Publications

Hegeman Google Scholar Profile

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Research Articles

  1. Wilson MB, Pawlus AD, Brinkman D, Gardner G, Hegeman AD, Spivak M, & Cohen JD (2017) 3-Acyl dihydroflavonols from poplar resins collected by honey bees are active against the bee pathogens Paenibacillus larvae and Ascosphaera apis. Phytochemistry138: 83-92.
  2. Freund DM, Hegeman AD (2017) Recent Advances in Stable Isotope-Enabled Mass Spectrometry-Based Plant Metabolomics, Current Opinion in Biotechnology, 43, 41-48. 
  3. Yang DQ, Freund DM, Harris BR, Wang D, Cleary MP, Hegeman AD (2016) Measuring relative utilization of aerobic glycolysis in breast cancer cells by positional isotopic discrimination, FEBS Lett. 590(18): 3179-87.
  4. Tivendale, N. D., Jewett, E. M., Hegeman, A. D., & Cohen, J. D. (2016). Extraction, purification, methylation and GC–MS analysis of short-chain carboxylic acids for metabolic flux analysis. Journal of Chromatography B1028: 165–174.
  5. Fan, K.-T., Rendahl, A. K., Chen, W.-P., Freund, D. M., Gray, W. M., Cohen, J. D., and Hegeman, A. D. (2016) Proteome Scale-Protein Turnover Analysis Using High Resolution Mass Spectrometric Data from Stable-Isotope Labeled Plants, J of Proteome Res,15(3), 851-67.
  6. Abate-Pella D, Freund DM, Ma Y, Simón-Manso Y, Hollender J, Broeckling CD, Huhman DV, Krokhin OV, Stoll DR, Hegeman AD, Kind T, Fiehn O, Schymanski EL, Prenni JE, Sumner LW, Boswell PG (2015) Retention Projection Enables Accurate Calculation of Liquid Chromatographic Retention Times Across Labs and Methods, J Chromatog A1412: 43-51.
  7. Yu P, Lor P, Ludwig-Müller J, Hegeman AD, and Cohen JD (2015) Quantitative evaluation of IAA conjugate pools in Arabidopsis thaliana, Planta241(2): 539-48.
  8. Moore M, Ostry M, Hegeman AD, and Martin AC (2015) Inhibition of Ophiognomonia clavigignenti-juglandacearum by Juglans species bark extracts, Plant Dis99(3): 401-8.
  9. Martin AC, Johnston E, Xing C, and Hegeman AD (2014) Measuring the chemical and cytotoxic variability of commercially available kava (Piper methysticum G. Forster), PLOS One9(11): e111572.
  10. Yu P, Hegeman AD, Cohen JD (2014) A facile means for the identification of indolic compounds from plant tissues, Plant J79(6): 1065–75.
  11. Roe MR, Carlson JL, McManimon TM, Hegeman AD, and Tong CBS (2014) Differential accumulation and degradation of anthocyanins in Red Norland periderm is dependent on soil type and tuber storage duration,Am J Potato Res,  91(6): 696-705.
  12. Martin AC, Pawlus AD, Jewett EM, Wyse DL, Angerhofer CK, Hegeman AD (2014) Evaluating solvent extraction systems using metabolomics approaches, RSC Adv, 4: 26325-26334.
  13. Unger L, Nicholson A, Jewett EM, Gerber V, Hegeman AD, Sweetman L. and Valberg S (2014), Hypoglycin A concentrations in seeds of Acer pseudoplatanus trees growing on atypical myopathy-affected and control pastures. J Vet Intern Med28(4): 1289–1293.
  14. Wang Y, Freund DM, Magdaong NM, Urban VS, Frank HA, Hegeman AD, Tang JK (2014) Impact of esterified bacteriochlorophylls on the biogenesis of chlorosomes in Chloroflexus aurantiacusPhotosynth Res122(1): 69-86.
