Gram-negative bacteria characteristically are surrounded by an additional membrane layer,
the outer membrane. Although outer membrane components often play important roles in …

Nucleic acid polymerases and helicases often contain additional domains that possess
nuclease or phosphohydrolase activity; these domains also tend to occur as 'stand …

Identifying master regulators of biological processes and mapping their downstream gene
networks are key challenges in systems biology. We developed a computational method …

Since its first release in 2001 as mainly a software package for phylogenetic analysis, data
analysis for molecular biology and evolution (DAMBE) has gained many new functions that …

PlantCARE is a database of plant cis-acting regulatory elements, enhancers and repressors.
Regulatory elements are represented by positional matrices, consensus sequences and …

This book provides a self-contained and up-to-date treatment of the Monte Carlo method
and develops a common framework under which various Monte Carlo techniques can be" …

Improving the accuracy of prediction of gene starts is one of a few remaining open problems
in computer prediction of prokaryotic genes. Its difficulty is caused by the absence of …

We sought to create a comprehensive catalog of yeast genes whose transcript levels vary
periodically within the cell cycle. To this end, we used DNA microarrays and samples from …

Using a combination of computer methods for iterative database searches and multiple
sequence alignment, we show that protein sequences related to the AAA family of ATPases …

MOTIVATION: To illustrate an intuitive and statistically valid method for combining
independent sources of evidence that yields a p-value for the complete evidence, and to …