DNA Fragment assembly - an NP-Hard problem - is one of the major steps in of DNA sequencing. Multiple strategies have been used for this problem, including greedy graph-based algorithms, deBruijn graphs, and the overlap-layout-consensus approach. Thi...
Genome-wide association studies (GWASs) have mined many common genetic variants associated with human complex traits like diseases. After that, the functional annotation and enrichment analysis of significant SNPs are important tasks. Classic methods...
Journal of computational biology : a journal of computational molecular cell biology
Jun 27, 2016
Genomics has been used with varying degrees of success in the context of drug discovery and in defining mechanisms of action for diseases like cancer and neurodegenerative and rare diseases in the quest for orphan drugs. To improve its utility, accur...
BACKGROUND: Targeted sequencing of discrete gene sets is a cost effective strategy to screen subjects for monogenic forms of disease. One method to achieve this pairs microfluidic PCR with next generation sequencing. The PCR step of this pipeline cre...
IEEE/ACM transactions on computational biology and bioinformatics
May 3, 2016
The transcription factors (TFs) can activate or suppress gene expression by binding to specific sites, hence are crucial regulatory elements for transcription. Recently, series of discriminative motif finders have been tailored to offering promising ...
The rapid improvement of next-generation sequencing performance now enables us to analyze huge sample sets with more than ten thousand specimens. However, DNA extraction can still be a limiting step in such metagenomic approaches. In this study, we a...
UNLABELLED: We present a new R package for training gapped-kmer SVM classifiers for DNA and protein sequences. We describe an improved algorithm for kernel matrix calculation that speeds run time by about 2 to 5-fold over our original gkmSVM algorith...
Modeling the properties and functions of DNA sequences is an important, but challenging task in the broad field of genomics. This task is particularly difficult for non-coding DNA, the vast majority of which is still poorly understood in terms of fun...
Recombination is crucial for biological evolution, which provides many new combinations of genetic diversity. Accurate identification of recombination spots is useful for DNA function study. To improve the prediction accuracy, researchers have propos...
Journal of computational biology : a journal of computational molecular cell biology
Feb 1, 2016
Constructing coexpression and association networks with omics data is crucial for studying gene-gene interactions and underlying biological mechanisms. In recent years, learning the structure of a Gaussian graphical model from high-dimensional data u...