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    Al Burlingame, PhD

    TitleProfessor
    SchoolUCSF School of Pharmacy
    DepartmentPharmaceutical Chemistry
    Address600 16th Street
    San Francisco CA 94158
    Phone415-476-5641
    vCardDownload vCard

      Collapse Biography 
      Collapse Awards and Honors
      1970John Simon Guggenheim Memorial Fellowship
      Academia Sinica, People's Republic of China1981Official Guest
      Japanese Society for Medical Mass Spectrometry1982Honorary Member
      Academy of Sciences of the USSR1986Official Guest, Academy of Sciences of the USSR
      American Association for the Advancement of Science1990Fellow, American Association for the Advancement of Science
      Virginia Polytechnic University1996The Peters Lecturer
      Northeastern University1999Barnett Lectureship
      Indiana University2001Lilly Distinguished Lecturer
      Nobel Forum, Stockholm, Sweden2007Lecturer, Proteomics in Medicine
      International Forum of Proteomics2012Achievement Award

      Collapse Overview 
      Collapse Overview
      My group has long-standing, extensive expertise and experience in mass spectrometry, proteomics and systems biology, especially focused on sequencing, identification and study of unknown proteins, and the detection, assignment and site-specific dynamics of posttranslational modifications of proteins, particularly OGlcNAcylation, phosphorylation, acetylation, methylation and ubiquitinylation. Over many years we have collaborated with the neurobiological community extensively, including structural characterization of the GPI membrane anchor of the prion protein, structure of the lysyl oxidase co-factor, identification and PTM regulation of proteins in the retrograde signaling complexes in damaged axons, the O-GlcNAc/phosphorylation dynamics at the murine synapse, identification of new proteins involved in the Nodes of Ranvier, etc.

      In addition to the work in proteomics and epigenetics above, we have focused significant effort on other studies concerning the architecture of protein complexes and machines for which angstrom resolution structural information has not yet been tractable. For example we have developed a new lysine-lysine cross-linking strategy based on chemical reductive amination that provides comprehensive sequence and cross-link site assignments using electron transfer dissociation (ETD). This information provides accurate distance constraints that complement cryoEM and computer modeling efforts. In parallel software algorithms and scoring strategies have been developed that greatly facilitates the assignment of cross-linked peptides in general. Very recently we have initiated a thrust into development and application of methodology to measure protein complexes directly in the gas phase using a newly acquired high mass Orbitrap Exactive instrument (m/z < 22,000). This effort will complement our long-standing work on chemical cross-linking of protein complexes and machines.

      Finally, we have developed a general suite of programs and software tools required for processing large scale mass spectral data sets (HCD, ETD, etc) and stable isotopic labeling experiments (SILAC, iTRAQ, etc) called Protein Prospector.

      Collapse Interests
      Proteomics & the Molecular Compositions of Biological Systems, Molecular Structure Determinations, Identification of Cell Constituents and Correlation with Gene Expression, Structures of Modified Macromolecules and protein machines in Structural Biology, e.g., Posttranslational Modifications of Proteins, Epigenetics, Glucoconjugates, Antigenic Determinants, Molecular Immunochemistry, Metabolic Activation and Covalent Binding of Xenobiotics to Cellular Macromolecules, Molecular Nature of Chemical Toxicity, Mass Spectrometry, Molecular Composition of Biological Systems

      Collapse ORNG Applications 
      Collapse Websites
      Collapse Awarded Grants

      Collapse Bibliographic 
      Collapse Publications
      Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Researchers can login to make corrections and additions, or contact us for help.
      List All   |   Timeline
      1. Levin RS, Hertz NT, Burlingame AL, Shokat KM, Mukherjee S, et al. Innate immunity kinase TAK1 phosphorylates Rab1 on a hotspot for posttranslational modifications by host and pathogen. Proc Natl Acad Sci U S A. 2016 Aug 1. PMID: 27482120.
        View in: PubMed
      2. Perry RB, Rishal I, Doron-Mandel E, Kalinski AL, Medzihradszky KF, Terenzio M, Alber S, Koley S, Lin A, Rozenbaum M, Yudin D, Sahoo PK, Gomes C, Shinder V, Geraisy W, Huebner EA, Woolf CJ, Yaron A, Burlingame AL, Twiss JL, Fainzilber M. Nucleolin-Mediated RNA Localization Regulates Neuron Growth and Cycling Cell Size. Cell Rep. 2016 Aug 9; 16(6):1664-76. PMID: 27477284.
        View in: PubMed
      3. Lee S, Shang Y, Redmond SA, Urisman A, Tang AA, Li KH, Burlingame AL, Pak RA, Jovicic A, Gitler AD, Wang J, Gray NS, Seeley WW, Siddique T, Bigio EH, Lee VM, Trojanowski JQ, Chan JR, Huang EJ, et al. Activation of HIPK2 Promotes ER Stress-Mediated Neurodegeneration in Amyotrophic Lateral Sclerosis. Neuron. 2016 Jul 6; 91(1):41-55. PMID: 27321923.
        View in: PubMed
      4. Burlingame AL. On Strengthening the MCP Editorial Leadership. Mol Cell Proteomics. 2016 Jul; 15(7):2214-6. PMID: 27281785.
        View in: PubMed
      5. Sanlorenzo M, Vujic I, Posch C, Ma J, Lin K, Lai K, Lee D, Vujic M, Oses-Prieto JA, Chand S, Rodriguez-Peralto JL, Burlingame A, Ortiz-Urda S. Oncogenic KIT mutations in different exons lead to specific changes in melanocyte phospho-proteome. J Proteomics. 2016 Jul 20; 144:140-7. PMID: 27216642.
        View in: PubMed
      6. To TL, Medzihradszky KF, Burlingame AL, DeGrado WF, Jo H, Shu X. Photoactivatable protein labeling by singlet oxygen mediated reactions. Bioorg Med Chem Lett. 2016 Jul 15; 26(14):3359-63. PMID: 27220724.
        View in: PubMed
      7. Lewis BA, Burlingame AL, Myers SA. Human RNA Polymerase II Promoter Recruitment in Vitro Is Regulated by O-Linked N-Acetylglucosaminyltransferase (OGT). J Biol Chem. 2016 Jul 1; 291(27):14056-61. PMID: 27129214.
        View in: PubMed
      8. Li C, Gu L, Gao L, Chen C, Wei CQ, Qiu Q, Chien CW, Wang S, Jiang L, Ai LF, Chen CY, Yang S, Nguyen V, Qi Y, Snyder MP, Burlingame AL, Kohalmi SE, Huang S, Cao X, Wang ZY, Wu K, Chen X, Cui Y. Concerted genomic targeting of H3K27 demethylase REF6 and chromatin-remodeling ATPase BRM in Arabidopsis. Nat Genet. 2016 Jun; 48(6):687-93. PMID: 27111034.
        View in: PubMed
      9. Xu SL, Medzihradszky KF, Wang ZY, Burlingame AL, Chalkley RJ. N-Glycopeptide Profiling in Arabidopsis Inflorescence. Mol Cell Proteomics. 2016 Jun; 15(6):2048-54. PMID: 27067053.
        View in: PubMed
      10. Myers SA, Peddada S, Chatterjee N, Friedrich T, Tomoda K, Krings G, Thomas S, Maynard J, Broeker M, Thomson M, Pollard K, Yamanaka S, Burlingame AL, Panning B. SOX2 O-GlcNAcylation alters its protein-protein interactions and genomic occupancy to modulate gene expression in pluripotent cells. Elife. 2016; 5. PMID: 26949256.
        View in: PubMed
      11. Portnoy V, Lin SH, Li KH, Burlingame A, Hu ZH, Li H, Li LC. saRNA-guided Ago2 targets the RITA complex to promoters to stimulate transcription. Cell Res. 2016 Mar; 26(3):320-35. PMID: 26902284.
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      12. Roh SH, Kasembeli M, Galaz-Montoya JG, Trnka M, Lau WC, Burlingame A, Chiu W, Tweardy DJ. Chaperonin TRiC/CCT Modulates the Folding and Activity of Leukemogenic Fusion Oncoprotein AML1-ETO. J Biol Chem. 2016 Feb 26; 291(9):4732-41. PMID: 26706127.
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      13. Zhang B, Wang X, Zhao Z, Wang R, Huang X, Zhu Y, Yuan L, Wang Y, Xu X, Burlingame AL, Gao Y, Sun Y, Tang W. OsBRI1 Activates BR Signaling by Preventing Binding between the TPR and Kinase Domains of OsBSK3 via Phosphorylation. Plant Physiol. 2016 Feb; 170(2):1149-61. PMID: 26697897.
        View in: PubMed
      14. Rys JP, DuFort CC, Monteiro DA, Baird MA, Oses-Prieto JA, Chand S, Burlingame AL, Davidson MW, Alliston TN. Discrete spatial organization of TGFß receptors couples receptor multimerization and signaling to cellular tension. Elife. 2015; 4. PMID: 26652004.
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      15. Wang R, Liu M, Yuan M, Oses-Prieto JA, Cai X, Sun Y, Burlingame AL, Wang ZY, Tang W. The Brassinosteroid-Activated BRI1 Receptor Kinase Is Switched off by Dephosphorylation Mediated by Cytoplasm-Localized PP2A B' Subunits. Mol Plant. 2016 Jan 4; 9(1):148-57. PMID: 26517938.
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      16. Didonna A, Isobe N, Caillier SJ, Li KH, Burlingame AL, Hauser SL, Baranzini SE, Patsopoulos NA, Oksenberg JR. A non-synonymous single-nucleotide polymorphism associated with multiple sclerosis risk affects the EVI5 interactome. Hum Mol Genet. 2015 Dec 15; 24(24):7151-8. PMID: 26433934.
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      17. Kim EJ, Youn JH, Park CH, Kim TW, Guan S, Xu S, Burlingame AL, Kim YP, Kim SK, Wang ZY, Kim TW. Oligomerization between BSU1 Family Members Potentiates Brassinosteroid Signaling in Arabidopsis. Mol Plant. 2016 Jan 4; 9(1):178-81. PMID: 26432287.
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      18. Robinson PJ, Trnka MJ, Pellarin R, Greenberg CH, Bushnell DA, Davis R, Burlingame AL, Sali A, Kornberg RD. Molecular architecture of the yeast Mediator complex. Elife. 2015; 4. PMID: 26402457; PMCID: PMC4631838.
      19. Doron-Mandel E, Alber S, Oses JA, Medzihradszky KF, Burlingame AL, Fainzilber M, Twiss JL, Lee SJ. Isolation and analyses of axonal ribonucleoprotein complexes. Methods Cell Biol. 2016; 131:467-86. PMID: 26794529.
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      20. Lu J, Trnka MJ, Roh SH, Robinson PJ, Shiau C, Fujimori DG, Chiu W, Burlingame AL, Guan S. Improved Peak Detection and Deconvolution of Native Electrospray Mass Spectra from Large Protein Complexes. J Am Soc Mass Spectrom. 2015 Dec; 26(12):2141-51. PMID: 26323614.
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      21. Guan S, Trnka MJ, Bushnell DA, Robinson PJ, Gestwicki JE, Burlingame AL. Deconvolution method for specific and nonspecific binding of ligand to multiprotein complex by native mass spectrometry. Anal Chem. 2015 Aug 18; 87(16):8541-6. PMID: 26189511.
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      22. Morris M, Knudsen GM, Maeda S, Trinidad JC, Ioanoviciu A, Burlingame AL, Mucke L. Tau post-translational modifications in wild-type and human amyloid precursor protein transgenic mice. Nat Neurosci. 2015 Aug; 18(8):1183-9. PMID: 26192747.
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      23. Onizawa M, Oshima S, Schulze-Topphoff U, Oses-Prieto JA, Lu T, Tavares R, Prodhomme T, Duong B, Whang MI, Advincula R, Agelidis A, Barrera J, Wu H, Burlingame A, Malynn BA, Zamvil SS, Ma A. Erratum: The ubiquitin-modifying enzyme A20 restricts ubiquitination of the kinase RIPK3 and protects cells from necroptosis. Nat Immunol. 2015 Jul; 16(7):785. PMID: 26086145.
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      24. Burlingame A, Carr SA, Bradshaw RA, Chalkley RJ. On Credibility, Clarity, and Compliance. Mol Cell Proteomics. 2015 Jul; 14(7):1731-3. PMID: 26041845; PMCID: PMC4587320.
      25. Muller M, Hutin S, Marigold O, Li KH, Burlingame A, Glaunsinger BA. A ribonucleoprotein complex protects the interleukin-6 mRNA from degradation by distinct herpesviral endonucleases. PLoS Pathog. 2015 May; 11(5):e1004899. PMID: 25965334; PMCID: PMC4428876.
      26. Onizawa M, Oshima S, Schulze-Topphoff U, Oses-Prieto JA, Lu T, Tavares R, Prodhomme T, Duong B, Whang MI, Advincula R, Agelidis A, Barrera J, Wu H, Burlingame A, Malynn BA, Zamvil SS, Ma A. The ubiquitin-modifying enzyme A20 restricts ubiquitination of the kinase RIPK3 and protects cells from necroptosis. Nat Immunol. 2015 Jun; 16(6):618-27. PMID: 25939025; PMCID: PMC4439357 [Available on 12/01/15].
      27. Bradshaw RA, Burlingame AL. Minireviews revisited. Mol Cell Proteomics. 2015 Mar; 14(3):455. PMID: 25657218; PMCID: PMC4349968 [Available on 03/01/16].
      28. Duong BH, Onizawa M, Oses-Prieto JA, Advincula R, Burlingame A, Malynn BA, Ma A. A20 restricts ubiquitination of pro-interleukin-1ß protein complexes and suppresses NLRP3 inflammasome activity. Immunity. 2015 Jan 20; 42(1):55-67. PMID: 25607459; PMCID: PMC4302274 [Available on 01/20/16].
      29. Doll S, Burlingame AL. Mass spectrometry-based detection and assignment of protein posttranslational modifications. ACS Chem Biol. 2015 Jan 16; 10(1):63-71. PMID: 25541750; PMCID: PMC4301092 [Available on 12/26/15].
      30. Wang Y, Kim SM, Trnka MJ, Liu Y, Burlingame AL, Correia MA. Human liver cytochrome P450 3A4 ubiquitination: molecular recognition by UBC7-gp78 autocrine motility factor receptor and UbcH5a-CHIP-Hsc70-Hsp40 E2-E3 ubiquitin ligase complexes. J Biol Chem. 2015 Feb 6; 290(6):3308-32. PMID: 25451919; PMCID: PMC4319004 [Available on 02/06/16].
      31. Bradshaw RA, Pundavela J, Biarc J, Chalkley RJ, Burlingame AL, Hondermarck H. NGF and ProNGF: Regulation of neuronal and neoplastic responses through receptor signaling. Adv Biol Regul. 2015 May; 58:16-27. PMID: 25491371; PMCID: PMC4426037 [Available on 05/01/16].
      32. Ultanir SK, Yadav S, Hertz NT, Oses-Prieto JA, Claxton S, Burlingame AL, Shokat KM, Jan LY, Jan YN. MST3 kinase phosphorylates TAO1/2 to enable Myosin Va function in promoting spine synapse development. Neuron. 2014 Dec 3; 84(5):968-82. PMID: 25456499; PMCID: PMC4407996.
      33. Sos ML, Levin RS, Gordan JD, Oses-Prieto JA, Webber JT, Salt M, Hann B, Burlingame AL, McCormick F, Bandyopadhyay S, Shokat KM. Oncogene mimicry as a mechanism of primary resistance to BRAF inhibitors. Cell Rep. 2014 Aug 21; 8(4):1037-48. PMID: 25127139; PMCID: PMC4294625.
      34. Pando-Robles V, Oses-Prieto JA, Rodríguez-Gandarilla M, Meneses-Romero E, Burlingame AL, Batista CV. Quantitative proteomic analysis of Huh-7 cells infected with Dengue virus by label-free LC-MS. J Proteomics. 2014 Dec 5; 111:16-29. PMID: 25009145.
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      35. Ni W, Xu SL, Tepperman JM, Stanley DJ, Maltby DA, Gross JD, Burlingame AL, Wang ZY, Quail PH. A mutually assured destruction mechanism attenuates light signaling in Arabidopsis. Science. 2014 Jun 6; 344(6188):1160-4. PMID: 24904166; PMCID: PMC4414656.
      36. Deng Z, Oses-Prieto JA, Kutschera U, Tseng TS, Hao L, Burlingame AL, Wang ZY, Briggs WR. Blue light-induced proteomic changes in etiolated Arabidopsis seedlings. J Proteome Res. 2014 May 2; 13(5):2524-33. PMID: 24712693; PMCID: PMC4015686.
