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Amy-Joan Ham

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Josane F Sousa; Corbin Whitwell; Han-Kwang Yang; Bing Zhang; Amy-Joan L Ham; Woo Ho Kim; Bonnie LaFleur; Hyuk-Joon Lee; Ming Li; Daniel C Liebler; Ki Taek Nam; James R Goldenring
Proteomic profiling of paraffin-embedded samples identifies metaplasia-specific and early-stage gastric cancer biomarkers.
Surendra Dasari; Amy-Joan L Ham; Misti A Martinez; Kristin L Carpenter; Matthew C Chambers; Lorenzo J Vega-Montoto; David L Tabb
Pepitome: evaluating improved spectral library search for identification complementarity and quality assessment.
Esra Mutlu; Patricia B Upton; Darrell W Winsett; Leonard B Collins; Paul Evansky; Amy-Joan L Ham; Gary Hatch; Yo-Chan Jeong; James A Swenberg
A new LC-MS/MS method for the quantification of endogenous and vinyl chloride-induced 7-(2-Oxoethyl)guanine in sprague-dawley rats.

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2012: Josane F Sousa; Corbin Whitwell; Han-Kwang Yang; Bing Zhang; Amy-Joan L Ham; Woo Ho Kim; Bonnie LaFleur; Hyuk-Joon Lee; Ming Li; Daniel C Liebler; Ki Taek Nam; James R Goldenring
Proteomic profiling of paraffin-embedded samples identifies metaplasia-specific and early-stage gastric cancer biomarkers.
The American journal of pathology 2012;181(5):1560-72.
2012: Surendra Dasari; Amy-Joan L Ham; Misti A Martinez; Kristin L Carpenter; Matthew C Chambers; Lorenzo J Vega-Montoto; David L Tabb
Pepitome: evaluating improved spectral library search for identification complementarity and quality assessment.
Journal of proteome research 2012;11(3):1686-95.
2012: Esra Mutlu; Patricia B Upton; Darrell W Winsett; Leonard B Collins; Paul Evansky; Amy-Joan L Ham; Gary Hatch; Yo-Chan Jeong; James A Swenberg
A new LC-MS/MS method for the quantification of endogenous and vinyl chloride-induced 7-(2-Oxoethyl)guanine in sprague-dawley rats.
Chemical research in toxicology 2012;25(2):391-9.
2011: Ze-Qiang Ma; Michael R Oreto; William C Schultz; Scott M Sobecki; David L Tabb; Tina Y Tsui; Gregory R Wernke; Joseph Burden; Michael J Cantrell; Matthew C Chambers; Matthew B Cox; Amy-Joan L Ham; Michael D Litton; Daniel C Liebler
Supporting tool suite for production proteomics.
Bioinformatics (Oxford, England) 2011;27(22):3214-5.
2011: Sunil K Halder; Amy-Joan L Ham; Govindaraj Anumanthan; David P Carbone; Yong-Jig Cho; Arunima Datta; Pran K Datta
Elucidating the mechanism of regulation of transforming growth factor β Type II receptor expression in human lung cancer cell lines.
Neoplasia (New York, N.Y.) 2011;13(10):912-22.
2011: Ze-Qiang Ma; Aaron W Miller; Birgit Schilling; Hans Aerni; Richard M Caprioli; Matthew C Chambers; Kristin L Cheek; Amy-Joan L Ham; Corbin W Whitwell; David L Tabb
ScanRanker: Quality assessment of tandem mass spectra via sequence tagging.
Journal of proteome research 2011;10(7):2896-904.
2011: Haixia Zhang; Qinfeng Liu; Lisa J Zimmerman; Amy-Joan L Ham; Robbert J C Slebos; Jamshedur Rahman; Takefume Kikuchi; Pierre P Massion; David P Carbone; Dean Billheimer; Daniel C Liebler
Methods for peptide and protein quantitation by liquid chromatography-multiple reaction monitoring mass spectrometry.
