Quantifying similarity between motifs

Tomtom allows for the statistical measurement of similarity between pairs of motifs, thereby enabling searching a motif database with a motif query.

This paper presents WiSee, a novel gesture recognition system that leverages wireless signals (e.g., Wi-Fi) to enable whole-home sensing and recognition of human gestures. Since wireless signals do not require line-of-sight and can traverse through walls, WiSee can enable wholehome gesture recognition using few wireless sources. Further, it achieves this goal without requiring instrumentation of the human body with sensing devices. We implement a proof-ofconcept prototype of WiSee using USRP-N210s and evaluate it in both an office environment and a two-bedroom apartment. Our results show that WiSee can identify and classify a set of nine gestures with an average accuracy of 94%.

Nucleosomes are the fundamental repeating unit of chromatin and comprise the structural building blocks of the living eukaryotic genome. Micrococcal nuclease (MNase) has long been used to delineate nucleosomal organization. Microarray-based nucleosome mapping experiments in yeast chromatin have revealed regularly-spaced translational phasing of nucleosomes. These data have been used to train computational models of sequence-directed nuclesosome positioning, which have identified ubiquitous strong intrinsic nucleosome positioning signals. Here, we successfully apply this approach to nucleosome positioning experiments from human chromatin. The predictions made by the human-trained and yeast-trained models are strongly correlated, suggesting a shared mechanism for sequence-based determination of nucleosome occupancy. In addition, we observed striking complementarity between classifiers trained on experimental data from weakly versus heavily digested MNase samples. In the former case, the resulting model accurately identifies nucleosome-forming sequences; in the latter, the classifier excels at identifying nucleosome-free regions. Using this model we are able to identify several characteristics of nucleosome-forming and nucleosome-disfavoring sequences. First, by combining results from each classifier applied de novo across the human ENCODE regions, the classifier reveals distinct sequence composition and periodicity features of nucleosome-forming and nucleosome-disfavoring sequences. Short runs of dinucleotide repeat appear as a hallmark of nucleosome-disfavoring sequences, while nucleosome-forming sequences contain short periodic runs of GC base pairs. Second, we show that nucleosome phasing is most frequently predicted flanking nucleosome-free regions. The results suggest that the major mechanism of nucleosome positioning in vivo is boundary-event-driven and affirm the classical statistical positioning theory of nucleosome organization.

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