  15. Roe MR, Cohen JD, Hegeman AD (2014) Regioselective solvent-phase deuteration of polyphenolic compounds informs their identification by mass spectrometry, Anal Biochem452: 76-85.
  16. Kwak H, Hegeman AD, and Park S (2014) Seasonal changes in metabolic profiles of galls and leaves ofRhus chinensis using gas chromatography mass spectrometry and liquid chromatography quadrupole time-of-flight mass spectrometry, J Plant Biol57: 127-135.
  17. Smith AG, Eberle CA, Moss NG, Anderson NO, Clasen BM, Hegeman AD (2013) The transmitting tissue ofNicotiana tabacum is not essential to pollen tube growth, and its ablation can reverse prezygotic interspecific barriers, Plant Reprod26(4): 339-50.
  18. Wilson MB, Marla Spivak M, Hegeman AD, Rendahl A, and Cohen JD (2013) Metabolomics Reveals the Origins of Antimicrobial Plant Resins Collected by Honey Bees, PLOS One8(10): e77512.
  19. Ivancic MM, Huttlin EL, Chen X, Pleiman JK, Irving AA, Hegeman AD, Dove WF and Sussman MR (2013) Candidate Serum Biomarkers for Early Intestinal Cancer Using 15N Metabolic Labeling and Quantitative Proteomics in the ApcMin/+ Mouse, J. Prot. Res., 12(9): 4152-66.
  20. Yerramsetty V, Roe MR, Cohen JD, Hegeman AD, Ismail B (2013) Development of a Simple, Fast and Accurate Method for the Direct Quantification of Selective Estrogen Receptor Modulators using Stable Isotope Dilution Mass Spectrometry, J Agric Food Chem, 61(29): 7028–7037.
  21. Eberle CA, Anderson NO, Clasen BM, Hegeman AD, Smith AG (2013) PELPIII: the Class III Pistil-Specific Extensin-Like Nicotiana tabacum proteins are essential for interspecific incompatibility, Plant J. 74(5): 805-814.
  22. Valberg S, Sponseller B, Hegeman AD, Earing J, Bender J, Martinson K, Patterson S, and Sweetman L (2013) Seasonal pasture myopathy/atypical myopathy in North America associated with ingestion of hypoglycin A within seeds of the box elder tree, Equine Vet J, 45(4): 419-26.
  23. Boswell, P. G., Carr, P. W., Cohen, J. D., and Hegeman, A. D. (2012) Easy and Accurate Calculation of Programmed Temperature Gas Chromatographic Retention Times by Back-Calculation of Temperature and Hold-up Time Profiles, J Chromatogr A, 1263: 179-88. 
  24. Liu X, Hegeman AD, Gardner G, and Cohen, JD (2012) Protocol: High-throughput and quantitative assays of auxin and auxin precursors from minute tissue samples, Plant Methods8(1): 31.
  25. Boswell PG, Schellenberg JR, Carr PW, Cohen JD, and Hegeman AD (2011) A study on retention “projection” as a supplementary means for compound identification by liquid chromatography-mass spectrometry capable of predicting retention with different gradients, flow rates, and instruments, J Chromatogr A1218(38): 6732-41.
  26. Boswell, P. G., Schellenberg, J. R., Carr, P. W., Cohen, J. D., and Hegeman, A. D. (2011) Easy and accurate high-performance liquid chromatography retention prediction with different gradients, flow rates, and instruments by back-calculation of gradient and flow rate profiles, J Chromatogr A1218(38): 6742-9.
  27. Estrada AER, Hegeman AD, Kistler HC, and May G (2011) In vitro interactions between Fusarium verticillioides and Ustilago maydis through real-time PCR and metabolic profiling, Fungal Genetics and Biology48, 874–885.
  28. Charve, J., Chen, C., Hegeman, A. D., and Reineccius, G. A. (2011) Evaluation of instrumental methods for the untargeted analysis of chemical stimuli of orange juice flavour, Flavour Fragr J26(6), 429-440.
