Current Bioinformatics - Volume 8, Issue 2, 2013

Epigenetic modification refers to heritable changes in genotypes or phenotypes through biochemical modifications without altering the underlying DNA sequence. In humans, DNA methylation is a major epigenetic modification that adds a methyl group mainly to the carbon-5 position of the cytosine pyrimidine ring in the cytosine guanine dinucleotide. This epigenetic modification is crucial to normal development and cellular Read More

Correlated mutation is regarded as a phenomenon induced by the demand of maintaining the structure and/or function of a protein during its biological evolution. Since it is closely related to the underlying mechanism of protein structure and function, tremendous efforts have been made to reveal the relationship between correlated mutations and the structure and function of the protein. In the past few decades, different Read More

Owing to the biological significance of single amino acid polymorphism (SAP), there has been an increasing interest in understanding how certain amino acid substitutions give rise to functional change and consequent disease association, while others remain neutral polymorphisms. With the increasing availability of biological data, our knowledge regarding functional elements of the proteome continues to expand. As experim Read More

High-throughput experimental technologies continue to alter the study of current system biology. Investigators are understandably eager to harness the power of these new technologies. Protein-protein interactions on these platforms, however, present numerous production and bioinformatics challenges. Some issues like feature extraction, feature representation, prediction algorithm and results analysis have be Read More

Protein signal peptides play a vital role in targeting and translocation of most secreted proteins and many integral membrane proteins in both prokaryotes and eukaryotes. Consequently, accurate prediction of signal peptides and their cleavage sites is an important task in molecular biology. In the present study, firstly, we develop a novel discriminative scoring method for classifying proteins with or without signal peptides. Thi Read More

Chloroplasts are subcellular organelles found only in green plants and eukaryotic algae. Chloroplasts are of central importance in the photosynthesis process. The subchloroplast localizations of chloroplast proteins are critical in understanding their functions and important for fully decipher the photosynthesis process. Although there are several existing methods that computationally determine protein subchloroplas Read More

In systems biology, it is a great challenge for researchers to identify whether the given set of organic compounds can combine together and form a meaningful pathway. Fortunately, it becomes more and more feasible to address and solve such a problem with the rapidly accumulated information on various organisms. Based on the attainable information, a novel computational approach is proposed to investigate this Read More

In recent years, binary coding of image features, such as local binary patterns and local phase quantization, have become popular in a large variety of image quantification tasks. Lately, some non-binary codings, such as local ternary pattern, have been proposed to improve the performance of these binary based approaches. In these methods it is very important to correctly choose the thresholds applied for building the coding Read More

Proteins interact among them and different interactions are represented as graphs named Protein to Protein Interaction (PPI) networks. From a physical point of view, interactions are performed by contacts among protein structure. Consequently, the study and the comparison of protein structure is an important field in Bioinformatics and Computational Biology. The TM-Align algorithm is a method that presents one of the Read More

Bioinformatics is a promising and innovative research field in 21st century. Automatic gene prediction has been an actively researched field of bioinformatics. Despite a high number of techniques specifically dedicated to bioinformatics problems as well as many successful applications, we are in the beginning of a process to massively integrate the aspects and experiences in the different core subjects such as biology, medi Read More

External stimuli may activate the stress response in Arabidopsis thaliana. The molecules which play important roles in the stress response have been widely studied. However, the interactions, especially logic interactions, among these molecules, need to be studied. In this paper, logic networks are constructed based on gene expression profiles of Arabidopsis under the normal condition and four different stimuli conditi Read More

High energy consumption nowadays alongside with concerns on the environment had caused rising demand for synthetic alternative fuels. These include biofuels that can be produced from a variety of engineered microbes such as Escherichia coli. In the metabolic engineering field, this is done by genetically modifying the target microbes to obtain optimal production of a particular biochemical. Conventional metabolic engi Read More

With advances in biotechnology, a huge amount of high throughput biological data has been and will continuously be produced. The information contained in such data is very useful in understanding the biological process from which such data is collected. Generally, high throughput biological data such as gene expression data is presented in a data matrix. Through matrix decomposition methods, we can often discover some v Read More

The periodic transference of nucleotide strings in bacterial and archaeal complete genomes is investigated by using the metric representation and the recurrence plot method. The generated periodic correlation structures exhibit four kinds of fundamental transferring characteristics: a single increasing period, several increasing periods, an increasing quasi-period and almost noincreasing period. The mechanism of the periodi Read More