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Gene set enrichment testing can enhance the biological interpretation of ChIP-seq data. Here, we develop a method, ChIP-Enrich, for this analysis which empirically adjusts for gene locus length (the length of the gene body and its surrounding non-coding sequence). Adjustment for gene locus length is necessary because it is often positively associated with(More)
A chromosomal translocation results in production of an oncogenic PAX8-PPARG fusion protein (PPFP) in thyroid carcinomas. PAX8 is a thyroid transcription factor, and PPARG is a transcription factor that plays important roles in adipocytes and macrophages. PPFP retains the DNA binding domains of both proteins; however, the genomic binding sites of PPFP have(More)
The size of electronic devices becomes smaller and smaller and the utilized components and materials are subjected to complex environments including high temperatures, electrical current, mechanical stresses, and others. We need to evaluate the performance of these small-scale materials that are used in such devices. We have shown that these small-scale(More)
UNLABELLED Tests for differential gene expression with RNA-seq data have a tendency to identify certain types of transcripts as significant, e.g. longer and highly-expressed transcripts. This tendency has been shown to bias gene set enrichment (GSE) testing, which is used to find over- or under-represented biological functions in the data. Yet, there(More)
The electrical properties of boron nitride (BN) nanostructures, particularly BN nanotubes (NTs), have been studied less in comparison to the counterpart carbon nanotubes. The present work investigates the field emission (FE) behavior of BNNTs under multiple cycles of FE experiments and demonstrates a strain-engineering pathway to tune the electronic(More)
The recent observation of high flexibility in buckled boron nitride nanotubes (BNNTs) contradicts the pre-existing belief about BN nanotube brittleness due to the partially ionic character of bonding between the B and N atoms. However, the underlying mechanisms and relationships within the nanotube remained unexplored. This study reports for the first time(More)
BACKGROUND Unexpected results were recently reported about the poor surrogacy of Gynecologic Cancer Intergroup (GCIG) defined CA-125 response in recurrent ovarian cancer (ROC) patients. Mathematical modeling may help describe CA-125 decline dynamically and discriminate prognostic kinetic parameters. METHODS Data from CALYPSO phase III trial comparing 2(More)
MOTIVATION Functional enrichment testing facilitates the interpretation of Chromatin immunoprecipitation followed by high-throughput sequencing (ChIP-seq) data in terms of pathways and other biological contexts. Previous methods developed and used to test for key gene sets affected in ChIP-seq experiments treat peaks as points, and are based on the number(More)
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