We describe algorithms to explore the space of all possible reconciliations between a gene tree and a species tree. We propose an algorithm for generating a random reconciliation, ...
Background: To meet the needs of gene annotation for newly sequenced organisms, optimized spaced seeds can be implemented into cross-species sequence alignment programs to accurat...
Background: Sequence alignment is a common tool in bioinformatics and comparative genomics. It is generally assumed that multiple sequence alignment yields better results than pai...
Background: Identifying protein-protein interactions is fundamental for understanding the molecular machinery of the cell. Proteome-wide studies of protein-protein interactions ar...
Nan Lin, Baolin Wu, Ronald Jansen, Mark Gerstein, ...
Many recommendation and retrieval tasks can be represented as proximity queries on a labeled directed graph, with typed nodes representing documents, terms, and metadata, and labe...