The main overarching focus on the Eisen lab is on the mechanisms by which new functions original and in particular the causes and effects of variation in these mechanisms between taxa. Among our current research topics are:
Improving phylogenetic coverage of genomes.
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. Examples of our work on this include:
The evolution of intracellular and mutualistic symbioses.
One of the simplest ways for organisms to acquire new functions is to engage in symbioses with other species. We use genomic sequencing of a diversity of such symbioses to better understand what the rules are for these symbioses to evolve. Examples of our past projects on this topic 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: wMel genome as well as a few other Wolbachia papers BAC from Brugia Wolbachia, letter about Wolbachia classification.
The functioning of communities of microbes in nature.
For many years, we focused on studies of microbes grown in pure culture in the laboratory. Recently, we have shifted much of our focus to using genome sequencing to study microbes directly in their natural habitats. See for example
Computational methods for analyzing metagenomic data.
We are currently working on multiple projects focusing on designing methods for analyzing metagenomic data. Our work on this includes
- iSEEM (a collaboration with the labs of Jessica Green and Katherine Pollard; see http://openwetware.org/wiki/ISEEM for more detail)
- a collaboration with Simon Levin and Josh Weitz as part of the DARPA Fundamental laws of Biology program.
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 (e.g., Eisen1995; Eisen1997, Eisen1998 Eisen2002, Wu2005, EisenWu2002)
The genomics and evolution of carbon fixation.
We use the evolution of carbon fixation as a model for studying the origin and evolution and processes and pathways. Our work includes genomic studies of the reverse TCA cycle (e.g., here, here and here), methylotrophy (here), Carboxydotrophs (e.g., here), plastid evolution and/or the Calvin cycle (e.g., here, here, here, here, and here), and chemosynthetic symbionts (here, here).