Current Bioinformatics - Volume 1, Issue 2, 2006

It has recently been recognized that pseudoknots of RNAs have important roles and not a small number of RNAs contain pseudoknots. Therefore, recent studies on RNA secondary structure prediction focus on pseudoknots. Several algorithms have been developed based on dynamic programming. Though optimality of a solution is guaranteed, these algorithms suffer from high time complexities. Thus, heuristic algorit Read More

Whole genome duplication has played a major role in the evolution of many eukaryotic lineages. Polyploidy has long been postulated as a powerful mechanism for evolutionary innovation, and recent analyses have provided convincing evidence that independent ancient genome duplications occurred in the ancestors of yeast, plants, vertebrates and fish. It is the growing availability of whole genome sequences that has facilita Read More

The potential of systems-based approaches are increasingly being realised in drug discovery, metabolic engineering and related areas. Developments in high-throughput experimental techniques and explosion of genomic data have fuelled progress in this area. Modelling and simulation of metabolic and regulatory pathways is an important step in systems analysis. In this review, we discuss the principles of pat Read More

Recently, Bayesian statistical thinking has been considered as a revolutionary force within genetics and bioinformatics. Novel computational algorithms have enabled use of probability models of unprecedented degree of complexity in many applications. Pattern recognition within bioinformatics is a multifaceted field which poses an enormous challenge for the Bayesian approach to data analysis. Advantages of this Read More

In recent years, there has been a considerable amount of interest in the area of Genomic Signal Processing, which is the engineering discipline that studies the processing of genomic signals. Since regulatory decisions within the cell utilize numerous inputs, analytical tools are necessary to model the multivariate influences on decision-making produced by complex genetic networks. Signal processing approaches such as detection, Read More

We review recent research and development in high performance computing (HPC) for computational biology and discuss the great challenges to both biomedical scientists and IT professionals. During the last decades, research in the fields of molecular biology and biomedicine has provided the scientific community with huge amount of data through sequencing, genome-wide annotation and gene expression profiling projects Read More

The development of high-throughput technologies that expedite the discovery of interactions between proteins has made it possible to screen entire genomes and produce large protein-protein interaction (PPI) datasets. The availability of these datasets is now enabling researchers to perform PPI data mining activities of theoretical and practical importance, including prediction of novel PPIs and protein function, sub-ce Read More

Predicting genes and gene regions undergoing adaptive evolution is one of the most important aims of geneticists and of new emerging areas of investigation. As more genomes are being sequenced and computational tools to detect selection are being developed, the number of genes uncovered as being positively selected is overwhelming. Several statistical methods have been devised to test if specific amino acid regi Read More

The use of the term 'network' is more and more widespread in all fields of biology. It evokes a systemic approach to biological problems able to overcome the evident limitations of the strict reductionism of the past twenty years. The expectations produced by taking into considerations not only the single elements but even the intermingled 'web' of links connecting different parts of biological entities, are huge. Nevertheless, Read More

The impact of the internet in Biology is undeniable. The next stage in the evolution of the Internet for biological and molecular resource discovery must be towards what has been described as a semantic Web, where not only humans but machines can make "biologically intelligent" decisions based on collections of authenticable assertions about biology and molecular sciences. This vision requires agreed common representati Read More

Protein sequence clustering is one of the oldest problems addressed in the field of computational biology. Back in the 60s, when the first protein sequence database was published as printed version, Margaret Dayhoff defined the basic principles of this discipline with only a small number of sequences at hand. With up to a million sequences available in public databases nowadays and several well known methods for automat Read More

Two-dimensional gel electrophoresis in combination with mass spectrometry constitutes the backbone of proteomic analysis. With the availability of powerful software tools addressing the specific needs for analyzing twodimensional gels, several typical procedures have been elaborated. In the first part of this review, we will describe and discuss the procedure of analyzing two-dimensional electrophoretic gels consisting of (i) digi Read More