BACKGROUND The frequency of synonymous codon usage varies widely between organisms. Suboptimal codon content limits expression of viral, experimental or therapeutic heterologous proteins due to limiting cognate tRNAs. Codon content is therefore often adjusted to match codon bias of the host organism. Codon content also varies between genes within individual mammalian species. However, little at...

Preference elicitation is a serious bottleneck in many decision support applications and agent specification tasks. CP-nets were designed to make the preference elicitation process simpler and more intuitive for lay users by graphically structuring a set of Ceteris Paribus (CP) preference statements preference statements most people find natural and intuitive. In various contexts, CP-nets with ...

In recent years, CP-nets have emerged as a useful tool for supporting preference elicitation, reasoning, and representation. CP-nets capture and support reasoning with qualitative conditional preference statements, statements that are relatively natural for users to express. In this paper, we extend the CP-nets formalism to handle another class of very natural qualitative statements one often u...

When faced with large or complex decision problems, human decision makers (DM) can make costly mistakes, due to inherent limitations of their memory, attention, and knowledge. Preference elicitation tools assist the decision maker in overcoming these limitations. They do so by interactively learning the DM’s preferences through appropriately chosen queries and suggesting high-quality outcomes b...

The X circular code is a set of 20 trinucleotides (codons) that has been identified in the protein-coding genes most organisms (bacteria, archaea, eukaryotes, plasmids, viruses). It shown previously important mathematical property being an error-correcting code. Thus, motifs code, i.e. series codons belonging to and called motifs, allow identification maintenance reading frame genes. are signif...

Optimization and relaxation are two important operations that naturally arise in many applications requiring the use of constraints, e.g., engineering design, scheduling, decision support, etc. In optimization , we are interested in nding the optimal solutions to a set of constraints with respect to an objective function. In many applications, optimal solutions may be diicult or impossible to o...

We study the interrelations between tRNA gene copy numbers, gene expression levels and measures of codon bias in the human genome. First, we show that isoaccepting tRNA gene copy numbers correlate positively with expression-weighted frequencies of amino acids and codons. Using expression data of more than 14,000 human genes, we show a weak positive correlation between gene expression level and ...