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United States Department of Agriculture

Agricultural Research Service

Rex T Nelson
Corn Insects and Crop Genetics Research
Computational Biologist

Phone: (515) 294-1297
Fax: (515) 294-9359
1575 AGRONOMY HALL
IOWA STATE UNIVERSITY
AMES, IA, 50011

Projects
SoyBase and the Legume Clade Database
Appropriated (D)
  Accession Number: 425040

Publications (Clicking on the reprint icon Reprint Icon will take you to the publication reprint.)
Transcriptome analyses and virus induced gene silencing identify genes in the Rpp4-mediated Asian soybean rust resistance pathway - (Peer Reviewed Journal)
Morales, A., O'Rourke, J.A., Van De Mortel, M., Schneider, K., Bancroft, T., Borem, A., Nelson, R., Nettleton, D., Baum, T., Shoemaker, R.C., Frederick, R.D., Abdelnoor, R.V., Pedley, K.F., Whitham, S.A., Graham, M.A. 2013. Transcriptome analyses and virus induced gene silencing identify genes in the Rpp4-mediated Asian soybean rust resistance pathway. Functional Plant Biology. DOI:10.1071/FP12296.
Towards a reference plant trait ontology for modeling knowledge of plant traits and phenotypes - (Abstract Only)
Arnaud, E., Cooper, L., Shrestha, R., Menda, N., Nelson, R., Ramil, M., Matteis, L., Skofic, M., Bastow, R., Jaiswal, P., Mueller, L., Mclaren, G. 2012. Towards a reference plant trait ontology for modeling knowledge of plant traits and phenotypes. Meeting Abstract. Paper No. 67.
Biphasic gene expression changes elicited by Phakopsora pachyrhizi in soybean correlates with fungal penetration and haustoria formation - (Peer Reviewed Journal)
Schneider, K.T., Van De Mortel, M., Bancroft, T.J., Nelson, R., Nettleton, D., Braun, E., Frederick, R.D., Baum, T.J., Graham, M.A., Whitham, S.A. 2011. Biphasic gene expression changes elicited by Phakopsora pachyrhizi in soybean correlates with fungal penetration and haustoria formation. Plant Physiology. 157:355-371.
Phenotypic and genomic analyses of a fast neutron mutant population resource in soybean Reprint Icon - (Peer Reviewed Journal)
Bolon, Y.E., Haun, W.J., Xu, W.W., Grant, D.M., Stacey, M.G., Nelson, R., Gerhardt, D.J., Jeddeloh, J.A., Stacey, G., Muehlbauer, G.J., Orf, J.H., Naeve, S.L., Stupar, R.M., Vance, C.P. 2011. Phenotypic and genomic analyses of a fast neutron mutant population resource in soybean. Plant Physiology. 156(1):240-253.
Soybean transcriptome analysis using the SoyBase soybean metabolic database SoyCyc - (Abstract Only)
Nelson, R., Grant, D.M., Cannon, S.B., Chi, A., Zhang, P., Rhee, S., Shoemaker, R.C. 2011. Soybean transcriptome analysis using the SoyBase soybean metabolic database SoyCyc [abstract]. Plant and Animal Genome Conference. Poster 772.
Fast neutron mutants database and web displays at SoyBase - (Abstract Only)
Grant, D.M., Bolon, Y.E., Nelson, R., Vance, C.P., Shoemaker, R.C. 2011. Fast neutron mutants database and web displays at SoyBase [abstract]. Plant and Animal Genome Conference. Poster 389.
Gene expression patterns are correlated with genomic and genic structure in soybean Reprint Icon - (Peer Reviewed Journal)
Woody, J.L., Severin, A., Bolon, Y.E., Joseph, B., Diers, B.W., Farmer, A.T., Weeks, N.T., Muehlbauer, G.J., Nelson, R., Grant, D.M., Specht, J.E., Graham, M.A., Cannon, S.B., May, G.D., Vance, C.P., Shoemaker, R.C. 2011. Gene expression patterns are correlated with genomic and genic structure in soybean. Genome. 54(1):10-18.
Abundance of SSR motifs and development of candidate polymorphic SSR markers (BARCSOYSSR_1.0) in soybean Reprint Icon - (Peer Reviewed Journal)
Song, Q., Jia, G., Zhu, Y., Hwang, E., Hyten, D.L., Cregan, P.B., Grant, D.M., Nelson, R. 2010. Abundance of SSR motifs and development of candidate polymorphic SSR markers (BARCSOYSSR_1.0) in soybean. Crop Science. 50:1950-1960.
