Current Bioinformatics - Volume 14, Issue 2, 2019

Background: Tuberculosis (TB) is still a major public health concern world-wide. The increasing global burden of TB is linked to HIV infection. HIV-TB coinfection has also conditioned clinical aspects of the TB. Since the HIV is beginning in the 1980s, the HIV infection poses a significant challenge in global TB control. Objective: In this review we focused on the challenges of epidemiological and clinical feature of tuberculosis presente Read More

Background: There have been numerous experiments and studies on liver cancer by biomedical scientists, while no comprehensive and systematic exploration has yet been conducted. Therefore, this study aimed to systematically dissect the transcriptional and non-coding RNAmediated mechanisms of liver cancer dysfunction. Method: At first, we collected 974 liver cancer associated genes from the Online Mendelian Inh Read More

Background: Dye-exclusion based cell viability analysis has been broadly used in cell biology including anticancer drug discovery studies. Viability analysis refers to the whole decision making process for the distinction of dead cells from live ones. Basically, cell culture samples are dyed with a special stain called trypan blue, so that the dead cells are selectively colored to darkish. This distinction provides critical information that Read More

Background: Self Interacting Proteins (SIPs) play an essential role in various aspects of the structural and functional organization of the cell. Objective: In the study, we presented a novelty sequence-based computational approach for predicting Self-interacting proteins using Weighed-Extreme Learning Machine (WELM) model combined with an Autocorrelation (AC) descriptor protein feature representation. Method: Th Read More

Background: Biological sequence data have increased at a rapid rate due to the advancements in sequencing technologies and reduction in the cost of sequencing data. The huge increase in these data presents significant research challenges to researchers. In addition to meaningful analysis, data storage is also a challenge, an increase in data production is outpacing the storage capacity. Data compression is used to Read More

Background: Accurate and exhaustive identification of genomic deletion events is the basis for understanding their roles in phenotype variation. Developing effective algorithms to identify deletions using next generation sequencing (NGS) data remains a challenge. Objective: The accurate and exhaustive identification of genomic deletion events is important; we present a new approach, Defind, to detect deletions using NGS Read More

Background: Lung cancer is a greatest threat to people's health and life. CT image leads to unclear boundary segmentation. Segmentation of irregular nodules and complex structure, boundary information is not well considered and lung nodules have always been a hot topic. Objective: In this study, the pulmonary nodule segmentation is accomplished with the new graph cut algorithm. The problem of segmenting the juxta- Read More

Background: Specific combinations of Histone Modifications (HMs) contributing towards histone code hypothesis lead to various biological functions. HMs combinations have been utilized by various studies to divide the genome into different regions. These study regions have been classified as chromatin states. Mostly Hidden Markov Model (HMM) based techniques have been utilized for this purpose. In case of chromatin studies Read More

Background: One of the pivotal challenges in nowadays genomic research domain is the fast processing of voluminous data such as the ones engendered by high-throughput Next-Generation Sequencing technologies. On the other hand, BLAST (Basic Local Alignment Search Tool), a longestablished and renowned tool in Bioinformatics, has shown to be incredibly slow in this regard. Objective: To improve the performa Read More

Background: Various properties of Protein-Protein Interaction (PPI) network have been widely exploited to discover the topological organizing principle and the crucial function motifs involving specific biological pathway or disease process. The current motifs of PPI network are either detected by the topology-based coarse grain algorithms, i.e. community discovering, or depended on the limited-accessible protein ann Read More