Current Bioinformatics - Volume 1, Issue 3, 2006

In a gene network, genes may be expressed constantly, or expressed based on molecular signals. Transcription is a key process in gene expression. Through evolution, biological organisms have developed internal regulatory mechanisms for transcription control. Such mechanisms dictate how the network will function under certain environmental conditions and respond to changes in the environment. To develop formal approa Read More

In recent years, the broad utilization of high-throughput experimental techniques resulted in a vast amount of expression and interaction data, accompanied by information on metabolic, cell signaling and gene regulatory pathways accumulated in the literature and databases. Thus, one of the major goals of modern bioinformatics is to process and integrate heterogeneous biological data to provide an insight into the inner Read More

A major breakthrough in classifying proteins from different microbial genomes in terms of sequence similarity was the development of the COG concept by Tatusov et al. in 1997. The authors defined clusters of orthologous groups of proteins (COGs) by strictly applying all against all BLAST alignments of protein sequences from completely sequenced microbial genomes. The latest update of the COG database already cover Read More

Inferring comprehensive regulatory networks from high-throughput data is one of the foremost challenges of modern computational biology. As high-throughput expression profiling experiments have gained common ground in many laboratories, different techniques have been proposed to infer transcriptional regulatory networks from them. Furthermore, with the advent of diverse types of high-throughput data, the researc Read More

Computational modeling and simulation have become invaluable tools for the biological sciences. Both aid in the formulation of new hypothesis and supplement traditional experimental research. Many different types of models using various mathematical formalisms can be created to represent any given biological system. Here we review a class of modeling techniques based on particle-based stochastic approaches. In these mo Read More

Discovery of transcription regulatory elements has been an enormous challenge, both to biologists and computational scientists. Over the last three decades, significant progress has been achieved by various laboratories around the world. Earlier, laborious experimental methods were used to detect one or handful of elements at a time. With recent advances in DNA sequencing technology, many completed genomes became a Read More

We have conducted a dedicated analysis on the frequency distribution of the TATA Box and TATA extension sequences on six data sets of human promoters. Promoters in these sets have different lengths and are from different types of genes (housekeeping genes, tissue specific genes, and all genes). The statistical approach developed in this study will firstly partition the promoters into bins of 20 bp long, then calculate the freq Read More

To a great extent, our phenotype is determined by our genetic material. Many genotypic modifications may ultimately become manifest in more or less pronounced changes in phenotype. Despite the importance of how specific genetic alterations contribute to the development of diseases, surprisingly little effort has been made towards exploiting systematically the current knowledge of genotype-phenotype relationships. In Read More

The genome projects in human and other species have made genetic data widely available and pose challenges as well as opportunities for statistical analysis. In this paper we elaborate the concept of integrated analysis of genetic data, such that most aspects of analyses can be done effectively and efficiently in environments with facility for database accessibility, graphics, mathematical/statistical routines, flexible prog Read More