Hajduch M, Matusova R, Houston NL, Thelen JJ (2010) Comparative proteomics of seed maturation in oilseeds reveals differences in intermediary metabolism. Proteomics. In press

Oliver MJ, Jain R, Balbuena TS, Agrawal GK, Gasulla F, Thelen JJ (2010) Proteome analysis of leaves of the desiccation-tolerant grass, Sporobolus stapfianus, in response to desiccation. Phytochemistry. In press

Houston NL, Lee DG, Stevenson SE, Ladics GS, Bannon GA, McClain s, Privalle L, Stagg N, Herouet-Guicheney C, MacIntosh SC, Thelen JJ (2010) Quantitation of soybean allergens using tandem mass spectrometry. J. Proteome Res. In press

Demartini D, Thelen JJ, Carlini C (2010) Global and targeted proteomics in developing jack bean (Canavalia ensiformis) seedlings: an investigation of urease isoform mobilization in early stages of development. Plant Mol. Biol. In press

Stevenson SE, Houston NL, Thelen JJ (2010) Evolution of seed allergen quantification ¨C from antibodies to mass spectrometry. Reg. Tox. Pharm. In press

Gao J, Thelen JJ, Dunker AK, Xu D (2010) Musite: a tool for global prediction of general and kinase-specific phosphorylation sites. Mol. Cell. Prot. In press

Lee, DG, Houston NL, Stevenson SE, Ladics GS, McClain S, Privalle L, Thelen JJ (2010) Mass spectrometry analysis of soybean seed proteins: optimization of gel-free quantitative workflow. Anal. Methods In press

Huang Y, Houston NL, Tovar-Mendez A, Stevenson SE, Miernyk JA, Randall DD, Thelen JJ (2010) A quantitative mass spectrometry-based approach for identifying protein kinase ¨Cclients and quantifying kinase activity. Anal. Biochem. 402:69-76

Chen M, Thelen JJ (2010) The essential role of plastidial triose phosphate isomerase in the integration of seed reserve mobilization and seedling establishment. Plant Signal. Behav. 5:1-5

Hajduch M, Hearne LB, Miernyk JA, Casteel JE, Joshi T, Agrawal GK, Song Z, Zhou M, Xu D, Thelen JJ (2010) Systems analysis of seed filling in Arabidopsis thaliana: using general linear modeling to assess concordance of transcript and protein expression. Plant Physiol. 152:2078-87

Chen M, Thelen JJ (2010) The plastid isoform of triose phosphate isomerase is required for the postgerminative transition from heterotrophic to autotrophic growth in Arabidopsis. Plant Cell 22:77-90

Houston NL, Hajduch M, Thelen JJ (2009) Quantitative Proteomics of Seed Filling in Castor: Comparison with Soybean and Rapeseed Reveals Differences between Photosynthetic and Non-photosynthetic Seed Metabolism. Plant Physiol. 151:857-868

Chen M, Mooney BP, Hajduch M, Joshi T, Zhou M, Xu D, Thelen JJ (2009) System analysis of an Arabidopsis mutant altered in de novo fatty acid synthesis reveals diverse changes in seed composition and metabolic regulation. Plant Physiol. 150:27-41

Stevenson S, Ozias-Akins P, Thelen JJ (2009) Validation of label-free quantitative proteomics approaches: Applications for seed allergen profiling. J. Proteomics 72:555-566

Thelen JJ (2009) Proteomics tools and resources for investigating protein allergens in oilseeds. Regul. Toxicol. Pharmacol. 54:41-45

Ozias-Akins P, Ramos ML, Faustinelli P, Chu Y, Maleki S, Thelen JJ, Huntley J, Arias K, Jordana M. (2009) Spontaneous and induced variability of allergens in commodity crops: Ara h 2 in peanut as a case study. Regul. Toxicol. Pharmacol. 54:37-40

