The field of genomics holds incredible potential, and it is imperative that students are exposed to the opportunities that the field offers to prepare the future generations of scientists and leaders. However, as a discipline that continues to develop, genomics still provides many issues that must be addressed, particularly with regards to the computerized and automated tools used to analyze en...

We consider regression under the “extremely small n large p” condition. In particular, we focus on problems with so small sample sizes n compared to the dimensionality p, even n → 1, that predictors cannot be estimated without prior knowledge. Furthermore, we assume all prior knowledge that can be automatically extracted from databases has already been taken into account. This setup occurs in p...

Structure determination has already proven useful for lead optimization and direct drug design. The number of high-resolution structures available in public databases today exceeds 30,000 and will definitely aid in structure-based drug design. Structural genomics approaches covering whole genomes, topologically similar proteins or gene families are great assets for further progress in the devel...

One of the recent critical issues in linking genetic variation to clinical phenotypes is to apply population genetic analyses to high-throughput genomics data to investigate underlying patterns of variation in the human genome. Especially, relating drug response to genetic variation has been emerging in the field of pharmacogenomics [2] with the combined use of genetics and functional genomics ...

The starlet sea anemone, Nematostella vectensis, is a basal metazoan organism that has recently emerged as an important model system in developmental biology and evolutionary genomics. StellaBase, the Nematostella Genomics Database (http://stellabase.org), was developed in 2005 as a resource to support the Nematostella research community. Recently, it has become apparent that Nematostella may b...

The successful identification of drug targets requires an understanding of the high-level functional interactions between the key components of cells, organs and systems, and how these interactions change in disease states. This information does not reside in the genome, or in the individual proteins that genes code for, it is to be found at a higher level. Genomics will succeed in revolutionis...

Binary subcomplexes in proteins database (BISC) is a new protein-protein interaction (PPI) database linking up the two communities most active in their characterization: structural biology and functional genomics researchers. The BISC resource offers users (i) a structural perspective and related information about binary subcomplexes (i.e. physical direct interactions between proteins) that are...

Besides domain-specific problems, biologists are confronted with many computational problems. The large amount of varying, heterogeneous, and semi-structured biological data, the increasing complexity of biological applications, methods, and tools afflicted with uncertainty and missing knowledge, as well as the lacking interoperability of available tools necessitate integrative measures to enab...

Dollo's Law, the idea that the loss of complex features in evolution is irreversible, is a popular concept in evolutionary biology. Here we review how application of recent phylogenetic methods, genomics and evo-devo approaches is changing our view of Dollo's Law and its underlying mechanisms. Phylogenetic studies have recently demonstrated cases where seemingly complex features such as digits ...

Recent advances in our understanding of the human genome have raised high hopes for the creation of personalized medicine able to predict diseases well before they occur, or that will lead to individualized and therefore more effective treatments. This possibility of a more accurate science of the prevention and surveillance of disease also illuminates the field of public health, where the tran...