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Insulators are DNA sequences that control the interactions among genomic regulatory elements and act as chromatin boundaries. A thorough understanding of their location and function is necessary to address the complexities of metazoan gene regulation. We studied by ChIP-chip the genome-wide binding sites of 6 insulator-associated proteins-dCTCF, CP190,(More)
We systematically generated large-scale data sets to improve genome annotation for the nematode Caenorhabditis elegans, a key model organism. These data sets include transcriptome profiling across a developmental time course, genome-wide identification of transcription factor-binding sites, and maps of chromatin organization. From this, we created more(More)
BACKGROUND Chromatin immunoprecipitation (ChIP), coupled with massively parallel short-read sequencing (seq) is used to probe chromatin dynamics. Although there are many algorithms to call peaks from ChIP-seq datasets, most are tuned either to handle punctate sites, such as transcriptional factor binding sites, or broad regions, such as histone modification(More)
To gain insight into how genomic information is translated into cellular and developmental programs, the Drosophila model organism Encyclopedia of DNA Elements (modENCODE) project is comprehensively mapping transcripts, histone modifications, chromosomal proteins, transcription factors, replication proteins and intermediates, and nucleosome properties(More)
BACKGROUND One challenge facing biologists is to tease out useful information from massive data sets for further analysis. A pathway-based analysis may shed light by projecting candidate genes onto protein functional relationship networks. We are building such a pathway-based analysis system. RESULTS We have constructed a protein functional interaction(More)
A new method for temporal pattern matching of a time series is developed using pattern wavelets and genetic algorithms. The pattern wavelet is applied to the matching of an embedded time series. A problem-specific fitness factor is introduced in the new algorithm, which is useful to construct a fitness function of the feature space. A two-step process(More)
The iPlant Collaborative (iPlant) is a United States National Science Foundation (NSF) funded project that aims to create an innovative, comprehensive, and foundational cyberinfrastructure in support of plant biology research (PSCIC, 2006). iPlant is developing cyberinfrastructure that uniquely enables scientists throughout the diverse fields that comprise(More)
—A new method for analyzing time series data is introduced in this paper. Inspired by data mining, the new method employs time-delayed embedding and identifies temporal patterns in the resulting phase spaces. An optimization method is applied to search the phase spaces for optimal heterogeneous temporal pattern clusters that reveal hidden temporal patterns,(More)
This paper presents a method for improving genetic algorithm (GA) performance. Typically, zero diversity in the population's fitness values signals the stopping point for a GA. As the population evolves, diversity diminishes, causing the same chromosomes to be frequently reevaluated. For real world problems, the computational effort spent on evaluating the(More)