DNA research : an international journal for rapid publication of reports on genes and genomes
Dec 1, 2018
Ancient DNA (aDNA) studies often rely on standard methods of mutation calling, optimized for high-quality contemporary DNA but not for excessive contamination, time- or environment-related damage of aDNA. In the absence of validated datasets and desp...
MOTIVATION: Gene expression data represents a unique challenge in predictive model building, because of the small number of samples (n) compared with the huge amount of features (p). This 'n≪p' property has hampered application of deep learning techn...
MOTIVATION: Nucleosome positioning plays significant roles in proper genome packing and its accessibility to execute transcription regulation. Despite a multitude of nucleosome positioning resources available on line including experimental datasets o...
Annals of oncology : official journal of the European Society for Medical Oncology
Apr 1, 2018
BACKGROUND: Tumor-specific mutations form novel immunogenic peptides called neoantigens. Neoantigens can be used as a biomarker predicting patient response to cancer immunotherapy. Although a predicted binding affinity (IC50) between peptide and majo...
MOTIVATION: Although many machine learning techniques have been proposed for distinguishing miRNA hairpins from other stem-loop sequences, most of the current methods use supervised learning, which requires a very good set of positive and negative ex...
Methods in molecular biology (Clifton, N.J.)
Jan 1, 2017
The GO captures many aspects of functional annotations, but there are other alternative complementary sources of protein function information. For example, enzyme functional annotations are described in a range of resources from the Enzyme Commission...
Methods in molecular biology (Clifton, N.J.)
Jan 1, 2017
Two avenues to understanding gene function are complementary and often overlapping: experimental work and computational prediction. While experimental annotation generally produces high-quality annotations, it is low throughput. Conversely, computati...
MOTIVATION: DNA methylation is an intensely studied epigenetic mark, yet its functional role is incompletely understood. Attempts to quantitatively associate average DNA methylation to gene expression yield poor correlations outside of the well-under...