifiers is challenging, as the individual answers are embedded spatially on the surface of the molecules, yet the performance needs to be understood(More)
Many bioinformatics applications utilize machine learning techniques to create models for predicting which parts of proteins will bind to targets. Understanding the results of these protein surface binding classifiers is challenging, as the individual answers are embedded spatially on the surface of the molecules, yet the performance needs to be understood(More)