BACKGROUND: The accurate screening of tumor genomic landscapes for somatic mutations using high-throughput sequencing involves a crucial step in precise clinical diagnosis and targeted therapy. However, the complex inherent features of cancer tissue,...
High-throughput sequencing techniques have accelerated functional metagenomics studies through the generation of large volumes of omics data. The integration of these data using computational approaches is potentially useful for predicting metagenomi...
BACKGROUND: The postmortem microbiome can provide valuable information to a death investigation and to the human health of the once living. Microbiome sequencing produces, in general, large multi-dimensional datasets that can be difficult to analyze ...
Correct identification of different human epithelial materials such as from skin, saliva and vaginal origin is relevant in forensic casework as it provides crucial information for crime reconstruction. However, the overlap in human cell type composit...
IEEE/ACM transactions on computational biology and bioinformatics
Apr 3, 2019
DNA methylation plays an important role in the regulation of some biological processes. Up to now, with the development of machine learning models, there are several sequence-based deep learning models designed to predict DNA methylation states, whic...
With the rapid development of high-throughput sequencing technology, a large number of transcript sequences have been discovered, and how to identify long non-coding RNAs (lncRNAs) from transcripts is a challenging task. The identification and inclus...
A major limitation of RNA sequencing (RNA-seq) analysis of alternative splicing is its reliance on high sequencing coverage. We report DARTS (https://github.com/Xinglab/DARTS), a computational framework that integrates deep-learning-based predictions...
Blood-based diagnostics tests, using individual or panels of biomarkers, may revolutionize disease diagnostics and enable minimally invasive therapy monitoring. However, selection of the most relevant biomarkers from liquid biosources remains an imme...
Molecular testing is increasingly important in cancer diagnosis. Targeted next generation sequencing (NGS) is widely accepted method but structural variation (SV) detection by targeted NGS remains challenging. In the brain tumor, identification of mo...
Transposon insertion sequencing (TIS) is a widely used technique for conducting genome-scale forward genetic screens in bacteria. However, few methods enable comparison of TIS data across multiple replicates of a screen or across independent screens,...
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