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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)
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)
We describe a novel software verification primitive called Oblivious Hashing. Unlike previous techniques that mainly verify the static shape of code, this primitive allows implicit computation of a hash value based on the actual execution (i.e., space-time history of computation) of the code. We also discuss its applications in local software tamper(More)
We present a graph theoretic approach for watermarking software in a robust fashion. While watermarking typical software that are small in size (e.g. a few kilobytes) may be infeasible through this approach, it seems to be a viable scheme for large applications. Our approach works with program ow graphs and uses some abstractions, approximate k-partitions,(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 discovery of cis-regulatory modules in metazoan genomes is crucial for understanding the connection between genes and organism diversity. RESULTS We develop a computational method that uses Hidden Markov Models and an Expectation Maximization algorithm to detect such modules, given the weight matrices of a set of transcription factors known(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)
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)
— Analysis techniques, such as control flow, data flow, and control dependence, are used for a variety of software-engineering tasks, including structural and regression testing, dynamic execution profiling, static and dynamic slicing, and program understanding. To be applicable to programs in languages, such as Java and C++, these analysis techniques must(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)