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In this paper, we present a brief overview of Pellet: a complete OWL-DL reasoner with acceptable to very good performance, extensive iddleware, and a number of unique features. Pellet is the first sound and complete OWL-DL reasoner with extensive support for reasoning ith individuals (including nominal support and conjunctive query), user-defined datatypes,(More)
Through alternative splicing, most human genes express multiple isoforms that often differ in function. To infer isoform regulation from high-throughput sequencing of cDNA fragments (RNA-seq), we developed the mixture-of-isoforms (MISO) model, a statistical model that estimates expression of alternatively spliced exons and isoforms and assesses confidence(More)
Technologies allowing for specific regulation of endogenous genes are valuable for the study of gene functions and have great potential in therapeutics. We created the CRISPR-on system, a two-component transcriptional activator consisting of a nuclease-dead Cas9 (dCas9) protein fused with a transcriptional activation domain and single guide RNAs (sgRNAs)(More)
The homeodomain transcription factor Nanog is a central part of the core pluripotency transcriptional network and plays a critical role in embryonic stem cell (ESC) self-renewal. Several reports have suggested that Nanog expression is allelically regulated and that transient downregulation of Nanog in a subset of pluripotent cells predisposes them toward(More)
MOTIVATION Analysis of RNA sequencing (RNA-Seq) data revealed that the vast majority of human genes express multiple mRNA isoforms, produced by alternative pre-mRNA splicing and other mechanisms, and that most alternative isoforms vary in expression between human tissues. As RNA-Seq datasets grow in size, it remains challenging to visualize isoform(More)
Recently, there have been a number of proposals for languages for expressing web service constraints and capabilities, with WSPolicy and WSPL leading the way. The proposed languages, although relatively inexpressive, suffer from a lack of formal semantics. In this paper, we provide a mapping of WS-Policy to the description logic fragment species of the Web(More)
Supplementary Figure 1 Annotated isoforms in human and mouse genomes. Supplementary Figure 2 Estimates of  using single‐end reads. Supplementary Figure 3 Steps of MISO statistical inference procedure Supplementary Figure 4 Evidence for exon size‐dependent qRT‐PCR bias. Supplementary Figure 5 MISO estimation for 52 alternative exons in breast cancer(More)