Molecular interactions are often represented as network models which have become the
common language of many areas of biology. Graphs serve as convenient mathematical …

Studying biological networks, such as protein-protein interactions, is key to understanding
complex biological activities. Various types of large-scale biological datasets have been …

Automated annotation of protein function is challenging. As the number of sequenced
genomes rapidly grows, the overwhelming majority of protein products can only be …

Background A major bottleneck in our understanding of the molecular underpinnings of life
is the assignment of function to proteins. While molecular experiments provide the most …

With the development of next generation sequencing techniques, it is fast and cheap to
determine protein sequences but relatively slow and expensive to extract useful information …

One of the most important and challenging problems in biomedicine and genomics is how to
identify the disease genes. In this study, we developed a computational method to identify …

Enhancing xylose utilization has been a major focus in Saccharomyces cerevisiae strain-
engineering efforts. The incentive for these studies arises from the need to use all sugars in …

Background With the huge amount of uncharacterized protein sequences generated in the
post-genomic age, it is highly desirable to develop effective computational methods for …

We surveyed the iron nutrition-responsive transcriptome of Chlamydomonas reinhardtii
using RNA-Seq methodology. Presumed primary targets were identified in comparisons …

Due to its ease to donate or accept electrons, iron (Fe) plays a crucial role in respiration and
metabolism, including tetrapyrrole synthesis, in virtually all organisms. In plants, Fe is a …