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United States Department of Agriculture

Agricultural Research Service

Research Project: GENOMICS AND PROTEOMICS APPROACHES TO BROADENING RESISTANCE OF SOYBEAN TO PESTS AND PATHOGENS Publications (Clicking on the reprint icon Reprint Icon will take you to the publication reprint.)

Gene expression study of phakopsoara pachyrzhiz-glycine max in interaction in susceptible plant using next generation sequencing - (Peer Reviewed Journal)
Tremblay, A., Hosseini, P., Alkharouf, N.W., Li, S., Matthews, B.F. 2011. Gene expression study of phakopsoara pachyrzhiz-glycine max in interaction in susceptible plant using next generation sequencing. Sequencing. doi:10.1155/2011/827250.
Proteomic Responses in Arabidopsis thaliana Seedlings Treated with Ethylene     Reprint Icon - (Peer Reviewed Journal)
Chen, R., Binder, B.M., Garrett, W.M., Tucker, M.L., Cooper, B., Chang, C. 2011. Proteomic Responses in Arabidopsis thaliana Seedlings Treated with Ethylene. Molecular Biosystems. 7:2637-2650.
Analysis of gene expression profiles for cell wall modifying proteins and ACC synthases in soybean cyst nematode colonized roots, adventitious rooting hypocotyls, root tips, flooded roots, and IBA and ACC treatment roots - (Peer Reviewed Journal)
Tucker, M.L., Murphy, C.A., Yang, R. 2011. Analysis of gene expression profiles for cell wall modifying proteins and ACC synthases in soybean cyst nematode colonized roots, adventitious rooting hypocotyls, root tips, flooded roots, and IBA and ACC treatment roots. Plant Physiology. 156:319-329.
The problem with peptide presumption and low mascot scoring     Reprint Icon - (Peer Reviewed Journal)
Cooper, B. 2011. The problem with peptide presumption and low mascot scoring. Journal of Proteome Research. 10:1432-1435.
Differences in gene expression occurring between the rapid and potent localized resistant soybean cv Peking as compared to PI 88788 in response to rust - (Peer Reviewed Journal)
Klink, V.P., Hosseini, P., Matsye, P.D., Alkharouf, N.W., Matthews, B.F. 2010. Differences in gene expression occurring between the rapid and potent localized resistant soybean cv Peking as compared to PI 88788 in response to rust. Plant Molecular Biology. 75:141-165.
Nuclear proteomic changes linked to soybean rust resistance     Reprint Icon - (Peer Reviewed Journal)
Cooper, B., Campbell, K., Feng, J., Garrett, W.M., Frederick, R.D. 2010. Nuclear proteomic changes linked to soybean rust resistance. Molecular Biosystems. 7:773-783.
An integrative approach to genomic introgression mapping - (Peer Reviewed Journal)
Severin, A.J., Peiffer, G., Xu, W.W., Hyten, D.L., Bucciarelli, B., O'Rourke, J.A., Bolon, Y.E., Grant, D.M., Farmer, A.D., May, G.D., Vance, C.P., Shoemaker, R.C., Stupar, R.M. 2010. An integrative approach to genomic introgression mapping. Plant Physiology. 154(1):3-12.
An efficient annotation and gene expression derivation tool for Illumina Solexa datasets     Reprint Icon - (Peer Reviewed Journal)
Hosseini, P., Tremblay, A., Matthews, B.F., Alkharouf, N. 2010. An efficient annotation and gene expression derivation tool for Illumina Solexa datasets. Biomed Central (BMC) Genomics. 3:183.
Relative, label-free protein quantitation: spectral counting error statistics from nine replicate MudPIT samples     Reprint Icon - (Peer Reviewed Journal)
Cooper, B., Feng, J., Garrett, W.M. 2010. Relative, label-free protein quantitation: spectral counting error statistics from nine replicate MudPIT samples. Journal of American Society for Mass Spectrometry. 21:1534-1546.
Transcriptome analysis of a compatible response by Glycine max to Phakopsora pachyrhizi infection - (Peer Reviewed Journal)
Tremblay, A., Hosseini, P., Alkharouf, N., Li, S., Matthews, B.F. 2010. Transcriptome Analysis of a Compatible Response by Glycine max to Phakopsora pachyrhizi Infection. Plant Science. 179:183-193.
