Biomedical Research Education & Training
Faculty Member

Ham, Amy-Joan Lorna, Ph.D.
Adjunct Research Associate Professor of Biochemistry

Lab Url: http://www.vicc.org/jimayersinstitute/

Phone Number: 615-322-2948

Email Address: amy.ham@vanderbilt.edu

Ham, Amy-Joan's picture
Academic history
B.S., Univ of Arizona
M.S., Univ of Arizona
Ph.D., Univ of Arizona

Office Address   Mailing Address

B3301A Medical Center North

465 21st Avenue South U1213 MRB III 37232-6350


Publications
Ma, ZQ, Chambers, MC, Ham, AJ, Cheek, KL, Whitwell, CW, Aerni, HR, Schilling, B, Miller, AW, Caprioli, RM, Tabb, DL. ScanRanker: Quality Assessment of Tandem Mass Spectra via Sequence Tagging. J Proteome Res, 2011

Rexer, BN, Ham, AJ, Rinehart, C, Hill, S, de Matos Granja-Ingram, N, Gonz?!lez-Angulo, AM, Mills, GB, Dave, B, Chang, JC, Liebler, DC, Arteaga, CL. Phosphoproteomic mass spectrometry profiling links Src family kinases to escape from HER2 tyrosine kinase inhibition. Oncogene, 2011

Tomasiak, TM, Archuleta, TL, Andr??ll, J, Luna-Ch?!vez, C, Davis, TA, Sarwar, M, Ham, AJ, McDonald, WH, Yankovskaya, V, Stern, HA, Johnston, JN, Maklashina, E, Cecchini, G, Iverson, TM. Geometric restraint drives on- and off-pathway catalysis by the Escherichia coli menaquinol:fumarate reductase. J Biol Chem, 286(4), 3047-56, 2011

Zhang, H, Liu, Q, Zimmerman, LJ, Ham, AJ, Slebos, RJ, Rahman, J, Kikuchi, T, Massion, PP, Carbone, DP, Billheimer, D, Liebler, DC. Methods for Peptide and protein quantitation by liquid chromatography-multiple reaction monitoring mass spectrometry. Mol Cell Proteomics, 10(6), M110.006593, 2011

Baucum, AJ, Jalan-Sakrikar, N, Jiao, Y, Gustin, RM, Carmody, LC, Tabb, DL, Ham, AJ, Colbran, RJ. Identification and validation of novel spinophilin-associated proteins in rodent striatum using an enhanced ex vivo shotgun proteomics approach. Mol Cell Proteomics, 9(6), 1243-59, 2010 PMCID:2877984

Dasari, S, Chambers, MC, Slebos, RJ, Zimmerman, LJ, Ham, AJ, Tabb, DL. TagRecon: high-throughput mutation identification through sequence tagging. J Proteome Res, 9(4), 1716-26, 2010 PMCID:2859315

Tabb, DL, Vega-Montoto, L, Rudnick, PA, Variyath, AM, Ham, AJ, Bunk, DM, Kilpatrick, LE, Billheimer, DD, Blackman, RK, Cardasis, HL, Carr, SA, Clauser, KR, Jaffe, JD, Kowalski, KA, Neubert, TA, Regnier, FE, Schilling, B, Tegeler, TJ, Wang, M, Wang, P, Whiteaker, JR, Zimmerman, LJ, Fisher, SJ, Gibson, BW, Kinsinger, CR, Mesri, M, Rodriguez, H, Stein, SE, Tempst, P, Paulovich, AG, Liebler, DC, Spiegelman, C. Repeatability and reproducibility in proteomic identifications by liquid chromatography-tandem mass spectrometry. J Proteome Res, 9(2), 761-76, 2010 PMCID:2818771

Cai, Y, Xu, Z, Xie, J, Ham, AJ, Koury, MJ, Hiebert, SW, Brandt, SJ. Eto2/MTG16 and MTGR1 are heteromeric corepressors of the TAL1/SCL transcription factor in murine erythroid progenitors. Biochem Biophys Res Commun, 390(2), 295-301, 2009 PMCID:2774815

Falin, RA, Morrison, R, Ham, AJ, Strange, K. Identification of regulatory phosphorylation sites in a cell volume- and Ste20 kinase-dependent ClC anion channel. J Gen Physiol, 133(1), 29-42, 2009 PMCID:2606941

Kolobova, E, Efimov, A, Kaverina, I, Rishi, AK, Schrader, JW, Ham, AJ, Larocca, MC, Goldenring, JR. Microtubule-dependent association of AKAP350A and CCAR1 with RNA stress granules. Exp Cell Res, 315(3), 542-55, 2009

