Brian O’Meara is co-PI on a newly funded, nearly $1 million NSF grant entitled “Collaborative Research: ABI Development: An open infrastructure to disseminate phylogenetic knowledge.” Brian’s part is to make trees with time information more available, and includes funds for a postdoc (~$140K for UT). Congratulations, Brian!
Both Katie Massana (O’Meara Lab) and Rachel Wooliver (Schweitzer Lab) won NSF East Asia and Pacific Summer Institute (EAPSI) grants last week!
Katie will be going to New Zealand and Rachel will be going to Tasmania this summer.
EEB faculty Joe Williams and Brian O’Meara, together with former grad student Mackenzie Taylor, have a new article out in the American Journal of Botany that has been getting attention in the press. Read the EurekAlert press release, “Which came first, bi- or tricellular pollen? New research updates a classic debate.” Or, read the original, open-access article:
Congratulations to Brian O’Meara and Mike Gilchrist, who were recently awarded a new grant from NSF for “Population genetics-based codon models.” They will be developing new methods of phylogenetic reconstruction using protein coding sequences of DNA. Unlike most work in this area, their methods will be based on evolutionary models that explicitly include the forces of mutation, natural selection and genetic drift. Their work will result in more accurate inferences of the evolutionary relationships between different taxa and, simultaneously, estimates of the strength of natural selection on the coding sequences.
Five Six current or incoming EEB students were awarded NSF Graduate Research Fellowships or honorable mentions:
Awards:
Update 2: Angela Chuang has decided to enter EEB in the fall; numbers have been updated to reflect this.
| Institution | Awards + Honorable Mentions |
|---|---|
| University of California-Davis | 16 |
| University of Washington | 13 |
| University of California-Berkeley | 9 |
| University of California-Santa Cruz | 9 |
| Cornell University | 8 |
| University of Minnesota-Twin Cities | 8 |
| Princeton University | 7 |
| Texas A & M University Main Campus | 7 |
| University of Tennessee Knoxville, all departments | 7 |
| University of Tennessee Knoxville, EEB only | 6 |
| Colorado State University | 6 |
| Michigan State University | 6 |
| University of Florida | 6 |
| University of Arizona | 5 |
| University of Colorado at Boulder | 5 |
| University of Georgia | 5 |
| University of Illinois at Urbana-Champaign | 5 |
| Utah State University | 5 |
| Indiana University | 4 |
| Oregon State University | 4 |
| University of California-Santa Barbara | 4 |
| University of Chicago | 4 |
| University of Michigan Ann Arbor | 4 |
| University of Wisconsin-Madison | 4 |
| Pennsylvania State Univ University Park | 3 |
| Stanford University | 3 |
| University of California-Los Angeles | 3 |
| University of California-San Diego | 3 |
| University of Montana | 3 |
| University of South Florida | 3 |
| Yale University | 3 |
| Arizona State University | 2 |
| Harvard University | 2 |
| Montana State University | 2 |
| Oklahoma State University | 2 |
| Purdue University | 2 |
| SUNY at Stony Brook | 2 |
| University of California-Irvine | 2 |
| University of Hawaii | 2 |
| University of Idaho | 2 |
| University of Illinois at Chicago | 2 |
| University of Kansas Main Campus | 2 |
| University of Missouri-Columbia | 2 |
| University of Notre Dame | 2 |
| University of Pittsburgh | 2 |
| University of Texas at Austin | 2 |
| University of Utah | 2 |
| University of Vermont & State Agricultural College | 2 |
| Virginia Polytechnic Institute and State University | 2 |
| American Museum Natural History | 1 |
| Boise State University | 1 |
| Boston University | 1 |
| Central Michigan University | 1 |
| College of William and Mary | 1 |
| Dartmouth College | 1 |
| Emory University | 1 |
| Florida Gulf Coast University | 1 |
| Florida International University | 1 |
| Florida State University | 1 |
| Hawaii Institute of Marine Biology – University of Hawaii Manoa | 1 |
| Humboldt State University | 1 |
| Humboldt State University Foundation | 1 |
| Kent State University | 1 |
| Massachusetts Institute of Technology | 1 |
| Miami University | 1 |
| Missouri State University | 1 |
| North Carolina State University | 1 |
| North Dakota State University Fargo | 1 |
| Old Dominion University | 1 |
| Portland State University | 1 |
| Rutgers University New Brunswick | 1 |
| Salisbury University | 1 |
| San Francisco State University | 1 |
| San Jose State University | 1 |
| Syracuse University | 1 |
| Texas State University – San Marcos | 1 |
| Trustees of Boston University | 1 |
| Tufts University | 1 |
| University of Alaska Fairbanks Campus | 1 |
| University of California-Riverside | 1 |
| University of Central Florida | 1 |
| University of Connecticut | 1 |
| University of Maine | 1 |
| University of Massachusetts Amherst | 1 |
| University of Nevada Reno | 1 |
| University of New Hampshire | 1 |
| University of North Carolina at Chapel Hill | 1 |
| University of North Carolina at Charlotte | 1 |
| University of Oklahoma Norman Campus | 1 |
| University of Puerto Rico-Rio Piedras | 1 |
| University of Virginia Main Campus | 1 |
| Woods Hole Oceanographic Institution | 1 |
Institutions with no awards or honorable mentions not listed.
