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= Laboratory of Jonathan A. Eisen =
= Laboratory of Jonathan A. Eisen =
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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 [http://genomics.ucdavis.edu/ U. C. Davis Genome Center].  Dr. Eisen has appointments in the [http://www-eve.ucdavis.edu/ Section of Evolution and Ecology] and the [http://www.ucdmc.ucdavis.edu/medmicro/ Department of Medical Microbiology] at [http://www.ucdmc.ucdavis.edu/medmicro/ U. C. Davis] and an Adjunct Appointment at the [http://www.jgi.doe.gov/ Joint Genome Institute], where he runs a small "Phylogenomics" group.
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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 [http://genomics.ucdavis.edu/ U. C. Davis Genome Center].  Dr. Eisen has appointments in the [http://www-eve.ucdavis.edu/ Section of Evolution and Ecology] and the [http://www.ucdmc.ucdavis.edu/medmicro/ Department of Medical Microbiology] at [http://www.ucdmc.ucdavis.edu/medmicro/ U. C. Davis] and an Adjunct Appointment at the [http://www.jgi.doe.gov/ Joint Genome Institute].
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== '''General research areas -- Phylogenomics and the Origin of Novelty.''' ** More detail is available [[Eisen:Research| Here]].==
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Dr. Eisen is also a strong proponent of the Open Access movement in scientific publishing and is Academic Editor in Chief of [http://www.plosbiology.org PLoS Biology]. Dr. Eisen is also an active and award winning science blogger (see [http://phylogenomics.blogspot.com his Tree of Life blog here]). More detail is available [[Eisen:Research| Here]].
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* Mechanisms of novelty generation.
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* Evolvability.
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* Predicting organisms biology from their genome sequences.
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* Phylogenomic methods development.
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== '''Model systems for studying novelty.''' More detail is available [[Eisen:Research| Here]].==
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== General research areas -- Phylogenomics and the Origin of Novelty ==
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* Phylogenomics and the tree of life.
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* '''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.  
-
* The evolution of intracellular symbioses.
+
*'''Evolvability.''' We are particularly interested in constraints and biases in these novelty generating mechanisms that differ within and between species.
-
* The functioning of communities of microbes in nature.
+
* '''Predicting organisms biology from their genome sequences.''' We make use of information on novelty generation to improve predictions of the biology of organisms from their genome sequences.  
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* The genomics and evolution of carbon fixation
+
* '''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., [http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=7651832 Eisen1995]; [http://www.ncbi.nlm.nih.gov/pubmed/9334711?ordinalpos=1&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum Eisen1997], [http://www.genome.org/cgi/content/full/8/3/163 Eisen1998] [http://www.pnas.org/cgi/content/full/99/14/9509 Eisen2002], [http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.0010065 Wu2005], [http://www.ncbi.nlm.nih.gov/pubmed/12167367?ordinalpos=20&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum EisenWu2002])
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== '''Recent News'''==
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== Current projects and model systems for studying novelty ==
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* Jonathan Eisen is the new Academic Editor in Chief of PLoS Biology. For more detail see my first editorial [http://biology.plosjournals.org/perlserv/?request=get-document&doi=10.1371/journal.pbio.0060048 here].
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* '''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: a past NSF Tree of Life project [http://www.tigr.org/tol see here] and GEBA (A Genomic Encyclopedia of Bacteria and Archaea)  [http://www.jgi.doe.gov/programs/GEBA/pilot.html here].
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* Jonathan Eisen's [http://evolution-textbook.org/ 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.  
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* '''The evolution of intracellular 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 projects include studies of symbionts of the  glassy winged sharpshooter [http://biology.plosjournals.org/perlserv/?request=get-document&doi=10.1371/journal.pbio.0040188 here],  chemosynthetic symbionts (e.g.,  [http://www.sciencemag.org/cgi/content/full/315/5814/998 here]), Wolbachia ([http://biology.plosjournals.org/perlserv/?request=get-document&doi=10.1371/journal.pbio.0020069 wMel genome], [http://www.ncbi.nlm.nih.gov/pubmed/11812492?ordinalpos=3&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum BAC from Brugia Wolbachia], [http://www.ncbi.nlm.nih.gov/pubmed/17684235?ordinalpos=1&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum letter about Wolbachia classification]).
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** I am creating a Wiki Page for the Textbook that anyone can edit [[Eisen:EvolutionTextbook | Here]]
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* '''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  [http://biology.plosjournals.org/perlserv/?request=get-document&doi=10.1371/journal.pbio.0050082 Review], [http://biology.plosjournals.org/perlserv/?request=get-document&doi=10.1371/journal.pbio.0050016 GOS Proteins]; [http://biology.plosjournals.org/perlserv/?request=get-document&doi=10.1371/journal.pbio.0050077 GOS Survey]; [http://www.ncbi.nlm.nih.gov/pubmed/15001713?ordinalpos=3&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum Sargasso metagenomics], [http://www.ncbi.nlm.nih.gov/pubmed/11832943?ordinalpos=1&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum Phototroph metagenomics].
