Wilkerson, M.D., Ru, Y., and Brendel, V.P. (2009) Common introns within orthologous genes: software and application to plants Briefings in Bioinformatics, 10(6), 631-644. [abstract] [PDF]
PlantGDB News:Community-annotated maize gene models (see an example at ZmGDB) are now displayed at both MaizeGDB and maizesequence.org, by means of Distributed Annotation Service (DAS) (November 21, 2009).
Brachypodium distachyon browser: BdGDB, a genome browser for the model grass species Brachypodium distachyon, is now available, based on the JGI v1.0 8x genome assembly. The assembly displayed comprises 271.15 Mb arranged in 5 pseudochromosomes. Display includes gene models, splice-aligned EST, cDNA, PUT assembly and Arabidopsis and rice predicted proteins (October 30, 2009).
| Date | Location | Host | Title |
| October 15, 2010 | Brno, Czech Republic | INTERNATIONAL WORKSHOP: Structural and functional diversity of the eukaryotic genome |
To be announced |
| May 13, 2010 | Indiana University, Bloomington | Department of Biology | Continuing the paradigm shift in biology: Advances towards characterization, modeling, and prediction of the plant transcriptome |
| February 5, 2010 | University of North Carolina at Charlotte | Bioinformatics and Genomics | Opportunities and Challenges for Automated Genome Annotation and Modeling in a Time of Unlimited Access to Sequence Data |
| December 11, 2009 | Michigan State University | Joint Graduate Program Symposium | Advances towards characterization, modeling, prediction, and visualization of the plant transcriptome |
| December 6-8, 2009 | Welcome Trust Conference Center, Hinxton, UK | EC-US Task force on Plant Biotechnology Workshop on Plant Bioinformatics |
Data analysis |
| October 13, 2009 | Gainesville, FL | University of Florida Genetics Institute | Genome-wide studies of intron evolution in the context of orthologous genes |
| June 16-19, 2009 | St. Louis, MO | iPlant Genomics in Education: Gene Annotation and Comparison |
Community-enabled Genome Annotation at PlantGDB |
| June 11-14, 2009 | Kansas City, MO | 3rd Annual Arthropod Genomics Symposium Frontiers in Arthropod Genomics |
Opportunities and challenges for automated genome annotation and modeling in a time of unlimited access to sequence data |
| March 12-15, 2009 | Pheasant Run, St. Charles, IL | 51st Annual Maize Genetics Conference | Community annotation of the maize transcriptome @ MaizeGDB |
| December 8, 2008 postponed |
Vermillion, SD | University of South Dakota, Biology Department | Comprehensive annotation and comparative analysis of minor classes of introns in eukaryotic genes |
| November 15, 2007 | Manhattan, KS | Kansas State University, Computing and Information Sciences, Distinguished Lecturer Series | Necesssity and Promise of Automated and Community Genome Annotation |
| October 17, 2007 | Ann Arbor, MI | University of Michigan Bioinformatics Graduate Program | Catching up with DNA Sequencing Technology: Steps towards automated and community genome annotation |
| February 22, 2007 | Thousand Oaks, California | Ceres | Tools and resources for comparative plant genomics, with applications to the analysis of alternative pre-mRNA splicing |
| May 26, 2006 | Research Triangle Park, North Carolina | BASF Plant Science | Alternative splicing in plants |
| April 27, 2006 | Limburgerhof, Germany | BASF Plant Science | Cyberinfrastructure for plant genomics |
| November 17-19, 2005 | Atlanta, Georgia | The Fifth Georgia Tech International Conference on Bioinformatics | Incorporation of splice site probability models for non-canonical introns improves gene structure prediction in plants. |
| March 10-13, 2005 | Lake Geneva, Wisconsin | 47th Maize Genetics Conference | Estimating and annotating the maize gene space |
| December 14, 2004 | Berlin, Germany | International BCB-Workshop on Gene Annotation Analysis and Alternative Splicing | Assessment of the number and roles of microRNA genes in Arabidopsis |
| November 3, 2004 | Vermillion, South Dakota | South Dakota Biomedical Research Infrastructure Network | Bioinformatics tools and resources for the maize genome sequencing project |
| October 17, 2004 | Irvine, California | Sackler Colloquium: Frontiers in Bioinformatics: Unsolved Problems and Challenges | Comparative plant genomics: evaluation of the model genome concept |
| August 6, 2004 | Ames, Iowa | Iowa State University - University of Iowa Joint Bioinformatics Workshop | Computational identification of microRNAs and their targets |