Raman, D, Neel, NF, Sai, J, Mernaugh, RL, Ham, AJ, Richmond, AJ. Characterization of chemokine receptor CXCR2 interacting proteins using a proteomics approach to define the CXCR2 "chemosynapse". Methods Enzymol, 460, 315-30, 2009 PMCID:2876822

Vanacore, R, Ham, AJ, Voehler, M, Sanders, CR, Conrads, TP, Veenstra, TD, Sharpless, KB, Dawson, PE, Hudson, BG. A sulfilimine bond identified in collagen IV. Science, 325(5945), 1230-4, 2009 PMCID:2876822

Brown, KA, Ham, AJ, Clark, CN, Meller, N, Law, BK, Chytil, A, Cheng, N, Pietenpol, JA, Moses, HL. Identification of novel Smad2 and Smad3 associated proteins in response to TGF-beta1. J Cell Biochem, 105(2), 596-611, 2008 PMCID:2700048

Burgess, EF, Ham, AJ, Tabb, DL, Billheimer, D, Roth, BJ, Chang, SS, Cookson, MS, Hinton, TJ, Cheek, KL, Hill, S, Pietenpol, JA. Prostate cancer serum biomarker discovery through proteomic analysis of alpha-2 macroglobulin protein complexes. Proteomics Clin Appl, 2(9), 1223, 2008 PMCID:2811579

Cao, Z, Li, C, Higginbotham, JN, Franklin, JL, Tabb, DL, Graves-Deal, R, Hill, S, Cheek, K, Jerome, WG, Lapierre, LA, Goldenring, JR, Ham, AJ, Coffey, RJ. Use of fluorescence-activated vesicle sorting for isolation of Naked2-associated, basolaterally targeted exocytic vesicles for proteomics analysis. Mol Cell Proteomics, 7(9), 1651-67, 2008 PMCID:2528074

Chetyrkin, SV, Mathis, ME, Ham, AJ, Hachey, DL, Hudson, BG, Voziyan, PA. Propagation of protein glycation damage involves modification of tryptophan residues via reactive oxygen species: inhibition by pyridoxamine. Free Radic Biol Med, 44(7), 1276-85, 2008

Erickson, JR, Joiner, ML, Guan, X, Kutschke, W, Yang, J, Oddis, CV, Bartlett, RK, Lowe, JS, O''Donnell, SE, Aykin-Burns, N, Zimmerman, MC, Zimmerman, K, Ham, AJ, Weiss, RM, Spitz, DR, Shea, MA, Colbran, RJ, Mohler, PJ, Anderson, ME. A dynamic pathway for calcium-independent activation of CaMKII by methionine oxidation. Cell, 133(3), 462-74, 2008 PMCID:2435269

Fang, WB, Brantley-Sieders, DM, Hwang, Y, Ham, AJ, Chen, J. Identification and functional analysis of phosphorylated tyrosine residues within EphA2 receptor tyrosine kinase. J Biol Chem, 283(23), 16017-26, 2008 PMCID:2414276

Luo, W, Slebos, RJ, Hill, S, Li, M, Br?!bek, J, Amanchy, R, Chaerkady, R, Pandey, A, Ham, AJ, Hanks, SK. Global impact of oncogenic Src on a phosphotyrosine proteome. J Proteome Res, 7(8), 3447-60, 2008 PMCID:2579752

Slebos, RJ, Brock, JW, Winters, NF, Stuart, SR, Martinez, MA, Li, M, Chambers, MC, Zimmerman, LJ, Ham, AJ, Tabb, DL, Liebler, DC. Evaluation of Strong Cation Exchange versus Isoelectric Focusing of Peptides for Multidimensional Liquid Chromatography-Tandem Mass Spectrometry. J Proteome Res, 2008 PMCID:2669493

Tabb, DL, Ma, ZQ, Martin, DB, Ham, AJ, Chambers, MC. DirecTag: accurate sequence tags from peptide MS/MS through statistical scoring. J Proteome Res, 7(9), 3838-46, 2008

Vanacore, RM, Ham, AJ, Cartailler, JP, Sundaramoorthy, M, Todd, P, Pedchenko, V, Sado, Y, Borza, DB, Hudson, BG. A role for collagen IV cross-links in conferring immune privilege to the Goodpasture autoantigen: structural basis for the crypticity of B cell epitopes. J Biol Chem, 283(33), 22737-48, 2008 PMCID:2504875

