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United States Department of Agriculture

Agricultural Research Service

Research Project: Enhancing Breeding of Small Grains Through Improved Bioinformatics

Location: Plant, Soil and Nutrition Research

Publications (Clicking on the reprint icon Reprint Icon will take you to the publication reprint.)

Identification of black bean (Phaseolus vulgaris L.) polyphenols that inhibit and promote iron uptake by caco-2 cells - (Peer Reviewed Journal)
Hart, J.J., Tako, E.N., Kochian, L.V., Glahn, R.P. 2015. Identification of black bean (Phaseolus vulgaris L.) polyphenols that inhibit and promote iron uptake by caco-2 cells. Journal of Agricultural and Food Chemistry. DOI: 10.1021/acs.jafc.5b00531.
Optimization of genomic selection training populations with a genetic algorithm     Reprint Icon - (Peer Reviewed Journal)
Akdemir, D., Sanchez, J., Jannink, J. 2015. Optimization of genomic selection training populations with a genetic algorithm. Genetics Selection Evolution. 47:38.
Increased prediction accuracy in wheat breeding trials using a marker x environment interaction genomic selection model     Reprint Icon - (Peer Reviewed Journal)
Cruz, M., Crossa, J., Bonnett, D., Dreisigacker, S., Poland, J.A., Jannink, J., Singh, R., De Los Campos, G. 2015. Increased prediction accuracy in wheat breeding trials using a marker x environment interaction genomic selection model. Genes, Genomes, Genetics. 5(4):569-582.
Increased prediction accuracy in wheat breeding trials using a marker x environment interaction genomic selection model     Reprint Icon - (Peer Reviewed Journal)
Lopez-Cruz, M., Crossa, J., Bonnett, D., Dreisigacker, S., Poland, J., Jannink, J., Singh, R.P., Antrique, E., De Los Campos, G. 2015. Increased prediction accuracy in wheat breeding trials using a marker x environment interaction genomic selection model. Genes, Genomes, Genetics. 5(4):569-582.
Locally epistatic genomic relationship matrices for genomic association and prediction - (Peer Reviewed Journal)
Akdemir, D., Jannink, J. 2015. Locally epistatic genomic relationship matrices for genomic association and prediction. Genetics. 199(3):857-871.
Locally epistatic genomic relationship matrices for genomic association     Reprint Icon - (Peer Reviewed Journal)
Akdemir, D., Jannink, J. 2015. Locally epistatic genomic relationship matrices for genomic association. Genetics. 199:857-871.
solGS: a web-based tool for genomic selection     Reprint Icon - (Peer Reviewed Journal)
Tecle, I., Edwards, J., Egesi, C., Rabbi, I., Kulakow, P., Jannink, J., Mueller, L.A. 2014. solGS: a web-based tool for genomic selection. BMC Bioinformatics. 15:398.
Efficient use of historical data for genomic selection: a case study of rust resistance in wheat - (Peer Reviewed Journal)
Rutkoski, J., Singh, R., Huerta-Espino, J., Bhavani, S., Poland, J.A., Jannink, J., Sorrells, M. 2015. Efficient use of historical data for genomic selection: a case study of rust resistance in wheat. The Plant Genome. DOI: 10.3835/plantgenome2014.09.0046.
Training set optimization under population structure in genomic selection     Reprint Icon - (Peer Reviewed Journal)
Isidro, J., Jannink, J., Akdemir, D., Poland, J., Heslot, N., Sorrells, M. 2015. Training set optimization under population structure in genomic selection. Theoretical and Applied Genetics. 128(1):145-158.
Training set optimization under population structure in genomic selection     Reprint Icon - (Peer Reviewed Journal)
Isidro, J., Jannink, J., Akdemir, D., Poland, J.A., Heslot, N., Sorrells, M. 2015. Training set optimization under population structure in genomic selection. Theoretical and Applied Genetics. 128(1):145-158.
Genomic prediction in bi-parental tropical maize populations in water-stressed and well-watered environments using low density and GBS SNPs     Reprint Icon - (Peer Reviewed Journal)
Zhang, X., Perez-Rodriquez, P., Kassa, S., Beyene, Y., Babu, R., Lopez Cruz, M., San Vicente, F., Olsen, M., Buckler IV, E.S., Jannink, J., Prasanna, B.M., Crossa, J. 2014. Genomic prediction in bi-parental tropical maize populations in water-stressed and well-watered environments using low density and GBS SNPs. Heredity. 114:291-299.
Assessing genomic selection prediction accuracy in a dynamic barley breeding - (Peer Reviewed Journal)
Sallam, A., Endelman, J., Jannink, J., Smith, K. 2014. Assessing genomic selection prediction accuracy in a dynamic barley breeding. The Plant Genome. DOI: 10.3835/plantgenome2014.05.0020.
Perspectives for genomic selection applications and research in plants     Reprint Icon - (Peer Reviewed Journal)
