U.S. flagAn official website of the United States government
                    Here's how you know **Official websites use .gov**
                            
                            A **.gov** website belongs to an official government organization in the United States.
 **Secure .gov websites use HTTPS**
                            
                            A **lock** (                            
                              A locked padlock                                                      
                            
                            ) or **https://** means you’ve safely connected to the .gov website. Share sensitive information only on official, secure websites.


Menu Agricultural Research Service
						
                    U.S. DEPARTMENT OF AGRICULTURE
 Corn Insects and Crop Genetics Research: Ames, IA
 close



    Research

                    Research Projects
                                    Publications
                                    Collaborations
                                    News
                People

                    Staff Listing
                                    Careers


        


                    Database Projects
                        MaizeGDB
                                    SoyBase
                                    PeanutBase
                                    Legume Information System
                                    Maize Newsletter
                                    Maize Mutant Phenotypes
                                    Maize Genetics Conference
                                    Shiny Soybase CNV
                                    Shiny Soybase SNP
                                    Common Bean and Alfalfa - PvGEA
                                    Common Bean and Alfalfa - AGEDSearch small
                    Search
            
            ARS Home
                                About ARS
                                Contact Us




ARS Home Midwest Area Ames, Iowa Corn Insects and Crop Genetics Research People







Rex T Nelson    Computational Biologist Corn Insect & Crop Genetics Research Unit  /ARSUserFiles/50300500/images/Rex Nelson 2.jpg