      37. Cho Y, Di Liberto V, Carlin D, Abe N, Li KH, Burlingame AL, Guan S, Michaelevski I, Cavalli V. Syntaxin13 expression is regulated by mammalian target of rapamycin (mTOR) in injured neurons to promote axon regeneration. J Biol Chem. 2014 May 30; 289(22):15820-32. PMID: 24737317; PMCID: PMC4140936.
      38. Hirsch J, Chalkley RJ, Bentley T, Burlingame AL, Frank JA. Double impact of cigarette smoke and mechanical ventilation on the alveolar epithelial type II cell. Crit Care. 2014; 18(2):R50. PMID: 24666941; PMCID: PMC4056080.
      39. Carr SA, Abbatiello SE, Ackermann BL, Borchers C, Domon B, Deutsch EW, Grant RP, Hoofnagle AN, Hüttenhain R, Koomen JM, Liebler DC, Liu T, MacLean B, Mani DR, Mansfield E, Neubert H, Paulovich AG, Reiter L, Vitek O, Aebersold R, Anderson L, Bethem R, Blonder J, Boja E, Botelho J, Boyne M, Bradshaw RA, Burlingame AL, Chan D, Keshishian H, Kuhn E, Kinsinger C, Lee JS, Lee SW, Moritz R, Oses-Prieto J, Rifai N, Ritchie J, Rodriguez H, Srinivas PR, Townsend RR, Van Eyk J, Whiteley G, Wiita A, Weintraub S. Targeted peptide measurements in biology and medicine: best practices for mass spectrometry-based assay development using a fit-for-purpose approach. Mol Cell Proteomics. 2014 Mar; 13(3):907-17. PMID: 24443746; PMCID: PMC3945918.
      40. Abernathy E, Clyde K, Yeasmin R, Krug LT, Burlingame A, Coscoy L, Glaunsinger B. Gammaherpesviral gene expression and virion composition are broadly controlled by accelerated mRNA degradation. PLoS Pathog. 2014 Jan; 10(1):e1003882. PMID: 24453974; PMCID: PMC3894220.
      41. Asmussen J, Lasater EA, Tajon C, Oses-Prieto J, Jun YW, Taylor BS, Burlingame A, Craik CS, Shah NP. MEK-dependent negative feedback underlies BCR-ABL-mediated oncogene addiction. Cancer Discov. 2014 Feb; 4(2):200-15. PMID: 24362263; PMCID: PMC4248023.
      42. Trnka MJ, Baker PR, Robinson PJ, Burlingame AL, Chalkley RJ. Matching cross-linked peptide spectra: only as good as the worse identification. Mol Cell Proteomics. 2014 Feb; 13(2):420-34. PMID: 24335475; PMCID: PMC3916644.
      43. Young LC, Hartig N, Muñoz-Alegre M, Oses-Prieto JA, Durdu S, Bender S, Vijayakumar V, Vietri Rudan M, Gewinner C, Henderson S, Jathoul AP, Ghatrora R, Lythgoe MF, Burlingame AL, Rodriguez-Viciana P. An MRAS, SHOC2, and SCRIB complex coordinates ERK pathway activation with polarity and tumorigenic growth. Mol Cell. 2013 Dec 12; 52(5):679-92. PMID: 24211266.
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      44. Wiita AP, Ziv E, Wiita PJ, Urisman A, Julien O, Burlingame AL, Weissman JS, Wells JA. Global cellular response to chemotherapy-induced apoptosis. Elife. 2013; 2:e01236. PMID: 24171104; PMCID: PMC3808542.
      45. Xu P, Xu SL, Li ZJ, Tang W, Burlingame AL, Wang ZY. A brassinosteroid-signaling kinase interacts with multiple receptor-like kinases in Arabidopsis. Mol Plant. 2014 Feb; 7(2):441-4. PMID: 24051702; PMCID: PMC3900014.
      46. Wang C, Shang JX, Chen QX, Oses-Prieto JA, Bai MY, Yang Y, Yuan M, Zhang YL, Mu CC, Deng Z, Wei CQ, Burlingame AL, Wang ZY, Sun Y. Identification of BZR1-interacting proteins as potential components of the brassinosteroid signaling pathway in Arabidopsis through tandem affinity purification. Mol Cell Proteomics. 2013 Dec; 12(12):3653-65. PMID: 24019147; PMCID: PMC3861714.
      47. Hertz NT, Berthet A, Sos ML, Thorn KS, Burlingame AL, Nakamura K, Shokat KM. A neo-substrate that amplifies catalytic activity of parkinson's-disease-related kinase PINK1. Cell. 2013 Aug 15; 154(4):737-47. PMID: 23953109; PMCID: PMC3950538.
      48. Ni W, Xu SL, Chalkley RJ, Pham TN, Guan S, Maltby DA, Burlingame AL, Wang ZY, Quail PH. Multisite light-induced phosphorylation of the transcription factor PIF3 is necessary for both its rapid degradation and concomitant negative feedback modulation of photoreceptor phyB levels in Arabidopsis. Plant Cell. 2013 Jul; 25(7):2679-98. PMID: 23903316; PMCID: PMC3753391.
      49. Nishino M, Choy JW, Gushwa NN, Oses-Prieto JA, Koupparis K, Burlingame AL, Renslo AR, McKerrow JH, Taunton J. Hypothemycin, a fungal natural product, identifies therapeutic targets in Trypanosoma brucei [corrected]. Elife. 2013; 2:e00712. PMID: 23853713; PMCID: PMC3707081.
      50. Trinidad JC, Schoepfer R, Burlingame AL, Medzihradszky KF. N- and O-glycosylation in the murine synaptosome. Mol Cell Proteomics. 2013 Dec; 12(12):3474-88. PMID: 23816992; PMCID: PMC3861701.
      51. Aebersold R, Burlingame AL, Bradshaw RA. Western blots versus selected reaction monitoring assays: time to turn the tables? Mol Cell Proteomics. 2013 Sep; 12(9):2381-2. PMID: 23756428; PMCID: PMC3769317.
      52. Xu J, Wang AH, Oses-Prieto J, Makhijani K, Katsuno Y, Pei M, Yan L, Zheng YG, Burlingame A, Brückner K, Derynck R. Arginine Methylation Initiates BMP-Induced Smad Signaling. Mol Cell. 2013 Jul 11; 51(1):5-19. PMID: 23747011; PMCID: PMC3951972.
      53. Bellodi C, McMahon M, Contreras A, Juliano D, Kopmar N, Nakamura T, Maltby D, Burlingame A, Savage SA, Shimamura A, Ruggero D. H/ACA small RNA dysfunctions in disease reveal key roles for noncoding RNA modifications in hematopoietic stem cell differentiation. Cell Rep. 2013 May 30; 3(5):1493-502. PMID: 23707062; PMCID: PMC3857015.
      54. Susuki K, Chang KJ, Zollinger DR, Liu Y, Ogawa Y, Eshed-Eisenbach Y, Dours-Zimmermann MT, Oses-Prieto JA, Burlingame AL, Seidenbecher CI, Zimmermann DR, Oohashi T, Peles E, Rasband MN. Three mechanisms assemble central nervous system nodes of Ranvier. Neuron. 2013 May 8; 78(3):469-82. PMID: 23664614; PMCID: PMC3756512.
      55. Gautam V, Trinidad JC, Rimerman RA, Costa BM, Burlingame AL, Monaghan DT. Nedd4 is a specific E3 ubiquitin ligase for the NMDA receptor subunit GluN2D. Neuropharmacology. 2013 Nov; 74:96-107. PMID: 23639431; PMCID: PMC3855079.
      56. Shiau C, Trnka MJ, Bozicevic A, Ortiz Torres I, Al-Sady B, Burlingame AL, Narlikar GJ, Fujimori DG. Reconstitution of nucleosome demethylation and catalytic properties of a Jumonji histone demethylase. Chem Biol. 2013 Apr 18; 20(4):494-9. PMID: 23601638; PMCID: PMC3704229.
      57. Biarc J, Chalkley RJ, Burlingame AL, Bradshaw RA. Dissecting the roles of tyrosines 490 and 785 of TrkA protein in the induction of downstream protein phosphorylation using chimeric receptors. J Biol Chem. 2013 Jun 7; 288(23):16606-18. PMID: 23589303; PMCID: PMC3675596.
      58. Greninger AL, Knudsen GM, Betegon M, Burlingame AL, DeRisi JL. ACBD3 interaction with TBC1 domain 22 protein is differentially affected by enteroviral and kobuviral 3A protein binding. MBio. 2013; 4(2):e00098-13. PMID: 23572552; PMCID: PMC3622926.
      59. Bessat M, Knudsen G, Burlingame AL, Wang CC. A minimal anaphase promoting complex/cyclosome (APC/C) in Trypanosoma brucei. PLoS One. 2013; 8(3):e59258. PMID: 23533609; PMCID: PMC3606461.
      60. Liu W, Baker SS, Trinidad J, Burlingame AL, Baker RD, Forte JG, Virtuoso LP, Egilmez NK, Zhu L. Inhibition of lysosomal enzyme activities by proton pump inhibitors. J Gastroenterol. 2013 Dec; 48(12):1343-52. PMID: 23478938.
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      61. Myers SA, Daou S, Affar el B, Burlingame A. Electron transfer dissociation (ETD): the mass spectrometric breakthrough essential for O-GlcNAc protein site assignments-a study of the O-GlcNAcylated protein host cell factor C1. Proteomics. 2013 Mar; 13(6):982-91. PMID: 23335398; PMCID: PMC3988289.
      62. Le DD, Cortesi AT, Myers SA, Burlingame AL, Fujimori DG. Site-specific and regiospecific installation of methylarginine analogues into recombinant histones and insights into effector protein binding. J Am Chem Soc. 2013 Feb 27; 135(8):2879-82. PMID: 23398247; PMCID: PMC4260808.
      63. Kaasik K, Kivimäe S, Allen JJ, Chalkley RJ, Huang Y, Baer K, Kissel H, Burlingame AL, Shokat KM, Ptácek LJ, Fu YH. Glucose sensor O-GlcNAcylation coordinates with phosphorylation to regulate circadian clock. Cell Metab. 2013 Feb 5; 17(2):291-302. PMID: 23395175; PMCID: PMC3597447.
      64. Ilagan JO, Chalkley RJ, Burlingame AL, Jurica MS. Rearrangements within human spliceosomes captured after exon ligation. RNA. 2013 Mar; 19(3):400-12. PMID: 23345524; PMCID: PMC3677250.
      65. Choy JW, Bryant C, Calvet CM, Doyle PS, Gunatilleke SS, Leung SS, Ang KK, Chen S, Gut J, Oses-Prieto JA, Johnston JB, Arkin MR, Burlingame AL, Taunton J, Jacobson MP, McKerrow JM, Podust LM, Renslo AR. Chemical-biological characterization of a cruzain inhibitor reveals a second target and a mammalian off-target. Beilstein J Org Chem. 2013; 9:15-25. PMID: 23400640; PMCID: PMC3566858.
      66. Ouellet H, Chow ED, Guan S, Cox JS, Burlingame AL, de Montellano PR. Genetic and mass spectrometric tools for elucidating the physiological function(s) of cytochrome P450 enzymes from Mycobacterium tuberculosis. Methods Mol Biol. 2013; 987:79-94. PMID: 23475669.
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      67. Just S, Illing S, Trester-Zedlitz M, Lau EK, Kotowski SJ, Miess E, Mann A, Doll C, Trinidad JC, Burlingame AL, von Zastrow M, Schulz S. Differentiation of opioid drug effects by hierarchical multi-site phosphorylation. Mol Pharmacol. 2013 Mar; 83(3):633-9. PMID: 23239825; PMCID: PMC3583494.
      68. Zhuang M, Guan S, Wang H, Burlingame AL, Wells JA. Substrates of IAP ubiquitin ligases identified with a designed orthogonal E3 ligase, the NEDDylator. Mol Cell. 2013 Jan 24; 49(2):273-82. PMID: 23201124; PMCID: PMC3557559.
      69. Bradshaw RA, Chalkley RJ, Biarc J, Burlingame AL. Receptor tyrosine kinase signaling mechanisms: Devolving TrkA responses with phosphoproteomics. Adv Biol Regul. 2013 Jan; 53(1):87-96. PMID: 23266087; PMCID: PMC3577974.
      70. Robinson PJ, Bushnell DA, Trnka MJ, Burlingame AL, Kornberg RD. Structure of the mediator head module bound to the carboxy-terminal domain of RNA polymerase II. Proc Natl Acad Sci U S A. 2012 Oct 30; 109(44):17931-5. PMID: 23071300; PMCID: PMC3497735.
      71. Trinidad JC, Thalhammer A, Burlingame AL, Schoepfer R. Activity-dependent protein dynamics define interconnected cores of co-regulated postsynaptic proteins. Mol Cell Proteomics. 2013 Jan; 12(1):29-41. PMID: 23035237; PMCID: PMC3536907.
      72. O'Donoghue AJ, Eroy-Reveles AA, Knudsen GM, Ingram J, Zhou M, Statnekov JB, Greninger AL, Hostetter DR, Qu G, Maltby DA, Anderson MO, Derisi JL, McKerrow JH, Burlingame AL, Craik CS. Global identification of peptidase specificity by multiplex substrate profiling. Nat Methods. 2012 Nov; 9(11):1095-100. PMID: 23023596; PMCID: PMC3707110.
      73. Nagano K, Akpan A, Warnasuriya G, Corless S, Totty N, Yang A, Stein R, Zvelebil M, Stensballe A, Burlingame A, Waterfield M, Cramer R, Timms JF, Naaby-Hansen S. Functional proteomic analysis of long-term growth factor stimulation and receptor tyrosine kinase coactivation in Swiss 3T3 fibroblasts. Mol Cell Proteomics. 2012 Dec; 11(12):1690-708. PMID: 22956732; PMCID: PMC3518109.
      74. Crawford ED, Seaman JE, Barber AE, David DC, Babbitt PC, Burlingame AL, Wells JA. Conservation of caspase substrates across metazoans suggests hierarchical importance of signaling pathways over specific targets and cleavage site motifs in apoptosis. Cell Death Differ. 2012 Dec; 19(12):2040-8. PMID: 22918439; PMCID: PMC3504717.
      75. Beltrao P, Albanèse V, Kenner LR, Swaney DL, Burlingame A, Villén J, Lim WA, Fraser JS, Frydman J, Krogan NJ. Systematic functional prioritization of protein posttranslational modifications. Cell. 2012 Jul 20; 150(2):413-25. PMID: 22817900; PMCID: PMC3404735.
      76. Shimbo K, Hsu GW, Nguyen H, Mahrus S, Trinidad JC, Burlingame AL, Wells JA. Quantitative profiling of caspase-cleaved substrates reveals different drug-induced and cell-type patterns in apoptosis. Proc Natl Acad Sci U S A. 2012 Jul 31; 109(31):12432-7. PMID: 22802652; PMCID: PMC3412033.
      77. Stowe IB, Mercado EL, Stowe TR, Bell EL, Oses-Prieto JA, Hernández H, Burlingame AL, McCormick F. A shared molecular mechanism underlies the human rasopathies Legius syndrome and Neurofibromatosis-1. Genes Dev. 2012 Jul 1; 26(13):1421-6. PMID: 22751498; PMCID: PMC3403010.
      78. Trinidad JC, Barkan DT, Gulledge BF, Thalhammer A, Sali A, Schoepfer R, Burlingame AL. Global identification and characterization of both O-GlcNAcylation and phosphorylation at the murine synapse. Mol Cell Proteomics. 2012 Aug; 11(8):215-29. PMID: 22645316; PMCID: PMC3412957.
      79. Bhattacharya M, Su G, Su X, Oses-Prieto JA, Li JT, Huang X, Hernandez H, Atakilit A, Burlingame AL, Matthay MA, Sheppard D. IQGAP1 is necessary for pulmonary vascular barrier protection in murine acute lung injury and pneumonia. Am J Physiol Lung Cell Mol Physiol. 2012 Jul 1; 303(1):L12-9. PMID: 22561460; PMCID: PMC3426434.
      80. Guan S, Price JC, Ghaemmaghami S, Prusiner SB, Burlingame AL. Compartment modeling for mammalian protein turnover studies by stable isotope metabolic labeling. Anal Chem. 2012 May 1; 84(9):4014-21. PMID: 22444387; PMCID: PMC3923578.
      81. Burlingame AL, Stults JT. Mass spectrometry: reconnaissance at the Frontiers of biology. Mol Cell Proteomics. 2012 May; 11(5):1-2. PMID: 22511459; PMCID: PMC3418840.
