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).
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Michael Sparks is currently a research computational biologist with the USDA-ARS. Home town: Cicero, Illinois. B.S. in Biology, 2002, University of Kentucky. Ph.D. in Bioinformatics and Computational Biology, 2007, Iowa State University. @ ISU from 2002-2008, in Brendel Group since 2002. Research interests: Gene structure prediction. Most recent publication: Sparks, M.E. and Brendel, V. (2008) MetWAMer: eukaryotic translation initiation site prediction. BMC Bioinformatics, 9, 381. Web site: http://brendelgroup.org/mespar1/. |
 | Matt Wilkerson is currently a postdoctoral associate at the University of North Carolina. Home town: Bethesda, Maryland. B.S. Biological Sciences, Notre Dame University, 2003. Ph.D. in Bioinformatics and Computational Biology, Iowa State University, 2007. @ ISU from 2003-2007, Brendel Group since 2003, student since 2004. Research interests: Genome annotation, U12-intron splicing. Most recent publication: Wilkerson, M.D., Schlueter, S.D. & Brendel, V. (2006) yrGATE: a web-based gene-structure annotation tool for the identification and dissemination of eukaryotic genes. Genome Biol. 7, R58 |
 | Qunfeng Dong is currently Bioinformatics Director at the Center for Bioinformatics and Genomics, Indiana University, Bloomington, IN. Home town: Wuhan, Hubei, China. Ph.D., Biochemistry, Iowa State University, 2000. Qunfeng was with the Brendel Group from 2001-2006. Most recent publication (13 total): Dong, Q., Wilkerson, M.D. & Brendel, V. (2007) Tracembler - software for in silico chromosome walking in unassembled genomes. BMC Bioinformatics 8, 151. (*Co-first author). Website: http://people.cgb.indiana.edu/qfdong/web/ |
 | Carolyn Lawrence is a USDA-ARS group leader at Iowa State University and the Director of www.maizegdb.org, a database of maize genome information. Ph.D., University of Georgia, 2003. Carolyn was with the Brendel Group as a postdoc from 2003 to 2005??. Most recent publication: Carolyn J. Lawrence and Virginia Walbot (2007) Translational Genomics for Bioenergy Production from Fuelstock Grasses: Maize as the Model Species. The Plant Cell 19:2091-2094. Website: http://www.lawrencelab.org/index.html |
 | Xiaokang Pan is currently with the Department of Biochemistry, Center for Eukaryotic Structural Genomics, U. of Wisconsin-Madison, Madison WI. B.S., Agronomy, Jiangxi Agricultural University, China, 1985. M.S., Computational Plant Biology, U. of Illinois at Urbana-Champaign, 1996. Ph.D., Computational Plant Biology, U. of Illinois at Urbana-Champaign, 1999. Xiaokang was with the Brendel Group from 2003-2006?. Research Interests: Comparative Genomics. Most recent publication: Brendel, V., Kurtz, S. & Pan, X. (2007) Visualization of syntenic relationships with SynBrowse. In N.H Bergman (ed.), Comparative Genomics, Volume II. Methods in Molecular Biology 396, 153-163. Humana Press, Totowa, NJ. Website: ttp://www.synbrowse.org/ |
 | Bing-Bing Wang is currently an Information Management specialist at Pioneer Hi-Bred, International, Johnston, Iowa. Home town: Anxiang, Hunan province, China. B.S. Hunan Agricultural University, 1995. M.S. China Agricultural University, 1999. Ph.D., Interdepartmental Genetics, Iowa State University. Bing-Bing was with the Brendel Group from 2000-2005. Research interests: plant pre-mRNA splicing. Most recent publication: Bing-Bing Wang and Volker Brendel (2006) Genomewide comparative analysis of alternative splicing in plants. Proc. Nat. Acad. Sci (USA) 103(18) 7175-7180 |
 | Shannon D. Schlueter is currently an Assistant Professor in the Department of Computer and Information Technology, Purdue University, West Lafayette, IN. Home town: Sweetwater, TX. B.S., Genetics, Texas A&M University, 2000. Ph.D., Bioinformatics and Computational Biology, Iowa State University, 2006. Shannon was with the Brendel Group from 2001-2006. Research interests: Genome database development, Genome annotation, and Transcriptional control of gene expression. Most recent publication (6 total): Wilkerson, M.D., Schlueter, S.D. & Brendel, V. (2006) yrGATE: a web-based gene-structure annotation tool for the identification and dissemination of eukaryotic genes. Genome Biol. 7, R58 |
 | Trent Seigfried is formerly the Database Manager at MaizeGDB, USDA-ARS, Iowa State University. Home town: Niota, Illinois. B.S., Biology and Computer Science, Iowa State University, 2002. @ ISU from 1996 to 2008, Brendel Group from 1998 - 2003. Publications: Lawrence, C.J., Seigfried, T.E. & Brendel, V. (2005) MaizeGDB - the community resource for access to diverse maize data. Plant Physiol., 138, 55-58. Lawrence, C.J., Dong, Q., Polacco, M.L., Seigfried, T.E. & Brendel, V. (2004) MaizeGDB, the community database for maize genetics and genomics. Nucl. Acids Res. 32, D393-D397 |
 | Darwin Campbell. is the Database Administrator at MaizeGDB, USDA-ARS, Iowa State University. Home town: Mount Ayr, Iowa. B.S., Agricultural Education, Northwest Missouri State University, 1985. @ ISU since April 2002, Brendel Group since April 2002. |