  29. Chen, W.-P., Yang, X.-Y., Harms, G. L., Gray, W. M., Hegeman, A. D., and Cohen, J. D. (2011) An automated growth enclosure for metabolic labeling of Arabidopsis thaliana with 13C-carbon dioxide – An in vivo labeling system for proteomics and metabolomics research. Proteome Sci. 9:9.
  30. Ballhorn DJ, Kautz S, Jensen M, Schmitt I, Heil M, Hegeman AD (2011) Genetic and environmental interactions determine plant defences against herbivores. J Ecol, 99(1):313–326.
  31. Chen, W.-P., Yang, X.-Y., Hegeman, A. D., Gray, W. M., and Cohen, J. D. (2010) Microscale analysis of amino acids using gas chromatography-mass spectrometry after methyl chloroformate derivatization. J. Chromatogr B 878:2199-2208.
  32. Yang, X. -Y., Chen, W.-P., Rendahl, A. K., Hegeman, A. D., Gray, W. M., and Cohen, J. D. (2010) Measuring the turnover rates of Arabidopsis proteins using deuterium oxide: an auxin signaling case study. Plant J.,63(4):680-95.
  33. Ballhorn, D., Kautz, S., Heil, M., and Hegeman, A. D. (2009) Analyzing plant defenses in nature, Plant Signal Behav. 2009, 4(8), 743-5.
  34. Huttlin, E. L., Chen, X., Barrett-Wilt, G. A., Hegeman A. D., Halberg, R. B., Harm, A. C., Newton, M. A., William F. Dove, W. F., and Sussman, M. R. (2009) Discovery and Validation of Colonic Tumor-Associated Proteins via Metabolic Labeling and Stable Isotopic Dilution, Proc. Natl. Acad. Sci. U S A, 106(40), 17235-40.
  35. Ballhorn, D., Kautz, S., Heil, M., and Hegeman, A. D. (2009) Cyanogenesis of wild lima bean (Phaseolus lunatus L.) is an efficient direct defence in nature, submitted to PLoS One, 4(5), e5450.
  36. Cui, Q., Lewis, I. A., Hegeman, A. D., Anderson, M. E., Li, J., Schulte, C. F., Westler, W.M., Eghbalnia, H. R., Sussman, M. R., Markley, J. L. (2008) Metabolite identification via the Madison Metabolomics Consortium Database, Nat. Biotechnol., 26(2), 162-4.
  37. Hegeman, A. D., Schulte, C. F., Cui, Q., Lewis, I. A., Huttlin, E. L., Eghbalnia, H., Harms, A. C., Ulrich, E. L., Markley, J. L., and Sussman, M. R. (2007) Stable Isotope Assisted Assignment of Elemental Compositions for Metabolomics, Anal. Chem., 79(18), 6912-21.
  38. *Nelson, C. J.,*Huttlin, E. L., Hegeman, A. D., Harms, A. C., and Sussman, M. R. (2007) Implications of 15N-Metabolic Labeling for Automated Peptide Identification in Arabidopsis thaliana, Proteomics, 7(8), 1279-92.
  39. *Huttlin, E. L., *Hegeman, A. D., Harms, A. C., and Sussman, M. R. (2007) Comparison of full versus partial metabolic labeling for quantitative proteomic analysis in Arabidopsis thaliana, Mol. Cell Proteomics, 6(5), 860-81.
  40. Huttlin, E. L., Hegeman, A. D., Harms, A. C., and Sussman, M. R. (2007) Prediction of error associated with false positive rate determination for peptide identification in large-scale proteomics experiments using a combined reverse and forward peptide sequence database strategy. J. Prot. Res., 6(1), 392-398.
