The International Journal of Biocomputing and Nano Technology (IJBNT) is an open access peer-reviewed journal that publishes articles which contribute new results in all the areas of Biocomputing and Nano Technology. Authors are solicited... more
The International Journal of Biocomputing and Nano Technology (IJBNT) is an open access peer-reviewed journal that publishes articles which contribute new results in all the areas of Biocomputing and Nano Technology. Authors are solicited to contribute to the journal by submitting articles that illustrate research results, projects, surveying works and industrial experiences that describe significant advances in this area.
High-throughput protein interaction data, with ever-increasing volume, are becoming the foundation of many biological discoveries. However, high-throughput protein interaction data are often associated with high false positive and false... more
High-throughput protein interaction data, with ever-increasing volume, are becoming the foundation of many biological discoveries. However, high-throughput protein interaction data are often associated with high false positive and false negative rates. It is desirable to develop scalable methods to identify these errors. In this paper, we develop a computational method to identify spurious interactions and missing interactions from high-throughput protein interaction data. Our method uses both local and global topological information of ...
Metabolism is one of the best studied fields of biochemistry, but its regulation involves processes on many different levels, some of which are still not understood well enough to allow for quantitative modeling and prediction. Glycolysis... more
Metabolism is one of the best studied fields of biochemistry, but its regulation involves processes on many different levels, some of which are still not understood well enough to allow for quantitative modeling and prediction. Glycolysis in yeast is a good example: although high-quality quantitative data are available, well-established mathematical models typically only cover direct regulation of the involved enzymes by metabolite binding. The effect of various metabolites on the enzyme kinetics is summarized in carefully developed mathematical formulae. However, this approach implicitly assumes that the enzyme concentrations themselves are constant, thus neglecting other regulatory levels--e.g. transcriptional and translational regulation--involved in the regulation of enzyme activities. It is believed, however, that different experimental conditions result in different enzyme activities regulated by the above mechanisms. Detailed modeling of all regulatory levels is still out of ...
Nucleosome configuration in eukaryotic genomes is an important clue to clarify the mechanisms of regulation for various nuclear events. In the past few years, numerous computational tools have been developed for the prediction of... more
Nucleosome configuration in eukaryotic genomes is an important clue to clarify the mechanisms of regulation for various nuclear events. In the past few years, numerous computational tools have been developed for the prediction of nucleosome positioning, but there is no third-party benchmark about their performance. Here we present a performance evaluation using genome-scale in vivo nucleosome maps of two vertebrates and three invertebrates. In our measurement, two recently updated versions of Segal's model and Gupta's SVM with the RBF kernel, which was not implemented originally, showed higher prediction accuracy although their performances differ significantly in the prediction of medaka fish and candida yeast. The cross-species prediction results using Gupta's SVM also suggested rather specific characters of nucleosomal DNAs in medaka and budding yeast. With the analyses for over- and under-representat ion of DNA oligomers, we found both general and species-specific mo...
The high osmolarity glycerol (HOG) signalling system in yeast belongs to the class of Mitogen Activated Protein Kinase (MAPK) pathways that are found in all eukaryotic organisms. It includes at least three scaffold proteins that form... more
The high osmolarity glycerol (HOG) signalling system in yeast belongs to the class of Mitogen Activated Protein Kinase (MAPK) pathways that are found in all eukaryotic organisms. It includes at least three scaffold proteins that form complexes, and involves reactions that are strictly dependent on the set of species bound to a certain complex. The scaffold proteins lead to a combinatorial increase in the number of possible states. To date, representations of the HOG pathway have used simplifying assumptions to avoid this combinatorial problem. Such assumptions are hard to make and may obscure or remove essential properties of the system. This paper presents a detailed generic formal representation of the HOG system without such assumptions, showing the molecular interactions known from the literature. The model takes complexes into account, and summarises existing knowledge in an unambiguous and detailed representation. It can thus be used to anchor discussions about the HOG system....
Complete genome sequences of more than 30 organisms have been determined today. When manycompletegenomesequencesbecomeavailable,oneofthefirstquestionsiswhichregionsareconservedamong various genome sequences. For the purpose, however, most... more
Complete genome sequences of more than 30 organisms have been determined today. When manycompletegenomesequencesbecomeavailable,oneofthefirstquestionsiswhichregionsareconservedamong various genome sequences. For the purpose, however, most existing tools are not availablebecause they can not treat large sequences such as complete genome sequences, or even when theycantreatcompletegenomesequences,theyareoftentooslow.We have developed a software tool
