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The prediction of regulatory elements is a problem where computational methods offer great hope. Over the past few years, numerous tools have become available for this task. The purpose of the current assessment is twofold: to provide some guidance to users regarding the accuracy of currently available tools in various settings, and to provide a benchmark(More)
The zebra finch is an important model organism in several fields with unique relevance to human neuroscience. Like other songbirds, the zebra finch communicates through learned vocalizations, an ability otherwise documented only in humans and a few other animals and lacking in the chicken-the only bird with a sequenced genome until now. Here we present a(More)
Regression testing is applied to modified software to provide confidence that the changed parts behave as intended and that the unchanged parts have not been adversely affected by the modifications. To reduce the cost of regression testing, test cases are selected from the test suite that was used to test the original version of the software---this process(More)
BACKGROUND This paper addresses the problem of discovering transcription factor binding sites in heterogeneous sequence data, which includes regulatory sequences of one or more genes, as well as their orthologs in other species. RESULTS We propose an algorithm that integrates two important aspects of a motif's significance - overrepresentation and(More)
A prominent theory states that animal phenotypes arise by evolutionary changes in gene regulation, but the extent to which this theory holds true for behavioral evolution is not known. Because "nature and nurture" are now understood to involve hereditary and environmental influences on gene expression, we studied whether environmental influences on a(More)
Program-dependence information is useful for a variety of applications, such as software testing and maintenance tasks, and code optimization. Properly defined, control and data dependences can be used to identify semantic dependences. To function effectively on whole programs, tools that utilize dependence information require information about(More)
Aging is characterized by specific alterations in gene expression, but their underlying mechanisms and functional consequences are not well understood. Here we develop a systematic approach to identify combinatorial cis-regulatory motifs that drive age-dependent gene expression across different tissues and organisms. Integrated analysis of 365 microarrays(More)
Understanding the complex and varied mechanisms that regulate gene expression is an important and challenging problem. A fundamental sub-problem is to identify DNA binding sites for unknown regulatory factors, given a collection of genes believed to be co-regulated. We discuss a computational method that identifies good candidates for such binding sites.(More)
Understanding the mechanisms that determine the regulation of gene expression is an important and challenging problem. A fundamental subproblem is to identify DNA-binding sites for unknown regulatory factors, given a collection of genes believed to be coregulated, and given the noncoding DNA sequences near those genes. We present an enumerative statistical(More)
MOTIVATION The similarity of two biological sequences has traditionally been assessed within the well-established framework of alignment. Here we focus on the task of identifying functional relationships between cis-regulatory sequences that are non-orthologous or greatly diverged. 'Alignment-free' measures of sequence similarity are required in this(More)