Dynamic regulation and packaging of genetic information is achieved by the organization of DNA into chromatin. Nucleosomal core histones, which form the basic repeating unit of chromatin, are subject to various post-translational modifications such as acetylation, methylation, phosphorylation, and ubiquitinylation. These modifications have effects on chromatin structure and, along with DNA methylation, regulate gene transcription. The goal of this study was to determine if patterns in modific...

To evaluate the early diagnostic value of circulating miRNA-21 in diagnosis of lung cancer, databases such as Wan Fang, VIP, PubMed, and Elsevier were systematically searched from 2005 to 2013 to collect relevant references in which the diagnostic value had been evaluated. The statistics were consolidated and the qualities of the studies were classified. The data were analyzed using Meta Disc1.4 software. The diagnostic value of circulating miRNA-21 in lung cancer was assessed by pooling sens...

Numerical characterizations of DNA sequence can facilitate analysis of similar sequences. To visualize and compare different DNA sequences in less space, a novel descriptors extraction approach was proposed for numerical characterizations and similarity analysis of sequences. Initially, a transformation method was introduced to represent each DNA sequence with dinucleotide physicochemical property matrix. Then, based on the approximate joint diagonalization theory, an eigenvalue vector was ex...

The identification of communities is imperative in the understanding of network structures and functions. Using community detection algorithms in biological networks, the community structure of biological networks can be determined, which is helpful in analyzing the topological structures and predicting the behaviors of biological networks. In this paper, we analyze the diseasome network using a new method called disease-gene network detecting algorithm based on principal component analysis, ...

It has been well accepted that the folding energy landscape may resemble a funnel according to the theory of protein folding. This theory of "folding funnel" has been extensively studied and thought to play an important role in guiding the sampling process of the protein folding and refinement in protein structure prediction. Here, we have investigated the relationship between the "funnel likeness" of protein folding and the size/structure of the proteins based on a set of...

Network motif is defined as a frequent and unique subgraph pattern in a network, and the search involves counting all the possible instances or listing all patterns, testing isomorphism known as NP-hard and large amounts of repeated processes for statistical evaluation. Although many efficient algorithms have been introduced, exhaustive search methods are still infeasible and feasible approximation methods are yet implausible. Additionally, the fast and continual growth of biological networks...

Phylogenetic trees have been widely used in the study of evolutionary biology for representing the tree-like evolution of a collection of species. However, different data sets and different methods often lead to the construction of different phylogenetic trees for the same set of species. Therefore, comparing these trees to determine similarities or, equivalently, dissimilarities, becomes the fundamental issue. Typically, Tree Bisection and Reconnection (TBR) and Subtree Prune and Regraft (SP...

The recent breakthroughs in next-generation sequencing technologies, such as those of Roche 454, Illumina/Solexa, and ABI SOLID, have dramatically reduced the cost of producing short reads of the genome of new species. The huge volume of reads, along with short read length, high coverage, and sequencing errors, poses a great challenge to de novo genome assembly. However, the paired-end information provides a new solution to these problems. In this paper, we review and compare some current ass...

Similarities and dissimilarities between biomolecular networks cannot be intuitively recognized even after the development of several comparison algorithms because of the lack of visualization tools. In this paper, an integrated tool kit named Biomolecular Network Match (BNMatch) is designed and developed based on Cytoscape—a popular and open-source tool for analyzing and visualizing networks. BNMatch integrates the comparison of the outputs of algorithms used for processing biomolecular netw...

A novel avian-origin H7N9 influenza virus was discovered in March in China and has caused a total of 131 people infected including 39 deaths in China as of June 9, 2013. Adaptation of avian viruses to efficiently infect humans requires the viral hemagglutinin (HA) binding switches from avian to human type receptors with help of some mutations in HA. As such it is critical for pandemic assessment to discover these mutations as hallmarks of adaptation. To continue our previous study of this nov...

Current methods for the detection of differential gene expression focus on finding individual genes that may be responsible for certain diseases or external irritants. However, for common genetic diseases, multiple genes and their interactions should be understood and treated together during the exploration of disease causes and possible drug design. The present study focuses on analyzing the dynamic patterns of co-regulated modules during biological progression and determining those having r...