Rna-Seq Atlas of Glycine Max: a Guide to the Soybean Transcriptome Reprint Icon - (Peer Reviewed Journal)
Severin, A.J., Woody, J.L., Bolon, Y.E., Joseph, B., Diers, B.W., Farmer, A.D., Muehlbauer, G.J., Nelson, R., Grant, D.M., Specht, J.E., Graham, M.A., Cannon, S.B., May, G.D., Vance, C.P., Shoemaker, R.C. 2010. RNA-Seq Atlas of Glycine max: a guide to the soybean transcriptome. Biomed Central (BMC) Plant Biology. 10:610.
SoyTEdb: A Comprehensive Database of Transposable Elements in the Soybean Genome - (Peer Reviewed Journal)
Du, J., Grant, D.M., Tian, Z., Nelson, R., Zhu, L., Shoemaker, R.C., Ma, J. 2010. SoyTEdb: A Comprehensive Database of Transposable Elements in the Soybean Genome. Biomed Central (BMC) Genomics. 11:113.
Applications and Methods Utilizing the Simple Semantic Web Architecture and Protocol (SSWAP) for Bioinformatics Resource Discovery and Disparate Data and Service Integration - (Peer Reviewed Journal)
Nelson, R., Avraham, S., Shoemaker, R.C., May, G., Ware, D., Gessler, D.D. 2009. Applications and Methods Utilizing the Simple Semantic Web Architecture and Protocol (SSWAP) for Bioinformatics Resource Discovery and Disparate Data and Service Integration. BioMed Central (BMC) BioData Mining. 10:309.
Sswap: a Simple Semantic Web Architecture and Protocol for Semantic Web Services Reprint Icon - (Peer Reviewed Journal)
Gessler, D.D., Schiltz, G.S., May, G.D., Avraham, S., Town, C.D., Grant, D.M., Nelson, R. 2009. SSWAP: A Simple Semantic Web Architecture and Protocol for Semantic Web Services. BMC Bioinformatics. 10:309doi:10.1186/1471-2105-10-309.
SoyBase, The USDA-ARS Soybean Genetics and Genomics Database - (Peer Reviewed Journal)
Grant, D.M., Nelson, R., Cannon, S.B., Shoemaker, R.C. 2009. SoyBase, The USDA-ARS Soybean Genetics and Genomics Database. Nucleic Acids Research. Doi: 10.1093/nar/gkp798.
Integrating Microarray Analysis and the Soybean Genome to Understand the Soybean's Iron Deficiency Response - (Peer Reviewed Journal)
O'Rourke, J.A., Nelson, R., Grant, D.M., Schmutz, J., Grimwald, J., Cannon, S.B., Vance, C.P., Graham, M.A., Shoemaker, R.C. 2009. Integrating Microarray Analysis and the Soybean Genome to Understand the Soybean's Iron Deficiency Response. Biomed Central(BMC)Genomics. 10:376. Available: http://www.biomedcentral.com/1471-2164/10/376.
SoyBase Soybean Ontologies: Pathways to Soybean Growth and Developmental Description - (Abstract Only)
Nelson, R., Grant, D.M., Cannon, S.B., Shoemaker, R.C. 2009. SoyBase Soybean Ontologies: Pathways to Soybean Growth and Developmental Description [abstract]. Plant and Animal Genome Conference. Poster No. P797.
SoyBase Simple Semantic Web Architecture and Protocol (SSWAP) Services - (Abstract Only)
Nelson, R., Grant, D.M., Gangwal, P., Shoemaker, R.C. 2009. SoyBase Simple Semantic Web Architecture and Protocol (SSWAP) Services [abstract]. Plant and Animal Genome Conference. Poster No. P798.
Soybase and The Soybean Breeder's Toolbox: Updated Features and New Data - (Abstract Only)
Grant, D.M., Nelson, R., Cannon, S.B., Shoemaker, R.C. 2009. Soybase and The Soybean Breeder's Toolbox: Updated Features and New Data [abstract]. Plant and Animal Genome Conference. Poster No. P364.
The Soybean Breeder’s Toolbox: Updated Features and New Data - (Abstract Only) - (20-Jul-08)
Microsatellite Discovery from BAC End Sequences and Genetic Mapping to Anchor the Soybean Physical and Genetic Maps - (Peer Reviewed Journal)
