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In vitro selection of oligonucleotides that bind double-stranded DNA in the presence of triplex-stabilizing agents

In vitro selection of oligonucleotides that bind double-stranded DNA in the presence of triplex-stabilizing agents - A SELEX approach has been developed in order to select oligonucleotides that bind double-stranded DNA in the presence of a triplex-stabilizing agent, and was applied to a target sequence containing an ol

SBRML: a markup language for associating systems biology data with models

SBRML: a markup language for associating systems biology data with models - Motivation: Research in systems biology is carried out through a combination of experiments and models.

Standard virtual biological parts: a repository of modular modeling components for synthetic biology

Standard virtual biological parts: a repository of modular modeling components for synthetic biology - Motivation: Fabrication of synthetic biological systems is greatly enhanced by incorporating engineering design principles and techniques such as computer-aided design.

Gene function prediction from synthetic lethality networks via ranking on demand

Gene function prediction from synthetic lethality networks via ranking on demand - Motivation: Synthetic lethal interactions represent pairs of genes whose individual mutations are not lethal, while the double mutation of both genes does incur lethality.

GO-Bayes: Gene Ontology-based overrepresentation analysis using a Bayesian approach

GO-Bayes: Gene Ontology-based overrepresentation analysis using a Bayesian approach - Motivation: A typical approach for the interpretation of high-throughput experiments, such as gene expression microarrays, is to produce groups of genes based on certain criteria (e.g.

Protein secondary structure appears to be robust under in silico evolution while protein disorder appears not to be

Protein secondary structure appears to be robust under in silico evolution while protein disorder appears not to be - Motivation: The mutation of amino acids often impacts protein function and structure. Mutations without negative effect sustain evolutionary pressure.

Active site prediction using evolutionary and structural information

Active site prediction using evolutionary and structural information - Motivation: The identification of catalytic residues is a key step in understanding the function of enzymes. While a variety of computational methods have been developed for this task, accuracies have remained fairly low.

RNAsnoop: efficient target prediction for H/ACA snoRNAs

RNAsnoop: efficient target prediction for H/ACA snoRNAs - Motivation: Small nucleolar RNAs are an abundant class of non-coding RNAs that guide chemical modifications of rRNAs, snRNAs and some mRNAs. In the case of many ‘orphan’ snoRNAs, the targeted nucleotides remain unknown, however.

ProteinWorldDB: querying radical pairwise alignments among protein sets from complete genomes

ProteinWorldDB: querying radical pairwise alignments among protein sets from complete genomes - Motivation: Many analyses in modern biological research are based on comparisons between biological sequences, resulting in functional, evolutionary and structural inferences.

Xper2: introducing e-taxonomy

Xper2: introducing e-taxonomy - Motivation: Computer Aided Identification systems provide users with the resources to relate morpho-anatomic observations with taxa names and to subsequently access other knowledge about the organisms.