Yang, Z, Browning, CF, Hallaq, H, Yermalitskaya, L, Esker, J, Hall, MR, Link, AJ, Ham, AJ, McGrath, MJ, Mitchell, CA, Murray, KT. Four and a half LIM protein 1: a partner for KCNA5 in human atrium. Cardiovasc Res, 78(3), 449-57, 2008

Bender, RP, Ham, AJ, Osheroff, N. Quinone-induced enhancement of DNA cleavage by human topoisomerase IIalpha: adduction of cysteine residues 392 and 405. Biochemistry, 46(10), 2856-64, 2007

Donowitz, M, Singh, S, Salahuddin, FF, Hogema, BM, Chen, Y, Gucek, M, Cole, RN, Ham, A, Zachos, NC, Kovbasnjuk, O, Lapierre, LA, Broere, N, Goldenring, J, deJonge, H, Li, X. Proteome of murine jejunal brush border membrane vesicles. J Proteome Res, 6(10), 4068-79, 2007

Druckova, A, Mernaugh, RL, Ham, AJ, Marnett, LJ. Identification of the protein targets of the reactive metabolite of teucrin A in vivo in the rat. Chem Res Toxicol, 20(10), 1393-408, 2007

Hill, KE, Zhou, J, Austin, LM, Motley, AK, Ham, AJ, Olson, GE, Atkins, JF, Gesteland, RF, Burk, RF. The selenium-rich C-terminal domain of mouse selenoprotein P is necessary for the supply of selenium to brain and testis but not for the maintenance of whole body selenium. J Biol Chem, 282(15), 10972-80, 2007

Lapierre, LA, Avant, KM, Caldwell, CM, Ham, AJ, Hill, S, Williams, JA, Smolka, AJ, Goldenring, JR. Characterization of immunoisolated human gastric parietal cells tubulovesicles: identification of regulators of apical recycling. Am J Physiol Gastrointest Liver Physiol, 292(5), G1249-62, 2007

Mohler, PJ, Zhu, MY, Blade, AM, Ham, AJ, Shelness, GS, Swift, LL. Identification of a novel isoform of microsomal triglyceride transfer protein. J Biol Chem, 282(37), 26981-8, 2007

Myers, JS, Zhao, R, Xu, X, Ham, AJ, Cortez, D. Cyclin-dependent kinase 2 dependent phosphorylation of ATRIP regulates the G2-M checkpoint response to DNA damage. Cancer Res, 67(14), 6685-90, 2007 PMCID:2728292

Ducharme, NA, Hales, CM, Lapierre, LA, Ham, AJ, Oztan, A, Apodaca, G, Goldenring, JR. MARK2/EMK1/Par-1Balpha phosphorylation of Rab11-family interacting protein 2 is necessary for the timely establishment of polarity in Madin-Darby canine kidney cells. Mol Biol Cell, 17(8), 3625-37, 2006 PMCID:1525241

Grueter, CE, Abiria, SA, Dzhura, I, Wu, Y, Ham, AJ, Mohler, PJ, Anderson, ME, Colbran, RJ. L-type Ca2+ channel facilitation mediated by phosphorylation of the beta subunit by CaMKII. Mol Cell, 23(5), 641-50, 2006

Luka, Z, Ham, AJ, Norris, JL, Yeo, EJ, Yermalitsky, V, Glenn, B, Caprioli, RM, Liebler, DC, Wagner, C. Identification of phosphorylation sites in glycine N-methyltransferase from rat liver. Protein Sci, 15(4), 785-94, 2006 PMCID:2242492

Popescu, DC, Ham, AJ, Shieh, BH. Scaffolding protein INAD regulates deactivation of vision by promoting phosphorylation of transient receptor potential by eye protein kinase C in Drosophila. J Neurosci, 26(33), 8570-7, 2006 PMCID:1577681

Tabb, DL, Friedman, DB, Ham, AJ. Verification of automated peptide identifications from proteomic tandem mass spectra. Nat Protoc, 1(5), 2213-22, 2006

Wu, ZL, Bartleson, CJ, Ham, AJ, Guengerich, FP. Heterologous expression, purification, and properties of human cytochrome P450 27C1. Arch Biochem Biophys, 445(1), 138-46, 2006

Hansen, BT, Davey, SW, Ham, AJ, Liebler, DC. P-Mod: an algorithm and software to map modifications to peptide sequences using tandem MS data. J Proteome Res, 4(2), 358-68, 2005

Manza, LL, Stamer, SL, Ham, AJ, Codreanu, SG, Liebler, DC. Sample preparation and digestion for proteomic analyses using spin filters. Proteomics, 5(7), 1742-5, 2005

