Current Bioinformatics - Volume 13, Issue 1, 2018

Background: The post-translational modification of tyrosine nitration is an important covalently substituted process in many biochemical processes that are closely related to several human diseases. Objective: Therefore, the correct recognition of nitration sites is useful for diseases diagnosis and the design of effective treatments. However, traditional experimental techniques and methods for the identification of nitration sites Read More

Background: As a crucial component of the entire protein-protein interaction (PPI) network, protein-peptide interactions are ubiquitous in living cells. These interactions play important roles in signaling transduction and regulation. Compared with laborious and time-consuming experimental approaches, predicting protein-peptide interactions with effective computational methods could be convenient and rapid. Method: This s Read More

Background: Data compression is essential for efficient large-scale data processing, so that a number of studies have been done. Grammar-based compression is to find a small grammar that generates input data, and it has been used not only for data compression but also for analysis of biological data since it is useful for pattern extraction. Objective: Recently, for rooted ordered trees, a special kind of network structures Read More

Background: MicroRNAs (miRNAs) are short non-coding RNAs that serve as key regulators at post-transcriptional level in many important biological processes. In recent years, miRNA expression profiles have been largely investigated and demonstrated to be promising biomarkers for discriminating subtypes of complex human diseases and measuring treatment effects. Methods: Most of the analysis approaches for DN Read More

Background: The phospholipase D genes have been identified to play critical roles in plant growth and stress responses. There are 12 and 17 PLD members conformed in Arabidopsis and Oryza sativa respectively. Different PLD isoforms have distinct regulatory and catalytic properties. Method: In this study, the VvPLD genes were cloned using the genome-wide search and RT-PCR amplification from suspenson-cultured grape cell Read More

Background: The flow cytometry (FCM) has been widely used in both basic and clinical research applications. However, the conventional noncoherent fluorescence and the bright or dark field images acquired spatially integrated and can only yield limited information. Few 3D morphological features of cells can be unveiled. Objective: Diffraction imaging techniques can be used to improve the flow cytometry sy Read More

Background: IsomiR is an isoform of microRNA (miRNA), and its sequences vary from those of a reference miRNA, which arose with the advencements of deep sequencing, high miRNA variability has been detected from the same miRNA precursor. IsomiR exists in four main types formed through the following processes: 5' or 3' trimming, Nucleotide addition, Nucleotide removal, and posttranscriptional RNA editing. Read More

Background: We are living in an era that is in general characterized by a lot of data but little information. An enormous amount of biological data collected over several years is now presented as annotations and databases. In this context, all this data properly combined and grouped has great potential for enabling novel discoveries which would then, finally and hopefully, lead to advances in biology and medicine. The inference Read More

Background: Hepatitis C Virus causes the most severe form of chronic liver disease and nearly 200 million people worldwide are estimated to be infected with this virus. Much about the HCV pathogenesis process is still unknown. The study of interactions between HCV and human proteins will lead to deeper understanding of HCV mechanism. Objective: The objective of this paper is to predict potentially new HCV-Human protein Read More

Background: Transcription Factors (TFs) play a pivotal role in a Gene Regulatory Network (GRN) by differentially regulating genes across conditions. In some cases, it requires coordinated regulation of multiple TFs to control a Differentially Expressed (DE) gene. In this line, we have also developed simple architectures to unveil the parallel regulatory control by TFs. Objective: To date there are few works that have conducted active r Read More

Background: Cardamom (Elettaria cardamomum Maton) is an important commodity spice that comes under the ginger family (Zingiberaceae). Several genetic markers are widely being used to analyze plant genomes. However, genetic mapping of cardamom has never been attempted owing to the lack of sufficient number of high quality genetic markers and other pertinent genome information. Objective: The goals of t Read More

Background: Modelling and analysis of metabolic networks can be carried out with different levels of granularity, ranging from structural (topological) analysis to constraint-based methods to kinetic modelling. The increasing number of genome-scale metabolic reconstructions and the growing importance of metabolic modelling intensify the need for integrated approaches allowing the application of different analysis m Read More