      82. Ruperez P, Gago-Martinez A, Burlingame AL, Oses-Prieto JA. Quantitative phosphoproteomic analysis reveals a role for serine and threonine kinases in the cytoskeletal reorganization in early T cell receptor activation in human primary T cells. Mol Cell Proteomics. 2012 May; 11(5):171-86. PMID: 22499768; PMCID: PMC3418841.
      83. Sivaramakrishnan S, Ouellet H, Matsumura H, Guan S, Moënne-Loccoz P, Burlingame AL, Ortiz de Montellano PR. Proximal ligand electron donation and reactivity of the cytochrome P450 ferric-peroxo anion. J Am Chem Soc. 2012 Apr 18; 134(15):6673-84. PMID: 22444582; PMCID: PMC3329582.
      84. Sherman J, Molloy MP, Burlingame AL. Why complexity and entropy matter: information, posttranslational modifications, and assay fidelity. Proteomics. 2012 Apr; 12(8):1147-50. PMID: 22577016.
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      85. Ultanir SK, Hertz NT, Li G, Ge WP, Burlingame AL, Pleasure SJ, Shokat KM, Jan LY, Jan YN. Chemical genetic identification of NDR1/2 kinase substrates AAK1 and Rabin8 Uncovers their roles in dendrite arborization and spine development. Neuron. 2012 Mar 22; 73(6):1127-42. PMID: 22445341; PMCID: PMC3333840.
      86. Agard NJ, Mahrus S, Trinidad JC, Lynn A, Burlingame AL, Wells JA. Global kinetic analysis of proteolysis via quantitative targeted proteomics. Proc Natl Acad Sci U S A. 2012 Feb 7; 109(6):1913-8. PMID: 22308409; PMCID: PMC3277568.
      87. Hengeveld RC, Hertz NT, Vromans MJ, Zhang C, Burlingame AL, Shokat KM, Lens SM. Development of a chemical genetic approach for human aurora B kinase identifies novel substrates of the chromosomal passenger complex. Mol Cell Proteomics. 2012 May; 11(5):47-59. PMID: 22267324; PMCID: PMC3418839.
      88. Greninger AL, Knudsen GM, Betegon M, Burlingame AL, Derisi JL. The 3A protein from multiple picornaviruses utilizes the golgi adaptor protein ACBD3 to recruit PI4KIIIß. J Virol. 2012 Apr; 86(7):3605-16. PMID: 22258260; PMCID: PMC3302542.
      89. Xu SL, Chalkley RJ, Wang ZY, Burlingame AL. Identification of O-linked ß-D-N-acetylglucosamine-modified proteins from Arabidopsis. Methods Mol Biol. 2012; 876:33-45. PMID: 22576084; PMCID: PMC3699408.
      90. Jäger S, Kim DY, Hultquist JF, Shindo K, LaRue RS, Kwon E, Li M, Anderson BD, Yen L, Stanley D, Mahon C, Kane J, Franks-Skiba K, Cimermancic P, Burlingame A, Sali A, Craik CS, Harris RS, Gross JD, Krogan NJ. Vif hijacks CBF-ß to degrade APOBEC3G and promote HIV-1 infection. Nature. 2012 Jan 19; 481(7381):371-5. PMID: 22190037; PMCID: PMC3310910.
      91. Jäger S, Cimermancic P, Gulbahce N, Johnson JR, McGovern KE, Clarke SC, Shales M, Mercenne G, Pache L, Li K, Hernandez H, Jang GM, Roth SL, Akiva E, Marlett J, Stephens M, D'Orso I, Fernandes J, Fahey M, Mahon C, O'Donoghue AJ, Todorovic A, Morris JH, Maltby DA, Alber T, Cagney G, Bushman FD, Young JA, Chanda SK, Sundquist WI, Kortemme T, Hernandez RD, Craik CS, Burlingame A, Sali A, Frankel AD, Krogan NJ. Global landscape of HIV-human protein complexes. Nature. 2012 Jan 19; 481(7381):365-70. PMID: 22190034; PMCID: PMC3310911.
      92. Deng Z, Xu S, Chalkley RJ, Oses-Prieto JA, Burlingame AL, Wang ZY, Kutschera U. Rapid auxin-mediated changes in the proteome of the epidermal cells in rye coleoptiles: implications for the initiation of growth. Plant Biol (Stuttg). 2012 May; 14(3):420-7. PMID: 22117532; PMCID: PMC3312047.
      93. Wang Y, Guan S, Acharya P, Liu Y, Thirumaran RK, Brandman R, Schuetz EG, Burlingame AL, Correia MA. Multisite phosphorylation of human liver cytochrome P450 3A4 enhances Its gp78- and CHIP-mediated ubiquitination: a pivotal role of its Ser-478 residue in the gp78-catalyzed reaction. Mol Cell Proteomics. 2012 Feb; 11(2):M111.010132. PMID: 22101235; PMCID: PMC3277751.
      94. Bohlen CJ, Chesler AT, Sharif-Naeini R, Medzihradszky KF, Zhou S, King D, Sánchez EE, Burlingame AL, Basbaum AI, Julius D. A heteromeric Texas coral snake toxin targets acid-sensing ion channels to produce pain. Nature. 2011 Nov 17; 479(7373):410-4. PMID: 22094702; PMCID: PMC3226747.
      95. Biarc J, Chalkley RJ, Burlingame AL, Bradshaw RA. The induction of serine/threonine protein phosphorylations by a PDGFR/TrkA chimera in stably transfected PC12 cells. Mol Cell Proteomics. 2012 May; 11(5):15-30. PMID: 22027198; PMCID: PMC3418849.
      96. Guan S, Price JC, Prusiner SB, Ghaemmaghami S, Burlingame AL. A data processing pipeline for mammalian proteome dynamics studies using stable isotope metabolic labeling. Mol Cell Proteomics. 2011 Dec; 10(12):M111.010728. PMID: 21937731; PMCID: PMC3237081.
      97. Kim TW, Guan S, Burlingame AL, Wang ZY. The CDG1 kinase mediates brassinosteroid signal transduction from BRI1 receptor kinase to BSU1 phosphatase and GSK3-like kinase BIN2. Mol Cell. 2011 Aug 19; 43(4):561-71. PMID: 21855796; PMCID: PMC3206214.
      98. Lau EK, Trester-Zedlitz M, Trinidad JC, Kotowski SJ, Krutchinsky AN, Burlingame AL, von Zastrow M. Quantitative encoding of the effect of a partial agonist on individual opioid receptors by multisite phosphorylation and threshold detection. Sci Signal. 2011 Aug 9; 4(185):ra52. PMID: 21868358; PMCID: PMC3625704.
      99. Ge W, Song Y, Zhang C, Zhang Y, Burlingame AL, Guo Y. Proteomic analyses of apoplastic proteins from germinating Arabidopsis thaliana pollen. Biochim Biophys Acta. 2011 Dec; 1814(12):1964-73. PMID: 21798377; PMCID: PMC3214693.
      100. Francone OL, Ishida BY, de la Llera-Moya M, Royer L, Happe C, Zhu J, Chalkey RJ, Schaefer P, Cox C, Burlingame A, Kane JP, Rothblat GH. Disruption of the murine procollagen C-proteinase enhancer 2 gene causes accumulation of pro-apoA-I and increased HDL levels. J Lipid Res. 2011 Nov; 52(11):1974-83. PMID: 21771977; PMCID: PMC3196229.
      101. Charles GM, Chen C, Shih SC, Collins SR, Beltrao P, Zhang X, Sharma T, Tan S, Burlingame AL, Krogan NJ, Madhani HD, Narlikar GJ. Site-specific acetylation mark on an essential chromatin-remodeling complex promotes resistance to replication stress. Proc Natl Acad Sci U S A. 2011 Jun 28; 108(26):10620-5. PMID: 21673141; PMCID: PMC3127919.
      102. Myers SA, Panning B, Burlingame AL. Polycomb repressive complex 2 is necessary for the normal site-specific O-GlcNAc distribution in mouse embryonic stem cells. Proc Natl Acad Sci U S A. 2011 Jun 7; 108(23):9490-5. PMID: 21606357; PMCID: PMC3111310.
      103. Coltri P, Effenberger K, Chalkley RJ, Burlingame AL, Jurica MS. Breaking up the C complex spliceosome shows stable association of proteins with the lariat intron intermediate. PLoS One. 2011; 6(4):e19061. PMID: 21526149; PMCID: PMC3079748.
      104. Brennan DF, Dar AC, Hertz NT, Chao WC, Burlingame AL, Shokat KM, Barford D. A Raf-induced allosteric transition of KSR stimulates phosphorylation of MEK. Nature. 2011 Apr 21; 472(7343):366-9. PMID: 21441910.
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      105. Song Y, Zhang C, Ge W, Zhang Y, Burlingame AL, Guo Y. Identification of NaCl stress-responsive apoplastic proteins in rice shoot stems by 2D-DIGE. J Proteomics. 2011 Jun 10; 74(7):1045-67. PMID: 21420516; PMCID: PMC3107904.
      106. Sterling HJ, Cassou CA, Trnka MJ, Burlingame AL, Krantz BA, Williams ER. The role of conformational flexibility on protein supercharging in native electrospray ionization. Phys Chem Chem Phys. 2011 Nov 7; 13(41):18288-96. PMID: 21399817; PMCID: PMC3415327.
      107. Tang W, Yuan M, Wang R, Yang Y, Wang C, Oses-Prieto JA, Kim TW, Zhou HW, Deng Z, Gampala SS, Gendron JM, Jonassen EM, Lillo C, DeLong A, Burlingame AL, Sun Y, Wang ZY. PP2A activates brassinosteroid-responsive gene expression and plant growth by dephosphorylating BZR1. Nat Cell Biol. 2011 Feb; 13(2):124-31. PMID: 21258370; PMCID: PMC3077550.
      108. Li T, Xu SL, Oses-Prieto JA, Putil S, Xu P, Wang RJ, Li KH, Maltby DA, An LH, Burlingame AL, Deng ZP, Wang ZY. Proteomics analysis reveals post-translational mechanisms for cold-induced metabolic changes in Arabidopsis. Mol Plant. 2011 Mar; 4(2):361-74. PMID: 21242321; PMCID: PMC3063518.
      109. Wang Y, Guan S, Acharya P, Koop DR, Liu Y, Liao M, Burlingame AL, Correia MA. Ubiquitin-dependent proteasomal degradation of human liver cytochrome P450 2E1: identification of sites targeted for phosphorylation and ubiquitination. J Biol Chem. 2011 Mar 18; 286(11):9443-56. PMID: 21209460; PMCID: PMC3058980.
      110. Chu F, Ren X, Chasse A, Hickman T, Zhang L, Yuh J, Smith MT, Burlingame AL. Quantitative mass spectrometry reveals the epigenome as a target of arsenic. Chem Biol Interact. 2011 Jun 30; 192(1-2):113-7. PMID: 21075096; PMCID: PMC4360996.
      111. Biarc J, Chalkley RJ, Burlingame AL, Bradshaw RA. Receptor tyrosine kinase signaling--a proteomic perspective. Adv Enzyme Regul. 2011; 51(1):293-305. PMID: 21056590; PMCID: PMC3079071.
      112. Su T, Bryant DM, Luton F, Vergés M, Ulrich SM, Hansen KC, Datta A, Eastburn DJ, Burlingame AL, Shokat KM, Mostov KE. A kinase cascade leading to Rab11-FIP5 controls transcytosis of the polymeric immunoglobulin receptor. Nat Cell Biol. 2010 Dec; 12(12):1143-53. PMID: 21037565; PMCID: PMC3072784.
      113. Wang F, Bai MY, Deng Z, Oses-Prieto JA, Burlingame AL, Lu T, Chong K, Wang ZY. Proteomic study identifies proteins involved in brassinosteroid regulation of rice growth. J Integr Plant Biol. 2010 Dec; 52(12):1075-85. PMID: 21106006.
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      114. Bradshaw RA, Burlingame AL. Technological innovation revisited. Mol Cell Proteomics. 2010 Nov; 9(11):2335-6. PMID: 20943599; PMCID: PMC2984236.
      115. Ferreyra ML, Biarc J, Burlingame AL, Casati P. Arabidopsis L10 ribosomal proteins in UV-B responses. Plant Signal Behav. 2010 Oct; 5(10):1222-5. PMID: 20855946; PMCID: PMC3115351.
      116. Trnka MJ, Burlingame AL. Topographic studies of the GroEL-GroES chaperonin complex by chemical cross-linking using diformyl ethynylbenzene: the power of high resolution electron transfer dissociation for determination of both peptide sequences and their attachment sites. Mol Cell Proteomics. 2010 Oct; 9(10):2306-17. PMID: 20813910; PMCID: PMC2953922.
      117. Wang D, Oses-Prieto JA, Li KH, Fernandes JF, Burlingame AL, Walbot V. The male sterile 8 mutation of maize disrupts the temporal progression of the transcriptome and results in the mis-regulation of metabolic functions. Plant J. 2010 Sep; 63(6):939-51. PMID: 20626649; PMCID: PMC2974755.
      118. David DC, Ollikainen N, Trinidad JC, Cary MP, Burlingame AL, Kenyon C. Widespread protein aggregation as an inherent part of aging in C. elegans. PLoS Biol. 2010; 8(8):e1000450. PMID: 20711477; PMCID: PMC2919420.
      119. Price JC, Guan S, Burlingame A, Prusiner SB, Ghaemmaghami S. Analysis of proteome dynamics in the mouse brain. Proc Natl Acad Sci U S A. 2010 Aug 10; 107(32):14508-13. PMID: 20699386; PMCID: PMC2922600.
      120. Michaelevski I, Segal-Ruder Y, Rozenbaum M, Medzihradszky KF, Shalem O, Coppola G, Horn-Saban S, Ben-Yaakov K, Dagan SY, Rishal I, Geschwind DH, Pilpel Y, Burlingame AL, Fainzilber M. Signaling to transcription networks in the neuronal retrograde injury response. Sci Signal. 2010; 3(130):ra53. PMID: 20628157; PMCID: PMC3645873.
      121. Ouellet H, Guan S, Johnston JB, Chow ED, Kells PM, Burlingame AL, Cox JS, Podust LM, de Montellano PR. Mycobacterium tuberculosis CYP125A1, a steroid C27 monooxygenase that detoxifies intracellularly generated cholest-4-en-3-one. Mol Microbiol. 2010 Aug; 77(3):730-42. PMID: 20545858; PMCID: PMC2909382.
      122. Oda Y, Chalkley RJ, Burlingame AL, Bikle DD. The transcriptional coactivator DRIP/mediator complex is involved in vitamin D receptor function and regulates keratinocyte proliferation and differentiation. J Invest Dermatol. 2010 Oct; 130(10):2377-88. PMID: 20520624; PMCID: PMC4114506.
      123. Falcone Ferreyra ML, Pezza A, Biarc J, Burlingame AL, Casati P. Plant L10 ribosomal proteins have different roles during development and translation under ultraviolet-B stress. Plant Physiol. 2010 Aug; 153(4):1878-94. PMID: 20516338; PMCID: PMC2923885.
      124. He N, Liu M, Hsu J, Xue Y, Chou S, Burlingame A, Krogan NJ, Alber T, Zhou Q. HIV-1 Tat and host AFF4 recruit two transcription elongation factors into a bifunctional complex for coordinated activation of HIV-1 transcription. Mol Cell. 2010 May 14; 38(3):428-38. PMID: 20471948; PMCID: PMC3085314.
      125. Hallows KR, Bhalla V, Oyster NM, Wijngaarden MA, Lee JK, Li H, Chandran S, Xia X, Huang Z, Chalkley RJ, Burlingame AL, Pearce D. Phosphopeptide screen uncovers novel phosphorylation sites of Nedd4-2 that potentiate its inhibition of the epithelial Na+ channel. J Biol Chem. 2010 Jul 9; 285(28):21671-8. PMID: 20466724; PMCID: PMC2898378.
      126. Burlingame AL, Stults JT. Mass spectrometry and the evolution of proteomics. Mol Cell Proteomics. 2010 May; 9(5):753. PMID: 20439911; PMCID: PMC2871410.
      127. Kutschera U, Deng Z, Oses-Prieto JA, Burlingame AL, Wang ZY. Cessation of coleoptile elongation and loss of auxin sensitivity in developing rye seedlings: a quantitative proteomic analysis. Plant Signal Behav. 2010 May; 5(5):509-17. PMID: 20234181.
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      128. Hertz NT, Wang BT, Allen JJ, Zhang C, Dar AC, Burlingame AL, Shokat KM. Chemical genetic approach for kinase-substrate mapping by covalent capture of thiophosphopeptides and analysis by mass spectrometry. Curr Protoc Chem Biol. 2010 Mar 1; 2(1):15-36. PMID: 23836541; PMCID: PMC3894912.
