A computational evolution lab at Harvey Mudd College

Research

Our current work is in the area of microbial genome evolution. We've developed an approach to reconstructing the history of genomic island insertions in clades of closely related microbes. We are currently working on improving various aspects of this method, and in using it to study patterns of horizontal transfer across the tree of life.

Data Sets and Tools

• xenoGI, a tool for reconstructing the history of genomic island insertions in clades of microbes

• PHANTASM, PHylogenomic ANalyses for the TAxonomy and Systematics of Microbes

• Calculate the relative abundance of words in DNA: relab.c

• Calculate the relative abundance of substitution patterns: relabSub.tar.gz

• Metabolic simulation code: coop.tar.gz

• 3d reconstructions of mammalian brains

Publications

• *Liu, N., *Gonzalez TA, *Fischer J, *Hong C, *Johnson M, Mawhorter R, *Mugnatto F, *Soh R, *Somji S, Wirth JS, Libeskind-Hadas R, and Bush EC. xenoGI 3: using the DTLOR model to reconstruct the evolution of gene families in clades of microbes. BMC Bioinformatics. 24(295). 2023.

• Wirth JS, Bush EC. Automating microbial taxonomy workflows with PHANTASM: PHylogenomic ANalyses for the TAxonomy and Systematics of Microbes. Nucleic Acids Research. 51(7). 2023.

• *Liu J, Mawhorter R, *Liu I, *Santichaivekin S, Bush E, Libeskind-Hadas R. Maximum Parsimony Reconciliation in the DTLOR Model. BMC Bioinformatics. 22(394). 2021.

• Bush EC, Adolph SC, Donaldson-Matasci MC, Hur JH, and Schulz D. Incorporating Programming, Modeling and Data Analysis into an Introductory Biology Course. Journal of College Science Teaching. 50(3). 2021. [PDF]

• 
  

• Bush EC, *Clark AE, *DeRanek CA, *Eng A, *Forman J, *Heath K, *Lee AB, Stoebel DM, *Wang Z, *Wilber M, *Wu H. xenoGI: reconstructing the history of genomic island insertions in clades of closely related bacteria. BMC Bioinformatics. 19(32). 2018. (article)

• *Wong GT, Bonocora RP, *Schep AN, *Beeler SM, Fong AJ, *Shull LM, Batachari LE, *Dillon M, Evans C, *Becker CJ, Bush EC, Hardin J, Wade JT, and Stoebel DM. Genome-Wide Transcriptional Response to Varying RpoS Levels in Escherichia coli K-12. J Bacteriol. 199:e00755-16. 2017.

• Drewell, RA, Bush EC, Remnant EJ, *Wong GT, *Beeler SM, *Stringham JL, Lim J, Gouldie F, and Oldroyd BP. The dynamic DNA methylation cycle from egg to sperm in the honey bee Apis mellifera. Development. 141(13):2702-11. 2014.

• *Beeler, SM, *Wong GT, Zheng JM, Bush EC, Remnant EJ, Oldroyd BP, and Drewell RA. Whole Genome DNA Methylation Profile of the Jewel Wasp (Nasonia vitripennis). G3: Genes Genomes Genetics, g3-113. 2013.

• Bush EC, Clark AE*, DeBoever CM*, Haynes LE*, Hussain S*, Ma S*, McDermott MM*, Novak AM*, Wentworth JS*. (2012) Modeling the Role of Negative Cooperativity in Metabolic Regulation and Homeostasis. PLoS ONE 7(11): e48920. (article)

• 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)