Current Bioinformatics - Volume 7, Issue 1, 2012

What can be compared to travel thousands of miles from your place, arriving for the first time in a new country and suddenly finding you at home? This is the experience the great writer and philosopher Gilbert Keith Chesterton described one hundred years ago equating his spiritual and intellectual experience to an English explorer that arrives, after a long and dangerous journey, to an island and suddenly discovers it is G Read More

Bioinformatics research in the last three decades has contributed quite a large number of methodologies for compressing genomic sequence data. However, recent progress in the next generation sequencing (NGS) techniques requires the development of more effective compression methods. In this review paper, a comprehensive overview of the state-of-the-art DNA sequence compression techniques for handling the exponen Read More

Several graph representations have been introduced for different data in theoretical biology. For instance, Complex Networks based on Graph theory are used to represent the structure and/or dynamics of different large biological systems such as protein-protein interaction networks. In addition, Randic, Liao, Nandy, Basak, and many others developed some special types of graph-based representations. This special type Read More

This paper presents a transformation method of original score matrix by correspondently normalizing its elements in row and column. The sequence alignment of 4830 superfamilies and 9570 fold related protein pairs showed that the quality of the alignment based on the transformed matrices is significantly improved compared to that based on the original matrices, especially for the fold related protein pairs, which is Read More

Biclustering analysis is a useful methodology to discover the local coherent patterns hidden in a data matrix. Unlike the traditional clustering procedure, which searches for groups of coherent patterns using the entire feature set, biclustering performs simultaneous pattern classification in both row and column directions in a data matrix. The technique has found useful applications in many fields but notably in bioinformatic Read More

As a paradigm for modeling gene regulatory networks, synchronous or asynchronous probabilistic Boolean networks (PBNs) provide us an effective tool to design therapeutic intervention strategies. However, most of the previous works focused on the former and only few studied the latter. This paper deals with an optimal control problem in a generalized asynchronous PBN by applying the theory on semi-Markov decision proces Read More

In this article, we discuss the basic challenges of clustering on gene expression data. In particular, we divide the methods of clustering into eight different categories. Then, we present specific characteristics pertinent to each clustering category. We compare the results of 27 clustering/biclustering algorithms on various gene expression datasets using different cluster validation indices. Comparison is made in t Read More

Metabolic flux analysis (MFA) has become a fundamental tool for quantifying metabolic pathways, which is essential for in-depth understanding of biological systems. In experimentally based MFA, isotopically labeled substrates are supplied to a biological system and the resulting labeling patterns are analyzed to obtain internal flux information. Three main techniques are necessary for 13C MFA: (i) a steady state cell cultur Read More

Biological aggregation is a process where bio-macromolecules such as proteins, lipids and nucleic acids essentially self-associate in an ordered fashion into functional complexes (that may be normal or pathological) and finally precipitate out due to formation of higher order conglomerates of low solubility. Neurodegenerative diseases are, in general, associated with the deposition of pathogenic aggregates composed of amy Read More

Biological systems are increasingly being studied in a holistic manner, using omics approaches, to provide quantitative and qualitative descriptions of the diverse collection of cellular components. Among the omics approaches, metabolomics, which deals with the quantitative global profiling of small molecules or metabolites, is being used extensively to explore the dynamic response of living systems, such as organelles, cells, tis Read More