Saurabh Sinha

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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)
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)
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)
We report here genome sequences and comparative analyses of three closely related parasitoid wasps: Nasonia vitripennis, N. giraulti, and N. longicornis. Parasitoids are important regulators of arthropod populations, including major agricultural pests and disease vectors, and Nasonia is an emerging genetic model, particularly for evolutionary and(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)
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)
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)
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)
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)