Context-dependent DNA recognition code for C2H2 zinc-finger transcription factors

Context-dependent DNA recognition code for C2H2 zinc-finger transcription factors - Motivation: Modeling and identifying the DNA-protein recognition code is one of the most challenging problems in computational biology.

Artificial neural network for prediction of antigenic activity for a major epitope in the hepatitis C virus NS3 protein

Artificial neural network for prediction of antigenic activity for a major conformational epitope in the hepatitis C virus NS3 protein - Motivation: Insufficient knowledge of general principles for accurate quantitative inference of biological properties from sequences is a major obstacle in the rat

Rapid and efficient construction of markerless deletions in the Escherichia coli genome

Rapid and efficient construction of markerless deletions in the Escherichia coli genome - We have developed an improved and rapid genomic engineering procedure for the construction of custom-designed microorganisms.

PhosphoPOINT: a comprehensive human kinase interactome and phospho-protein database

PhosphoPOINT: a comprehensive human kinase interactome and phospho-protein database - Motivation: To fully understand how a protein kinase regulates biological processes, it is imperative to first identify its substrate(s) and interacting protein(s).

A protein-DNA docking benchmark

A protein-DNA docking benchmark - We present a protein–DNA docking benchmark containing 47 unbound–unbound test cases of which 13 are classified as easy, 22 as intermediate and 12 as difficult cases. The latter shows considerable structural rearrangement upon complex formation.

Organization and integration of biomedical knowledge with concept maps for key peroxisomal pathways

Organization and integration of biomedical knowledge with concept maps for key peroxisomal pathways - Motivation: One important area of clinical genomics research involves the elucidation of molecular mechanisms underlying (complex) disorders which eventually may lead to new diagnostic or drug target

Expanded molecular diversity generation during directed evolution by trinucleotide exchange (TriNEx)

Expanded molecular diversity generation during directed evolution by trinucleotide exchange (TriNEx) - Trinucleotide exchange (TriNEx) is a method for generating novel molecular diversity during directed evolution by random substitution of one contiguous trinucleotide sequence for another.

Linking the functions of unrelated proteins using a novel directed evolution domain insertion method

Linking the functions of unrelated proteins using a novel directed evolution domain insertion method - We have successfully developed a new directed evolution method for generating integral protein fusions comprising of one domain inserted within another.

Impact of whole genome amplification on analysis of copy number variants

Impact of whole genome amplification on analysis of copy number variants - Large-scale copy number variants (CNVs) have recently been recognized to play a role in human genome variation and disease.

Primase-based whole genome amplification

Primase-based whole genome amplification - In vitro DNA amplification methods, such as polymerase chain reaction (PCR), rely on synthetic oligonucleotide primers for initiation of the reaction. In vivo, primers are synthesized on-template by DNA primase.