Chu Y, Faustinelli P, Ramos ML, Hajduch M, Stevenson S, Thelen JJ, Maleki SJ, Ozias-Akins P (2008) Reduction of IgE binding and nonpromotion of Aspergillus flavus growth by simultaneously silencing Ara h 2 and Ara h 6 in peanut. J. Agric. Food Chem. 56:11225-11233

Gao J, Agrawal GK, Thelen JJ, Xu D (2008) P3DB: A plant protein phosphorylation database. Nucl. Acids Res. 37:D960-962

Agrawal GK, Hajduch M, Graham, K, Thelen JJ (2008) In-depth investigation of soybean seed-filling proteome and comparison with a parallel study of rapeseed. Plant Physiol. 48:504-518

Jain R, Katavic V, Agrawal GK, Guzov VM, Thelen JJ (2008) Purification and proteomic characterization of plastids from Brassica napus developing embryos. Proteomics. 8:3397-3405

Miernyk JA, Thelen JJ (2008) Biochemical approaches for discovering protein-protein interactions. Plant J. 53:597–609

Thelen JJ, Peck SC (2007) Quantitative proteomics in plants: choices in abundance. Plant Cell. 19:3339–46

Hajduch M, Casteel JE, Tang S, Hearne LB, Knapp S, Thelen JJ (2007) Proteomic analysis of near isogenic sunflower varieties differing in seed oil traits. J. Proteome Res. 6:3232–41

Mooney BP, Miernyk JA, Greenlief CM, Thelen JJ (2006) Using quantitative proteomics of Arabidopsis roots and leaves to predict metabolic activity. Physiol. Plant. 128:237-250

Kojima M, Casteel J, Miernyk JA, Thelen JJ (2006) The effects of down-regulating expression of Arabidopsis thaliana membrane-associated acyl-CoA binding protein 2 on acyl-lipid composition. Plant Science. 172:36-44

Agrawal GK, Thelen JJ. Large-scale identification and quantification of phosphoproteins during seed filling in oilseed rape. Molecular and Cellular Proteomics 5: 2044-2059

Katavic V, Agrawal GK, Hajduch M, Harris SL, Thelen JJ. (2006) Protein and lipid compositional analysis of oil bodies from two Brassica napus cultivars. Proteomics In press

Hajduch M, Casteel JE, Hurrelmeyer KE, Song Z, Agrawal GK, Thelen JJ. (2006) Proteomic analysis of seed filling in Brassica napus: Developmental characterization of metabolic isozymes using high-resolution two-dimensional gel electrophoresis. Plant Physiol 141(1):32-46.

Agrawal GK, Thelen JJ (2005) Development of a simplified, economical polyacrylamide gel staining protocol for phosphoproteins. Proteomics 5(18):4684-8

Hajduch M, Ganapathy A, Stein JW, Thelen JJ (2005) A Systematic Proteomic Study Of Seed-Filling In Soybean: Establishment Of High-Resolution Two-Dimensional Reference Maps, Expression Profiles, and an Interactive Proteome Database. Plant Physiol 137 (4):1397-419

Wan J, Torres M, Ganapathy A, Thelen JJ, DaGue BB, Mooney B, Xu D, Stacey G. (2005) Proteomic analysis of soybean root hairs after infection by Bradyrhizobium japonicum. Mol. Plant Microbe Interact. 18:458-467

Phinney B, Thelen JJ (2005) Proteomic characterization of a Triton X-100 insoluble fraction from chloroplasts defines a novel group of proteins associated with macromolecular structures. J. Proteome Res. 4:497-506 Supplementary information

Mooney BP, Thelen JJ (2004) High-throughput peptide mass fingerprinting of soybean
seed proteins: automated workflow and utility of Unigene expressed sequence tag databases for protein identification. Phytochemistry 65:1733-44

Ganapathy A, Wan X-F, Wan J, Thelen JJ, Emerich DW, Stacey G, Xu D (2004) Statistical assessment for mass-spec protein identification using peptide fingerprinting approach. Conf Proc IEEE Eng Med Biol Soc. 4:3051-3054