These mainstream methods of motif-searching involve testing a very large number of hypotheses in parallel, with an associated high risk of false positive results. For example, the total number of possible 6-node motif candidates is over 1.5 million, meaning that if all are tested for, roughly ...
meaning that MHC-I–peptide binding prediction is an extremely imbalanced classification process. In fact, the imbalance among classes is a common issue in machine learning, and some methods have been developed to deal with it21. In MHCfovea, we used the ensemble strategy with downsampling22,23...
we reject the null hypothesis, meaning we assume that the two rows were not sampled from the same distribution. The quantity - log10(p-value(a|M))can be considered as a quantitative measure of strand bias and is called thestrand bias score...
In this work, we thoroughly examine the most common network motifs2,6with explicit delays and present an approachable, step-by-step view of the mathematical analysis (applying established DDE methods34,51) in order to make such delay equations easy to use for biologists and others. We show th...
Here, we illustrate an analytical model to derive the mean number of occurrences of an induced motif in an unlabeled network with respect to a random graph model. A comprehensive experimental analysis shows the effectiveness of our approach for the computation of the expected number of induced ...
For example, the QGRS GGGACGTTCGGATTGGGTTACCAGGG would be considered (only for the purposes of the tetrad similarity computation) to have a tetrad length of 2.75 - as three of the four tracts have an adjacent extra guanine, meaning that a single mutation in the other tract would have ...
Transcription factors (TFs) control transcription by binding to specific regions of DNA called transcription factor binding sites (TFBSs). The identification of TFBSs is a crucial problem in computational biology and includes the subtask of predicting th
In biological networks, network motifs represent meaning to protein family and to pathway conservation26, which has been shown theoretically and experimentally27. Herein, we studied network motifs by relabelling nucleotide positions with codon positions. Despite the tremendous advancements in the field of...
C. Epigenetic regulation of the neural transcriptome: the meaning of the marks. Nat Neurosci 13, 1313–8 (2010). Article CAS Google Scholar Cheng, C. et al. A statistical framework for modeling gene expression using chromatin features and application to modENCODE datasets. Genome Biol 12, ...
such adaptations and modifications are intended to be within the meaning and range of equivalents of the disclosed embodiments, based on the teaching and guidance presented herein. It is to be understood that the phraseology or terminology herein is for the purpose of description and not of limitat...