CoP: a database for characterizing co-expressed gene modules with biological information in plants

CoP: a database for characterizing co-expressed gene modules with biological information in plants - Summary: Using a large dataset (10 022 assays) obtained from public plant microarray databases, we developed the CoP database for associating co-expressed gene modules with biological information such

PCRPi: Presaging Critical Residues in Protein interfaces, a new computational tool to chart hot spots in protein interfaces

PCRPi: Presaging Critical Residues in Protein interfaces, a new computational tool to chart hot spots in protein interfaces - Protein–protein interactions (PPIs) are ubiquitous in Biology, and thus offer an enormous potential for the discovery of novel therapeutics.

Beyond Affymetrix arrays: expanding the set of known hybridization isotherms and observing pre-wash signal intensities

Beyond Affymetrix arrays: expanding the set of known hybridization isotherms and observing pre-wash signal intensities - Microarray hybridization studies have attributed the nonlinearity of hybridization isotherms to probe saturation and post-hybridization washing.

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.