Molecular & cellular proteomics : MCP 2011;10(6):M110.006593.
2011: Nicole F Neel; Amy-Joan L Ham; Raymond L Mernaugh; Jiqing Sai; Tammy Sobolik-Delmaire; Ann Richmond
IQGAP1 is a novel CXCR2-interacting protein and essential component of the "chemosynapse".
PloS one 2011;6(8):e23813.
2010: Anthony J Baucum; Nidhi Jalan-Sakrikar; Yuxia Jiao; Richard M Gustin; Leigh C Carmody; David L Tabb; Amy-Joan L Ham; Roger J Colbran
Identification and validation of novel spinophilin-associated proteins in rodent striatum using an enhanced ex vivo shotgun proteomics approach.
Molecular & cellular proteomics : MCP 2010;9(6):1243-59.
2010: Surendra Dasari; Matthew C Chambers; Robbert J Slebos; Lisa J Zimmerman; Amy-Joan L Ham; David L Tabb
TagRecon: high-throughput mutation identification through sequence tagging.
Journal of proteome research 2010;9(4):1716-26.
2010: Amanda Paulovich; Dean Billheimer; Amy-Joan L Ham; Lorenzo Vega-Montoto; Paul A Rudnick; David L Tabb; Pei Wang; Ronald K Blackman; David M Bunk; Helene L Cardasis; Karl R Clauser; Christopher R Kinsinger; Birgit Schilling; Tony J Tegeler; Asokan Mulayath Variyath; Mu Wang; Jeffrey Whiteaker; Lisa J Zimmerman; David Fenyo; Steven A Carr; Susan J Fisher; Bradford W Gibson; Mehdi Mesri; Thomas A Neubert; Fred E Regnier; Henry Rodriguez; Cliff Spiegelman; Stephen E Stein; Paul Tempst; Daniel C Liebler
Interlaboratory study characterizing a yeast performance standard for benchmarking LC-MS platform performance.
Molecular & cellular proteomics : MCP 2010;9(2):242-54.
2009: Ying Cai; Zhixiong Xu; Jingping Xie; Amy-Joan L Ham; Mark J Koury; Scott W Hiebert; Stephen J Brandt
Eto2/MTG16 and MTGR1 are heteromeric corepressors of the TAL1/SCL transcription factor in murine erythroid progenitors.
Biochemical and biophysical research communications 2009;390(2):295-301.
2009: Daniel C Liebler; Amy-Joan L Ham
Spin filter-based sample preparation for shotgun proteomics.
Nature methods 2009;6(11):785; author reply 785-6.
2009: Roberto Vanacore; Amy-Joan L Ham; Markus Voehler; Charles R Sanders; Thomas P Conrads; Timothy D Veenstra; K Barry Sharpless; Philip E Dawson; Billy G Hudson
A sulfilimine bond identified in collagen IV.
Science (New York, N.Y.) 2009;325(5945):1230-4.
2009: Dayanidhi Raman; Nicole F Neel; Jiqing Sai; Raymond L Mernaugh; Amy-Joan L Ham; Ann Richmond
Characterization of chemokine receptor CXCR2 interacting proteins using a proteomics approach to define the CXCR2 "chemosynapse".
Methods in enzymology 2009;460():315-30.
2009: Rebecca A Falin; Rebecca Morrison; Amy-Joan L Ham; Kevin Strange
Identification of regulatory phosphorylation sites in a cell volume- and Ste20 kinase-dependent ClC anion channel.
The Journal of general physiology 2009;133(1):29-42.
2008: Kimberly A Brown; Amy-Joan L Ham; Cara N Clark; Nahum Meller; Brian K Law; Anna Chytil; Nikki Cheng; Jennifer A Pietenpol; Harold L Moses
Identification of novel Smad2 and Smad3 associated proteins in response to TGF-beta1.
Journal of cellular biochemistry 2008;105(2):596-611.
2008: David L Tabb; Ze-Qiang Ma; Daniel B Martin; Amy-Joan L Ham; Matthew C Chambers
DirecTag: accurate sequence tags from peptide MS/MS through statistical scoring.
