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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)
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)
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)
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)
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)
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)
BACKGROUND The high comorbidity between depressive and anxiety disorders, especially among females, has called into question the independence of these two symptom groups. It is possible that childhood anxiety typically precedes depression in girls. Comparing of the predictive utility of symptoms of anxiety with the predictive utility of symptoms of(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)
OBJECTIVE Given the risk for adolescent depression in girls to lead to a chronic course of mental illness, prevention of initial onset could have a large impact on reducing chronicity. If symptoms of depression that emerge during childhood were stable and predictive of later depressive disorders and impairment, then secondary prevention of initial onset of(More)
BACKGROUND Little is known about the role of oppositional defiant disorder (ODD) dimensions on the temporal unfolding of conduct disorder (CD) and depression in girls between childhood and adolescence. METHOD The year-to-year associations between CD and depressive symptomatology were examined using nine waves of annually collected data (ages 8 through 16(More)