      129. Phan VT, Ding VW, Li F, Chalkley RJ, Burlingame A, McCormick F. The RasGAP proteins Ira2 and neurofibromin are negatively regulated by Gpb1 in yeast and ETEA in humans. Mol Cell Biol. 2010 May; 30(9):2264-79. PMID: 20160012; PMCID: PMC2863595.
      130. Eliuk SM, Maltby D, Panning B, Burlingame AL. High resolution electron transfer dissociation studies of unfractionated intact histones from murine embryonic stem cells using on-line capillary LC separation: determination of abundant histone isoforms and post-translational modifications. Mol Cell Proteomics. 2010 May; 9(5):824-37. PMID: 20133344; PMCID: PMC2871417.
      131. Rishal I, Michaelevski I, Rozenbaum M, Shinder V, Medzihradszky KF, Burlingame AL, Fainzilber M. Axoplasm isolation from peripheral nerve. Dev Neurobiol. 2010 Feb; 70(2):126-33. PMID: 19885832; PMCID: PMC2857660.
      132. Ogawa Y, Oses-Prieto J, Kim MY, Horresh I, Peles E, Burlingame AL, Trimmer JS, Meijer D, Rasband MN. ADAM22, a Kv1 channel-interacting protein, recruits membrane-associated guanylate kinases to juxtaparanodes of myelinated axons. J Neurosci. 2010 Jan 20; 30(3):1038-48. PMID: 20089912; PMCID: PMC2811262.
      133. Chalkley RJ, Medzihradszky KF, Lynn AJ, Baker PR, Burlingame AL. Statistical analysis of Peptide electron transfer dissociation fragmentation mass spectrometry. Anal Chem. 2010 Jan 15; 82(2):579-84. PMID: 20028093; PMCID: PMC2836188.
      134. Darula Z, Chalkley RJ, Baker P, Burlingame AL, Medzihradszky KF. Mass spectrometric analysis, automated identification and complete annotation of O-linked glycopeptides. Eur J Mass Spectrom (Chichester, Eng). 2010; 16(3):421-8. PMID: 20530845; PMCID: PMC2963623.
      135. Guan S, Burlingame AL. High mass selectivity for top-down proteomics by application of SWIFT technology. J Am Soc Mass Spectrom. 2010 Mar; 21(3):455-9. PMID: 20060315; PMCID: PMC3384707.
      136. Guan S, Burlingame AL. Data processing algorithms for analysis of high resolution MSMS spectra of peptides with complex patterns of posttranslational modifications. Mol Cell Proteomics. 2010 May; 9(5):804-10. PMID: 19955076; PMCID: PMC2871415.
      137. Michaelevski I, Medzihradszky KF, Lynn A, Burlingame AL, Fainzilber M. Axonal transport proteomics reveals mobilization of translation machinery to the lesion site in injured sciatic nerve. Mol Cell Proteomics. 2010 May; 9(5):976-87. PMID: 19955087; PMCID: PMC2871428.
      138. Chu F, Baker PR, Burlingame AL, Chalkley RJ. Finding chimeras: a bioinformatics strategy for identification of cross-linked peptides. Mol Cell Proteomics. 2010 Jan; 9(1):25-31. PMID: 19809093; PMCID: PMC2808265.
      139. Ilagan J, Yuh P, Chalkley RJ, Burlingame AL, Jurica MS. The role of exon sequences in C complex spliceosome structure. J Mol Biol. 2009 Nov 27; 394(2):363-75. PMID: 19761775; PMCID: PMC2783800.
      140. Kim TW, Guan S, Sun Y, Deng Z, Tang W, Shang JX, Sun Y, Burlingame AL, Wang ZY. Brassinosteroid signal transduction from cell-surface receptor kinases to nuclear transcription factors. Nat Cell Biol. 2009 Oct; 11(10):1254-60. PMID: 19734888; PMCID: PMC2910619.
      141. Jo WJ, Ren X, Chu F, Aleshin M, Wintz H, Burlingame A, Smith MT, Vulpe CD, Zhang L. Acetylated H4K16 by MYST1 protects UROtsa cells from arsenic toxicity and is decreased following chronic arsenic exposure. Toxicol Appl Pharmacol. 2009 Dec 15; 241(3):294-302. PMID: 19732783; PMCID: PMC2784148.
      142. Tomizawa M, Talley TT, Park JF, Maltby D, Medzihradszky KF, Durkin KA, Cornejo-Bravo JM, Burlingame AL, Casida JE, Taylor P. Nicotinic agonist binding site mapped by methionine- and tyrosine-scanning coupled with azidochloropyridinyl photoaffinity labeling. J Med Chem. 2009 Jun 25; 52(12):3735-41. PMID: 19459645; PMCID: PMC2748672.
      143. Beltrao P, Trinidad JC, Fiedler D, Roguev A, Lim WA, Shokat KM, Burlingame AL, Krogan NJ. Evolution of phosphoregulation: comparison of phosphorylation patterns across yeast species. PLoS Biol. 2009 Jun 16; 7(6):e1000134. PMID: 19547744; PMCID: PMC2691599.
      144. Chalkley RJ, Thalhammer A, Schoepfer R, Burlingame AL. Identification of protein O-GlcNAcylation sites using electron transfer dissociation mass spectrometry on native peptides. Proc Natl Acad Sci U S A. 2009 Jun 2; 106(22):8894-9. PMID: 19458039; PMCID: PMC2690010.
      145. Ortiz-Muñoz G, Houard X, Martín-Ventura JL, Ishida BY, Loyau S, Rossignol P, Moreno JA, Kane JP, Chalkley RJ, Burlingame AL, Michel JB, Meilhac O. HDL antielastase activity prevents smooth muscle cell anoikis, a potential new antiatherogenic property. FASEB J. 2009 Sep; 23(9):3129-39. PMID: 19417089; PMCID: PMC2735359.
      146. Skibbe DS, Fernandes JF, Medzihradszky KF, Burlingame AL, Walbot V. Mutator transposon activity reprograms the transcriptomes and proteomes of developing maize anthers. Plant J. 2009 Aug; 59(4):622-33. PMID: 19453454.
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      147. Fernandez F, Trinidad JC, Blank M, Feng DD, Burlingame AL, Garner CC. Normal protein composition of synapses in Ts65Dn mice: a mouse model of Down syndrome. J Neurochem. 2009 Jul; 110(1):157-69. PMID: 19453946; PMCID: PMC2735138.
      148. Coan KE, Maltby DA, Burlingame AL, Shoichet BK. Promiscuous aggregate-based inhibitors promote enzyme unfolding. J Med Chem. 2009 Apr 9; 52(7):2067-75. PMID: 19281222; PMCID: PMC2664636.
      149. Conrad F, Zhu X, Zhang X, Chalkley RJ, Burlingame AL, Marks JD, Liu B. Human antibodies targeting cell surface antigens overexpressed by the hormone refractory metastatic prostate cancer cells: ICAM-1 is a tumor antigen that mediates prostate cancer cell invasion. J Mol Med (Berl). 2009 May; 87(5):507-14. PMID: 19219419; PMCID: PMC2796542.
      150. Zhang W, St-Gelais F, Grabner CP, Trinidad JC, Sumioka A, Morimoto-Tomita M, Kim KS, Straub C, Burlingame AL, Howe JR, Tomita S. A transmembrane accessory subunit that modulates kainate-type glutamate receptors. Neuron. 2009 Feb 12; 61(3):385-96. PMID: 19217376; PMCID: PMC2803770.
      151. Thalhammer A, Trinidad JC, Burlingame AL, Schoepfer R. Densin-180: revised membrane topology, domain structure and phosphorylation status. J Neurochem. 2009 Apr; 109(2):297-302. PMID: 19187442; PMCID: PMC2846389.
      152. Joubel A, Chalkley RJ, Medzihradszky KF, Hondermarck H, Burlingame AL. Identification of new p53 acetylation sites in COS-1 cells. Mol Cell Proteomics. 2009 Jun; 8(6):1167-73. PMID: 19155208; PMCID: PMC2690490.
      153. McCord RA, Michishita E, Hong T, Berber E, Boxer LD, Kusumoto R, Guan S, Shi X, Gozani O, Burlingame AL, Bohr VA, Chua KF. SIRT6 stabilizes DNA-dependent protein kinase at chromatin for DNA double-strand break repair. Aging (Albany NY). 2009 Jan; 1(1):109-21. PMID: 20157594; PMCID: PMC2815768.
      154. Yam AY, Xia Y, Lin HT, Burlingame A, Gerstein M, Frydman J. Defining the TRiC/CCT interactome links chaperonin function to stabilization of newly made proteins with complex topologies. Nat Struct Mol Biol. 2008 Dec; 15(12):1255-62. PMID: 19011634; PMCID: PMC2658641.
      155. Lee SH, Sterling H, Burlingame A, McCormick F. Tpr directly binds to Mad1 and Mad2 and is important for the Mad1-Mad2-mediated mitotic spindle checkpoint. Genes Dev. 2008 Nov 1; 22(21):2926-31. PMID: 18981471; PMCID: PMC2577792.
      156. Casado P, Prado MA, Zuazua-Villar P, Del Valle E, Artime N, Cabal-Hierro L, Rupérez P, Burlingame AL, Lazo PS, Ramos S. Microtubule interfering agents and KSP inhibitors induce the phosphorylation of the nuclear protein p54(nrb), an event linked to G2/M arrest. J Proteomics. 2009 Jan 30; 71(6):592-600. PMID: 18832053.
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      157. Mahrus S, Trinidad JC, Barkan DT, Sali A, Burlingame AL, Wells JA. Global sequencing of proteolytic cleavage sites in apoptosis by specific labeling of protein N termini. Cell. 2008 Sep 5; 134(5):866-76. PMID: 18722006; PMCID: PMC2566540.
      158. Tang W, Kim TW, Oses-Prieto JA, Sun Y, Deng Z, Zhu S, Wang R, Burlingame AL, Wang ZY. BSKs mediate signal transduction from the receptor kinase BRI1 in Arabidopsis. Science. 2008 Jul 25; 321(5888):557-60. PMID: 18653891; PMCID: PMC2730546.
      159. Chalkley RJ, Baker PR, Medzihradszky KF, Lynn AJ, Burlingame AL. In-depth analysis of tandem mass spectrometry data from disparate instrument types. Mol Cell Proteomics. 2008 Dec; 7(12):2386-98. PMID: 18653769; PMCID: PMC2596346.
      160. Gräub R, Lancero H, Pedersen A, Chu M, Padmanabhan K, Xu XQ, Spitz P, Chalkley R, Burlingame AL, Stokoe D, Bernstein HS. Cell cycle-dependent phosphorylation of human CDC5 regulates RNA processing. Cell Cycle. 2008 Jun 15; 7(12):1795-803. PMID: 18583928; PMCID: PMC2940709.
      161. Li Z, Lee JH, Chu F, Burlingame AL, Günzl A, Wang CC. Identification of a novel chromosomal passenger complex and its unique localization during cytokinesis in Trypanosoma brucei. PLoS One. 2008; 3(6):e2354. PMID: 18545648; PMCID: PMC2396291.
      162. Hirsch J, Niemann CU, Hansen KC, Choi S, Su X, Frank JA, Fang X, Hirose R, Theodore P, Sapru A, Burlingame AL, Matthay MA. Alterations in the proteome of pulmonary alveolar type II cells in the rat after hepatic ischemia-reperfusion. Crit Care Med. 2008 Jun; 36(6):1846-54. PMID: 18496381; PMCID: PMC2442403.
      163. Casati P, Campi M, Chu F, Suzuki N, Maltby D, Guan S, Burlingame AL, Walbot V. Histone acetylation and chromatin remodeling are required for UV-B-dependent transcriptional activation of regulated genes in maize. Plant Cell. 2008 Apr; 20(4):827-42. PMID: 18398050; PMCID: PMC2390752.
      164. Tomizawa M, Maltby D, Talley TT, Durkin KA, Medzihradszky KF, Burlingame AL, Taylor P, Casida JE. Atypical nicotinic agonist bound conformations conferring subtype selectivity. Proc Natl Acad Sci U S A. 2008 Feb 5; 105(5):1728-32. PMID: 18230720; PMCID: PMC2234212.
      165. Tang W, Deng Z, Oses-Prieto JA, Suzuki N, Zhu S, Zhang X, Burlingame AL, Wang ZY. Proteomics studies of brassinosteroid signal transduction using prefractionation and two-dimensional DIGE. Mol Cell Proteomics. 2008 Apr; 7(4):728-38. PMID: 18182375; PMCID: PMC2401332.
      166. Trinidad JC, Thalhammer A, Specht CG, Lynn AJ, Baker PR, Schoepfer R, Burlingame AL. Quantitative analysis of synaptic phosphorylation and protein expression. Mol Cell Proteomics. 2008 Apr; 7(4):684-96. PMID: 18056256.
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      167. Walther TC, Aguilar PS, Fröhlich F, Chu F, Moreira K, Burlingame AL, Walter P. Pkh-kinases control eisosome assembly and organization. EMBO J. 2007 Dec 12; 26(24):4946-55. PMID: 18034155; PMCID: PMC2094096.
      168. Olsen O, Funke L, Long JF, Fukata M, Kazuta T, Trinidad JC, Moore KA, Misawa H, Welling PA, Burlingame AL, Zhang M, Bredt DS. Renal defects associated with improper polarization of the CRB and DLG polarity complexes in MALS-3 knockout mice. J Cell Biol. 2007 Oct 8; 179(1):151-64. PMID: 17923534; PMCID: PMC2064744.
      169. Deng Z, Zhang X, Tang W, Oses-Prieto JA, Suzuki N, Gendron JM, Chen H, Guan S, Chalkley RJ, Peterman TK, Burlingame AL, Wang ZY. A proteomics study of brassinosteroid response in Arabidopsis. Mol Cell Proteomics. 2007 Dec; 6(12):2058-71. PMID: 17848588; PMCID: PMC2966871.
      170. Iacovides DC, O'Shea CC, Oses-Prieto J, Burlingame A, McCormick F. Critical role for arginine methylation in adenovirus-infected cells. J Virol. 2007 Dec; 81(23):13209-17. PMID: 17686851; PMCID: PMC2169124.
      171. Gampala SS, Kim TW, He JX, Tang W, Deng Z, Bai MY, Guan S, Lalonde S, Sun Y, Gendron JM, Chen H, Shibagaki N, Ferl RJ, Ehrhardt D, Chong K, Burlingame AL, Wang ZY. An essential role for 14-3-3 proteins in brassinosteroid signal transduction in Arabidopsis. Dev Cell. 2007 Aug; 13(2):177-89. PMID: 17681130; PMCID: PMC2000337.
      172. Tomizawa M, Maltby D, Medzihradszky KF, Zhang N, Durkin KA, Presley J, Talley TT, Taylor P, Burlingame AL, Casida JE. Defining nicotinic agonist binding surfaces through photoaffinity labeling. Biochemistry. 2007 Jul 31; 46(30):8798-806. PMID: 17614369.
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      173. Medzihradszky KF, Guan S, Maltby DA, Burlingame AL. Sulfopeptide fragmentation in electron-capture and electron-transfer dissociation. J Am Soc Mass Spectrom. 2007 Sep; 18(9):1617-24. PMID: 17629708.
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      174. Allen JJ, Li M, Brinkworth CS, Paulson JL, Wang D, Hübner A, Chou WH, Davis RJ, Burlingame AL, Messing RO, Katayama CD, Hedrick SM, Shokat KM. A semisynthetic epitope for kinase substrates. Nat Methods. 2007 Jun; 4(6):511-6. PMID: 17486086; PMCID: PMC2932705.
      175. Tomizawa M, Talley TT, Maltby D, Durkin KA, Medzihradszky KF, Burlingame AL, Taylor P, Casida JE. Mapping the elusive neonicotinoid binding site. Proc Natl Acad Sci U S A. 2007 May 22; 104(21):9075-80. PMID: 17485662; PMCID: PMC1885630.
      176. Maloney A, Clarke PA, Naaby-Hansen S, Stein R, Koopman JO, Akpan A, Yang A, Zvelebil M, Cramer R, Stimson L, Aherne W, Banerji U, Judson I, Sharp S, Powers M, deBilly E, Salmons J, Walton M, Burlingame A, Waterfield M, Workman P. Gene and protein expression profiling of human ovarian cancer cells treated with the heat shock protein 90 inhibitor 17-allylamino-17-demethoxygeldanamycin. Cancer Res. 2007 Apr 1; 67(7):3239-53. PMID: 17409432.
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      177. Hirsch J, Hansen KC, Sapru A, Frank JA, Chalkley RJ, Fang X, Trinidad JC, Baker P, Burlingame AL, Matthay MA. Impact of low and high tidal volumes on the rat alveolar epithelial type II cell proteome. Am J Respir Crit Care Med. 2007 May 15; 175(10):1006-13. PMID: 17363773; PMCID: PMC1899270.
