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





Research

We use computational approaches to study evolution. This includes some more traditional computational biology projects, developing algorithms to analyze sequence data. And some more theoretical projects that involve modeling both molecular processes and evolution.

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 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 of metabolism in a simple artificial chemistry. We are looking at the evolution of metabolic pathways in digital organisms that live and evolve in a simple artificial chemistry. The goal is to better understand aspects of the evolution of enzymes and metabolic pathways. This is a theoretical project, which we hope will allow us to develop hypotheses which can be tested in real biology.

People

Current

Eliot Bush
Ben Freeland (HMC '11)
Sean Laguna (HMC '12)
Helen Wu (HMC '12)
Adam Novak (HMC '12)
John Wentworth (HMC '13)
Anne Clark (HMC '13)


Former

Chris DeBoever (HMC '10)
Andrew Nevarez (HMC '09)
Marissa Quitt (HMC '09)
Singer Ma (HMC '11)
Karen Gragg (HMC '11)

Data Sets and Tools


Publications

  • Nevarez PA, DeBoever CM, Freeland BJ, Quitt MA, Bush EC. Context dependent substitution biases vary within the human genome. BMC Bioinformatics, 11(462), 2010. (article)
  • 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