Tag: eukaryotes

The need for a phylogeny driven genomic encyclopedia of eukaryotes

Monday I gave a talk for the SMBE Eukaryotic Omics satellite meeting that has been going on at UC Davis.  When Holly Bik, a post doc in my lab asked me to talk at the meeting, I said, basically “Well, OK, but I don’t really do much work on eukaryotes.”  And then I came up with an idea – I could make my talk about how it might be good to have a better phylogenetic sampling of eukaryotic genome sequences.  I have been a bit obsessed for many many years about phylogenetic sampling of genomes and, well, though I have avoided eukaryotes mostly in most of my genome sequencing work, I figured, I should still get on my soap box about how phylogenetic sampling is a good thing.  So, well, I did.  And I think we (i.e., the scientific community) really needs a better sampling of eukaryotic genomes.

I have posted my talk to Slideshare and I recorded audio of my talk in synch with the slides and posted that to Youtube.  These are below.

I hereby am calling for those people interested in participating in such a phylogeny driven genomic encyclopedia of eukaryotes to make yourselves known.  We NEED to do this.

Related posts

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This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

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Sign up: SMBE Satellite Mtg. on Eukaryotic-Omics 4/29-5/2 at #UCDavis

Going to be good:

Eukaryotes | SMBE Satellite Meeting on Eukaryotic -Omics – April 29 to May 2, UC Davis Conference Center

No bias here – given that it is organized by Holly Bik in my lab and it is at UC Davis. The lineup of speakers is great and the topic is timely.  So sign up  …

Speakers:

Rachel Adams UC Berkeley Groundtruthing next-gen sequencing for microbial ecology: is beta diversity robust to errors in pyrosequencing?
Nicholas A. Bokulich UC Davis Regional Patterns in Grape Fungal Consortia Define Wine Fermentation Communities
Sara Branco UC Berkeley Fungi at a small-scale: spatial zonation of fungal assemblages around single trees
C. Titus Brown Michigan State University Sequencing and assembly of diverse eukaryotes: like metagenomics, but much harder
Peter Countway Bigelow Laboratory for Ocean Sciences Title TBA
Simon Creer Bangor University, Wales Title TBA
Tom Delmont Marine Biological Laboratory, Woods Hole Phaeocystis antarctica spatiotemporal diversity, activity and its relation to prokaryotes and viruses using physiological and ‘omic approaches
Jonathan Eisen UC Davis The need for a phylogeny driven genomic encyclopedia of eukaryotes
Laura Eme Dalhousie University Large scale phylogenomic analyses of Blastocystis subtype 1 reveals a major role for lateral gene transfer in adaptation to parasitism of the human gut
Jack Gilbert Argonne National Lab Addressing microbial eukaryotic biogeography in home, hospitals and the world
Jean-David Grattepanche Smith College Title TBA
Victor Hanson-Smith UC San Francisco Identifying Loci of Functional Evolution in Ancestral Genes
Ian King University of Guelph Biomonitoring 2.0: A high-throughput genomics approach for comprehensive biological assessment of environmental change
Andrew Krohn Northern Arizona University Rhizosphere microbial community dynamics of drought-stressed pinyon pines (Poster)
Franck Lejzerowicz University of Geneva Exploring the deep-sea foraminiferal diversity by multiplexed RNA and DNA-based ultra-deep sequencing and ultra-fast bioinformatic analyses
Matthew Morgan CSIRO Australia Next-generation sequencing reveals the impacts of inundation and drought on eukaryote biodiversity in semi-arid floodplain soils
Laura Wegener Parfrey University of Colorado, Boulder Incorporating microbial eukaryotes into analyses of the human microbiome
Katherine Pollard UC San Francisco Title TBA
Dorota Porazinska University of Florida Discrimination of microscopic pests of agricultural importance with NGS
Thomas Richards NHM London Title TBA
Surya Saha Cornell University Composition of the Maize Endophytic Microbiome is Correlated with Maize Genotype (Poster)
Søren Sørensen University of Copenhagen Title TBA
Fabian Staubach Stanford University Host species and environmental effects on bacterial communities associated with Drosophila in the laboratory and in the natural environment
Sarah Stephenson CSIRO Australia Metagenetic examinations of benthic eukaryl estuarine communities
Joshua Stern Georgia Institute of Technology Searching for the Phylogenetic Place of Eukaryotes, Using Data from STORI
W. Kelley Thomas University of New Hampshire Title TBA
Xianfa Xie Virginia State University Comparative genomic study of the origin and evolution of eukaryotes
——–
This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

——–