Current Bioinformatics - Volume 13, Issue 5, 2018

Background: Due to the intrinsic compensatory mechanism and cross-talks mong cellular signaling pathways, single-target drugs often fail to inhibit the survival pathways in cancer cells. Some multi-target combination drugs have demonstrated their high sensitivities and low side effects in cancer therapies, and thus drawn intensive attentions from researchers and pharmaceutical enterprises. Method: Although a few computationa Read More

Background: Tandem mass spectrometry (MS/MS) peptide identification is an important research topic in molecular biology; the comparison between an experimental spectrum and a theoretically predicted spectrum is a crucial step for many identification methods. Consequently, the accurate prediction of the theoretical spectrum from a peptide sequence can potentially improve the performance of peptide identificat Read More

Background: It is very likely that RNA secondary structures, more so than the sequence itself, are closely related to their functions, especially for mRNAs and even short noncoding RNAs. However, secondary structure of most lncRNAs (long noncoding RNAs) remains poorly understood. Method: Here, we perform a large-scale investigation of lncRNA secondary structures especially for hairpin structural motif in human an Read More

Background: Protein S-Sulfenylation, the reversible oxidative modification of cysteine thiol groups to cysteine S-Sulfenic acids, is a post-translational modification (PTM) that plays a critical role in regulating protein function and signal transduction. The identification of specific protein Ssulfenylation sites is crucial to understand the underlying molecular mechanisms. Objective: We sought to develop a computational method that can Read More

Background: The classification of phenotypes on microarray data has drawn much attention in last few years. The known methods mainly focused on the selection or construction of features based on either genes or gene pairs on continuous-value gene expression data. However, few researches have been implemented to identify useful features based on both genes and gene pairs on binary-value gene expression dat Read More

Background: Approximate string matching algorithms are widely used in bioinformatics, among which the bit-parallel Myers algorithm is a popular approach to compute the Levenshtein distance between two genome sequences. The bit vector encoding of the Myers algorithm makes it feasible to extend to modern parallel architectures with wider-than-ever vector registers and many cores. Objective: Myers algorithm has alread Read More

Background: The purpose of phylogenetic analysis is to not only show the evolutionary history of taxa, but also comprehend the origin of life. Rooted phylogenetic trees are employed to express the result of phylogenetic analysis. Objective: Computing the dissimilarity of rooted phylogenetic trees has been instrumental in our understanding of the evolutionary relationship of species and the analysis of the reconst Read More

Objective: Small GTPase is an important molecular switch that plays an important role in numerous signaling transduction pathways, the aim is to explore its binary classification features with machine learning algorithms. Methods: The sequences including small GTPases and non small GTPases were clustered to remove similar entries, respectively. Then, they were divided into 10 datasets, each containing equal entries of small Read More

Background and Objective: Attention deficit hyperactivity disorder (ADHD) is a typical neurodevelopmental disorder occurs in children's early school-age, which often results in serious executive dysfunction. Recent ADHD studies highlight the great potential of non-invasive event-related potential (ERP) technique. It is thus worth combining multiple features to form sensitive and robust biomarkers to distinguish ADHD from Read More

Background: Sparse representation has achieved tremendous success recently. Low-rank representation is one of the successful methods. It is aimed to capture underlying low-dimensional structures of high dimensional data and attracted much attention in the area of the pattern recognition and signal processing. Such successful applications were mainly to its effectiveness in exploring lowdimensional manifolds e Read More

Background: The sequence Arginine-Glycine-Aspartic acid (RGD tripeptide) has been identified in most proteins implicated in cell adhesion and signal transduction. Moreover, the RGD paradigm extends to the plant and microbial kingdoms. Investigating this field can be facilitated by combining data from multiple databases into a single one. The RGD tripeptide database is a comprehensive resource with records includ Read More

Background: Alzheimer's disease (AD) has attracted more and more attention in recent years. Accurate diagnosis of AD is significant, especially its prodromal stage, i.e., mild cognitive impairment (MCI), for timely therapy is possibly beneficial to delay the disease progression. Some existing studies indicated that different biomarkers provide complementary information to discriminate MCI patients from healthy normal control Read More

Background: Major intrinsic proteins (MIPs) are membrane channel proteins which maintain water homeostasis and permeable to small molecules across the membrane. Objective: Genome analysis of Brachypodium MIPs (BdMIPs) gene family and in silico studies are based on available bioinformatic tools. Further comparison and evolutionary study of MIPs members were performed within grass family. Method: MIPs seq Read More

Background: In sequencing human and model organism DNA, the development of efficient computational techniques for the rapid prediction of short exons in eukaryotes is a major challenge. Objective: This paper presents a multiscale products-based method in B-spline wavelet domain for short exon detection. In our analysis, we find out the wavelet coefficients associated to introns are less correlated between consecutive Read More