Heslot, N., Jannink, J., Sorrells, M.E. 2014. Perspectives for genomic selection applications and research in plants. Genetics Selection Evolution. 55:1-12.
Genomic selection for quantitative adult plant stem rust resistance in wheat - (Peer Reviewed Journal)
Rutkoski, J.E., Sorrells, M., Poland, J.A., Singh, R.P., Huerta-Espino, J., Bhavani, S., Barbier, H., Rouse, M.N., Jannink, J. 2014. Genomic selection for quantitative adult plant stem rust resistance in wheat. The Plant Genome. DOI: 10.3835/plantgenome2014.02.0006.
Genetic mapping using genotyping-by-sequencing in the clonally-propagated cassava - (Peer Reviewed Journal)
Rabbi, I., Hamblin, M., Gedil, M., Kulakow, P., Ferguson, M., Ikpan, A.S., Ly, D., Jannink, J. 2014. Genetic mapping using genotyping-by-sequencing in the clonally-propagated cassava. Crop Science. DOI: 10.2135/cropsci2013.07.0482.
Genomic selection in plant breeding - (Book / Chapter)
Newell, M., Jannink, J. 2013. Genomic selection in plant breeding. In: Fleury, D., and WHitford, R., editors. Crop Breeding: Methods and Protocols. Humana Press, Springer New York, Heidelberg, dordrecht, London. p. 117-130.
High-resolution mapping of resistance to cassava mosaic geminiviruses in cassava using genotyping-by-sequencing and its implications for breeding - (Peer Reviewed Journal)
Rabbi, I., Hamblin, M., Kumar, P., Gedil, M., Ikpan, A.S., Jannink, J., Kulakow, P. 2013. High-resolution mapping of resistance to cassava mosaic geminiviruses in cassava using genotyping-by-sequencing and its implications for breeding. Virus Research. 186:87-96.
Barley - (Book / Chapter)
Blake, T.K., Blake, V.C., Wiersma, J. 2014. Barley. In: Smith, S., Diers, B., Specht, B., Carver, B. editors. Yield Gains in Major U.S. Field Crops. Madison, WI: ASA, CSSA, and SSSA. 33:1-12.
Integrating environmental covariates and crop modeling into the genomic selection framework to predict genotype by environment interactions - (Peer Reviewed Journal)
Heslot, N., Akdemir, D., Sorrells, M.E., Jannink, J. 2013. Integrating environmental covariates and crop modeling into the genomic selection framework to predict genotype by environment interactions. Theoretical and Applied Genetics. 127:463-480.
Genotype by environment interaction and the use of unbalanced historical data for genomic selection in an international wheat breeding program - (Peer Reviewed Journal)
Dawson, J.C., Endelman, J., Heslot, N., Crossa, J., Poland, J.A., Dreisigacker, S., Manes, Y., Sorrells, M., Jannink, J. 2013. Genotype by environment interaction and the use of unbalanced historical data for genomic selection in an international wheat breeding program. Field Crops Research. 154:12-22.
Optimal design of preliminary yield trials with genome-wide markers - (Peer Reviewed Journal)
Endelman, J., Atlin, G., Beyene, Y., Fentaye, K., Zhang, X., Sorrells, M., Jannink, J. 2014. Optimal design of preliminary yield trials with genome-wide markers. Crop Science. 54:48-59.
An algorithm for deciding the number of clusters and validating using simulated data with application to exploring crop population structure - (Peer Reviewed Journal)
Newell, M., Cook, D., Hofmann, H., Jannink, J. 2013. An algorithm for deciding the number of clusters and validating using simulated data with application to exploring crop population structure. Annals of Applied Statistics. 7:1898-1916.
Ensemble learning with trees and rules: supervised, semi-supervised, unsupervised     Reprint Icon - (Peer Reviewed Journal)
Akdemir, D., Jannink, J. 2014. Ensemble learning with trees and rules: supervised, semi-supervised, unsupervised. Intelligent Data Analysis (An International Journal). 18(5):857-872.
Genomic predictability of interconnected bi-parental maize populations     Reprint Icon - (Peer Reviewed Journal)
Riedelsheimer, C., Endelman, J., Stange, M., Sorrells, M., Jannink, J., Melchinger, A. 2013. Genomic predictability of interconnected bi-parental maize populations. Genetics. 194:493-503.
The effects of relatedness and GxE interaction on prediction accuracies in genomic selection: a study in cassava - (Peer Reviewed Journal)
Ly, D., Hamblin, M., Rabbi, I., Gedli, M., Bakare, M., Gauch, H., Okechukwu, R., Dixon, A., Kulakow, P., Jannink, J. 2013. The effects of relatedness and GxE interaction on prediction accuracies in genomic selection: a study in cassava. Crop Science. 53(4):1312-1325.
Imputation of unordered markers and the impact on genomic selection accuracy     Reprint Icon - (Peer Reviewed Journal)
Rutkoski, J., Poland, J.A., Jannink, J., Sorrells, M. 2013. Imputation of unordered markers and the impact on genomic selection accuracy. Genes, Genomes, and Genomics. 3(3):427-439.
Last Modified: 9/1/2015
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