Journal of proteome research 2008;7(9):3838-46.
2008: Zheng Cao; Cunxi Li; James N Higginbotham; Jeffrey L Franklin; David L Tabb; Ramona Graves-Deal; Salisha Hill; Kristin Cheek; W Gray Jerome; Lynne A Lapierre; James R Goldenring; Amy-Joan L Ham; Robert J Coffey
Use of fluorescence-activated vesicle sorting for isolation of Naked2-associated, basolaterally targeted exocytic vesicles for proteomics analysis.
Molecular & cellular proteomics : MCP 2008;7(9):1651-67.
2008: roberto marcelo vanacore; Amy-Joan L Ham; Jean-Philippe Cartailler; Munirathinam Sundaramoorthy; Parvin Todd; Vadim Pedchenko; Yoshikazu Sado; Dorin-Bogdan Borza; Billy G Hudson
A role for collagen IV cross-links in conferring immune privilege to the Goodpasture autoantigen: structural basis for the crypticity of B cell epitopes.
The Journal of biological chemistry 2008;283(33):22737-48.
2008: Weifeng Luo; Robbert J Slebos; Salisha Hill; Ming Li; Jan Brábek; Ramars Amanchy; Raghothama Chaerkady; Akhilesh Pandey; Amy-Joan L Ham; Steven K Hanks
Global impact of oncogenic Src on a phosphotyrosine proteome.
Journal of proteome research 2008;7(8):3447-60.
2008: Wei Bin Fang; Dana M Brantley-Sieders; Yoonha Hwang; Amy-Joan L Ham; Jin Chen
Identification and functional analysis of phosphorylated tyrosine residues within EphA2 receptor tyrosine kinase.
The Journal of biological chemistry 2008;283(23):16017-26.
2008: Zhenjiang Yang; Carrie F Browning; Haifa Hallaq; Liudmila Yermalitskaya; Jan Esker; Matthew R Hall; Andrew J Link; Amy-Joan L Ham; Meagan J McGrath; Christina A Mitchell; Katherine T Murray
Four and a half LIM protein 1: a partner for KCNA5 in human atrium.
Cardiovascular research 2008;78(3):449-57.
2008: Jeffrey R Erickson; Mei-ling A Joiner; Xiaoqun Guan; William Kutschke; Jinying Yang; Carmine V Oddis; Ryan K Bartlett; John S Lowe; Susan E O'Donnell; Nukhet Aykin-Burns; Matthew C Zimmerman; Kathy Zimmerman; Amy-Joan L Ham; Robert M Weiss; Douglas R Spitz; Madeline A Shea; Roger J Colbran; Peter J Mohler; Mark E Anderson
A dynamic pathway for calcium-independent activation of CaMKII by methionine oxidation.
Cell 2008;133(3):462-74.
2008: Sergei V Chetyrkin; Missy E Mathis; Amy-Joan L Ham; David L Hachey; Billy G Hudson; Paul A Voziyan
Propagation of protein glycation damage involves modification of tryptophan residues via reactive oxygen species: inhibition by pyridoxamine.
Free radical biology & medicine 2008;44(7):1276-85.
2007: Alexandra Druckova; Raymond L Mernaugh; Amy-Joan L Ham; Lawrence J Marnett
Identification of the protein targets of the reactive metabolite of teucrin A in vivo in the rat.
Chemical research in toxicology 2007;20(10):1393-408.
2007: Peter J Mohler; Mei-Ying Zhu; Anna M Blade; Amy-Joan L Ham; Gregory S Shelness; Larry L Swift
Identification of a novel isoform of microsomal triglyceride transfer protein.
The Journal of biological chemistry 2007;282(37):26981-8.
2007: Jeremy S Myers; Runxiang Zhao; Xin Xu; Amy-Joan L Ham; David Cortez
Cyclin-dependent kinase 2 dependent phosphorylation of ATRIP regulates the G2-M checkpoint response to DNA damage.
