Current Bioinformatics - Volume 10, Issue 4, 2015

The application of machine learning approaches to decode cognitive states through functional Magnetic Resonance Imaging (fMRI) is one of the emerging fields of research over the past decade. Multivoxel Pattern Analysis (MVPA) treats the activation of multiple voxels from the fMRI data as a pattern to decode the brain states using machine learning based classifiers. The potential in designing a classifier to accurately classif Read More

In recent years, research on bioinformatics has increasingly focused on the problem of class imbalance. A classification task is called class imbalance when the number of instances belonging to one class or several classes exceeds that of the other classes. Class imbalance often underestimates the performance of minority classes. This article provides a review of the most widely used class imbalance learning me Read More

MicroRNAs (miRNAs) are important regulators of cell biological processes with approximately 21–25 nucleotides in length. They are thought to suppress protein coding gene expression through translation inhibition or (and) mRNA decay through leading the RNAi-induced silencing complex (RISC) to complementary sites in the 3' untranslated region of the target mRNA. Studies have shown widespread regulation of protein le Read More

This article reviews and compares different existing statistical tests utilized in significance analysis of gene expression from DNA microarray data. Microarray gene expression study facilitates the investigation of genes that are differentially expressed with respect to different classes of samples. Many gene expression studies also aim to find groups of genes that do something together, or to find out molecular similarities among a Read More

This paper proposes a novel hybrid approach to solve the DNA sequence assembly problem by combining particle swarm optimization and iterative local search algorithms. One of the vital challenges in DNA sequence assembly is to arrange a long genome sequence that consists of millions of fragments in accurate order. This is an NP- hard combinatorial optimization problem. The prominence of this paper is to demonstrate ho Read More

Bioinformatics is an emerging interdisciplinary research area which holds great promise in the advancement of research and development in complex areas, such as medicine, biology, agriculture, environment, public health, drug design and so on. It is a blend of computer science and molecular biology. Most of the problems in bioinformatics are NP hard in nature so researchers have used soft computing and artificial i Read More

Prediction of gene co-expression has a great importance because of its role in explaining the molecular and functional mechanisms of the cells. For this reason, high performance methods should be developed to reduce errors. We have developed a novel method using heterogeneous features including gene expression values and various sequencebased features (SBF) via the random forest (RF) classifier to predict co-expresse Read More

Cryofixation of tissues in a cryostat chamber is a routine technique to investigate rapidly about the presence of tumours during a surgical procedure in patients (intraoperative consultation). The tissue is placed without cryoprotectant in contact with a cooled metal block inside the cryostat used for cutting and preparing the specimen, without or with a heavy weight. Until now, quantitative studies of the damages pr Read More

In this research an efficient gene selection method called Discriminant Mutual Information (DMI) algorithm is proposed. The DMI algorithm sequentially induces discrimination and relevance to identify the most significant genes for tumor classification. In particular, in the first step the entire gene population is decorrelated by the formation of gene-sets such that the genes with similar characteristics form a single gene- Read More

Interactions between human and viral proteins have proved to be the major cause of several critical ailments and research directions in the recent past have focused on predicting potential viralhost protein relations through computational techniques. This research aimed at detecting probable interactions between HIV-1 and human proteins by generating all possible high -confident (>80%) associations between the host and vir Read More

Two-component systems (TCSs) and small regulatory RNAs (sRNAs) form dense regulatory networks in bacteria. To expand the known repertoire of TCS regulons in the Bacillus cereus group, we employed an in silico strategy to identify sRNA genes that might be regulated by response regulators (RRs) of TCS. Using the whole genomes of 21 fully sequenced strains of the B. cereus group, we identified 12 different types of novel sR Read More

Next-generation high-throughput sequencing technologies have opened up new and challenging research opportunities. In particular, Next-generation sequencers produce a massive amount of short-reads data in a single run. However, the large amount of short-reads data produced is highly susceptible to errors, as compared to shotgun sequencing. Therefore, there is a peremptory demand to design fast and more acc Read More

Background: Nowadays, pathologists grade breast cancer histopathology slides by microscopes based on Nottingham as an international standard. In this standard, three factors are scored. One of these factors is mitotic counting. This counting is a rigid and time consuming activity which suffers from conflicts in inter- and intra- observations. Objective: To prevent the drawbacks occurred during mitotic counting, the experts fetch Read More

Drawing and comparing structures of homologous genes is an important way to study the gene evolution. In recent years, several programs and web tools have been proposed to draw gene structures according to genome sequences or GFF (General Feature Format) gene data. It is unfitted for them to draw a large number of gene structures due to time-consuming preparation of input data. The visualization tools for compar Read More