Sequence-Evolution-Function is an introduction to the computational approaches that play a
critical role in the emerging new branch of biology known as functional genomics. The book …

Cellular functions result from intricate networks of molecular interactions, which involve not
only proteins and nucleic acids but also small chemical compounds. Here we present an …

Although analysis of genome rearrangements was pioneered by Dobzhansky and
Sturtevant 65 years ago, we still know very little about the rearrangement events that …

Gene order in prokaryotes is conserved to a much lesser extent than protein sequences.
Only several operons, primarily those that code for physically interacting proteins, are …

Background The availability of multiple complete genome sequences from diverse taxa
prompts the development of new phylogenetic approaches, which attempt to incorporate …

The availability of computerized knowledge on biochemical pathways in the KEGG database
opens new opportunities for developing computational methods to characterize and …

A computational method was developed for delineating connected gene neighborhoods in
bacterial and archaeal genomes. These gene neighborhoods are not typically present, in …

Conservation of proximity of a pair of genes across multiple genomes generally indicates
that their functions could be linked. Here, we present a systematic evaluation using 42 …

Understanding protein‐protein interactions (PPIs) in a cell is essential for learning protein
functions, pathways, and mechanism of diseases. PPIs are also important targets for …

Motivation: The rapidly increasing set of sequenced genomes highlights the importance of
identifying the synteny blocks in multiple and/or highly duplicated genomes. Most synteny …