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* Recent publications
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* '''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 [http://iseem.org for more detail]) and a collaboration with Simon Levin and Josh Weitz as part of the DARPA Fundamental laws of Biology program.
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** [http://www.pnas.org/cgi/content/full/104/28/11784?maxtoshow=&HITS=10&hits=10&RESULTFORMAT=&fulltext=eisen&searchid=1&FIRSTINDEX=0&sortspec=date&resourcetype=HWCIT Maresca JA et al. Identification of a fourth family of lycopene cyclases in photosynthetic bacteria. PNAS 104: 11784-11789.]
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* '''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., [http://www.pnas.org/cgi/content/full/104/28/11784 here], [http://www.pnas.org/cgi/content/full/99/14/9509 here] and [http://www.ncbi.nlm.nih.gov/pubmed/9595663?ordinalpos=4&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum here]),  methylotrophy ([http://biology.plosjournals.org/perlserv/?request=get-document&doi=10.1371/journal.pbio.0020303 here]), Carboxydotrophs (e.g., [http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.0010065 here]),  plastid evolution and/or the Calvin cycle (e.g.,  [http://www.pnas.org/cgi/content/full/102/20/7315 here], [http://www.nature.com/nature/journal/v419/n6906/abs/nature01097.html here], [http://www.nature.com/nature/journal/v415/n6872/abs/415630a.html here], [http://www.nature.com/nature/journal/v402/n6763/abs/402761a0.html here], [http://www.nature.com/nature/journal/v408/n6814/abs/408796a0.html and here]), and chemosynthetic symbionts ([http://www.sciencemag.org/cgi/content/full/315/5814/998 here], [http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=1577710 here]).
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** [http://genetics.plosjournals.org/perlserv/?request=get-document&doi=10.1371/journal.pgen.0030077 Norais C et al. Genetic and physical mapping of DNA replication origins in Haloferax volcanii. PLoS Genet. 2007 May 18;3(5):e77.]
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* '''Other genome projects'''. The sequencing the genome of ''Tetrahymena thermophila'' a model ciliate [http://biology.plosjournals.org/perlserv/?request=get-document&doi=10.1371/journal.pbio.0040286 here].
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* For more news see [http://phylogenomics.blogspot.com Jonathan Eisen's Work Blog]
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* For non news see = Jonathan's [http://daviscalifornia.blogspot.com/ Davis, CA blog]
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== Recent Publications ==
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*  Amber L. Hartman, Denver M. Lough, Dinesh K. Barupal, Oliver Fiehn, Thomas Fishbein, Michael Zasloff, and Jonathan A. Eisen. Human gut microbiome adopts an alternative state following small bowel transplantation. [http://www.pnas.org/content/early/2009/09/16/0904847106.abstract . PNAS 2009 : 0904847106v1-pnas.0904847106]
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** [http://www.upi.com/Science_News/2009/09/16/Ileostomy-patients-Different-gut-bacteria/UPI-98081253114816/ UPI Story about this]
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** [http://www.sciencedaily.com/releases/2009/09/090915154905.htm Press release]
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*  Wu D, Hartman A, Ward N, Eisen JA (2008) An Automated Phylogenetic Tree-Based Small Subunit rRNA Taxonomy and Alignment Pipeline (STAP) [http://www.plosone.org/article/info:doi%2F10.1371%2Fjournal.pone.0002566 . PLoS ONE 3(7): e2566. doi:10.1371/journal.pone.0002566]
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** Blogged about by [http://www.genome-technology.com/issues/blog/general/148000-1.html Genome Technology] and [http://phylogenomics.blogspot.com/2008/07/my-first-plos-one-paper-yay.html Jonathan Eisen] and [http://scienceblogs.com/clock/2008/07/new_and_exciting_in_plos_one_42.php Bora]
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** Download [http://128.120.136.15/mediawiki/index.php/STAP_download here ]
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* Wu M and Eisen JA. A simple, fast, and accurate method of phylogenomic inference [http://genomebiology.com/2008/9/10/R151 Genome Biology 2008, 9:R151]
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** Blogged about by [http://sandwalk.blogspot.com/2008/10/bacteria-phylogeny-facing-up-to.html Larry Moran]
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== Software and Downloads ==
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* AMPHORA - automated phylogenomic analysis for genomes and metagenomics http://bobcat.genomecenter.ucdavis.edu/AMPHORA/
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* Compost Bin  - Metagenomic Binning by PCA. Download http://bobcat.genomecenter.ucdavis.edu/souravc/compostbin/
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* STAP - rRNA alignment and taxonomy pipeline. Download http://bobcat.genomecenter.ucdavis.edu/mediawiki/index.php/STAP_download
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* WATERS - a Workflow for the Alignment, Taxonomy and Ecology of Ribosomal Sequences: http://bobcat.genomecenter.ucdavis.edu/mediawiki/index.php/WATERS
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== Social Media and Such ==
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* For other sciency information about the lab see [http://phylogenomics.blogspot.com Jonathan Eisen's Work Blog]
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* For non sciency things see Jonathan's [http://daviscalifornia.blogspot.com/ Davis, CA blog]
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* To follow Jonathan Eisen on Twitter go to http://twitter.com/phylogenomics
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* To follow Jonathan Eisen on FriendFeed go to http://friendfeed.com/treeoflife
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* Jonathan Eisen's Linked In profile is here: http://www.linkedin.com/in/jonathaneisen

