eliotbush
 
Search this site

Navigation

Lab




We are a computational evolution lab at Harvey Mudd College in Claremont, CA





Research

Our interests are broadly focused on the flow of information in biological systems. One set of projects focuses on mutations--errors in the transmission of information as it passes from generation to generation. A second set are aimed at understanding the theoretical principles which underlie information transmission from genotype to phenotope.

Context biases in nucleotide substitution. Nucleotide substitution is the process by which one nucleotide replaces another over evolutionary time. The rate of this process is strongly influenced by natural selection, a fact that can be used to recognize functional elements or reconstruct the evolutionary history of a sequence. Because substitution rates cannot be observed directly they must be inferred from the sequences of living species. This is typically done using models of nucleotide substitution. Our ability to reconstruct the history of substitutions for a particular sequence depends on the quality of these models, and thus on our understanding of the substitution process.

We are focusing on an aspect of nucleotide substitution that is currently poorly characterized: how context at intermediate scales (up to 8 bp) biases the substitution process. The best described bias effects are those due to immediately adjacent nucleotides, however it is known that more distant nucleotides also affect substitution. These biases have not yet been systematically described because methods to do so have not been available. We have developed a method to characterize these biases, and are currently examining them in ancestral transposon insertions. Ultimately we will use our findings to develop better models of nucleotide substitution.

Evolution in a simple artificial chemistry. We are studying the evolution of closed catalytic systems in an artificial chemistry. The chemistry is extremely simple, and will permit us to address aspects of the evolution of polymers and metabolic pathways which cannot be inferred by comparing extant organisms on earth. We are particularly interested in the mapping between genotype and phenotype.

People

Eliot Bush
Chris DeBoever (HMC '10)
Andrew Nevarez (HMC '09)
Ben Freeland (HMC '11)
Marissa Quitt (HMC '09)
Singer Ma (HMC '11)

Data Sets and Tools

  • Code calculates the relative abundance of a DNA word given counts. It uses the "total compositional bias" method, as was used by Burge, C. et al. PNAS 1992 and others. Instructions for compiling and using it are in the source. relab.c
  • 3d reconstructions of mammalian brains

Publications

  • Bush EC, Lahn BT. A genome-wide screen for noncoding elements important in primate evolution. BMC Evolutionary Biology, 8:17, 2008. (article)
  • Bush EC, Allman JM. Frontal Cortex Evolution in Primates. In Larry R. Squire, Editor-in-Chief, Encyclopedia of Neuroscience, Academic Press, Oxford, 2008.
  • Bush EC, Lahn BT. The evolution of word composition in metazoan promoter sequence. PLoS Computational Biology, 2(11):e150, 2006. (article)
  • Choi SS, Bush EC, Lahn BT. Different classes of tissue-specific genes show different levels of noncoding conservation. Genomics , 87(3):433-436, 2006. (article)
  • Bush EC, Lahn BT. Selective Constraint on Noncoding Regions of Hominid Genomes. PLoS Computational Biology, 1(7):e73, 2005. (article)
  • Bush EC, Allman JM. The scaling of frontal cortex in primates and carnivores. Proceedings of the National Academy of Sciences of the United States of America, 101(11):3962-3966, 2004. (article)
  • Bush EC, Allman JM. The three dimensional structure and evolution of primate primary visual cortex. Anatomical Record Part A, 281A:1088-1094, 2004. (article)
  • Bush EC, Simons EL, Allman JM. A high resolution CT study of the cranium of a fossil anthropoid primate, Parapithecus grangeri: new insights into the evolutionary history of primate sensory systems. Anatomical Record Part A, 281A:1083-1087, 2004. (article)
  • Bush EC, Allman JM.The scaling of white matter to gray matter in cerebellum and neocortex. Brain Behavior and Evolution, 61(1):1-5, 2003. (article)


Funding