  41. Hegeman, A. D., Rodriguez, M., Han B. W., Uno, Y., Phillips G. N. Jr., Hrabak, E. M., John C. Cushman, Harper, J. F., Harmon, A. C., and Sussman, M. R. (2006) A phyloproteomic characterization of in vitro autophosphorylation in calcium-dependent protein kinases. Proteomics, 6(12), 3649-3664.
  42. Nelson, C. J., Hegeman, A. D., Harms, A. C., and Sussman, M. R. (2006) A quantitative analysis of Arabidopsis plasma membrane using trypsin-catalyzed 18O labeling. Mol. Cell Proteomics, 5(8), 1382-1395.
  43. Pischke, M. S., Huttlin, E. L., Hegeman, A. D., and Sussman, M. R. (2006) A transcriptome-based characterization of habituation in plant tissue culture. Plant Physiol. 140(4), 1255-78.
  44. Stolc, V., Samanta, M.P., Tongprasit, W., Sethi, H., Liang, S., Nelson, D.C., Hegeman, A., Nelson, C., Rancour, D., Bednarek, S., Ulrich, E.L., Zhao, Q., Wrobel, R.L., Newman, C.S., Fox, B.G., Phillips, G.N., Jr., Markley, J.L., and Sussman, M.R. (2005) Identification of transcribed sequences in Arabidopsis thaliana by using high-resolution genome tiling arrays. Proc. Natl. Acad. Sci. U S A, 102(12) 4453-8.
  45. Bingman, C. A., Johnson K. A., Peterson F. C., Frederick R. O., Zhao Q., Thao S., Fox B. G., Volkman B. F., Jeon W. B., Smith D. W., Newman C. S., Ulrich E. L., Hegeman A. D., Sussman M. R., Markley J. L., and Phillips G. N. Jr. (2004) Crystal structure of the protein from gene At3g17210 of Arabidopsis thaliana. Proteins, 57(1), 218-20.
  46. Chehab, E. W., Patharkar, O. R., Hegeman, A. D., Taybi, T., and Cushman, J. C. (2004) Autophosphorylation and Subcellular Localization Dynamics of a Salt- and Water Deficit-Induced Calcium-Dependent Protein Kinase from Ice Plant. Plant Physiol. 135(3), 1430-46.
  47. Hegeman, A. D., Harms, A. C., Bunner, A. E., Harper, J. F., and Sussman, M. R. (2004) An isotope labeling strategy for quantifying the degree of phosphorylation at multiple sites in proteins, J. Am. Soc. Mass Spec. 15(5), 647-653.
  48. Smith, D. W., Johnson, K. A., Bingman, C. A., Aceti, D. J., Blommel, P. G., Wrobel, R. L., Frederick, R. O., Zhao, Q., Sreenath, H., Fox, B. G., Volkman, B. F., Jeon, W. B., Newman, C. S., Ulrich, E. L., Hegeman, A. D., Kimball, T., Thao, S., Sussman, M. R., Markley, J. L., and Phillips, G. N. Jr. (2004) Crystal structure of At2g03760, a putative steroid sulfotransferase from Arabidopsis thaliana, Proteins, 57(4), 854-7.
  49. Beis, K., Allard, S. T. M., Hegeman, A. D., Murshudov, G., Philp, D., Naismith, J. H. (2003) The structure of NADH in the enzyme dTDP-D-glucose dehydratase (RmlB). J. Am. Chem. Soc. 125, 11872-8.
  50. Allard, S. T. M., Beis, K., Giraud, M.-F., Hegeman, A. D., Gross, J. W., Wilmouth, R. C., Whitfield, C., Graninger, M., Messner, P., Allen, A. G., Maskell, D. J., and Naismith, J. H. (2002) Toward a structural understanding of the dehydratase mechanism. Structure with Folding and Design, 10, 81-92.
  51. *Hegeman, A. D., *Gross, J. W., and Frey, P. A. (2002) Concerted and stepwise dehydration mechanisms observed in wild type and mutated Escherichia coli dTDP-glucose 4,6-dehydratase. Biochemistry, 41, 2797-804.
