Current Bioinformatics - Volume 13, Issue 6, 2018

Background: In many important crops genomic studies are generating large amounts of data from cDNA sequencing and RNA expression experiments. Genomic data is complementing the efforts at improving production of new plant varieties with resistance to major worldwide biotic problems, facing the climate change challenge and pursuing the quest for better quality. After the initial exploratory phase of genome s Read More

Background: The development of diagnostic decision support systems (DDSS) requires having a reliable and consistent knowledge based on diseases and their symptoms, signs, and diagnostic tests. Physicians are typically the source of this knowledge but it is not always possible to obtain all the desired information from them. Other valuable sources are medical books and articles describing the diagnosis of diseases, but a Read More

Background: Many bioinformatics pipelines are available nowadays to analyze transcriptomics data produced by high-throughput RNA sequencing. They implement different workflows that address several analysis tasks, supported by the use of third party programs. Nevertheless, a proper workflow definition for RNA-seq data analysis is still lacking. Objective: To proper define what a comprehensive RNA-seq data analysis wo Read More

Background: Unbalanced data is a well-known and common problem in many practical applications of machine learning, having remarkable effects on the performance of standard classifiers. Taking into account the enormous growth of biomedical literature publicly available over Internet, one relevant task for the biomedical community is the automatic classification of relevant documents for further research. Objective: Focusi Read More

Background: Dengue virus (DENV) has become a crucial health concern. The NS2B/NS3 Protease is a major drug target for DENV in rational drug design. At present, effective treatment of DENV is not possible due to unavailability of specific anti-viral drugs. Based on the drug repurposing studies, bromocriptine compound was found to be a potent anti-DENV drug-like compound and it is also an approved drug for treatment Read More

Background: Metallothioneins (MTs) are important proteins for phytoremediation, and are widely involved in heavy metal uptake, transport, and enrichment. Objective: The aim of this research was to clarify all the MT genes in Populus trichocarpa, and to determine their sequences, chromosome distribution, and codon-use preferences. The results of this study would further our understanding of the diversity of popla Read More

Background: The accurate classification of tumors types is mainly important for the treatment of cancer. With the progress of the microarray expression profile, many methods are proposed to deal with these data. However, because of the feature dimension of tumor gene expression profile is very high; many machine learning algorithms are failure. Objective & Methods: In this paper, a novel method named probabilist Read More

Background: Flavin mononucleotide (FMN) specific riboswitch, also known as RFN element is frequently found in prokaryotes and also in some eukaryotes. FMN riboswitch is directly involved in the expression of Rib DEAHT genes in the biosynthesis and transport of riboflavin (vitamin B2). In case of bacteria all the genes of Rib operon are involved and the RFN element is found in a number of species where as in eukaryotes o Read More

Background: Presence of missing values in databases causes serious threats for knowledge extraction. Especially in large databases which are integrated from multiple sources, the number of missing values may be high which in turn may lead to biased inferences. Many methods have been proposed by researchers for handling ignorable (Missing At Random and Missing Completely At Random) and non-ignorable missingness Read More

Background: Enhancers are short DNA regions that improve transcription efficiency by recruiting transcription factors. Identifying enhancer regions is important to understand the process of gene expression. As enhancers are independent of their distances and orientations to the target genes, it is difficult to locate enhancers accurately. Recently, with the development of highthroughput ChIP-seq (Chromatin Immunoprecipitation s Read More