Eisen:Research



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= Laboratory of Jonathan A. Eisen =

The Eisen Lab research focuses on understanding the genomic basis for the origin of novelty (new functions and processes) in microorganisms. For many years, studies in this area were of limited scope. However, the advent of genome sequencing has allowed one to study the origin of novelty on a more global level. The Eisen lab's main location is in the U. C. Davis Genome Center. Dr. Eisen has appointments in the Section of Evolution and Ecology and the Department of Medical Microbiology at U. C. Davis and an Adjunct Appointment at the Joint Genome Institute, where he runs a small "Phylogenomics" group.

= General research areas -- Phylogenomics and the Origin of Novelty =
 * Mechanisms of novelty generation. A major component of our work involves using genome sequences to better understand the mechanisms by which new processes originate in microbes. Mechanisms in which we are interested include lateral DNA transfer, gene duplication and divergence and invention of new genes.
 * Evolvability. In addition, we are particularly interested in constraints and biases in the use of these novelty generating mechanisms.  These constraints and biases generate differences in evolvability both within genomes and between individuals and species.  For example, we are interested in differences in DNA repair and recombination processes between species and how these shape mutation rates and patterns.
 * Predicting organisms biology from their genome sequences. One of the major goals behind our work in studies of the origin of novelty is to use this information to improve our ability to make predictions of the biology of organisms from their genome sequences. Examples of our work in this area include:
 * We were the first to outline a phylogenetic approach to functional prediction generally known as phylogenomics (e.g., Eisen, 1995; Eisen et al, 1997, Eisen, 1998)
 * We have used and developed methods for predicting function using phylogenetic profiling (e.g., Eisen et al. 2002, Wu et al 2005, Eisen and Wu, 2002)
 * Phylogenomic methods development. Embedded within all our work is the development of computational approaches in which evolutionary reconstructions and genome analyses are combined into a composite phylogenomic approach.

= Model systems for studying novelty = In our studies of the origin of novelty, we focus on a few fey biological systems and questions that are excellent model systems for studying novelty. These include


 * Phylogenomics and the tree of life. In order to get a full appreciation of microbial diversity and genomics we needs to understand more about the poorly studied branches in the tree of life. To help with this, we have been involved in multiple projects to generate genome sequence data from novel branches on the tree of life including:
 * An NSF Tree of Life program to sequence and characterize genomes from phyla of bacteria for which there are no complete genomes available. For more information see http://www.tigr.org/tol
 * An NSF-NIH funded project to sequence the genome of Tetrahymena thermophila a model ciliate. See our paper here
 * A new project at JGI to create a Genomic Encyclopedia of Bacteria and Archaea
 * The evolution of intracellular symbioses. One of the simplest ways for organisms to acquire new functions is to engage in symbioses with other species. Perhaps the most pervasive symbioses leading to new functions are those involving the plastid and mitochondria organelles of eukaryotes. In addition, there are 1000s of other symbioses between eukaryotes and intracellular bacteria at various stages of evolution. We are interested in characterizing a diversity of such symbioses to better understand what the rules are for these symbioses to evolve.  Examples of our projects include:
 * A collaboration with Nancy Moran's lab on studying the genomes of the symbionts inside the glassy winged sharpshooter. See PLoS Biology paper here
 * A collaboration with JGI and the lab of Colleen Cavanaugh (my undergraduate advisor) on the chemosynthetic symbionts found in the giant clam Calyptogena magnifica. See paper here
 * A collaboration with the lab of Scott O'Neill on the first Wolbachia genome. See paper here. See other lab papers on Wolbachia: BAC from Brugia Wolbachia, letter about Wolbachia classification
 * The functioning of communities of microbes in nature. For many years, we have asked questions about the origin of novelty in the context of analysis of the genome sequences of microbial species that have been grown in pure culture in the laboratory. In the last few years we have shifted much of our focus to using genome sequencing to study microbes directly in their natural habitats. We are working on methods to characterize such microbial communities and are applying these methods to characterize some model microbial communities:
 * A review I wrote on environmental shotgun sequencing
 * Metagenomics of ocean microbes: Global Ocean Sampling Protein Families; Global Ocean Sampling: Northwest Atlantic through Eastern Tropical Pacific; Sargasso Sea metagenomics Phototroph metagenomics with Ed Delong
 * The genomics and evolution of carbon fixation
 * Reverse TCA cycle: Genome sequencing and evolution of Chlorobium tepidum: here, here and here.
 * Methylotrophy: Genome sequencing of Methylococcus capsulatus
 * Carboxydotrophs: Genome sequencing of Carboxydothermus hydrogenoformans
 * Plastid evolution and/or Calvin cycle and genomics Prochloron symbionts, Plasmodium genome, uncultured bugs, Arabidopsis chromosome II, Arabidopsis genome
 * Chemosynthetic symbionts Calyptogena genome, Solemya symbionts

= Recent News =
 * Jonathan Eisen is the new Academic Editor in Chief of PLoS Biology. For more detail see my first editorial here.
 * Jonathan Eisen's Evolution Textbook has been published. Entitled creatively "Evolution" this is a new textbook jointly authored by Jonathan Eisen, Nick Barton, David Goldstein, Derek Briggs and Nipam Patel.  It is published by Cold Spring Harbor Press.
 * Recent publications
 * Maresca JA et al. Identification of a fourth family of lycopene cyclases in photosynthetic bacteria. PNAS 104: 11784-11789.
 * Norais C et al. Genetic and physical mapping of DNA replication origins in Haloferax volcanii. PLoS Genet. 2007 May 18;3(5):e77.
 * For more news see Jonathan Eisen's Work Blog
 * For non news see = Jonathan's Davis, CA blog

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