Rex NelsonResearch Geneticist716 Farmhouse LaneG329 Agronomy HallIowa State UniversityAmes, Iowa 50011-4014515-294-1297515-294-9359 (Fax) **Education**: A.A. Microbiology, Manatee Community College
B.S. Microbiology, University of Florida
M.S. Microbiology, University of South Florida
Ph.D. Microbiology, University of South Florida  **Research Interests**:Soybean biology and ontology to support data management at SoyBase Database. Data retrieval and processing to support SoyBase soybean molecular biology visualization tools that soybean researchers use to develop testable hypotheses for crop improvement. **Aims:**To accumulate soybean molecular and phenotypic data to facilitate soybean research and genetic improvement activities of U.S. scientists and breeders.  Make SoyBase Database a platform that can be used by researchers in other legume crops through ontology and web services development.**Background:**The U.S. and world population is expected to increase in the future.  At the same time agricultural acreage is expected to remain approximately constant, thus there is a need to increase the rate of production of current world crops including soybean.  Concomitantly, the amount of data generated by scientists world-wide is increasing rapidly. In order for these data to be efficiently utilized, it must be identified and presented in an integrated way to scientists in order for them to form hypotheses or breeding strategies for crop improvement.  To further increase the rate of general crop improvement, information and discoveries in one crop will need to be extrapolated to other similar crop species.  Thus, it will be necessary to utilize sequence information and ontologies as a tool to leverage information gained in one crop species to another.**Approach:**SoyBase Database focuses on the accumulation and integration of sequence, genetic and phenotypic data about soybean from soybean researchers world-wide.  These data are then processed, metadata about the data is assigned and the data is integrated into SoyBase Database.  These data are then delivered to soybean researchers in a concise way that presents both genetic, sequence and phenotypic data in an integrated report to support U.S. soybean research and genetic improvement. **Outcomes:**  SoyBase is used by U.S. and foreign scientists and breeders to improve soybean varieties and increase crop yield.  In addition, SoyBase Database is used by scientists to understand physiologic and genetic adaptations of soybean to changes in the environment.  Publications(Clicking on the reprint iconReprint Icon  will take you to the publication reprint.)Standardizing biocuration of genetic variation data to promote FAIRification-(Abstract Only)Data Sharing and Ontology use among Agricultural Genetics, Genomics and Breeding Databases and Resources of the AgBioData Consortium-(Pre-print Publication) Clarke, J., Cooper, L., Poelchau, M.F., Berardini, T., Elser, J., Farmer, A., Ficklin, S., Kumari, S., Laporte, M., Nelson, R., Sadohara, R., Selby, P., Thessen, A.E., Whitehead, B., Sen, T.Z. 2023. Data Sharing and Ontology use among Agricultural Genetics, Genomics and Breeding Databases and Resources of the AgBioData Consortium. ArXiv. arXiv:2307.08958. https://doi.org/10.48550/arXiv.2307.08958.Using crop databases to explore phenotypes: from QTL to candidate genes-(Peer Reviewed Journal) Brown, A.V., Grant, D.M., Nelson, R. 2021. Using crop databases to explore phenotypes: from QTL to candidate genes. Plants. 10(11). Article 2494. https://doi.org/10.3390/plants10112494.The legume information system and associated online genomic resources-(Peer Reviewed Journal) Berendzen, J., Brown, A.V., Cameron, C.T., Campbell, J.D., Cleary, A.M., Dash, S., Hokin, S., Huang, W., Kalberer, S.R., Nelson, R., Redsun, S., Weeks, N.T., Wilkey, A., Farmer, A.D., Cannon, S.B. 2021. The legume information system and associated online genomic resources. Legume Science. Article e74. https://doi.org/10.1002/leg3.74.A new decade and new data at SoyBase, the USDA-ARS soybean genetics and genomics database-(Peer Reviewed Journal) Brown, A.V., Connors, S., Huang, W., Wilkey, A., Grant, D.M., Weeks, N.T., Cannon, S.B., Graham, M.A., Nelson, R. 2020. A new decade and new data at SoyBase, the USDA-ARS soybean genetics and genomics database. Nucleic Acids Research. 49(D1):D1496-D1501. https://doi.org/10.1093/nar/gkaa1107.Genetic variation among 481 diverse soybean accessions, inferred from genomic re-sequencing-(Peer Reviewed Journal) Valliyodan, B., Brown, A.V., Wang, J., Patil, G., Liu, Y., Otyama, P.I., Nelson, R., Vuong, T., Song, Q., Musket, T.A., Wagner, R., Marri, P., Reddy, S., Sessions, A., Wu, X., Grant, D.M., Bayer, P., Roorkiwal, M., Varshney, R.K., Liu, X., Edwards, D., Xu, D., Joshi, T., Cannon, S.B., Nguyen, H.T. 2020. Genetic variation among 481 diverse soybean accessions, inferred from genomic re-sequencing. Scientific Data. 8. Article 50. https://doi.org/10.1038/s41597-021-00834-w.AgBioData consortium recommendations for sustainable genomics and genetics databases for agriculture-(Peer Reviewed Journal) Harper, E.C., Campbell, J., Cannon, E.K., Jung, S., Main, D., Poelchau, M.F., Walls, R.L., Andorf, C.M., Arnaud, E., Berardini, T.Z., Birkett, C.L., Cannon, S.B., Carson, J., Condon, B., Cooper, L., Dunn, N., Elsik, C., Farmer, A., Ficklin, S., Grant, D.M., Grau, E., Hendon, N., Hu, Z., Humann, J., Jaiswal, P., Jonquet, C., Laporte, M., Larmande, P., Lazo, G.R., McCarthy, F., Menda, N., Mungall, C., Munoz-Torres, M., Naithani, S., Nelson, R., Nesdill, D., Park, C., Reecy, J., Reiser, L., Sanderson, L., Sen, T.Z., Staton, M., Subramaniam, S., Karey, T., Unda, V., Unni, D., Wang, L., Ware, D., Wegrzyn, J., Williams, J., Woodhouse, M. 2018. AgBioData consortium recommendations for sustainable genomics and genetics databases for agriculture. Database: The Journal of Biological Databases and Curation. 2018(1):1-32. https://doi.org/10.1093/database/bay088.Ten quick tips for sharing open genomic data-(Peer Reviewed Journal) Brown, A.V., Campbell, J.D., Assefa, T., Grant, D.M., Nelson, R., Weeks, N.T., Cannon, S.B. 2018. Ten quick tips for sharing open genomic data. PLoS Computational Biology. https://doi.org/10.1371/journal.pcbi.1006472.An ontology approach to comparative phenomics in plants-(Peer Reviewed Journal) Oellrich, A., Walls, R.L., Cannon, E., Cannon, S.B., Cooper, L., Gardiner, J., Gkoutos, G.V., Harper, E.C., He, M., Hoehndorf, R., Jaiswal, P., Kalberer, S.R., Lloyd, J., Meinke, D., Menda, N., Moore, L., Nelson, R., Pujar, A., Lawrence, C.J., Huala, E. 2015. An ontology approach to comparative phenomics in plants. Plant Methods. 11:10. DOI: 10.1186/s13007-015-0053-y.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-(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.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.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.Gene expression patterns are correlated with genomic and genic structure in soybean-(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-(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-(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-(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)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. ProjectsSoyBase and the Legume Information System - Information Infrastructure and Research for Legume Crop ImprovementIn-House Appropriated (D)Accession Number:444068 ARS News ArticlesNo news articles listed for this employee.


Return to top


Connect with ARS Sign up


ARS Home
                            USDA.gov
                            Plain Writing
                            Policies & Links
                            Civil Rights Statements
                            FOIA
                            Accessibility Statement
                            Privacy Policy
                            Non-Discrimination Statement
                            Quality of Information
                            USA.gov
                            WhiteHouse.gov