  52. *Gross, J. W., *Hegeman, A. D., Gerratana, B., and Frey, P. A. (2001) Dehydration is catalyzed by glutamate-136 and aspartic acid-135 active site residues in Escherichia coli dTDP-glucose 4,6-dehydratase. Biochemistry 40, 12497-504.
  53. *Hegeman, A. D., *Gross, J. W., and Frey, P. A. (2001) Probing catalysis by Escherichia coli dTDP-glucose 4,6-dehydratase: Identification and preliminary characterization of functional amino acid residues at the active site. Biochemistry 40, 6598-610.
  54. *Gross, J. W., *Hegeman, A. D., Vestling, M. M., and Frey, P. A. (2000) Characterization of enzymatic processes by rapid mix-quench mass spectrometry: The case of dTDP-glucose 4,6-dehydratase. Biochemistry 39, 13633-40.
  55. Gong, T. W., Hegeman, A. D., Shin, J. J., Lindberg, K. H., Barald, K. F., and Lomax, M. I. (1997) Novel genes expressed in the chick otocyst during development: identification using differential display of RNA. International Journal of Developmental Neuroscience 15, 585-94.
  56. Thoden, J. B., Hegeman, A. D., Wesenberg, G., Chapeau, M. C., Frey, P. A., and Holden, H. M. (1997) Structural analysis of UDP-sugar binding to UDP-galactose 4-epimerase from Escherichia coli. Biochemistry36, 6294-304.
  57. Liebert, M., Hubbel, A., Chung, M., Wedemeyer, G., Lomax M., Hegeman, A. D., Yuan, T. Y., Brozovich, M., Wheelock, M. J., and Grossman, H. B. (1997) Expression of mal is associated with urothelial differentiation in vitro: identification by differential display reverse-transcriptase polymerase chain reaction. Differentiation. 61, 177-85.
  58. Schuster, M. C., Mortell, K. H., Hegeman, A. D., and Kiessling, E. L. (1997) Neoglycopolymers produced by aqueous ring-opening metathesis polymerization: Decreasing saccharide density increases activity. J. Mol. Catal. A-Chem. 116, 209-16.
  59. Gong, T. W., Hegeman, A. D., Shin, J. J., Adler, H. J., Raphael, Y., and Lomax, M. I. (1996) Identification of genes expressed after noise exposure in the chick basilar papilla. Hearing Research 96, 20-32.
  60. Hegeman, A. D., Brown, J.S., and Lomax, M. I. (1995) Sequence of the cDNA for the heart/muscle isoform of mouse cytochrome C oxidase subunit VIII. Biochimica et Biophysica Acta 1261, 311-4.
  61. Walters, M. A., Hoem, A. B., Arcand, H. R., Hegeman, A. D., and McDonough, C. S. (1993) An extremely mild 3-aza-claisen reaction. 2. New conditions and the rearrangement of a-heteroatom substituted amides.Tetrahedron Lett. 34, 1453-6.

 

Review Articles, Book Chapters, Letters

  1. Park S, Seo Y-S and Hegeman AD (2014) Plant metabolomics for plant chemical responses to belowground community change by climate change, J Plant Biol57:137-149.
  2. Gillman JH, Hegeman AD, Sharp RG (2014) Clarifying the role of maples in atypical myopathy, Equine Vet J,46(2):135-6. doi: 10.1111/evj.12176.
  3. Roe MR, Cohen JD, Hegeman AD (2014) Targeted deuteration of polyphenolics for their qualitative and quantitative metabolomic analysis in plant-derived extracts, Methods Mol Biol1083:17-29. doi: 10.1007/978-1-62703-661-0_2.
  4. Frey, P. A. and Hegeman A. D. (2013) Chemical and Stereochemical Actions of UDP-galactose 4-Epimerase, Acc. Chem. Res.46(7): 1417-1426.
