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tRFs, 14 to 32 nt long single-stranded RNA derived from mature or precursor tRNAs, are a recently discovered class of small RNA that have been found to be present in diverse organisms at read counts comparable to miRNAs. Currently, there is a debate about their biogenesis and function. This is the first meta-analysis of tRFs. Analysis of more than 50 short(More)
UNLABELLED Long noncoding RNAs (lncRNA) are emerging as major regulators of cellular phenotypes and implicated as oncogenes or tumor suppressors. Here, we report a novel tumor-suppressive locus on human chromosome 15q23 that contains two multiexonic lncRNA genes of 100 kb each: DRAIC (LOC145837) and the recently reported PCAT29. The DRAIC lncRNA was(More)
We have created tRFdb, the first database of transfer RNA fragments (tRFs), available at http://genome.bioch.virginia.edu/trfdb/. With over 100 small RNA libraries analyzed, the database currently contains the sequences and read counts of the three classes of tRFs for eight species: R. sphaeroides, S. pombe, D. melanogaster, C. elegans, Xenopus, zebra fish,(More)
In addition to the core catalytic machinery, bacterial replicative DNA polymerases contain a Polymerase and Histidinol Phosphatase (PHP) domain whose function is not entirely understood. The PHP domains of some bacterial replicases are active metal-dependent nucleases that may play a role in proofreading. In E. coli DNA polymerase III, however, the PHP(More)
BACKGROUND Each year, over 16,000 patients die from malignant brain cancer in the US. Long noncoding RNAs (lncRNAs) have recently been shown to play critical roles in regulating neurogenesis and brain tumor progression. To better understand the role of lncRNAs in brain cancer, we performed a global analysis to identify and characterize all annotated and(More)
Numerous studies have identified prognostic genes in individual cancers, but a thorough pan-cancer analysis has not been performed. In addition, previous studies have mostly used microarray data instead of RNA-SEQ, and have not published comprehensive lists of associations with survival. Using recently available RNA-SEQ and clinical data from The Cancer(More)
Background: We present the results of a reanalysis of four articles from the Cornell Food and Brand Lab based on data collected from diners at an Italian restaurant buffet. Method: We calculated whether the means, standard deviations, and test statistics were compatible with the sample size. Test statistics and p values were recalculated. We also applied(More)
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