      178. Simon MD, Chu F, Racki LR, de la Cruz CC, Burlingame AL, Panning B, Narlikar GJ, Shokat KM. The site-specific installation of methyl-lysine analogs into recombinant histones. Cell. 2007 Mar 9; 128(5):1003-12. PMID: 17350582; PMCID: PMC2932701.
      179. Osés-Prieto JA, Zhang X, Burlingame AL. Formation of epsilon-formyllysine on silver-stained proteins: implications for assignment of isobaric dimethylation sites by tandem mass spectrometry. Mol Cell Proteomics. 2007 Feb; 6(2):181-92. PMID: 17138591.
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      180. Chu F, Mahrus S, Craik CS, Burlingame AL. Isotope-coded and affinity-tagged cross-linking (ICATXL): an efficient strategy to probe protein interaction surfaces. J Am Chem Soc. 2006 Aug 16; 128(32):10362-3. PMID: 16895390.
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      181. Chalkley RJ, Brinkworth CS, Burlingame AL. Side-chain fragmentation of alkylated cysteine residues in electron capture dissociation mass spectrometry. J Am Soc Mass Spectrom. 2006 Sep; 17(9):1271-4. PMID: 16809046.
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      182. Chu F, Maynard JC, Chiosis G, Nicchitta CV, Burlingame AL. Identification of novel quaternary domain interactions in the Hsp90 chaperone, GRP94. Protein Sci. 2006 Jun; 15(6):1260-9. PMID: 16731965; PMCID: PMC2242539.
      183. Conway MC, Whittal RM, Baldwin MA, Burlingame AL, Balhorn R. Electrospray mass spectrometry of NeuAc oligomers associated with the C fragment of the tetanus toxin. J Am Soc Mass Spectrom. 2006 Jul; 17(7):967-76. PMID: 16713287.
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      184. Bradshaw RA, Burlingame AL, Carr S, Aebersold R. Reporting protein identification data: the next generation of guidelines. Mol Cell Proteomics. 2006 May; 5(5):787-8. PMID: 16670253.
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      185. Rodriguez-Viciana P, Oses-Prieto J, Burlingame A, Fried M, McCormick F. A phosphatase holoenzyme comprised of Shoc2/Sur8 and the catalytic subunit of PP1 functions as an M-Ras effector to modulate Raf activity. Mol Cell. 2006 Apr 21; 22(2):217-30. PMID: 16630891.
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      186. Recht J, Tsubota T, Tanny JC, Diaz RL, Berger JM, Zhang X, Garcia BA, Shabanowitz J, Burlingame AL, Hunt DF, Kaufman PD, Allis CD. Histone chaperone Asf1 is required for histone H3 lysine 56 acetylation, a modification associated with S phase in mitosis and meiosis. Proc Natl Acad Sci U S A. 2006 May 2; 103(18):6988-93. PMID: 16627621; PMCID: PMC1459006.
      187. Zhou Q, Cadrin M, Herrmann H, Chen CH, Chalkley RJ, Burlingame AL, Omary MB. Keratin 20 serine 13 phosphorylation is a stress and intestinal goblet cell marker. J Biol Chem. 2006 Jun 16; 281(24):16453-61. PMID: 16608857.
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      188. Hirsch J, Hansen KC, Choi S, Noh J, Hirose R, Roberts JP, Matthay MA, Burlingame AL, Maher JJ, Niemann CU. Warm ischemia-induced alterations in oxidative and inflammatory proteins in hepatic Kupffer cells in rats. Mol Cell Proteomics. 2006 Jun; 5(6):979-86. PMID: 16500929.
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      189. Vosseller K, Trinidad JC, Chalkley RJ, Specht CG, Thalhammer A, Lynn AJ, Snedecor JO, Guan S, Medzihradszky KF, Maltby DA, Schoepfer R, Burlingame AL. O-linked N-acetylglucosamine proteomics of postsynaptic density preparations using lectin weak affinity chromatography and mass spectrometry. Mol Cell Proteomics. 2006 May; 5(5):923-34. PMID: 16452088.
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      190. Trinidad JC, Specht CG, Thalhammer A, Schoepfer R, Burlingame AL. Comprehensive identification of phosphorylation sites in postsynaptic density preparations. Mol Cell Proteomics. 2006 May; 5(5):914-22. PMID: 16452087.
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      191. Jiménez CR, Spijker S, de Schipper S, Lodder JC, Janse CK, Geraerts WP, van Minnen J, Syed NI, Burlingame AL, Smit AB, Li K. Peptidomics of a single identified neuron reveals diversity of multiple neuropeptides with convergent actions on cellular excitability. J Neurosci. 2006 Jan 11; 26(2):518-29. PMID: 16407549.
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      192. Chu F, Nusinow DA, Chalkley RJ, Plath K, Panning B, Burlingame AL. Mapping post-translational modifications of the histone variant MacroH2A1 using tandem mass spectrometry. Mol Cell Proteomics. 2006 Jan; 5(1):194-203. PMID: 16210244.
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      193. Baxter BK, Abeliovich H, Zhang X, Stirling AG, Burlingame AL, Goldfarb DS. Atg19p ubiquitination and the cytoplasm to vacuole trafficking pathway in yeast. J Biol Chem. 2005 Nov 25; 280(47):39067-76. PMID: 16186126.
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      194. Olsen O, Moore KA, Fukata M, Kazuta T, Trinidad JC, Kauer FW, Streuli M, Misawa H, Burlingame AL, Nicoll RA, Bredt DS. Neurotransmitter release regulated by a MALS-liprin-alpha presynaptic complex. J Cell Biol. 2005 Sep 26; 170(7):1127-34. PMID: 16186258; PMCID: PMC2171538.
      195. Bradshaw RA, Burlingame AL, Carr S, Aebersold R. Protein identification: the good, the bad, and the ugly. Mol Cell Proteomics. 2005 Sep; 4(9):1221-2. PMID: 16160099.
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      196. Burlingame AL, Zhang X, Chalkley RJ. Mass spectrometric analysis of histone posttranslational modifications. Methods. 2005 Aug; 36(4):383-94. PMID: 16112065.
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      197. Casati P, Zhang X, Burlingame AL, Walbot V. Analysis of leaf proteome after UV-B irradiation in maize lines differing in sensitivity. Mol Cell Proteomics. 2005 Nov; 4(11):1673-85. PMID: 16043824.
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      198. Wysocka J, Swigut T, Milne TA, Dou Y, Zhang X, Burlingame AL, Roeder RG, Brivanlou AH, Allis CD. WDR5 associates with histone H3 methylated at K4 and is essential for H3 K4 methylation and vertebrate development. Cell. 2005 Jun 17; 121(6):859-72. PMID: 15960974.
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      199. Chalkley RJ, Baker PR, Huang L, Hansen KC, Allen NP, Rexach M, Burlingame AL. Comprehensive analysis of a multidimensional liquid chromatography mass spectrometry dataset acquired on a quadrupole selecting, quadrupole collision cell, time-of-flight mass spectrometer: II. New developments in Protein Prospector allow for reliable and comprehensive automatic analysis of large datasets. Mol Cell Proteomics. 2005 Aug; 4(8):1194-204. PMID: 15937296.
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      200. Chalkley RJ, Baker PR, Hansen KC, Medzihradszky KF, Allen NP, Rexach M, Burlingame AL. Comprehensive analysis of a multidimensional liquid chromatography mass spectrometry dataset acquired on a quadrupole selecting, quadrupole collision cell, time-of-flight mass spectrometer: I. How much of the data is theoretically interpretable by search engines? Mol Cell Proteomics. 2005 Aug; 4(8):1189-93. PMID: 15923566.
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      201. Fukata Y, Tzingounis AV, Trinidad JC, Fukata M, Burlingame AL, Nicoll RA, Bredt DS. Molecular constituents of neuronal AMPA receptors. J Cell Biol. 2005 May 9; 169(3):399-404. PMID: 15883194; PMCID: PMC2171936.
      202. Trester-Zedlitz M, Burlingame A, Kobilka B, von Zastrow M. Mass spectrometric analysis of agonist effects on posttranslational modifications of the beta-2 adrenoceptor in mammalian cells. Biochemistry. 2005 Apr 26; 44(16):6133-43. PMID: 15835901.
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      203. Tanaka M, Bateman R, Rauh D, Vaisberg E, Ramachandani S, Zhang C, Hansen KC, Burlingame AL, Trautman JK, Shokat KM, Adams CL. An unbiased cell morphology-based screen for new, biologically active small molecules. PLoS Biol. 2005 May; 3(5):e128. PMID: 15799708; PMCID: PMC1073692.
      204. Bradshaw RA, Burlingame AL. From proteins to proteomics. IUBMB Life. 2005 Apr-May; 57(4-5):267-72. PMID: 16036609.
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      205. Trinidad JC, Thalhammer A, Specht CG, Schoepfer R, Burlingame AL. Phosphorylation state of postsynaptic density proteins. J Neurochem. 2005 Mar; 92(6):1306-16. PMID: 15748150.
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      206. Vosseller K, Hansen KC, Chalkley RJ, Trinidad JC, Wells L, Hart GW, Burlingame AL. Quantitative analysis of both protein expression and serine / threonine post-translational modifications through stable isotope labeling with dithiothreitol. Proteomics. 2005 Feb; 5(2):388-98. PMID: 15648052.
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      207. Huang L, Burlingame AL. Comprehensive mass spectrometric analysis of the 20S proteasome complex. Methods Enzymol. 2005; 405:187-236. PMID: 16413316.
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      208. Cutillas PR, Biber J, Marks J, Jacob R, Stieger B, Cramer R, Waterfield M, Burlingame AL, Unwin RJ. Proteomic analysis of plasma membrane vesicles isolated from the rat renal cortex. Proteomics. 2005 Jan; 5(1):101-12. PMID: 15593129.
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      209. Smith-Beckerman DM, Fung KW, Williams KE, Auersperg N, Godwin AK, Burlingame AL. Proteome changes in ovarian epithelial cells derived from women with BRCA1 mutations and family histories of cancer. Mol Cell Proteomics. 2005 Feb; 4(2):156-68. PMID: 15591324.
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      210. Chu F, Shan SO, Moustakas DT, Alber F, Egea PF, Stroud RM, Walter P, Burlingame AL. Unraveling the interface of signal recognition particle and its receptor by using chemical cross-linking and tandem mass spectrometry. Proc Natl Acad Sci U S A. 2004 Nov 23; 101(47):16454-9. PMID: 15546976; PMCID: PMC528904.
      211. Baldwin MA, Burlingame AL, Nikolaev E. Victor L. Talroze: 1922-2004. J Am Soc Mass Spectrom. 2004 Oct; 15(10):1517-9. PMID: 27518148.
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      212. Vergés M, Luton F, Gruber C, Tiemann F, Reinders LG, Huang L, Burlingame AL, Haft CR, Mostov KE. The mammalian retromer regulates transcytosis of the polymeric immunoglobulin receptor. Nat Cell Biol. 2004 Aug; 6(8):763-9. PMID: 15247922.
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      213. Hirsch J, Hansen KC, Burlingame AL, Matthay MA. Proteomics: current techniques and potential applications to lung disease. Am J Physiol Lung Cell Mol Physiol. 2004 Jul; 287(1):L1-23. PMID: 15187006.
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      214. Medzihradszky KF, Zhang X, Chalkley RJ, Guan S, McFarland MA, Chalmers MJ, Marshall AG, Diaz RL, Allis CD, Burlingame AL. Characterization of Tetrahymena histone H2B variants and posttranslational populations by electron capture dissociation (ECD) Fourier transform ion cyclotron mass spectrometry (FT-ICR MS). Mol Cell Proteomics. 2004 Sep; 3(9):872-86. PMID: 15199121.
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      215. Cutillas P, Burlingame A, Unwin R. Proteomic strategies and their application in studies of renal function. News Physiol Sci. 2004 Jun; 19:114-9. PMID: 15143205.
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      216. Cutillas PR, Chalkley RJ, Hansen KC, Cramer R, Norden AG, Waterfield MD, Burlingame AL, Unwin RJ. The urinary proteome in Fanconi syndrome implies specificity in the reabsorption of proteins by renal proximal tubule cells. Am J Physiol Renal Physiol. 2004 Sep; 287(3):F353-64. PMID: 15140760.
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      217. Oda Y, Sihlbom C, Chalkley RJ, Huang L, Rachez C, Chang CP, Burlingame AL, Freedman LP, Bikle DD. Two distinct coactivators, DRIP/mediator and SRC/p160, are differentially involved in VDR transactivation during keratinocyte differentiation. J Steroid Biochem Mol Biol. 2004 May; 89-90(1-5):273-6. PMID: 15225784.
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      218. Jiménez CR, ter Maat A, Pieneman A, Burlingame AL, Smit AB, Li KW. Spatio-temporal dynamics of the egg-laying-inducing peptides during an egg-laying cycle: a semiquantitative matrix-assisted laser desorption/ionization mass spectrometry approach. J Neurochem. 2004 May; 89(4):865-75. PMID: 15140186.
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      219. Carr S, Aebersold R, Baldwin M, Burlingame A, Clauser K, Nesvizhskii A. The need for guidelines in publication of peptide and protein identification data: Working Group on Publication Guidelines for Peptide and Protein Identification Data. Mol Cell Proteomics. 2004 Jun; 3(6):531-3. PMID: 15075378.
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      220. Perlson E, Medzihradszky KF, Darula Z, Munno DW, Syed NI, Burlingame AL, Fainzilber M. Differential proteomics reveals multiple components in retrogradely transported axoplasm after nerve injury. Mol Cell Proteomics. 2004 May; 3(5):510-20. PMID: 14973157.
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      221. Perlson E, Hanz S, Medzihradszky KF, Burlingame AL, Fainzilber M. From snails to sciatic nerve: Retrograde injury signaling from axon to soma in lesioned neurons. J Neurobiol. 2004 Feb 5; 58(2):287-94. PMID: 14704959.
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      222. Medzihradszky KF, Darula Z, Perlson E, Fainzilber M, Chalkley RJ, Ball H, Greenbaum D, Bogyo M, Tyson DR, Bradshaw RA, Burlingame AL. O-sulfonation of serine and threonine: mass spectrometric detection and characterization of a new posttranslational modification in diverse proteins throughout the eukaryotes. Mol Cell Proteomics. 2004 May; 3(5):429-40. PMID: 14752058.
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      223. Cutillas PR, Norden AG, Cramer R, Burlingame AL, Unwin RJ. Urinary proteomics of renal Fanconi syndrome. Contrib Nephrol. 2004; 141:155-69. PMID: 14650231.
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      224. Wignall SM, Gray NS, Chang YT, Juarez L, Jacob R, Burlingame A, Schultz PG, Heald R. Identification of a novel protein regulating microtubule stability through a chemical approach. Chem Biol. 2004 Jan; 11(1):135-46. PMID: 15113003.
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      225. Ishida BY, Bailey KR, Duncan KG, Chalkley RJ, Burlingame AL, Kane JP, Schwartz DM. Regulated expression of apolipoprotein E by human retinal pigment epithelial cells. J Lipid Res. 2004 Feb; 45(2):263-71. PMID: 14594998.
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      226. Oda Y, Sihlbom C, Chalkley RJ, Huang L, Rachez C, Chang CP, Burlingame AL, Freedman LP, Bikle DD. Two distinct coactivators, DRIP/mediator and SRC/p160, are differentially involved in vitamin D receptor transactivation during keratinocyte differentiation. Mol Endocrinol. 2003 Nov; 17(11):2329-39. PMID: 12893881.
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      227. Burlingame AL. Toward deciphering the knowledge encrypted in large datasets. Mol Cell Proteomics. 2003 Jul; 2(7):425. PMID: 12930872.
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      228. Hansen KC, Schmitt-Ulms G, Chalkley RJ, Hirsch J, Baldwin MA, Burlingame AL. Mass spectrometric analysis of protein mixtures at low levels using cleavable 13C-isotope-coded affinity tag and multidimensional chromatography. Mol Cell Proteomics. 2003 May; 2(5):299-314. PMID: 12766231.
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      229. Cutillas PR, Norden AG, Cramer R, Burlingame AL, Unwin RJ. Detection and analysis of urinary peptides by on-line liquid chromatography and mass spectrometry: application to patients with renal Fanconi syndrome. Clin Sci (Lond). 2003 May; 104(5):483-90. PMID: 12529166.
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      230. Kotite L, Zhang LH, Yu Z, Burlingame AL, Havel RJ. Human apoC-IV: isolation, characterization, and immunochemical quantification in plasma and plasma lipoproteins. J Lipid Res. 2003 Jul; 44(7):1387-94. PMID: 12700345.