Cancer research 2007;67(14):6685-90.
2007: Lynne A Lapierre; Kenya M Avant; Catherine M Caldwell; Amy-Joan L Ham; Salisha Hill; Janice A Williams; Adam J Smolka; James R Goldenring
Characterization of immunoisolated human gastric parietal cells tubulovesicles: identification of regulators of apical recycling.
American journal of physiology. Gastrointestinal and liver physiology 2007;292(5):G1249-62.
2007: Kristina E Hill; Jiadong Zhou; Lori M Austin; Amy K Motley; Amy-Joan L Ham; Gary E Olson; John F Atkins; Raymond F Gesteland; Raymond F Burk
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.
The Journal of biological chemistry 2007;282(15):10972-80.
2007: Ryan P Bender; Amy-Joan L Ham; Neil Osheroff
Quinone-induced enhancement of DNA cleavage by human topoisomerase IIalpha: adduction of cysteine residues 392 and 405.
Biochemistry 2007;46(10):2856-64.
2006: Chad E Grueter; Sunday A Abiria; Igor Dzhura; Yuejin Wu; Amy-Joan L Ham; Peter J Mohler; Mark E Anderson; Roger J Colbran
L-type Ca2+ channel facilitation mediated by phosphorylation of the beta subunit by CaMKII.
Molecular cell 2006;23(5):641-50.
2006: Daniela C Popescu; Amy-Joan L Ham; Bih-Hwa Shieh
Scaffolding protein INAD regulates deactivation of vision by promoting phosphorylation of transient receptor potential by eye protein kinase C in Drosophila.
The Journal of neuroscience : the official journal of the Society for Neuroscience 2006;26(33):8570-7.
2006: Nicole A Ducharme; Chadwick M Hales; Lynne A Lapierre; Amy-Joan L Ham; Asli Oztan; gerard apodaca; James R Goldenring
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.
Molecular biology of the cell 2006;17(8):3625-37.
2006: Zigmund Luka; Amy-Joan L Ham; Jeremy L Norris; Eui-Ju Yeo; Valery Yermalitsky; Byron Glenn; Richard M Caprioli; Daniel C Liebler; Conrad Wagner
Identification of phosphorylation sites in glycine N-methyltransferase from rat liver.
Protein science : a publication of the Protein Society 2006;15(4):785-94.
2006: David L Tabb; David B Friedman; Amy-Joan L Ham
Verification of automated peptide identifications from proteomic tandem mass spectra.
Nature protocols 2006;1(5):2213-22.
2006: Zhong-Liu Wu; Cheryl J Bartleson; Amy-Joan L Ham; F Peter Guengerich
Heterologous expression, purification, and properties of human cytochrome P450 27C1.
Archives of biochemistry and biophysics 2006;445(1):138-46.
2005: Vadim Pedchenko; Sergei V Chetyrkin; Peale Chuang; Amy-Joan L Ham; Moin A Saleem; Peter W Mathieson; Billy G Hudson; Paul A Voziyan
Mechanism of perturbation of integrin-mediated cell-matrix interactions by reactive carbonyl compounds and its implication for pathogenesis of diabetic nephropathy.
Diabetes 2005;54(10):2952-60.
2005: roberto marcelo vanacore; David B Friedman; Amy-Joan L Ham; Munirathinam Sundaramoorthy; Billy G Hudson
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.
The Journal of biological chemistry 2005;280(32):29300-10.
2005: Linda L Manza; Sheryl L Stamer; Amy-Joan L Ham; Simona G Codreanu; Daniel C Liebler
Sample preparation and digestion for proteomic analyses using spin filters.
Proteomics 2005;5(7):1742-5.
2005: Beau T Hansen; Sean W Davey; Amy-Joan L Ham; Daniel C Liebler
P-Mod: an algorithm and software to map modifications to peptide sequences using tandem MS data.
Journal of proteome research 2005;4(2):358-68.
