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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)
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)
— 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)
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)
A fundamental challenge facing biologists is to identify DNA binding sites for unknown regulatory factors, given a collection of genes believed to be coregulated. The program YMF identifies good candidates for such binding sites by searching for statistically overrepresented motifs. More specifically, YMF enumerates all motifs in the search space and is(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)
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)