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      231. Chalkley RJ, Burlingame AL. Identification of novel sites of O-N-acetylglucosamine modification of serum response factor using quadrupole time-of-flight mass spectrometry. Mol Cell Proteomics. 2003 Mar; 2(3):182-90. PMID: 12684542.
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      232. Allen NP, Patel SS, Huang L, Chalkley RJ, Burlingame A, Lutzmann M, Hurt EC, Rexach M. Deciphering networks of protein interactions at the nuclear pore complex. Mol Cell Proteomics. 2002 Dec; 1(12):930-46. PMID: 12543930.
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      233. Williams KE, Carver TA, Miranda JJ, Kautiainen A, Vogel JS, Dingley K, Baldwin MA, Turteltaub KW, Burlingame AL. Attomole detection of in vivo protein targets of benzene in mice: evidence for a highly reactive metabolite. Mol Cell Proteomics. 2002 Nov; 1(11):885-95. PMID: 12488464.
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      234. Hart SR, Waterfield MD, Burlingame AL, Cramer R. Factors governing the solubilization of phosphopeptides retained on ferric NTA IMAC beads and their analysis by MALDI TOFMS. J Am Soc Mass Spectrom. 2002 Sep; 13(9):1042-51. PMID: 12322952.
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      235. Zhang K, Tang H, Huang L, Blankenship JW, Jones PR, Xiang F, Yau PM, Burlingame AL. Identification of acetylation and methylation sites of histone H3 from chicken erythrocytes by high-accuracy matrix-assisted laser desorption ionization-time-of-flight, matrix-assisted laser desorption ionization-postsource decay, and nanoelectrospray ionization tandem mass spectrometry. Anal Biochem. 2002 Jul 15; 306(2):259-69. PMID: 12123664.
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      236. Zhang K, Williams KE, Huang L, Yau P, Siino JS, Bradbury EM, Jones PR, Minch MJ, Burlingame AL. Histone acetylation and deacetylation: identification of acetylation and methylation sites of HeLa histone H4 by mass spectrometry. Mol Cell Proteomics. 2002 Jul; 1(7):500-8. PMID: 12239278.
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      237. Zanata SM, Lopes MH, Mercadante AF, Hajj GN, Chiarini LB, Nomizo R, Freitas AR, Cabral AL, Lee KS, Juliano MA, de Oliveira E, Jachieri SG, Burlingame A, Huang L, Linden R, Brentani RR, Martins VR. Stress-inducible protein 1 is a cell surface ligand for cellular prion that triggers neuroprotection. EMBO J. 2002 Jul 1; 21(13):3307-16. PMID: 12093732; PMCID: PMC125391.
      238. Huang L, Baldwin MA, Maltby DA, Medzihradszky KF, Baker PR, Allen N, Rexach M, Edmondson RD, Campbell J, Juhasz P, Martin SA, Vestal ML, Burlingame AL. The identification of protein-protein interactions of the nuclear pore complex of Saccharomyces cerevisiae using high throughput matrix-assisted laser desorption ionization time-of-flight tandem mass spectrometry. Mol Cell Proteomics. 2002 Jun; 1(6):434-50. PMID: 12169684.
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      239. Michels J, Geyer A, Mocanu V, Welte W, Burlingame AL, Przybylski M. Structure and functional characterization of the periplasmic N-terminal polypeptide domain of the sugar-specific ion channel protein (ScrY porin). Protein Sci. 2002 Jun; 11(6):1565-74. PMID: 12021455; PMCID: PMC2373611.
      240. Hawkes DB, Adams GW, Burlingame AL, Ortiz de Montellano PR, De Voss JJ. Cytochrome P450(cin) (CYP176A), isolation, expression, and characterization. J Biol Chem. 2002 Aug 2; 277(31):27725-32. PMID: 12016226.
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      241. Benvenuti S, Cramer R, Quinn CC, Bruce J, Zvelebil M, Corless S, Bond J, Yang A, Hockfield S, Burlingame AL, Waterfield MD, Jat PS. Differential proteome analysis of replicative senescence in rat embryo fibroblasts. Mol Cell Proteomics. 2002 Apr; 1(4):280-92. PMID: 12096110.
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      242. Liu B, Huang L, Sihlbom C, Burlingame A, Marks JD. Towards proteome-wide production of monoclonal antibody by phage display. J Mol Biol. 2002 Feb 1; 315(5):1063-73. PMID: 11827476.
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      243. Greenbaum D, Baruch A, Hayrapetian L, Darula Z, Burlingame A, Medzihradszky KF, Bogyo M. Chemical approaches for functionally probing the proteome. Mol Cell Proteomics. 2002 Jan; 1(1):60-8. PMID: 12096141.
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      244. Chalkley RJ, Burlingame AL. Identification of GlcNAcylation sites of peptides and alpha-crystallin using Q-TOF mass spectrometry. J Am Soc Mass Spectrom. 2001 Oct; 12(10):1106-13. PMID: 11605972.
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      245. Person MD, Brown KC, Mahrus S, Craik CS, Burlingame AL. Novel inter-protein cross-link identified in the GGH-ecotin D137Y dimer. Protein Sci. 2001 Aug; 10(8):1549-62. PMID: 11468352; PMCID: PMC2374083.
      246. Allen NP, Huang L, Burlingame A, Rexach M. Proteomic analysis of nucleoporin interacting proteins. J Biol Chem. 2001 Aug 3; 276(31):29268-74. PMID: 11387327.
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      247. Jiménez CR, Huang L, Qiu Y, Burlingame AL. Sample preparation for MALDI mass analysis of peptides and proteins. Curr Protoc Protein Sci. 2001 May; Chapter 16:Unit 16.3. PMID: 18429130.
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      248. Jiménez CR, Huang L, Qiu Y, Burlingame AL. In-gel digestion of proteins for MALDI-MS fingerprint mapping. Curr Protoc Protein Sci. 2001 May; Chapter 16:Unit 16.4. PMID: 18429131.
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      249. Jiménez CR, Huang L, Qiu Y, Burlingame AL. Searching sequence databases over the internet: protein identification using MS-Fit. Curr Protoc Protein Sci. 2001 May; Chapter 16:Unit 16.5. PMID: 18429132.
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      250. Jiménez CR, Huang L, Qiu Y, Burlingame AL. Searching sequence databases over the internet: protein identification using MS-tag. Curr Protoc Protein Sci. 2001 May; Chapter 16:Unit 16.6. PMID: 18429133.
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      251. Jiménez CR, Huang L, Qiu Y, Burlingame AL. Enzymatic approaches for obtaining amino acid sequence: on-target ladder sequencing. Curr Protoc Protein Sci. 2001 May; Chapter 16:Unit 16.7. PMID: 18429134.
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      252. Huang L, Jacob RJ, Pegg SC, Baldwin MA, Wang CC, Burlingame AL, Babbitt PC. Functional assignment of the 20 S proteasome from Trypanosoma brucei using mass spectrometry and new bioinformatics approaches. J Biol Chem. 2001 Jul 27; 276(30):28327-39. PMID: 11309374.
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      253. Baldwin MA, Medzihradszky KF, Lock CM, Fisher B, Settineri TA, Burlingame AL. Matrix-assisted laser desorption/ionization coupled with quadrupole/orthogonal acceleration time-of-flight mass spectrometry for protein discovery, identification, and structural analysis. Anal Chem. 2001 Apr 15; 73(8):1707-20. PMID: 11338583.
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      254. Hoang VM, Foulk R, Clauser K, Burlingame A, Gibson BW, Fisher SJ. Functional proteomics: examining the effects of hypoxia on the cytotrophoblast protein repertoire. Biochemistry. 2001 Apr 3; 40(13):4077-86. PMID: 11300788.
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      255. Polson AG, Huang L, Lukac DM, Blethrow JD, Morgan DO, Burlingame AL, Ganem D. Kaposi's sarcoma-associated herpesvirus K-bZIP protein is phosphorylated by cyclin-dependent kinases. J Virol. 2001 Apr; 75(7):3175-84. PMID: 11238844; PMCID: PMC114111.
      256. Habelhah H, Shah K, Huang L, Burlingame AL, Shokat KM, Ronai Z. Identification of new JNK substrate using ATP pocket mutant JNK and a corresponding ATP analogue. J Biol Chem. 2001 May 25; 276(21):18090-5. PMID: 11259409.
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      257. Habelhah H, Shah K, Huang L, Ostareck-Lederer A, Burlingame AL, Shokat KM, Hentze MW, Ronai Z. ERK phosphorylation drives cytoplasmic accumulation of hnRNP-K and inhibition of mRNA translation. Nat Cell Biol. 2001 Mar; 3(3):325-30. PMID: 11231586.
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      258. Medzihradszky KF, Leffler H, Baldwin MA, Burlingame AL. Protein identification by in-gel digestion, high-performance liquid chromatography, and mass spectrometry: peptide analysis by complementary ionization techniques. J Am Soc Mass Spectrom. 2001 Feb; 12(2):215-21. PMID: 11212006.
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      259. Qiu Y, Benet LZ, Burlingame AL. Identification of hepatic protein targets of the reactive metabolites of the non-hepatotoxic regioisomer of acetaminophen, 3'-hydroxyacetanilide, in the mouse in vivo using two-dimensional gel electrophoresis and mass spectrometry. Adv Exp Med Biol. 2001; 500:663-73. PMID: 11765013.
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      260. Greenbaum D, Medzihradszky KF, Burlingame A, Bogyo M. Epoxide electrophiles as activity-dependent cysteine protease profiling and discovery tools. Chem Biol. 2000 Aug; 7(8):569-81. PMID: 11048948.
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      261. Whittal RM, Benz CC, Scott G, Semyonov J, Burlingame AL, Baldwin MA. Preferential oxidation of zinc finger 2 in estrogen receptor DNA-binding domain prevents dimerization and, hence, DNA binding. Biochemistry. 2000 Jul 25; 39(29):8406-17. PMID: 10913246.
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      262. Williamson TL, Corson LB, Huang L, Burlingame A, Liu J, Bruijn LI, Cleveland DW. Toxicity of ALS-linked SOD1 mutants. Science. 2000 Apr 21; 288(5465):399. PMID: 10798964.
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      263. Laiko VV, Baldwin MA, Burlingame AL. Atmospheric pressure matrix-assisted laser desorption/ionization mass spectrometry. Anal Chem. 2000 Feb 15; 72(4):652-7. PMID: 10701247.
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      264. Whittal RM, Ball HL, Cohen FE, Burlingame AL, Prusiner SB, Baldwin MA. Copper binding to octarepeat peptides of the prion protein monitored by mass spectrometry. Protein Sci. 2000 Feb; 9(2):332-43. PMID: 10716185; PMCID: PMC2144551.
      265. Medzihradszky KF, Campbell JM, Baldwin MA, Falick AM, Juhasz P, Vestal ML, Burlingame AL. The characteristics of peptide collision-induced dissociation using a high-performance MALDI-TOF/TOF tandem mass spectrometer. Anal Chem. 2000 Feb 1; 72(3):552-8. PMID: 10695141.
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      266. Chang WW, Huang L, Shen M, Webster C, Burlingame AL, Roberts JK. Patterns of protein synthesis and tolerance of anoxia in root tips of maize seedlings acclimated to a low-oxygen environment, and identification of proteins by mass spectrometry. Plant Physiol. 2000 Feb; 122(2):295-318. PMID: 10677424; PMCID: PMC58868.
      267. Cramer R, Burlingame AL. Employing target modifications for the investigation of liquid infrared matrix-assisted laser desorption/ionization mass spectrometry. Rapid Commun Mass Spectrom. 2000; 14(2):53-60. PMID: 10623929.
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      268. Yao Y, Toth CR, Huang L, Wong ML, Dias P, Burlingame AL, Coffino P, Wang CC. alpha5 subunit in Trypanosoma brucei proteasome can self-assemble to form a cylinder of four stacked heptamer rings. Biochem J. 1999 Dec 1; 344 Pt 2:349-58. PMID: 10567215; PMCID: PMC1220650.
      269. Yao Y, Huang L, Krutchinsky A, Wong ML, Standing KG, Burlingame AL, Wang CC. Structural and functional characterizations of the proteasome-activating protein PA26 from Trypanosoma brucei. J Biol Chem. 1999 Nov 26; 274(48):33921-30. PMID: 10567354.
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      270. Bossi A, Patel MJ, Webb EJ, Baldwin MA, Jacob RJ, Burlingame AL, Righetti PG. Analysis of cross-linked human hemoglobin by conventional isoelectric focusing, immobilized pH gradients, capillary electrophoresis, and mass spectrometry. Electrophoresis. 1999 Oct; 20(14):2810-7. PMID: 10546811.
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      271. Huang L, Shen M, Chernushevich I, Burlingame AL, Wang CC, Robertson CD. Identification and isolation of three proteasome subunits and their encoding genes from Trypanosoma brucei. Mol Biochem Parasitol. 1999 Aug 20; 102(2):211-23. PMID: 10498178.
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      272. Clauser KR, Baker P, Burlingame AL. Role of accurate mass measurement (+/- 10 ppm) in protein identification strategies employing MS or MS/MS and database searching. Anal Chem. 1999 Jul 15; 71(14):2871-82. PMID: 10424174.
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      273. Stimson E, Hope J, Chong A, Burlingame AL. Site-specific characterization of the N-linked glycans of murine prion protein by high-performance liquid chromatography/electrospray mass spectrometry and exoglycosidase digestions. Biochemistry. 1999 Apr 13; 38(15):4885-95. PMID: 10200178.
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      274. Wolfender JL, Chu F, Ball H, Wolfender F, Fainzilber M, Baldwin MA, Burlingame AL. Identification of tyrosine sulfation in Conus pennaceus conotoxins alpha-PnIA and alpha-PnIB: further investigation of labile sulfo- and phosphopeptides by electrospray, matrix-assisted laser desorption/ionization (MALDI) and atmospheric pressure MALDI mass spectrometry. J Mass Spectrom. 1999 Apr; 34(4):447-54. PMID: 10226369.
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      275. Swanson KD, Taylor LK, Haung L, Burlingame AL, Landreth GE. Transcription factor phosphorylation by pp90(rsk2). Identification of Fos kinase and NGFI-B kinase I as pp90(rsk2). J Biol Chem. 1999 Feb 5; 274(6):3385-95. PMID: 9920881.
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      276. Talrose VL, Person MD, Whittal RM, Walls FC, Burlingame AL, Baldwin MA. Insight into absorption of radiation/energy transfer in infrared matrix-assisted laser desorption/ionization: the roles of matrices, water and metal substrates. Rapid Commun Mass Spectrom. 1999; 13(21):2191-8. PMID: 10523780.
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      277. Cramer R, Richter WJ, Stimson E, Burlingame AL. Analysis of phospho- and glycopolypeptides with infrared matrix-assisted laser desorption and ionization. Anal Chem. 1998 Dec 1; 70(23):4939-44. PMID: 9852779.
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      278. Jiménez CR, Burlingame AL. Ultramicroanalysis of peptide profiles in biological samples using MALDI mass spectrometry. Exp Nephrol. 1998 Sep-Oct; 6(5):421-8. PMID: 9730658.
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      279. Burlingame AL, Boyd RK, Gaskell SJ. Mass spectrometry. Anal Chem. 1998 Aug 15; 70(16):647R-716R. PMID: 9726172.
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      280. Qiu Y, Benet LZ, Burlingame AL. Identification of the hepatic protein targets of reactive metabolites of acetaminophen in vivo in mice using two-dimensional gel electrophoresis and mass spectrometry. J Biol Chem. 1998 Jul 10; 273(28):17940-53. PMID: 9651401.
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      281. Prakobphol A, Thomsson KA, Hansson GC, Rosen SD, Singer MS, Phillips NJ, Medzihradszky KF, Burlingame AL, Leffler H, Fisher SJ. Human low-molecular-weight salivary mucin expresses the sialyl lewisx determinant and has L-selectin ligand activity. Biochemistry. 1998 Apr 7; 37(14):4916-27. PMID: 9538010.
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      282. Brown KC, Yu Z, Burlingame AL, Craik CS. Determining protein-protein interactions by oxidative cross-linking of a glycine-glycine-histidine fusion protein. Biochemistry. 1998 Mar 31; 37(13):4397-406. PMID: 9521759.
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      283. Qiu Y, Burlingame AL, Benet LZ. Mechanisms for covalent binding of benoxaprofen glucuronide to human serum albumin. Studies By tandem mass spectrometry. Drug Metab Dispos. 1998 Mar; 26(3):246-56. PMID: 9492388.
