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).
| DATES | SOURCE | AMOUNT (TOTAL COST) | TOPIC | PRINCIPAL INVESTIGATOR |
| 8/15/06 - 7/31/10 |
NSF EEC-0608769 | $450,000 | BBSI Bioinformatics and Computational Systems Biology Summer Institute at Iowa State University | Robert Jernigan, Iowa State University |
| 6/1/05 - 8/31/09 |
ARS/USDA Specific Cooperative Agreement No. 58-3625-5-124 | $217,194 | Relational Legume Genome Database: The Breeder's Toolbox | Volker Brendel |
| 1/1/04 - 12/31/07 |
NSF DBI-0321600 | $1,047,220 |
PlantGDB - Plant Genome Database and Analysis Tools | Volker Brendel |
| 10/1/02 - 9/30/07 |
NSF EEC-0234102 | $645,000 | NIH-NSF BBSI: Summer Institute in Bioinformatics and Computational Biology - Iowa State University | Volker Brendel |
| 10/1/01 - 9/30/07 | NSF DBI-0110189 | $445,247 (ISU subcontract expired 9/30/06) |
Regulation of Inflorescence Architecture in Maize | Sarah Hake, U.C. Berkeley |
| 9/1/03 - 8/31/06 |
BARD IS-3454-03 | $130,000 (ISU subcontract) |
Harnessing the Genetic Diversity Engendered by Alternative Gene Splicing | Robert Fluhr, The Weizmann Institute of Science, Israel |
| 9/15/02 - 9/30/06 | USDA-NRI CGP 52.1, Plant Genome Program - Bioinformatics and Data Management | $502,039 | BarleyBase, a Prototype Online Database for Cereal Microarrays with Integrated Tools for Data Visualization | Julie Dickerson, Iowa State University |
| 9/25/01 - 9/24/06 |
ARS/USDA Specific Cooperative Agreement No. 58-3625-1-192 | $818,976 | Database of Maize Genome Information (DBMGI) - A New Generation Maize Genome Database | Volker Brendel |
| 6/30/03 - 6/30/05 |
National Center for Genome Resources | $133,864 | Legume Information System (subcontract) | Volker Brendel |
| 9/5/03 - 8/31/04 |
ARS/USDA Specific Cooperative Agreement No. 58-3625-3-152 | $46,000 | Maize Genomic Sequences: Annotation and Curation in MaizeGDB | Volker Brendel |
| 7/1/02 - 12/31/04 |
NSF ACI-0203782 | $150,000 | Parallel Algorithms and Software for Gene Identification and Annotation from EST Collections | Srinivas Aluru, Iowa State University |
| 9/1/01 - 10/31/04 |
NSF DBI-0110254 | $158,996 | PlantGDB - Plant Genome Database and Analysis Tools | Volker Brendel |
| 9/1/03 - 12/31/03 |
NSF DBI-0319973 | $55,196 (Supplemental Award) |
PlantGDB - Plant Genome Database and Analysis Tools | Volker Brendel |
| 10/1/98 - 9/30/04 | NSF DBI-9872657 | $1,416,194 (ISU subcontract) |
Maize Gene Discovery, Sequencing and Phenotypic Analysis | Virginia Walbot, Stanford University |
| 9/15/01 - 8/31/04 |
NSF EIA-0130861 | $166,518 | CISE Research Resources: Acquisition of a cluster for experimental parallel computing research in scientific computing and computational biology | Srinivas Aluru, Iowa State University |
| 7/1/01 - 12/31/03 | NSF DBI-0090732 | $399,810 | Efficient Web-based Serving of Consolidated Multi-Source Biological Sequence Data Extracts | Volker Brendel |
| 7/1/01 - 6/30/03 | ISU Plant Sciences Institute Grant | $25,000 | Identification of Alternatively Spliced Genes in Arabidopsis | Volker Brendel |
| 7/1/00 - 6/30/02 | Iowa Corn Promotion Board | $32,000 | Gene Discovery and Annotation in the Maize Genome Database ZmDB | Volker Brendel |
| 7/1/99 - 6/30/01 | NIH 5R44HG001850-03 | $57,411 (VB part of ISU subcontract) |
An Integrated 'Field Stream' Bioinformatics Data System | Michael Bergman, VisualMetrics Inc. |
| 7/1/00 - 12/31/01 | ISU University Research Grant | $17,350 | Parallel Computational Methods for Gene Identification from EST Collections | Srinivas Aluru, Electrical and Computer Engineering |
| 10/1/00 | Hewlett-Packard Inc. | (1) R390 server (1) B180L workstation |
Equipment Gift (Loan from 4/1/99) | Volker Brendel |