Computational Biology Reflections

This column/blog is devoted to the exploration of current computational biology issues. It is designed for the typical biologist and will not be mathematically oriented. The idea is to present current papers or trends in the field that might be of interest to biologists while not focusing on computational or mathematical details. Occasionally, interesting computational concepts might be presented from earlier papers, especially those that reflect biological processes, for example neural networks or genetic algorithms. If you have comments on any of the entries, please respond by clicking on "Leave a comment" that follows every entry. Of course, if you want to respond privately, just send an email to us.

The entries will mostly be written by Bob Gross, President of Textco BioSoftware, Inc. and a professor at Dartmouth College. Dr. Gross' research site can be found here. Dr. Gross' lab developed and maintains the SCOPE algorithm for finding regulatory motifs in DNA. If you have an interesting topic that you would like to write about in this blog, we are seeking guest bloggers. Please send an email with your ideas. It would be wonderful to turn this into a community resource.

How living systems have helped in the evolution of computational problem solving

Today, we are being deluged with an enormous amount of biological data. Web sites abound that have genomes, gene expression data, transcription factor data, phylogenetic data, and the list goes on. The Genomes OnLine Database currently lists 6,423 genomes. They also list 249 metagenomes, which are “genomes” from whole microbial communities [1]. NCBI has [...]
Posted in computational biology reflections blog | Tagged , , | Leave a comment

Non-coding doesn’t ‘translate’ to non-functional when it comes to evolution

What is it that has allowed more “complex” species to evolve from simpler species? The popular notion that the addition of new protein coding genes is responsible for this increased complexity has been challenged over the last decade. It is becoming apparent that, although new proteins certainly are important, the amount of conserved sequence is [...]
Posted in computational biology reflections blog | Tagged , , , , , , | Leave a comment

Evolution, Conservation, Change, Robustness, Complexity and Degeneracy

For species to be successful and adapt to an ever changing environment, they must strike a delicate balance between allowing for some DNA alterations, while at the same time preserving the key developmental processes encoded in their unique genomes. This poses a problem, as even small changes in any given gene might lead to deleterious [...]
Posted in computational biology reflections blog | Tagged , , , , , | Leave a comment

Gene Expression and Transcription Regulation

One of the main beliefs in biology today is that there is a relationship between genes that share common promoter motifs and their expression. It makes sense that if genes share common regulatory elements that they would be turned on and off under similar conditions – and thus would have similar microarray expression profiles. A [...]
Posted in computational biology reflections blog | Tagged , , , , | Leave a comment