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      284. Jiménez CR, Li KW, Dreisewerd K, Spijker S, Kingston R, Bateman RH, Burlingame AL, Smit AB, van Minnen J, Geraerts WP. Direct mass spectrometric peptide profiling and sequencing of single neurons reveals differential peptide patterns in a small neuronal network. Biochemistry. 1998 Feb 17; 37(7):2070-6. PMID: 9485334.
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      285. Fainzilber M, Nakamura T, Lodder JC, Zlotkin E, Kits KS, Burlingame AL. gamma-Conotoxin-PnVIIA, a gamma-carboxyglutamate-containing peptide agonist of neuronal pacemaker cation currents. Biochemistry. 1998 Feb 10; 37(6):1470-7. PMID: 9484216.
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      286. Medzihradszky KF, Besman MJ, Burlingame AL. Reverse-phase capillary high performance liquid chromatography/high performance electrospray ionization mass spectrometry: an essential tool for the characterization of complex glycoprotein digests. Rapid Commun Mass Spectrom. 1998; 12(8):472-8. PMID: 9586235.
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      287. Grogan A, Reeves E, Keep N, Wientjes F, Totty NF, Burlingame AL, Hsuan JJ, Segal AW. Cytosolic phox proteins interact with and regulate the assembly of coronin in neutrophils. J Cell Sci. 1997 Dec; 110 ( Pt 24):3071-81. PMID: 9365277.
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      288. Yu Z, Friso G, Miranda JJ, Patel MJ, Lo-Tseng T, Moore EG, Burlingame AL. Structural characterization of human hemoglobin crosslinked by bis(3,5-dibromosalicyl) fumarate using mass spectrometric techniques. Protein Sci. 1997 Dec; 6(12):2568-77. PMID: 9416606; PMCID: PMC2143614.
      289. Machesky LM, Reeves E, Wientjes F, Mattheyse FJ, Grogan A, Totty NF, Burlingame AL, Hsuan JJ, Segal AW. Mammalian actin-related protein 2/3 complex localizes to regions of lamellipodial protrusion and is composed of evolutionarily conserved proteins. Biochem J. 1997 Nov 15; 328 ( Pt 1):105-12. PMID: 9359840; PMCID: PMC1218893.
      290. Caldera PS, Yu Z, Knegtel RM, McPhee F, Burlingame AL, Craik CS, Kuntz ID, Ortiz de Montellano PR. Alkylation of a catalytic aspartate group of the SIV protease by an epoxide inhibitor. Bioorg Med Chem. 1997 Nov; 5(11):2019-27. PMID: 9416419.
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      291. Medzihradszky KF, Besman MJ, Burlingame AL. Structural characterization of site-specific N-glycosylation of recombinant human factor VIII by reversed-phase high-performance liquid chromatography-electrospray ionization mass spectrometry. Anal Chem. 1997 Oct 1; 69(19):3986-94. PMID: 9322435.
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      292. Talwar N, Pilz RB, Yu Z, Burlingame A, Boss GR. A low molecular weight substance purified from human placenta inhibits cAMP-dependent protein kinase and activates protein kinase C. Mol Cell Biochem. 1997 May; 170(1-2):75-83. PMID: 9144320.
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      293. Sullivan CM, Smith DM, Matsui NM, Andrews LE, Clauser KR, Chapeaurouge A, Burlingame AL, Epstein LB. Identification of constitutive and gamma-interferon- and interleukin 4-regulated proteins in the human renal carcinoma cell line ACHN. Cancer Res. 1997 Mar 15; 57(6):1137-43. PMID: 9067284.
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      294. Matsui NM, Smith DM, Clauser KR, Fichmann J, Andrews LE, Sullivan CM, Burlingame AL, Epstein LB. Immobilized pH gradient two-dimensional gel electrophoresis and mass spectrometric identification of cytokine-regulated proteins in ME-180 cervical carcinoma cells. Electrophoresis. 1997 Mar-Apr; 18(3-4):409-17. PMID: 9150919.
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      295. Epstein LB, Smith DM, Matsui NM, Tran HM, Sullivan C, Raineri I, Burlingame AL, Clauser KR, Hall SC, Andrews LE. Identification of cytokine-regulated proteins in normal and malignant cells by the combination of two-dimensional polyacrylamide gel electrophoresis, mass spectrometry, Edman degradation and immunoblotting and approaches to the analysis of their functional roles. Electrophoresis. 1996 Nov; 17(11):1655-70. PMID: 8982598.
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      296. Yates JR, Eng JK, Clauser KR, Burlingame AL. Search of sequence databases with uninterpreted high-energy collision-induced dissociation spectra of peptides. J Am Soc Mass Spectrom. 1996 Nov; 7(11):1089-98. PMID: 24203070.
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      297. Wang SX, Mure M, Medzihradszky KF, Burlingame AL, Brown DE, Dooley DM, Smith AJ, Kagan HM, Klinman JP. A crosslinked cofactor in lysyl oxidase: redox function for amino acid side chains. Science. 1996 Aug 23; 273(5278):1078-84. PMID: 8688089.
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      298. Fainzilber M, Lodder JC, van der Schors RC, Li KW, Yu Z, Burlingame AL, Geraerts WP, Kits KS. A novel hydrophobic omega-conotoxin blocks molluscan dihydropyridine-sensitive calcium channels. Biochemistry. 1996 Jul 2; 35(26):8748-52. PMID: 8679638.
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      299. Burlingame AL, Boyd RK, Gaskell SJ. Mass spectrometry. Anal Chem. 1996 Jun 15; 68(12):599R-651R. PMID: 8686922.
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      300. Buckley N, Maltby D, Burlingame AL, Oppenheimer NJ. Reactions of Charged Substrates. 4. The Gas-Phase Dissociation of (4-Substituted benzyl)dimethylsulfoniums and -pyridiniums. J Org Chem. 1996 Apr 19; 61(8):2753-2762. PMID: 11667109.
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      301. Nakamura T, Yu Z, Fainzilber M, Burlingame AL. Mass spectrometric-based revision of the structure of a cysteine-rich peptide toxin with gamma-carboxyglutamic acid, TxVIIA, from the sea snail, Conus textile. Protein Sci. 1996 Mar; 5(3):524-30. PMID: 8868490; PMCID: PMC2143357.
      302. Burlingame AL. Characterization of protein glycosylation by mass spectrometry. Curr Opin Biotechnol. 1996 Feb; 7(1):4-10. PMID: 8742373.
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      303. Lipniunas PH, Townsend RR, Burlingame AL, Hindsgaul O. High-energy collision-induced dissociation mass spectrometry of synthetic mannose-6-phosphate oligosaccharides. J Am Soc Mass Spectrom. 1996 Feb; 7(2):182-8. PMID: 24203240.
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      304. Medzihradszky KF, Adams GW, Burlingame AL, Bateman RH, Green MR. Peptide sequence determination by matrix-assisted laser desorption ionization employing a tandem double focusing magnetic-Orthogonal acceleration time-of-flight mass spectrometer. J Am Soc Mass Spectrom. 1996 Jan; 7(1):1-10. PMID: 24202789.
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      305. Settineri CA, Burlingame AL. Structural characterization of protein glycosylation using HPLC/electrospray ionization mass spectrometry and glycosidase digestion. Methods Mol Biol. 1996; 61:255-78. PMID: 8930879.
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      306. Tsutakawa SE, Medzihradszky KF, Flint AJ, Burlingame AL, Koshland DE. Determination of in vivo phosphorylation sites in protein kinase C. J Biol Chem. 1995 Nov 10; 270(45):26807-12. PMID: 7592921.
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      307. Iwahara S, Satoh H, Song DX, Webb J, Burlingame AL, Nagae Y, Muller-Eberhard U. Purification, characterization, and cloning of a heme-binding protein (23 kDa) in rat liver cytosol. Biochemistry. 1995 Oct 17; 34(41):13398-406. PMID: 7577926.
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      308. Zia-Amirhosseini P, Ding A, Burlingame AL, McDonagh AF, Benet LZ. Synthesis and mass-spectrometric characterization of human serum albumins modified by covalent binding of two non-steroidal anti-inflammatory drugs: tolmetin and zomepirac. Biochem J. 1995 Oct 15; 311 ( Pt 2):431-5. PMID: 7487878; PMCID: PMC1136018.
      309. Pongracz K, Pathak DN, Nakamura T, Burlingame AL, Bodell WJ. Activation of the tamoxifen derivative metabolite E to form DNA adducts: comparison with the adducts formed by microsomal activation of tamoxifen. Cancer Res. 1995 Jul 15; 55(14):3012-5. PMID: 7606720.
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      310. Fainzilber M, Nakamura T, Gaathon A, Lodder JC, Kits KS, Burlingame AL, Zlotkin E. A new cysteine framework in sodium channel blocking conotoxins. Biochemistry. 1995 Jul 11; 34(27):8649-56. PMID: 7612605.
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      311. Clauser KR, Hall SC, Smith DM, Webb JW, Andrews LE, Tran HM, Epstein LB, Burlingame AL. Rapid mass spectrometric peptide sequencing and mass matching for characterization of human melanoma proteins isolated by two-dimensional PAGE. Proc Natl Acad Sci U S A. 1995 May 23; 92(11):5072-6. PMID: 7761450; PMCID: PMC41850.
      312. Schindler PA, Settineri CA, Collet X, Fielding CJ, Burlingame AL. Site-specific detection and structural characterization of the glycosylation of human plasma proteins lecithin:cholesterol acyltransferase and apolipoprotein D using HPLC/electrospray mass spectrometry and sequential glycosidase digestion. Protein Sci. 1995 Apr; 4(4):791-803. PMID: 7613477; PMCID: PMC2143102.
      313. Ding A, Zia-Amirhosseini P, McDonagh AF, Burlingame AL, Benet LZ. Reactivity of tolmetin glucuronide with human serum albumin. Identification of binding sites and mechanisms of reaction by tandem mass spectrometry. Drug Metab Dispos. 1995 Mar; 23(3):369-76. PMID: 7628303.
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      314. Adams GW, Mayer P, Medzihradszky KF, Burlingame AL. Mass spectrometric studies of the primary sequence and structure of bovine liver and serum amine oxidase. Methods Enzymol. 1995; 258:90-114. PMID: 8524166.
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      315. Robertson JG, Adams GW, Medzihradszky KF, Burlingame AL, Villafranca JJ. Complete assignment of disulfide bonds in bovine dopamine beta-hydroxylase. Biochemistry. 1994 Sep 27; 33(38):11563-75. PMID: 7918370.
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      316. Brown JD, Hann BC, Medzihradszky KF, Niwa M, Burlingame AL, Walter P. Subunits of the Saccharomyces cerevisiae signal recognition particle required for its functional expression. EMBO J. 1994 Sep 15; 13(18):4390-400. PMID: 7925282; PMCID: PMC395366.
      317. Fainzilber M, Hasson A, Oren R, Burlingame AL, Gordon D, Spira ME, Zlotkin E. New mollusc-specific alpha-conotoxins block Aplysia neuronal acetylcholine receptors. Biochemistry. 1994 Aug 16; 33(32):9523-9. PMID: 8068627.
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      318. Burlingame AL, Boyd RK, Gaskell SJ. Mass spectrometry. Anal Chem. 1994 Jun 15; 66(12):634R-683R. PMID: 8092481.
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      319. Medzihradszky KF, Maltby DA, Hall SC, Settineri CA, Burlingame AL. Characterization of protein iv-glycosylation by reversed-phase microbore liquid chromatography / electrospray mass spectrometry, complementary mobile phases, and sequential exoglycosidase digestion. J Am Soc Mass Spectrom. 1994 May; 5(5):350-8. PMID: 24222589.
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      320. Salto R, Babé LM, Li J, Rosé JR, Yu Z, Burlingame A, De Voss JJ, Sui Z, Ortiz de Montellano P, Craik CS. In vitro characterization of nonpeptide irreversible inhibitors of HIV proteases. J Biol Chem. 1994 Apr 8; 269(14):10691-8. PMID: 8144659.
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      321. Mu D, Medzihradszky KF, Adams GW, Mayer P, Hines WM, Burlingame AL, Smith AJ, Cai D, Klinman JP. Primary structures for a mammalian cellular and serum copper amine oxidase. J Biol Chem. 1994 Apr 1; 269(13):9926-32. PMID: 8144587.
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      322. Herrmann J, Turck CW, Atchison RE, Huflejt ME, Poulter L, Gitt MA, Burlingame AL, Barondes SH, Leffler H. Primary structure of the soluble lactose binding lectin L-29 from rat and dog and interaction of its non-collagenous proline-, glycine-, tyrosine-rich sequence with bacterial and tissue collagenase. J Biol Chem. 1993 Dec 15; 268(35):26704-11. PMID: 8253805.
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      323. Mel SF, Falick AM, Burlingame AL, Stroud RM. Mapping a membrane-associated conformation of colicin Ia. Biochemistry. 1993 Sep 14; 32(36):9473-9. PMID: 7690252.
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      324. Ding A, Ojingwa JC, McDonagh AF, Burlingame AL, Benet LZ. Evidence for covalent binding of acyl glucuronides to serum albumin via an imine mechanism as revealed by tandem mass spectrometry. Proc Natl Acad Sci U S A. 1993 May 1; 90(9):3797-801. PMID: 8483897; PMCID: PMC46392.
      325. Oda Y, Herrmann J, Gitt MA, Turck CW, Burlingame AL, Barondes SH, Leffler H. Soluble lactose-binding lectin from rat intestine with two different carbohydrate-binding domains in the same peptide chain. J Biol Chem. 1993 Mar 15; 268(8):5929-39. PMID: 8449956.
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      326. Stahl N, Baldwin MA, Teplow DB, Hood L, Gibson BW, Burlingame AL, Prusiner SB. Structural studies of the scrapie prion protein using mass spectrometry and amino acid sequencing. Biochemistry. 1993 Mar 2; 32(8):1991-2002. PMID: 8448158.
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      327. Hall SC, Smith DM, Masiarz FR, Soo VW, Tran HM, Epstein LB, Burlingame AL. Mass spectrometric and Edman sequencing of lipocortin I isolated by two-dimensional SDS/PAGE of human melanoma lysates. Proc Natl Acad Sci U S A. 1993 Mar 1; 90(5):1927-31. PMID: 8446611; PMCID: PMC45993.
      328. Kaur S, Pongracz K, Bodell WJ, Burlingame AL. Bis(hydroxyphenylethyl)deoxyguanosine adducts identified by [32P]-postlabeling and four-sector tandem mass spectrometry: unanticipated adducts formed upon treatment of DNA with styrene 7,8-oxide. Chem Res Toxicol. 1993 Jan-Feb; 6(1):125-32. PMID: 8448342.
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      329. Wen DX, Livingston BD, Medzihradszky KF, Kelm S, Burlingame AL, Paulson JC. Primary structure of Gal beta 1,3(4)GlcNAc alpha 2,3-sialyltransferase determined by mass spectrometry sequence analysis and molecular cloning. Evidence for a protein motif in the sialyltransferase gene family. J Biol Chem. 1992 Oct 15; 267(29):21011-9. PMID: 1400416.
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      330. Sanders DA, Gillece-Castro BL, Burlingame AL, Koshland DE. Phosphorylation site of NtrC, a protein phosphatase whose covalent intermediate activates transcription. J Bacteriol. 1992 Aug; 174(15):5117-22. PMID: 1321122; PMCID: PMC206329.
      331. Burlingame AL, Baillie TA, Russell DH. Mass spectrometry. Anal Chem. 1992 Jun 15; 64(12):467R-502R. PMID: 1626707.
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      332. Stahl N, Baldwin MA, Hecker R, Pan KM, Burlingame AL, Prusiner SB. Glycosylinositol phospholipid anchors of the scrapie and cellular prion proteins contain sialic acid. Biochemistry. 1992 Jun 2; 31(21):5043-53. PMID: 1350920.
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      333. Hines WM, Falick AM, Burlingame AL, Gibson BW. Pattern-based algorithm for peptide sequencing from tandem high energy collision-induced dissociation mass spectra. J Am Soc Mass Spectrom. 1992 May; 3(4):326-36. PMID: 24243043.
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      334. Pongracz K, Kaur S, Burlingame AL, Bodell WJ. Identification of N2-substituted 2'-deoxyguanosine-3'-phosphate adducts detected by 32P-postlabeling of styrene-oxide-treated DNA. Carcinogenesis. 1992 Mar; 13(3):315-9. PMID: 1547518.
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      335. Buechter DD, Medzihradszky KF, Burlingame AL, Kenyon GL. The active site of creatine kinase. Affinity labeling of cysteine 282 with N-(2,3-epoxypropyl)-N-amidinoglycine. J Biol Chem. 1992 Feb 5; 267(4):2173-8. PMID: 1733925.
