Current Bioinformatics - Volume 8, Issue 1, 2013

Protein-protein interactions play important roles in many biological progresses. Previous studies about proteinprotein interactions were mainly based on sequence analysis. As more 3D structural information can be obtained from protein-protein complexes, structural analysis becomes feasible and useful. In this study, we used structural alignment to predict protein-binding sites and analyzed interface properties using 3 Read More

Cancer and diabetes are two highly malignant diseases. Accumulating evidence suggests that cancer incidence might be associated with diabetes mellitus, especially Type-2 diabetes which is characterized by hyperinsulinemia, hyperglycemia, obesity, and overexpression of multiple components of the WNT pathway. These diabetes risk factors can activate a number of signaling pathways that are important in the dev Read More

Simultaneous activation of the agonist and antagonist muscles surrounding a joint, called co-contraction, is suggested to play a role in increasing joint stiffness to improve movement accuracy. However, it has not been clarified how co-contraction is related to movement accuracy, as most models for motor planning and control cannot deal with muscle co-contraction. In this study, the muscle activation and joint stiffness in r Read More

This paper presents a novel speckle smoothing method for ultrasound images. This smoothing method is designed to preserve both the edges and structural details of the image. Speckle noise is suppressed by extending the smoothness of the image in the wavelet-based Hölder spaces. We try to solve the performance of speckle reduction problem from the viewpoint of Besov norm. A comparison of smoothing speckles with the Read More

Gene regulation is a key factor in gaining a full understanding of molecular biology. microRNA (miRNA), a novel class of non-coding RNA, has recently been found to be one crucial class of post-transactional regulators, and play important roles in cancer. One essential step to understand the regulatory effect of miRNAs is the reliable prediction of their target mRNAs. Typically, the predictions are solely based on the sequen Read More

Most complex networks, such as biological networks, social networks, and information networks, are dynamic in nature. Therefore, analysis of these networks provides a better understanding of complex systems compared with analysis of static networks. In this paper, we define a new problem to find the substructures that are significant during the evolving periods, including conserved, appearing and disappearing subs Read More

Signaling pathways play central roles in responding to stimuli or transmitting signals from outside to inside of cells, which in turn regulate a series of complex biological processes that are vital for the function of cells. Unfortunately, the structure and function of most pathways are not complete or even not available. In the past decade, the availability of large amounts of high-throughput ‘omics’ data enables it possible to infer signa Read More

The expression of genes in three tissue types, adipose, liver and muscle, from normal (Wistar-Kyoto) and diabetic (Goto-Kakizaki) rats, was analyzed to gain insight into the potential functional relationships between these tissues in diabetes progression. For this purpose, the gene expression signatures during different periods of diabetes progression were first obtained, and were characterized by the biological func Read More

We designed a procedure to explore cellular relationships from sets of characteristic genes in distinctive cell types, by using a partial canonical correlation analysis. The present procedure was then applied to the characteristic gene sets of seven subtypes of testicular germ cell tumors, reported previously. The cellular relationships were reconstructed well, and were consistent with the general histologic lineage model. N Read More

The induced pluripotent stem cells (iPSCs), generated from transcription factor-induced reprogramming, hold the great promise as the next generation materials for regenerative medicine. Intensive follow-up studies have accumulated a large amount of high-throughput data in transcription, proteomics, methylation, and other levels, which makes the computational studies feasible. Here we briefly review the rec Read More

Amyotrophic lateral sclerosis (ALS) is a complicated and devastating neurodegenerative disease. To date, its diagnosis is still mainly based on clinical symptoms and electromyographic findings. High rates of misdiagnosis and delayed diagnosis are the major hurdles in ALS treatment. Thus, searching for biomarkers to improve clinical diagnosis of ALS is a highly desirable goal. Here we review current potential biomarkers deri Read More

Ion channels are integral membrane proteins that are responsible for most physiological functions including the electrical activity of excitable cells. Their expression and function are regulated by a variety of means including microRNAs (miRNAs). MicroRNAs are small non coding RNAs, 22 nucleotides in length, involved in regulation of gene expression. In this study, we attempt to predict the miRNA targets of ion channel ge Read More

The histone octamer induced bending of DNA into the superhelix structure in nucleosome core particle is important for DNA packing into chromatin, which is directly associated with gene expression and transcription regulation. In this paper, we review current computational methodologies of nucleosome positioning signal recognition based on the sequence and structural features. Sequence-based methods c Read More

Construction of the gene regulatory networks is a challenged problem in systems biology and bioinformatics. This paper presents construction of gene network using combined quantum-behaved PSO and K2 algorithm. Recent studies have shown that Bayesian Network is an effective way to learn the network structure. K2 algorithm is widely used because of its heuristic searching techniques and fast convergence, but it suffer Read More