2004: Amy-Joan L Ham; Bevin P Engelward; Hasan Koc; Ramiah Sangaiah; Lisiane Meira; Leona D Samson; James A Swenberg
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 2004;3(3):257-65.
2002: Eric J Morinello; Amy-Joan L Ham; Asoka Ranasinghe; Jun Nakamura; Patricia B Upton; James A Swenberg
Molecular dosimetry and repair of N(2),3-ethenoguanine in rats exposed to vinyl chloride.
Cancer research 2002;62(18):5189-95.
2002: James A Swenberg; Amy-Joan L Ham; Hasan Koc; David K La; Eric J Morinello; Brian F Pachkowski; Asoka Ranasinghe; Patricia B Upton
Methods for measuring DNA adducts and abasic sites II: methods for measurement of DNA adducts.
Current protocols in toxicology / editorial board, Mahin D. Maines (editor-in-chief) ... [et al.] 2002;Chapter 3():Unit3.9.
2002: James A Swenberg; Amy-Joan L Ham; Kevin S McDorman; Eric J Morinello; Jun Nakamura; Robert Schoonhoven
Methods for measuring DNA adducts and abasic sites I: isolation, purification, and analysis of DNA adducts in intact DNA.
Current protocols in toxicology / editorial board, Mahin D. Maines (editor-in-chief) ... [et al.] 2002;Chapter 3():Unit3.8.
2001: Eric J Morinello; Amy-Joan L Ham; Asoka Ranasinghe; Ramiah Sangaiah; James A Swenberg
Simultaneous quantitation of N(2),3-ethenoguanine and 1,N(2)-ethenoguanine with an immunoaffinity/gas chromatography/high-resolution mass spectrometry assay.
Chemical research in toxicology 2001;14(3):327-34.
2000: Amy-Joan L Ham; Asoka Ranasinghe; Hasan Koc; James A Swenberg
4-Hydroxy-2-nonenal and ethyl linoleate form N(2),3-ethenoguanine under peroxidizing conditions.
Chemical research in toxicology 2000;13(12):1243-50.
2000: James A Swenberg; Amy-Joan L Ham; Hasan Koc; Eric J Morinello; Asoka Ranasinghe; NY Tretyakova; Patricia B Upton; K Wu
DNA adducts: effects of low exposure to ethylene oxide, vinyl chloride and butadiene.
Mutation research 2000;464(1):77-86.
1999: Amy-Joan L Ham; Asoka Ranasinghe; Eric J Morinello; Jun Nakamura; Patricia B Upton; F Johnson; James A Swenberg
Immunoaffinity/gas chromatography/high-resolution mass spectrometry method for the detection of N(2),3-ethenoguanine.
Chemical research in toxicology 1999;12(12):1240-6.
1999: James A Swenberg; Matthew S Bogdanffy; Amy-Joan L Ham; S Holt; A Kim; Eric J Morinello; Asoka Ranasinghe; N Scheller; Patricia B Upton
Formation and repair of DNA adducts in vinyl chloride- and vinyl fluoride-induced carcinogenesis.
IARC scientific publications 1999;(150):29-43.
1999: Daniel C Liebler; J A Burr; Amy-Joan L Ham
Gas chromatography-mass spectrometry analysis of vitamin E and its oxidation products.
Methods in enzymology 1999;299():309-18.
1997: Amy-Joan L Ham; Daniel C Liebler
Antioxidant reactions of vitamin E in the perfused rat liver: product distribution and effect of dietary vitamin E supplementation.
Archives of biochemistry and biophysics 1997;339(1):157-64.
1996: Daniel C Liebler; J A Burr; L Philips; Amy-Joan L Ham
Gas chromatography-mass spectrometry analysis of vitamin E and its oxidation products.
Analytical biochemistry 1996;236(1):27-34.
1995: Amy-Joan L Ham; Daniel C Liebler
Vitamin E oxidation in rat liver mitochondria.
Biochemistry 1995;34(17):5754-61.