Predicting failure rate of PCR in large genomes

Predicting failure rate of PCR in large genomes - We have developed statistical models for estimating the failure rate of polymerase chain reaction (PCR) primers using 236 primer sequence-related factors. The model involved 1314 primer pairs and is based on more than 80 000 PCR experiments.

Identification of OBO nonalignments and its implications for OBO enrichment

Identification of OBO nonalignments and its implications for OBO enrichment - Motivation: Existing projects that focus on the semiautomatic addition of links between existing terms in the Open Biomedical Ontologies can take advantage of reasoners that can make new inferences between terms that are b

A global pathway crosstalk network

A global pathway crosstalk network - Motivation: Given the complex nature of biological systems, pathways often need to function in a coordinated fashion in order to produce appropriate physiological responses to both internal and external stimuli.

Fast grid layout algorithm for biological networks with sweep calculation

Fast grid layout algorithm for biological networks with sweep calculation - Motivation: Properly drawn biological networks are of great help in the comprehension of their characteristics. The quality of the layouts for retrieved biological networks is critical for pathway databases.

Comparative conservation analysis of the human mitotic phosphoproteome

Comparative conservation analysis of the human mitotic phosphoproteome - Motivation: A key challenge in phosphoproteomic studies is to distinguish functionally relevant phosphorylation sites from potentially ‘silent’ phosphorylation.

Positive selection drives a correlation between [non-]synonymous divergence and functional divergence

Positive selection drives a correlation between non-synonymous/synonymous divergence and functional divergence - Motivation: Functional divergence among proteins is often assumed to be strongly influenced by natural selection, as inferred from the ratio of non-synonymous nucleotide divergence (d<

Microarray-based global mapping of integration sites for the retrotransposon, intracisternal A-particle, in the mouse genome

Microarray-based global mapping of integration sites for the retrotransposon, intracisternal A-particle, in the mouse genome - Mammalian genomes contain numerous evolutionary harbored mobile elements, a part of which are still active and may cause genomic instability.

UniPrime: a workflow-based platform for improved universal primer design

UniPrime: a workflow-based platform for improved universal primer design - UniPrime is an open-source software (http://uniprime.batlab.eu), which automatically designs large sets of universal primers by simply inputting a gene ID reference.

Inter-individual variation of DNA methylation and its implications for large-scale epigenome mapping

Inter-individual variation of DNA methylation and its implications for large-scale epigenome mapping - Genomic DNA methylation profiles exhibit substantial variation within the human population, with important functional implications for gene regulation.