The aim of the motif recognition problem is to detect a set of mutually similar subsequences within a collection of biological sequences. The weak motif recognition problem on DNA ...
Background: The proliferation of structural and functional studies of RNA has revealed an increasing range of RNA's structural repertoire. Toward the objective of systematic ...
Daniela Fera, Namhee Kim, Nahum Shiffeldrim, Julie...
Background: In 2004, we presented a web resource for stimulating the search for novel RNAs, RNA-As-Graphs (RAG), which classified, catalogued, and predicted RNA secondary structur...
Joseph A. Izzo, Namhee Kim, Shereef Elmetwaly, Tam...
Background: Correct temporal and spatial gene expression during metazoan development relies on combinatorial interactions between different transcription factors. As a consequence...
: We introduce the novel concept of graph alignment, a generalization of graph isomorphism that is motivated by the commonly used multiple sequence alignments. Graph alignments and...