Affinity purification and mass spectrometry: an attractive choice to investigate protein-protein interactions in plant immunity     Reprint Icon - (Peer Reviewed Journal)
Chen, R., Chang, C., Tucker, M.L., Cooper, B. 2010. Affinity purification and mass spectrometry: an attractive choice to investigate protein-protein interactions in plant immunity. Current Protemics. 7:258-264.
Microarray detection calls as a means to compare transcripts within syncytial cells isolated from incompatible and compatible soybean (Glycine max) roots infected by the soybean cyst nematode (Heterodera glycines) - (Peer Reviewed Journal)
Klink, V.P., Overall, C.C., Alkharouf, N.W., Macdonald, M.H., Matthews, B.F. 2010. Microarray detection calls as a means to compare transcripts within syncytial cells isolated from incompatible and compatible soybean (Glycine max) roots infected by the soybean cyst nematode (Heterodera glycines). Journal of Biomedicine and Biotechnology. 2010(2010):Article ID 491217 30 pages.
Post-transcriptional gene silencing of root knot-nematode in transformed soybean roots - (Peer Reviewed Journal)
Ibrahim, H., Alkharouf, N., Meyer, S.L., Sanad, M., El-Din, A., Hussein, E., Matthews, B.F. 2010. Post-transcriptional gene silencing of root knot-nematode in transformed soybean roots. Experimental Parasitology. 127:90-99.
Syncytium gene expression in Glycine max [PI88788} roots undergoing a resistant reaction of the parasitic nematode Heterodera glycines - (Peer Reviewed Journal)
Klink, V., Houssein, P., Matsye, P., Alkharouf, N., Matthews, B.F. 2010. An expression analysis of syncytia isolated from the roots of the Glycine max (soybean) genotype PI 88788 undergoing a resistant reaction after infection by Heterodera glycines (soybean cyst nematode). Plant Physiology and Biochemistry. 48:176-193.
1-aminocyclopropane-1-carboxylic acid (ACC) concentration and ACC synthase expression in soybean roots and root tips and soybean cyst nematode (Heterodera glycines) colonized root pieces     Reprint Icon - (Peer Reviewed Journal)
Tucker, M.L., Ping, X., Yang, R. 2010. 1-aminocyclopropane-1-carboxylic acid (ACC) concentration and ACC synthase expression in soybean roots and root tips and soybean cyst nematode (Heterodera glycines) colonized root pieces. Journal of Experimental Botany. 61(2):463-472.
A gene expression analysis of syncytia isolated from the roots of the Glycine max (soybean) genotype PI 548402 (Peking) undergoing a resistant reaction after infection by Heterodera glycines (soybean cyst nematode) - (Peer Reviewed Journal)
Klink, V., Housseini, P., Matsye, P., Alkharouf, N., Matthews, B.F. 2009. A gene expression analysis of syncytia isolated from the roots of the Glycine max (soybean) genotype PI 548402 (Peking) undergoing a resistant reaction after infection by Heterodera glycines (soybean cyst nematode). Plant Molecular Biology. 71:525-567.
Emerging approaches to broaden the resistance of soybean to the soybean cyst nematode - (Peer Reviewed Journal)
Klink, V., Matthews, B.F. 2009. Emerging approaches to broaden the resistance of soybean to the soybean cyst nematode. Plant Physiology. 151:1017-1022.
Laser capture microdissection and expressed sequence tag analysis of uredinia formed by Phakopsora pachyrhizi, the causal agent of Asian soybean rust - (Peer Reviewed Journal)
Tremblay, A., Li, S., Scheffler, B.E., Matthews, B.F. 2009. Laser capture microdissection (LCM) and expressed sequence tag analysis of uredinia formed by Phakopsora pachyrhizi, the causal agent of Asian soybean rust. Physiological and Molecular Plant Pathology. 73(6):163-174.
Coding DNA repeated throughout intergenic regions of the Arabidopsis thaliana genome: Evolutionary footprints of RNA silencing - (Peer Reviewed Journal)
Feng, J., Naiman, D.Q., Cooper, B. 2009. Coding DNA repeated throughout intergenic regions of the Arabidopsis thaliana genome: Evolutionary footprints of RNA silencing. Molecular Biosystems. 5:1679-1687.
