We introduce relational grams (r-grams). They upgrade n-grams for modeling relational sequences of atoms. As n-grams, r-grams are based on smoothed n-th order Markov chains. Smoot...
A number of bioinformatics tools use regular expression (RE) matching to locate protein or DNA sequence motifs that have been discovered by researchers in the laboratory. For exam...
Amine Heddad, Markus Brameier, Robert M. MacCallum
Background: Empirical scoring functions have proven useful in protein structure modeling. Most such scoring functions depend on protein side chain conformations. However, backbone...
The protein-protein interaction networks of even well-studied model organisms are sketchy at best, highlighting the continued need for computational methods to help direct experim...
Background: An important challenge in eukaryotic gene prediction is accurate identification of alternatively spliced exons. Functional transcripts can go undetected in gene expres...