  5. Lewis IA, Shortreed MR, Hegeman AD, Markley JD (2012) “Novel NMR and MS Approaches to Metabolomics” in The Handbook of Metabolomics, Methods in Pharmacology and Toxicology, Teresa Whei-Mei Fan et al. Eds., Springer Science & Business Media, New York, vol. 17, 199-230, DOI 10.1007/978-1-61779-618-0_7.
  6. Menzel WI, Chen W-P, Hegeman AD, and Cohen JD (2012) “Qualitative and Quantitative Screening of Amino Acids in Plant Tissues”, High Throughput Phenotyping in Plants: Methods and Protocols, Normanly J. Ed. Methods in Molecular Biology, vol. 918, 165-178.
  7. Hegeman, A. D. (2011) “Proteomics and Metabolomics” in Genetics, Genomics and Breeding of Potato, Bradeen J. M., and Kole, C. Eds. , Science Publishers, Enfield NH, U.S.A., pp. 229–259.
  8. Hegeman, A. D. (2010) Plant metabolomics–meeting the analytical challenges of comprehensive metabolite analysis. Brief. Funct. Genomics, 9(2),139-48.
  9. Frey, P. A., Hegeman, A. D., and Ruzicka, F. J. (2008) The Radical SAM Superfamily, Crit Rev Biochem Mol Biol,43(1), 63-88.
  10. Huttlin, E. L., Hegeman, A. D., and Sussman, M. R. (2008) “Metabolic Labeling Approaches for the Relative Quantification of Proteins” In D. Barcelo. Editor: Comprehensive Analytical Chemistry, Vol 52, Protein Mass Spectrometry, Julian P. Whitelegge. Elsevier BV: Elsevier, pp. 479–513.
  11. Markley, J. L., Anderson, M. E., Cui, Q., Eghbalnia, H. R., Lewis, I. A., Hegeman, A. D., Li, J., Schulte, C. F., Sussman, M. R., Westler, W. M., Ulrich, E. L., and Zolnai, Z. (2007) “New bioinformatics resources for metabolomics”, in BIOCOMPUTING 2007, Proceedings of the Pacific Symposium, Maui, Hawaii, USA 3 – 7 January 2007, Altman, R. B., Dunker, A. K., Hunter, L., Murray, T., and Klein, T. E., Eds., World Scientific Publishing Company, Imperial College Press, London, U. K.
  12. Frey, P. A., Hegeman, A. D., and Reed, G. H. (2006) Free radical mechanisms in enzymology, Chem. Rev. 106(8), 3302-16.
  13. Aceti, D. J., Blommel, P. G., Endo, Y., Fox, B. G., Fredrick, R. O., Hegeman, A. D., Jeon, W. B., Kimball, T. L., Lee, J. M., Newman, C. S., Peterson, F. C., Sawasaki, T., Seder, K. D., Sussman, M. R., Ulrich, E. L., Wrobel, R. L., Thao, S., Vinarov, D.A., Volkman, B. F., and Zhao, Q. (2002) “Role of nucleic acid and protein manipulation technologies in high-throughput structural biology efforts.” in Biopolymers. Volume 4: Polyamides and Complex Proteinaceous Materials (Part B). Steinbüchel, A. Ed. Wiley-VCH Verlag GmbH, Weinheim, Germany, pp. 469-496.
  14. Sussman, M. R., Hegeman, A. D., Harms, A. C., Nelson, C. L. (2005) “Making elephants fly” in Human Embryonic Stem Cells, Odorico, J., Pederson, R., and Zhang, S.-C. Eds., BIOS Scientific Publishers Ltd., Oxford, UK, pp. 363-78.

 

Text Book

Enzymatic Reaction Mechanisms book cover.Frey, P. A., and Hegeman, A. D., Enzymatic Reaction Mechanisms, January 27, 2007, Oxford University Press, New York, NY.