Generation of Phaseolus vulgaris ESTs and investigation of the regulation upon Uromyces appendiculatus infection - (Peer Reviewed Journal)
Thibivilliers, S., Joshi, T., Campbell, K., Scheffler, B., Borerma, R., Xu, D., Cooper, B., Nguyen, H.T., Stacey, G. 2009. Generation of Phaseolus vulgaris ESTs and investigation of the regulation upon Uromyces appendiculatus infection. Biomed Central (BMC) Plant Biology. 9:46.
Laser capture microdissection, a new technique to collect specific cells - (Other)
Tremblay, A., Matthews, B.F. 2009. Laser capture microdissection, a new technique to collect specific cells. Extension Magazine. 4:4
Correlation of Multiple Peptide Mass Spectra for Phosphoprotein Identification - (Peer Reviewed Journal)
Feng, J., Garrett, W.M., Naiman, D., Cooper, B. 2009. Correlation of Multiple Peptide Mass Spectra for Phosphoprotein Identification. Journal of Proteome Research. 8(11):1021.
Establishment of a Protein Reference Map for Soybean Root Hair Cells - (Peer Reviewed Journal)
Brechenmacher, L., Lee, J., Sachdev, S., Song, Z., Nguyen, T., Joshi, T., Oehrle, N., Libault, M., Mooney, B., Xu, D., Cooper, B., Stacey, G. 2009. Establishment of a Protein Reference Map for Soybean Root Hair Cells. Plant Physiology. 149:670-68.
Population-specific gene expression in the pathogenic nematode Hederodera glycines exists prior to infection and during the onset of a resistant or susceptible reaction in the roots of Glycine max. - (Peer Reviewed Journal)
Klink, V.P., Hosseini, P., Macdonald, M.H., Alkharouf, N.W., Matthews, B.F. 2009. Population-specific gene expression in the pathogenic nematode Hederodera glycines exists prior to infection and during the onset of a resistant or susceptible reaction in the roots of Glycine max. Biomed Central (BMC) Genomics. 10:111. http://www.biomedcentral.com/1471-2164/10/111.
Quantitative Proteomic Analysis of Bean Plants Infected by a Virulent and Avirulent Obligate Rust Fungus - (Peer Reviewed Journal)
Lee, J., Campbell, K., Scheffler, B.E., Feng, J., Naiman, D.Q., Garrett, W.M., Thibivilliers, S., Stacey, G., Tucker, M.L., Pastor Corrales, M.A., Cooper, B. 2008. Quantitative Proteomic Analysis of Bean Plants Infected by a Virulent and Avirulent Obligate Rust Fungus. Molecular and Cellular Proteomics. 8:19-31.
Protease inhibitor expression in soybean roots exhibiting susceptible and resistance reactions to soybean cyst nematode - (Peer Reviewed Journal)
Nahed, R., Macdonald, M.H., Matthews, B.F. 2008. Protease inhibitor expression in soybean roots exhibiting susceptible and resistance reactions to soybean cyst nematode. Journal of Nematology. 40:138-146.
Analysis of expressed sequence tags from Uromyces appendiculatus hyphae and haustoria and their comparison to sequences from other rust fungi - (Peer Reviewed Journal)
Tucker, M.L., Puthoff, D.P., Neelam, A., Ehrenfried, M.L., Scheffler, B.E., Ballard, L.L., Campbell, K.B., Cooper, B. 2008. Analysis of expressed sequence tags from Uromyces appendiculatus hyphae and haustoria and their comparison to sequences from other rust fungi. Phytopathology. 98:1126-1135.
Combined Dynamic Arrays for Storing and Searching Semi-Ordered Tandem Mass Spectrometry Data - (Peer Reviewed Journal)
Feng, J., Naiman, D., Cooper, B. 2008. Combined Dynamic Arrays for Storing and Searching Semi-Ordered Tandem Mass Spectrometry Data. Journal of Computational Biology. 15:457-468.
MiniMax, a new diminutive Glycine max genotype with a rapid life cycle, embryonic potential and transformation capabilities - (Peer Reviewed Journal)
Klink, V.P., Macdonald, M.H., Martins, V., Park, S., Kim, K., Baek, S., Matthews, B.F. 2007. MiniMax, a new diminutive Glycine max genotype with a rapid life cycle, embryonic potential and transformation capabilities. Plant Cell Tissue And Organ Culture. 92:183-195.
Glycine max (soybean) roots and syncytia isolated by laser capture microdissection (LCM) exhibit differential gene expression - (Peer Reviewed Journal)
Klink, V.P., Matthews, B.F. 2007. Glycine max (soybean) roots and syncytia isolated by laser capture microdissection (LCM) exhibit differential gene expression. Plant Signaling and Behavior. 3(2):105-107.