Shoemaker, R.C., Grant, D.M., Olson, T., Warren, W.C., Wing, R., Yu, Y., Kim, H., Cregan, P.B., Joseph, B., Futrell-Griggs, M., Nelson, W., Davito, J., Walker, J., Wallis, J., Kremitski, C., Scheer, D., Clifton, S., Graves, T., Nguyen, H., Wu, X., Luo, M., Dvorak, J., Nelson, R., Cannon, S.B., Thomkins, J., Schmutz, J., Stacey, G., Jackson, S. 2008. Microsatellite Discovery from BAC End Sequences and Genetic Mapping to Anchor the Soybean Physical and Genetic Maps. Genome. 51:294-302.
Cel_interrogator: a Free and Open Source Package for Affymetrix Cel File Parsing - (Abstract Only)
Nelson, R., Shoemaker, R.C. 2008. Cel_interrogator: a free and open source package for affymetrix cel file parsing [abstract]. Plant and Animal Genome Conference. Paper No. P867.
Gene Duplication and Paleopolyploidy in Soybean and the Implications for Whole Genome Sequencing - (Peer Reviewed Journal)
Schlueter, J., Lin, J., Schlueter, S., Vasylenko-Sanders, I., Deshpandem, S., Yi, J., O'Bleness, M., Roe, B., Nelson, R., Scheffler, B.E., Jackson, S., Shoemaker, R.C. 2007. Gene duplication and paleopolyploidy in soybean and the implications for whole genome sequencing. Biomed Central (BMC) Genomics. 8:330.
Bioinformatic Resources for Soybean Genetic and Genomic Research - (Book / Chapter)
Grant, D.M., Nelson, R., Graham, M.A., Shoemaker, R.C. 2008. Bioinformatic resources for soybean genetic and genomic research. In: Stacey, Gary, editor. Genetics and Genomics of Soybean. New York, New York. Springer. p. 141-162.
Biphasic Responses of Resistant and Susceptible Soybean Plants to Soybean Rust, Phakopsora Pachyrhizi - (Peer Reviewed Journal)
Van De Mortel, M., Recknor, J.C., Graham, M.A., Nettleton, D., Dittman, J., Nelson, R., Godoy, C.V., Abdelnoor, R.V., Almeida, A.M., Baum, T.J., Whitham, S.A. 2007. Biphasic responses of resistant and susceptible soybean plants to soybean rust, Phakopsora pachyrhizi. Molecular Plant-Microbe Interactions. 20:887-899.
The Soybean Breeder's Toolbox: Integration of Genetic and Molecular Data for Soybean - (Abstract Only)
Nelson, R., Grant, D.M., Shoemaker, R.C. 2007. The soybean breeder's toolbox: integration of genetic and molecular data for soybean [abstract]. Plant and Animal Genome Conference. Paper No. P851.
Identification and Analysis of Gene Families from the Duplicated Genome of Soybean Using EST Sequences - (Peer Reviewed Journal)
Nelson, R., Shoemaker, R.C. 2006. Identification and Analysis of Gene Families from the Duplicated Genome of Soybean Using EST Sequences. Biomed Central (BMC) Genomics. 7:204.
The Soybean Breeder's Toolbox: a New Resource for Soybean Genetic and Genomic Information - (Abstract Only)
Nelson, R., Grant, D.M., Shoemaker, R.C. 2006. The soybean breeder's toolbox: a new resource for soybean genetic and genomic information [abstract]. Biennial Conference on Molecular and Cellular Biology of the Soybean. p. 4.
Preliminary Analysis of Single Nucleotide Polymorphisms in Soybean Detected B Estminer Analysis - (Abstract Only)
Nelson, R., Grant, D.M., Shoemaker, R.C. 2005. Preliminary analysis of single nucleotide polymorphisms in soybean detected b estminer analysis. Plant and Animal Genome Abstracts. p. 433.
The Legume Information Resource (Lis): An Integrated Information Resource for Comparative Legume Biology - (Abstract Only)
Gonzales, M.D., Beavis, B., Gajendran, K., Farmer, A., Archuletal, E., Grant, D.M., Nelson, R., Shoemaker, R.C., Waugh, M. 2005. The legume information resource (lis): an integrated information resource for comparative legume biology. Plant and Animal Genome Abstracts. p. 873.
Estminer: a Suite of Programs for Gene and Allele Identification - (Peer Reviewed Journal)
Nelson, R., Grant, D.M., Shoemaker, R.C. 2004. Estminer: a suite of programs for gene and allele identification. Bioinformatics. 21(5):691-693.
ARS News Articles
Last Modified: 7/31/2014
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