Pedchenko, VK, Chetyrkin, SV, Chuang, P, Ham, AJ, Saleem, MA, Mathieson, PW, Hudson, BG, Voziyan, PA. Mechanism of perturbation of integrin-mediated cell-matrix interactions by reactive carbonyl compounds and its implication for pathogenesis of diabetic nephropathy. Diabetes, 54(10), 2952-60, 2005

Vanacore, RM, Friedman, DB, Ham, AJ, Sundaramoorthy, M, Hudson, BG. Identification of S-hydroxylysyl-methionine as the covalent cross-link of the noncollagenous (NC1) hexamer of the alpha1alpha1alpha2 collagen IV network: a role for the post-translational modification of lysine 211 to hydroxylysine 211 in hexamer assembly. J Biol Chem, 280(32), 29300-10, 2005

Ham, AJ, Engelward, BP, Koc, H, Sangaiah, R, Meira, LB, Samson, LD, Swenberg, JA. New immunoaffinity-LC-MS/MS methodology reveals that Aag null mice are deficient in their ability to clear 1,N6-etheno-deoxyadenosine DNA lesions from lung and liver in vivo. DNA Repair (Amst), 3(3), 257-65, 2004

Morinello, EJ, Ham, AJ, Ranasinghe, A, Nakamura, J, Upton, PB, Swenberg, JA. Molecular dosimetry and repair of N(2),3-ethenoguanine in rats exposed to vinyl chloride. Cancer Res, 62(18), 5189-95, 2002

Morinello, EJ, Ham, AJ, Ranasinghe, A, Sangaiah, R, Swenberg, JA. Simultaneous quantitation of N(2),3-ethenoguanine and 1,N(2)-ethenoguanine with an immunoaffinity/gas chromatography/high-resolution mass spectrometry assay. Chem Res Toxicol, 14(3), 327-34, 2001

Ham, AJ, Ranasinghe, A, Koc, H, Swenberg, JA. 4-Hydroxy-2-nonenal and ethyl linoleate form N(2),3-ethenoguanine under peroxidizing conditions. Chem Res Toxicol, 13(12), 1243-50, 2000

Hussain, SP, Amstad, P, Raja, K, Ambs, S, Nagashima, M, Bennett, WP, Shields, PG, Ham, AJ, Swenberg, JA, Marrogi, AJ, Harris, CC. Increased p53 mutation load in noncancerous colon tissue from ulcerative colitis: a cancer-prone chronic inflammatory disease. Cancer Res, 60(13), 3333-7, 2000

Swenberg, JA, Ham, A, Koc, H, Morinello, E, Ranasinghe, A, Tretyakova, N, Upton, PB, Wu, K. DNA adducts: effects of low exposure to ethylene oxide, vinyl chloride and butadiene. Mutat Res, 464(1), 77-86, 2000

Ham, AJ, Ranasinghe, A, Morinello, EJ, Nakamura, J, Upton, PB, Johnson, F, Swenberg, JA. Immunoaffinity/gas chromatography/high-resolution mass spectrometry method for the detection of N(2),3-ethenoguanine. Chem Res Toxicol, 12(12), 1240-6, 1999

Liebler, DC, Burr, JA, Ham, AJ. Gas chromatography-mass spectrometry analysis of vitamin E and its oxidation products. Methods Enzymol, 299, 309-18, 1999

Swenberg, JA, Bogdanffy, MS, Ham, A, Holt, S, Kim, A, Morinello, EJ, Ranasinghe, A, Scheller, N, Upton, PB. Formation and repair of DNA adducts in vinyl chloride- and vinyl fluoride-induced carcinogenesis. IARC Sci Publ(150), 29-43, 1999

Ham, AJ, Liebler, DC. Antioxidant reactions of vitamin E in the perfused rat liver: product distribution and effect of dietary vitamin E supplementation. Arch Biochem Biophys, 339(1), 157-64, 1997

Liebler, DC, Burr, JA, Philips, L, Ham, AJ. Gas chromatography-mass spectrometry analysis of vitamin E and its oxidation products. Anal Biochem, 236(1), 27-34, 1996

Ham, AJ, Liebler, DC. Vitamin E oxidation in rat liver mitochondria. Biochemistry, 34(17), 5754-61, 1995

Sharpe, AL, Carter, DE. Substrate specificity of rat liver aldehyde dehydrogenase with chloroacetaldehydes. J Biochem Toxicol, 8(3), 155-60, 1993


Postdoctoral Position Available
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Postdoctoral Position Details
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Updated Date
06/20/2011