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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)
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. We have constructed a protein functional interaction network by extending(More)
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)
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)
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 marks; few(More)
This study examined the developmental trajectory of anxiety symptoms among 290 boys and evaluated the association of trajectory groups with child and family risk factors and children's internalizing disorders. Anxiety symptoms were measured using maternal reports from the Child Behavior Checklist (T. M. Achenbach, 1991, 1992) for boys between the ages of 2(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)
This study investigated the potential benefits of ultrasound-conditioned sludge dewatering treatments with specific energy dosages from 0 to 35,000 kJ/kg total solids (TS). Capillary suction time (CST) and specific resistance of filtration (SRF) were used to evaluate sludge dewaterability. Sludge water distribution was measured by the drying test and(More)
Minor histocompatibility antigens (mHAg's) are peptides encoded by polymorphic genes that are presented by major histocompatibility complex (MHC) molecules and recognized by T cells in recipients of allogeneic hematopoietic cell transplants. Here we report that an alternative transcript of the proliferation-associated nuclear element 1 (PANE1) gene encodes(More)