Revision as of 13:52, 12 December 2009


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Contents

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.

Dr. Eisen is also a strong proponent of the Open Access movement in scientific publishing and is Academic Editor in Chief of PLoS Biology. Dr. Eisen is also an active and award winning science blogger (see his Tree of Life blog here). More detail is available Here.

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.
  • Evolvability. We are particularly interested in constraints and biases in these novelty generating mechanisms that differ within and between species.
  • Predicting organisms biology from their genome sequences. We make use of information on novelty generation to improve predictions of the biology of organisms from their genome sequences.
  • 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)

Current projects and model systems for studying novelty

  • 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: a past NSF Tree of Life project see here and GEBA (A Genomic Encyclopedia of Bacteria and Archaea) here.
  • The evolution of intracellular 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 projects include studies of symbionts of the glassy winged sharpshooter here, chemosynthetic symbionts (e.g., here), Wolbachia (wMel genome, 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 Review, GOS Proteins; GOS Survey; Sargasso metagenomics, Phototroph metagenomics.
  • 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 for more detail) and a collaboration with Simon Levin and Josh Weitz as part of the DARPA Fundamental laws of Biology program.
  • 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).
  • Other genome projects. The sequencing the genome of Tetrahymena thermophila a model ciliate here.


Recent Publications

Software and Downloads


Social Media and Such

Personal tools