More bat TE data
The second chapter of Heidi Pagan's dissertation has been accepted
at Genome Biology and Evolution. Expect "Survey sequencing reveals
elevated DNA transposon activity, novel elements, and variation in repetitive
landscapes among bats" to be published in the near future. Great
3/9/12 - A non-LTR extinction in squirrels
Congratulations to PhD student, Neal Platt, on his first first-author
publication. The paper, "A non-LTR retroelement extinction in Spermophilus
tridecemlineatus" will appear in the journal Gene sometime in
the next month or so.
2/1/12 - Crocodilian genomes in print
Genome Biology has published our plan to sequence and assemble the
genomes of the three crocodilians discussed below. Currently, the publication
is the #1 Editors Pick at the journal.
1/26/12 - CrocGenomes.org
The website for the International Crocodilian Genomes Working Group
is up and running. There you can find information on our efforts to sequence
and assemble the genomes of three crocodilians - the American alligator,
the saltwater crocodile, and the Indian gharial. Enjoy! http://www.crocgenomes.org/
8/16/11 - NSF funding for the gharial genome!
NSF has just approved funding of our work to add a third genome to
our list of sequenced crocodilians. As per MCB-1052500, "Completing the
Crocodilian Triumvirate: A Genome Draft for the Indian Gharial", we will
immediately begin working to sequence and assemble the genome of Gavialis
8/9/11 - Mobile DNA in Mammalian Genomes
Neal Platt and Dr. Ray attended the FASEB sponsored Mobile DNA in
Mammalian Genomes meeting during the second week of August. Dr. Ray presented
some of Heidi Pagan's recent dissertation work and Neal presented his
recently submitted analyses of the Spermophilus tridecemlineatus
genome. Both the talk and poster were well-received and multiple collaborative
projects were initiated.
8/3/11 - Dr. Heidi Pagan
The Ray laboratory welcomes its first PhD. Dr. Heidi Pagan successfully
defended her dissertation, "A STUDY OF MOBILE DNA CONTENT AND ACTIVITY
IN NON-MODEL MAMMALIAN ORGANISMS". Heidi will be moving on to a postdoctoral
research position at Florida Atlantic University to study the impact of
environmental stress on marine mammals. Congratulations to her!
8/2/11 - First meeting of the International Crocodilian
Genome Working Group
MSU welcomed researchers from three countries and multiple
US universities to participate in a meeting to organize efforts to sequence
and assemble the genomes of Alligator mississippiensis (the American
alligator), Crocodylus porosus (the saltwater crocodile), and
Gavialis gangeticus (the Indian gharial). The meeting was a resounding
success with plans to complete the sequencing and assembly by mid-Fall
and to submit a high-profile genome assembly and analysis manuscript (as
well as multiple satellite papers) by mid-Spring).
1/3/11 - Papers, additional funding, and a new graduate
Over the last several months, we have had several publications submitted
and accepted. Postdoctoral researcher Meganathan has published two manuscripts
from his doctoral research in India (see pubs 40 and 44). Well, one is
published and the other is under revision. Dr. Ray has had a commentary
on recent developements in transposable element assays in humans accepted
at Genome Research (see pub 42). Finally, all of Jeremy's hard work in
analyzing the Anolis carolinensis genome is coming to fruition
(see pubs 37 and 41). In addition to our publication successes, we received
our second consecutive year of funding from the Mississippi Agricultural
and Forestry Experiment Station to continue our examination of TEs in
agriculturally and forensically important flies. Last but not least, we
welcome Christine Lavoie into the laboratory as a new MS student. She
will take over work on the fly TE research. Welcome Christine.
6/1/10 - NSF Funding for bat phylogenetics
NSF has recommended funding for our collaboration with Dr. Richard
Stevens at Louisiana State University entitled, "Collaborative Research:
A Novel Phylogenomic Approach to Bat Phylogenetics and Morphological Evolution".
This project will involve the development of a novel method for inferring
phylogenies using genome-wide analysis of SINEs. The resulting phylogenetic
hypotheses will allow us to answer questions about the evolution of morphological
characters in these unique mammals.
5/14/10 - Lemur transposons and the Biology of Genomes
Our research detailing DNA transposon activity and horizontal transfer
of piggyBac elements in the mouse lemur, Microcebus murinus,
at Genome Biology and Evolution. Congratulations to Heidi on her first
first-author publication! The laboratory also travelled to Cold Spring
Harbor in New York to attend the Biology of Genomes meeting. We presented
four posters detailing our work on squirrels, bats, lizards, and primates.
2/21/10 - MCBIOS awards.
The laboratory attended the MidSouth Computational Biology and Bioinformatics
Society conference in Jonesboro, AR. As a group, we presented three posters
and one oral presentation. Heidi Pagan won the title of best oral presentation
for her talk on lemur TEs and Neal Platt was awarded first prize for his
poster on TE discovery in Spermophilus tridecemlineatus.
1/6/10 - Postdoctoral research opportunity.
NSF funding (see below) has provided us. with funding to hire a postdoctoral
researcher for 2.5 years to perform research on crocodilian genome evolution.
The official announcement remains to be approved by MSU but will be posted
here in the near future. Apply to join our research team. Application
12/15/09 - Strategic Research Initiative Funding.
Our proposal to the Mississippi Agricultural and Forestry Experiment
Station (MAFES) was funded and will allow us to continue our research
into the TE content of oestroid flies (see pub #35 by Thompson
12/7/09 - Two new publications.
We have recently published two new papers. The first
is in collaboration with Dr. Mark Batzer at LSU and is a review of a recent
analysis of TEs in the genome of the extinct mammoth. The second
is the result of collaborative efforts with the laboratory of Stephane
Boissinot and explores the TE dynamics of the Anolis carolinensis
6/29/09 - NSF funding.
In July 2009, the Ray lab was awarded National Science Foundation
funding to study crocodilian genomics via a proposal titled Genome
Evolution and Mobile Element Dynamics in Crocodylia. Using these
funds, we will investigate aspects of genome structure, function and diversity
in representatives from all three crocodilian families (gharials, alligators
and caimans, and true crocodiles). Exciting work is ahead!