MOTIVATION: Estimating the future course of patients with cancer lesions is invaluable to physicians; however, current clinical methods fail to effectively use the vast amount of multimodal data that is available for cancer patients. To tackle this p...
MOTIVATION: Gene expression prediction is one of the grand challenges in computational biology. The availability of transcriptomics data combined with recent advances in artificial neural networks provide an unprecedented opportunity to create predic...
MOTIVATION: As one of important epigenetic modifications, DNA N4-methylcytosine (4mC) is recently shown to play crucial roles in restriction-modification systems. For better understanding of their functional mechanisms, it is fundamentally important ...
MOTIVATION: Recognition of different genomic signals and regions (GSRs) in DNA is crucial for understanding genome organization, gene regulation, and gene function, which in turn generate better genome and gene annotations. Although many methods have...
Since the discovery of 5-hydroxymethylcytosine (5hmC) as a prominent DNA modification found in mammalian genomes, an emergent question has been what role this mark plays in gene regulation. 5hmC is hypothesized to function as an intermediate in the d...
The importance of genomic sequence context in generating transcriptome diversity through RNA splicing is independently unmasked by two studies in this issue (Jaganathan et al., 2019; Baeza-Centurion et al., 2019).
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...
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