Note that for this table, ecology and systematics correspond to NSF categories “Life Sciences – Ecology”, “Life Sciences – Systematic Biology”.
Research assistant professor Barb Banbury and assistant professor Brian O’Meara recently received funding from the Encyclopedia of Life for creating an R interface to parse information from that site. This can be used to identify phylogenetic trends in amount of content for various groups, highlight taxonomic controversies, and in general make this data far more accessible for researchers. All their code is open source and is being developed in public. More information is available here. The figure above shows coverage of various plant species in different databases on a phylogeny of those plants (Asparagales); blue indicates better coverage.
The most recent version of the EEB Newsletter has appeared. You can download a PDF, submit items to the editor, or get an email subscription here.
The most recent version of the EEB Newsletter has appeared. You can download a PDF, submit items to the editor, or get an email subscription here.
PHYLOINFORMATICS SUMMER OF CODE 2011
http://informatics.nescent.org/wiki/Phyloinformatics_Summer_of_Code_2011
The Phyloinformatics Summer of Code program provides a unique opportunity for undergraduate, masters, and PhD students to obtain hands-on experience writing and extending open-source software for evolutionary informatics under the mentorship of experienced developers from around the world. The program is the participation of the US National Evolutionary Synthesis Center (NESCent) as a mentoring organization in the Google Summer of Code(tm) (http://code.google.com/soc/). EEB faculty member Brian O’Meara is one of the mentors of this program.
Students in the program will receive a stipend from Google (and possibly more importantly, a T-shirt solely available to successful participants), and may work from their home, or home institution, for the duration of the 3 month program. Each student will have at least one dedicated mentor to show them the ropes and help them complete their project.
NESCent is particularly targeting students interested in both evolutionary biology and software development. Initial project ideas are listed on the website. These range from visualizing viral epidemics to 3D protein structure evolution, rich annotation for TreeBASE content, exposing phenotype observations to the Encyclopedia of Life, to enhancing R packages for phylogenetic analysis. All project ideas are flexible and many can be adjusted in scope to match the skills of the student. We also welcome novel project ideas that dovetail with student interests.
TO APPLY: Apply online at the Google Summer of Code website (http://socghop.appspot.com/), where you will also find GSoC program rules and eligibility requirements. Each organization has a slightly different application format, and ours is at http://bit.ly/PhyloSoC2011-apptemplate. The 12-day application period for students opens on Monday, March 28th, and runs through Friday, April 8th, 2011.
INQUIRIES: phylosoc {at} nescent {dot} org. We strongly encourage all interested students to get in touch with us with their ideas as early on as possible. Working closely with potential mentors to develop your project proposal greatly increases your chance for acceptance. Do not underestimate the amount of time it takes to develop a competitive proposal.
2011 NESCent Phyloinformatics Summer of Code:
http://informatics.nescent.org/wiki/Phyloinformatics_Summer_of_Code_2011
Google Summer of Code FAQ:
http://socghop.appspot.com/document/show/gsoc_program/google/gsoc2011/faqs
PHYLOINFORMATICS SUMMER OF CODE 2011
http://informatics.nescent.org/wiki/Phyloinformatics_Summer_of_Code_2011
The Phyloinformatics Summer of Code program provides a unique opportunity for undergraduate, masters, and PhD students to obtain hands-on experience writing and extending open-source software for evolutionary informatics under the mentorship of experienced developers from around the world. The program is the participation of the US National Evolutionary Synthesis Center (NESCent) as a mentoring organization in the Google Summer of Code(tm) (http://code.google.com/soc/). EEB faculty member Brian O’Meara is one of the mentors of this program.
Students in the program will receive a stipend from Google (and possibly more importantly, a T-shirt solely available to successful participants), and may work from their home, or home institution, for the duration of the 3 month program. Each student will have at least one dedicated mentor to show them the ropes and help them complete their project.
NESCent is particularly targeting students interested in both evolutionary biology and software development. Initial project ideas are listed on the website. These range from visualizing viral epidemics to 3D protein structure evolution, rich annotation for TreeBASE content, exposing phenotype observations to the Encyclopedia of Life, to enhancing R packages for phylogenetic analysis. All project ideas are flexible and many can be adjusted in scope to match the skills of the student. We also welcome novel project ideas that dovetail with student interests.
TO APPLY: Apply online at the Google Summer of Code website (http://socghop.appspot.com/), where you will also find GSoC program rules and eligibility requirements. Each organization has a slightly different application format, and ours is at http://bit.ly/PhyloSoC2011-apptemplate. The 12-day application period for students opens on Monday, March 28th, and runs through Friday, April 8th, 2011.
INQUIRIES: phylosoc {at} nescent {dot} org. We strongly encourage all interested students to get in touch with us with their ideas as early on as possible. Working closely with potential mentors to develop your project proposal greatly increases your chance for acceptance. Do not underestimate the amount of time it takes to develop a competitive proposal.
2011 NESCent Phyloinformatics Summer of Code:
http://informatics.nescent.org/wiki/Phyloinformatics_Summer_of_Code_2011
Google Summer of Code FAQ:
http://socghop.appspot.com/document/show/gsoc_program/google/gsoc2011/faqs