Soybean GeneChip hybridizations to RNA isolated from root pieces colonized by soybean cyst nematode, Heterodera glycines - (Peer Reviewed Journal)
Tucker, M.L., Ehrenfried, M.L., Puthoff, D.P., Vinyard, B.T. 2007. Soybean GeneChip hybridizations to RNA isolated from root pieces colonized by soybean cyst nematode, Heterodera glycines. Journal of Experimental Botany. 58:3407-3418.
Tandem Mass Spectrometry for the Detection of Plant Pathogenic Fungi and the Effects of Database Composition on Protein Inferences - (Peer Reviewed Journal)
Cooper, B., Padliya, N., Garrett, W.M., Campbell, K., Tabb, D. 2007. Tandem Mass Spectrometry for the Detection of Plant Pathogenic Fungi and the Effects of Database Composition on Protein Inferences. Proteomics. 7:3932-3942.
A time-course comparative microarray analysis of an incompatible and compatible response by Glycine max (soybean) to Heterodera glycines (soybean cyst nematode) infection - (Peer Reviewed Journal)
Klink, V.P., Overall, C., Macdonald, M.H., Matthews, B.F. 2007. A time-course comparative microarray analysis of an incompatible and compatible response by Glycine max (soybean) to Heterodera glycines (soybean cyst nematode) infection. Planta. 226:1423-1447.
Laser capture microdissection (LCM) and comparative microarray expression analysis of syncytial cells isolated from incompatible and compatible soybean roots infected by soybean cyst nematode (Heterodera glycines) - (Peer Reviewed Journal)
Klink, V.P., Overall, C.C., Aklharouf, N.W., Macdonald, M.H., Matthews, B.F. 2007. Laser capture microdissection (LCM) and comparative microarray expression analysis of syncytial cells isolated from incompatible and compatible soybean roots infected by soybean cyst nematode (Heterodera glycines). Planta. 226:1389-1409.
Shotgun Proteomic Analysis of Arabidopsis thaliana Leaves - (Peer Reviewed Journal)
Lee, J., Garrett, W.M., Cooper, B. 2007. Shotgun Proteomic Analysis of Arabidopsis thaliana Leaves. Journal of Separation Science. 30:2225-2230.
Probability-Based Pattern Recognition and Statistical Framework for Randomization: Modeling Tandem Mass Spectrum/Peptide Sequence False Match Frequencies - (Peer Reviewed Journal)
Feng, J., Naiman, D., Cooper, B. 2007. Probability-Based Pattern Recognition and Statistical Framework for Randomization: Modeling Tandem Mass Spectrum/Peptide Sequence False Match Frequencies. Bioinformatics. 23:2210-2217.
Identification of Soybean Cyst Nematode, Heterodera Glycines, DNA Sequences with High Similarity to Those of Caenorhabditis Elegans with Mutant Lethal Phenotypes - (Peer Reviewed Journal)
Alkharouf, N., Klink, V.P., Matthews, B.F. 2007. Identification of soybean cyst nematode, heterodera glycines, dna sequences with high similarity to those of caenorhabditis elegans with mutant lethal phenotypes. Experimental Parasitology. 115:247-258.
Developing a systems biology approach to study disease progression caused by Heterodera glycines in Glycine max - (Peer Reviewed Journal)
Klink, V.P., Matthews, B.F. 2007. Developing a systems biology approach to study disease progression caused by Heterodera glycines in Glycine max. Gene Regulation and Systems Biology. 2:1-17.
Protein Accumulation Changes Associated with Germination of the Uromyces appendiculatus Uredospore - (Peer Reviewed Journal)
Cooper, B., Neelan, A., Campbell, K., Lee, J., Liu, G., Garrett, W.M., Scheffler, B.E., Tucker, M.L. 2007. Protein Accumulation Changes Associated with Germination of the Uromyces appendiculatus Uredospore. Molecular Plant-Microbe Interactions. 20(7):857-866.
Alternative Workflows to Replace 2d-Page for the Construction of Plant Proteome Maps - (Review Article)
Lee, J., Cooper, B. 2006. Alternative workflows to replace 2d-page for the construction of plant proteome maps. Molecular Biosystems. 2:621-626.
Last Modified: 12/19/2014
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