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.

The original entries were written by Dr. Robert Gross, the former President of Textco BioSoftware, Inc. and a former professor at Dartmouth College. Dr. Gross' lab developed the SCOPE algorithm for finding regulatory motifs in DNA. His research site can be found here.

How Genetic Algorithms Have Helped in Computational Problem Solving

[Note: you can download a Genetic Algorithm Demo program to go with this article (Mac, Win, Linux). This is explained later on.] In the last installment of this blog, I talked about how an improved understanding of the way in which biological systems handle complex decision making can be used to design computational approaches to […]
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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 a […]
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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 […]
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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 […]
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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 […]
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