Tuesday, December 7, 2010

Herbaria are a major frontier for species discovery

A very nice article published in PNAS enhancing the role of herbaria (and other museum collections, really!) in biodiversity research. Of all the new species I have described, only one I found in the field.  Discoveries are really made around the corner...in many cases.  The statistics presented is really interesting! Great read!  See paper here

Tuesday, November 23, 2010

Postdoc position available

I am still accepting applications for a NSF-funded postdoctoral position in biological informatics.  The successful candidate will work on data integration, data interoperability, analytical workflows, and will support the development of ontologies and web services.   Project activities will involve interaction with several informatics teams working on a variety of phyloinformatics and biodiversity informatics tools, e.g., TreeBASE, Global Name Architecture, PhyloWS, NeXML, CDAO and many others. 
The candidate must have a PhD in biology, computer science, computational biology or related fields. A strong background in data management and analysis is highly desirable. The position is available for 2 years with the possibility of extension. 
To apply, send me a CV, a description of your research interests and your PhD research, and contact information of at least two referees. 

Wednesday, November 17, 2010

A new course on Evolutionary Biogeography

Next semester (Spring 2011) I will teach a new Evolutionary Biogeography course with Keith Willmott (Curator of Lepidoptera, FLMNH). I have set up a blog where I will post topics, discussions, links to publications, etc.  Hopefully students will enjoy it and use it as a fun site to post comments, ideas, etc.  http://evobiogeography.blogspot.com

Thursday, November 4, 2010

PhD position available - Fall 2011

The successful applicant will work on the systematics, evolution, and biogeography of Mediterranean Campanulaceae with special focus on the origin and evolution of island endemics of the Aegean archipelago and surrounding, using chloroplast and nuclear DNA sequences.  Active interaction with international collaborators and extensive fieldwork in the Aegean Archipelago and surrounding areas are expected. Experience in molecular, phylogenetic methods and/or ecological niche modeling is desirable. Guidelines to apply can be found at http://www.biology.ufl.edu/Graduate/Application.aspx (applications are due the 15 December, 2010).
For any information, please contact me.

Monday, November 1, 2010

IBC Symposium: Data interoperability in evolutionary biology and the plant sciences

Karen Cranston (NESCent) and myself are organizing a Symposium as part of the International Botanical Congress that will be held in Melbourne, Australia on July 23-30, 2011. We would be happy to consider abstract submissions, although the deadline is soon, November 7, 2010. Here is the Symposium's abstract:

The well-known increase in the size of molecular sequence databases is paralleled by the online content in databases of names, traits, specimens and phylogenies. These data provide an opportunity for large-scale analysis based on a framework of hierarchical species relationships. By combining online phylogenies and metadata, we can ask questions in comparative biology, genomics and ecology without the need for time-consuming manual assembly of data files. These analyses are facilitated not only by the availability of data, but also by the development of standards and protocols that allow us to computationally access, search, retrieve and repurpose trees and associated metadata. Access to non-molecular data poses novel challenges about how we describe and query the data - for example, defining traits or searching for specific evolutionary relationships. Interoperability relies on appropriate file formats for data sharing, ontologies to describe terms and relationships and web services to construct queries and return results. This symposium will highlight recent advances in interoperability of evolutionary data across databases with a focus on the plant sciences. Talks will describe existing resources in plant biology, technologies for data interoperability and analyses that have been enabled through open access to evolutionary data. The list of confirmed speakers includes botanists, computational biologists and computer scientists, all with expertise in data interoperability. These speakers represent a number of projects in plant biology and biodiversity informatics, including the iPlant Collaborative, Encyclopedia of Life, Angiosperm Phylogeny Web (APWeb), Semantic Automated Discovery and Integration (SADI) framework, National Evolutionary Synthesis Center (NESCent) and TreeBASE.

Friday, October 29, 2010

Low-copy nuclear genes

Given the paucity of nuclear genes used in Campanulaceae, we are trying to identify low-copy genes that may be informative, especially within the Campanuloideae.  We have now isolated two markers: GapC exons 7-9 (with introns 7-8) and NIA (Nitrate reductase, intron3) AND we have our first sequences!  We are also exploring PepC, Waxy, Leafy, ADH, and TM6. Who needs ITS? :-)

BisciCol Tracker: Ready, set, go!

My Informatics Lab is happily involved with BiSciCol.  Check out the blog: http://biscicol.blogspot.com/