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      336. Medzihradszky KF, Gibson BW, Kaur S, Yu ZH, Medzihradszky D, Burlingame AL, Bass NM. The primary structure of fatty-acid-binding protein from nurse shark liver. Structural and evolutionary relationship to the mammalian fatty-acid-binding protein family. Eur J Biochem. 1992 Feb 1; 203(3):327-39. PMID: 1735421.
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      337. Gillece-Castro BL, Prakobphol A, Burlingame AL, Leffler H, Fisher SJ. Structure and bacterial receptor activity of a human salivary proline-rich glycoprotein. J Biol Chem. 1991 Sep 15; 266(26):17358-68. PMID: 1894623.
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      338. Poulter L, Karrer R, Burlingame AL. n-Alkyl p-aminobenzoates as derivatizing agents in the isolation, separation, and characterization of submicrogram quantities of oligosaccharides by liquid secondary ion mass spectrometry. Anal Biochem. 1991 May 15; 195(1):1-13. PMID: 1888004.
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      339. Kaur S, Hall SC, Burlingame AL. Strategies for identification of covalent xenobiotic modifications in proteins by mass spectrometry. Prog Clin Biol Res. 1991; 372:107-17. PMID: 1956909.
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      340. Medzihradszky KF, Gillece-Castro BL, Settineri CA, Townsend RR, Masiarz FR, Burlingame AL. Structure determination of O-linked glycopeptides by tandem mass spectrometry. Biomed Environ Mass Spectrom. 1990 Dec 5; 19(12):777-81. PMID: 1708302.
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      341. Baldwin MA, Stahl N, Reinders LG, Gibson BW, Prusiner SB, Burlingame AL. Permethylation and tandem mass spectrometry of oligosaccharides having free hexosamine: analysis of the glycoinositol phospholipid anchor glycan from the scrapie prion protein. Anal Biochem. 1990 Nov 15; 191(1):174-82. PMID: 1981823.
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      342. Settineri CA, Medzihradszky KF, Masiarz FR, Burlingame AL, Chu C, George-Nascimento C. Characterization of O-glycosylation sites in recombinant B-chain of platelet-derived growth factor expressed in yeast using liquid secondary ion mass spectrometry, tandem mass spectrometry and Edman sequence analysis. Biomed Environ Mass Spectrom. 1990 Nov; 19(11):665-76. PMID: 2076465.
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      343. Stahl N, Baldwin MA, Burlingame AL, Prusiner SB. Identification of glycoinositol phospholipid linked and truncated forms of the scrapie prion protein. Biochemistry. 1990 Sep 25; 29(38):8879-84. PMID: 1980209.
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      344. Pongracz K, Kaur S, Burlingame AL, Bodell WJ. Detection of (3'-hydroxy)-3,N4-benzetheno-2'-deoxycytidine-3'-phosphate by 32P-postlabeling of DNA reacted with p-benzoquinone. Carcinogenesis. 1990 Sep; 11(9):1469-72. PMID: 2205405.
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      345. Burlingame AL, Millington DS, Norwood DL, Russell DH. Mass spectrometry. Anal Chem. 1990 Jun 15; 62(12):268R-303R. PMID: 2196833.
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      346. Janes SM, Mu D, Wemmer D, Smith AJ, Kaur S, Maltby D, Burlingame AL, Klinman JP. A new redox cofactor in eukaryotic enzymes: 6-hydroxydopa at the active site of bovine serum amine oxidase. Science. 1990 May 25; 248(4958):981-7. PMID: 2111581.
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      347. Gillece-Castro BL, Burlingame AL. Oligosaccharide characterization with high-energy collision-induced dissociation mass spectrometry. Methods Enzymol. 1990; 193:689-712. PMID: 2074842.
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      348. Bodell WJ, Pongracz K, Kaur S, Burlingame AL, Liu SF, Rappaport SM. Investigation of styrene oxide-DNA adducts and their detection in workers exposed to styrene. Prog Clin Biol Res. 1990; 340C:271-82. PMID: 2381929.
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      349. Poulter L, Burlingame AL. Desorption mass spectrometry of oligosaccharides coupled with hydrophobic chromophores. Methods Enzymol. 1990; 193:661-89. PMID: 2074841.
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      350. Sanders DA, Gillece-Castro BL, Stock AM, Burlingame AL, Koshland DE. Identification of the site of phosphorylation of the chemotaxis response regulator protein, CheY. J Biol Chem. 1989 Dec 25; 264(36):21770-8. PMID: 2689446.
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      351. Kaur S, Hollander D, Haas R, Burlingame AL. Characterization of structural xenobiotic modifications in proteins by high sensitivity tandem mass spectrometry. Human hemoglobin treated in vitro with styrene 7,8-oxide. J Biol Chem. 1989 Oct 15; 264(29):16981-4. PMID: 2793839.
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      352. Haraguchi T, Fisher S, Olofsson S, Endo T, Groth D, Tarentino A, Borchelt DR, Teplow D, Hood L, Burlingame A. Asparagine-linked glycosylation of the scrapie and cellular prion proteins. Arch Biochem Biophys. 1989 Oct; 274(1):1-13. PMID: 2505674.
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      353. Poulter L, Earnest JP, Stroud RM, Burlingame AL. Structure, oligosaccharide structures, and posttranslationally modified sites of the nicotinic acetylcholine receptor. Proc Natl Acad Sci U S A. 1989 Sep; 86(17):6645-9. PMID: 2771948; PMCID: PMC297901.
      354. Hernández LM, Ballou L, Alvarado E, Gillece-Castro BL, Burlingame AL, Ballou CE. A new Saccharomyces cerevisiae mnn mutant N-linked oligosaccharide structure. J Biol Chem. 1989 Jul 15; 264(20):11849-56. PMID: 2663842.
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      355. Pongracz K, Kaur S, Burlingame AL, Bodell WJ. O6-substituted-2'-deoxyguanosine-3'-phosphate adducts detected by 32P post-labeling of styrene oxide treated DNA. Carcinogenesis. 1989 Jun; 10(6):1009-13. PMID: 2720897.
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      356. Gibson BW, Webb JW, Yamasaki R, Fisher SJ, Burlingame AL, Mandrell RE, Schneider H, Griffiss JM. Structure and heterogeneity of the oligosaccharides from the lipopolysaccharides of a pyocin-resistant Neisseria gonorrhoeae. Proc Natl Acad Sci U S A. 1989 Jan; 86(1):17-21. PMID: 2492099; PMCID: PMC286394.
      357. Poulter L, Earnest JP, Stroud RM, Burlingame AL. Cesium ion liquid secondary ion mass spectrometry of membrane-bound glycoproteins: structural and topological considerations of acetylcholine receptor from Torpedo californica. Biomed Environ Mass Spectrom. 1988 Oct; 16(1-12):25-30. PMID: 3242677.
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      358. Xu XB, Burlingame AL. Environmental applications of organic mass spectrometry in China. Biomed Environ Sci. 1988 Oct; 1(3):253-69. PMID: 3152059.
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      359. Aberth WH, Burlingame AL. Effect of primary beam energy on the secondary ion sputtering efficiency of liquid secondary ionization mass spectrometry in the 5-30-keV range. Anal Chem. 1988 Jul 15; 60(14):1426-8. PMID: 3064656.
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      360. Burlingame AL, Maltby D, Russell DH, Holland PT. Mass spectrometry. Anal Chem. 1988 Jun 15; 60(12):294R-342R. PMID: 3046425.
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      361. Gibson BW, Yu ZG, Aberth W, Burlingame AL, Bass NM. Revision of the blocked N terminus of rat heart fatty acid-binding protein by liquid secondary ion mass spectrometry. J Biol Chem. 1988 Mar 25; 263(9):4182-5. PMID: 3162235.
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      362. Webb JW, Jiang K, Gillece-Castro BL, Tarentino AL, Plummer TH, Byrd JC, Fisher SJ, Burlingame AL. Structural characterization of intact, branched oligosaccharides by high performance liquid chromatography and liquid secondary ion mass spectrometry. Anal Biochem. 1988 Mar; 169(2):337-49. PMID: 3132867.
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      363. Gillece-Castro BL, Fisher SJ, Tarentino AL, Peterson DL, Burlingame AL. Structure of the oligosaccharide portion of human hepatitis B surface antigen. Arch Biochem Biophys. 1987 Jul; 256(1):194-201. PMID: 3606122.
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      364. Burlingame AL, Baillie TA, Derrick PJ. Mass spectrometry. Anal Chem. 1986 Apr; 58(5):165R-211R. PMID: 3521386.
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      365. Wickramanayake PP, Deinzer ML, Burlingame AL. Positive and negative liquid secondary ion mass spectrometry of chloro- and nitrophenylglucuronides. Biomed Mass Spectrom. 1985 Mar; 12(3):127-33. PMID: 3160397.
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      366. Aberth W, Burlingame AL. Comparison of three geometries for a cesium primary beam liquid secondary ion mass spectrometry source. Anal Chem. 1984 Dec; 56(14):2915-8. PMID: 6524663.
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      367. Latini R, Reginato R, Burlingame AL, Kates RE. High-performance liquid chromatographic isolation and fast atom bombardment mass spectrometric identification of Di-N-desethylamiodarone, a new metabolite of amiodarone in the dog. Biomed Mass Spectrom. 1984 Sep; 11(9):466-71. PMID: 6509156.
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      368. Lampe MA, Burlingame AL, Whitney J, Williams ML, Brown BE, Roitman E, Elias PM. Human stratum corneum lipids: characterization and regional variations. J Lipid Res. 1983 Feb; 24(2):120-30. PMID: 6833889.
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      369. Straub KM, Burlingame AL. Carcinogen binding to DNA. Biomed Mass Spectrom. 1981 Sep; 8(9):431-5. PMID: 7306680.
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      370. Xu XB, Nachtman JP, Rappaport SM, Wei ET, Lewis S, Burlingame AL. Identification of 2-nitrofluorene in diesel exhaust particulates. J Appl Toxicol. 1981 Jun; 1(3):196-8. PMID: 6193162.
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      371. Eberhard A, Burlingame AL, Eberhard C, Kenyon GL, Nealson KH, Oppenheimer NJ. Structural identification of autoinducer of Photobacterium fischeri luciferase. Biochemistry. 1981 Apr 28; 20(9):2444-9. PMID: 7236614.
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      372. Linscheid M, D'Angona J, Burlingame AL, Dell A, Ballou CE. Field desorption mass spectrometry of oligosaccharides. Proc Natl Acad Sci U S A. 1981 Mar; 78(3):1471-5. PMID: 6940169; PMCID: PMC319152.
      373. Cronholm T, Sjövall J, Wilson DM, Burlingame AL. Exchange of methyl hydrogens in ethanol during incorporation in bile acids in vivo. Biochim Biophys Acta. 1979 Nov 21; 575(2):193-203. PMID: 508782.
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      374. Lewis S, Kenyon CN, Meili J, Burlingame AL. High resolution gas chromatographic/real-time high resolution mass spectrometric identification of organic acids in human urine. Anal Chem. 1979 Jul; 51(8):1275-85. PMID: 484857.
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      375. Straub KM, Meehan T, Burlingame AL, Calvin M. Identification of the major adducts formed by reaction of benzo(a)pyrene diol epoxide with DNA in vitro. Proc Natl Acad Sci U S A. 1977 Dec; 74(12):5285-9. PMID: 271953; PMCID: PMC431688.
      376. Burlingame AL. Assessment of the trace organic molecular composition of industrial and municipal wastewater effluents by capillary gas chromatography/real-time high-resolution mass spectrometry: a preliminary report. Ecotoxicol Environ Saf. 1977 Jun; 1(1):111-50. PMID: 617082.
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      377. Bowes CW, Mulvihill MJ, Simoneit BR, Burlingame AL, Risebrough RW. Identification of chlorinated dibenzofurans in American polychlorinated biphenyls. Nature. 1975 Jul 24; 256(5515):305-7. PMID: 806811.
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      378. Cronholm T, Burlingame AL, Sjövall J. Utilization of the carbon and hydrogen atoms of ethanol in the biosynthesis of steroids and bile acids. Eur J Biochem. 1974 Dec 2; 49(3):497-510. PMID: 4442424.
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      379. Wilson DM, Burlingame AL. Deuterium and carbon-13 tracer studies of ethanol metabolism in the rat by 2H, 1H-decoupled 13C nuclear magnetic resonance. Biochem Biophys Res Commun. 1974 Feb 4; 56(3):828-35. PMID: 4363753.
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      380. Burlingame AL, McPherron RV, Wilson DM. Nonheuristic computer determination of molecular structure based upon carbon-13 nuclear magnetic resonance data: branched alkanes. Proc Natl Acad Sci U S A. 1973 Dec; 70(12):3419-22. PMID: 4519635; PMCID: PMC427249.
      381. Simoneit BR, Smith DH, Eglinton G, Burlingame AL. Application of real-time mass spectrometric techniques to environmental organic geochemistry. II. Organic matter in San Francisco Bay area water. Arch Environ Contam Toxicol. 1973 Oct; 1(3):193-208. PMID: 4776414.
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      382. Bowes GW, Simoneit BR, Burlingame AL, de Lappe BW, Risebrough RW. The search for chlorinated dibenzofurans and chlorinated dibenzodioxins in wildlife populations showing elevated levels of embryonic death. Environ Health Perspect. 1973 Sep; 5:191-8. PMID: 4201766; PMCID: PMC1474954.
      383. Welch JW, Burlingame AL. Very long-chain fatty acids in yeast. J Bacteriol. 1973 Jul; 115(1):464-6. PMID: 4577752; PMCID: PMC246264.
      384. Holland PT, Simoneit BR, Wszolek PC, Burlingame AL. Study of carbon compounds in Apollo 12 and 14 lunar samples. Space Life Sci. 1972 Oct; 3(4):551-61. PMID: 4650306.
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      385. Burlingame AL, Johanson GA. Mass spectrometry. Anal Chem. 1972 Apr 1; 44(5):337-78. PMID: 22401018.
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      386. Balogh B, Wilson DM, Burlingame AL. Carbon-13 NMR study of the stereochemistry of steranes from oil shale of the Green River formation (Eocene). Nature. 1971 Sep 24; 233(5317):261-3. PMID: 16063320.
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      387. van Tamelen EE, Hanzlik RP, Clayton RB, Burlingame AL. Minimal substrate structural requirements for lanosterol-squalene 2,3-oxide cyclase action. 10'-norsqualene 2,3-oxide. J Am Chem Soc. 1970 Apr 8; 92(7):2137-9. PMID: 5435278.
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      388. Simoneit BR, Schnoes HK, Haug P, Burlingame AL. Nitrogenous compounds of the Colorado Green River Formation oil shale: a preliminary analysis by mass spectrometry. Nature. 1970 Apr 4; 226(5240):75-6. PMID: 16057113.
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      389. Burlingame AL, Calvin M, Han J, Henderson W, Reed W, Simoneit BR. Lunar organic compounds: search and characterization. Science. 1970 Jan 30; 167(3918):751-2. PMID: 17781577.
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      390. Kupchan SM, Anderson WK, Bollinger P, Doskotch RW, Smith RM, Renauld JA, Schnoes HK, Burlingame AL, Smith DH. Tumor inhibitors. XXXIX. Active principles of Acnistus arborescens. Isolation and structural and spectral studies of withaferin A and withacnistin. J Org Chem. 1969 Dec; 34(12):3858-66. PMID: 5357526.
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      391. Kupchan SM, Aynehchi Y, Cassady JM, Schnoes HK, Burlingame AL. Tumor inhibitors XL. The isolation and structural elucidation of elephantin and elephantopin, two novel sesquiterpenoid tumor inhibitors from Elephantopus elatus. J Org Chem. 1969 Dec; 34(12):3867-75. PMID: 5357527.
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      392. Kupchan SM, Davies AP, Barboutis SJ, Schnoes HK, Burlingame AL. Tumor inhibitors. 43. Solapalmitine and solapalmitenine, two novel alkaloid tumor inhibitors from Solanum tripartitium. J Org Chem. 1969 Dec; 34(12):3888-93. PMID: 5357530.
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      393. Simoneit BR, Burlingame AL, Flory DA, Smith ID. Apollo lunar module engine exhaust products. Science. 1969 Nov 7; 166(3906):733-8. PMID: 17776759.
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      394. Burlingame AL, Simoneit BR. Isoprenoid Fatty acids isolated from the kerogen matrix of the green river formation (eocene). Science. 1968 May 3; 160(3827):531-3. PMID: 17834267.
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      395. van Tamelen EE, Sharpless KB, Hanzlik R, Clayton RB, Burlingame AL, Wszolek PC. Enzymic cyclization of trans,trans,trans-18,19-dihydrosqualene 2,3-oxide. J Am Chem Soc. 1967 Dec 20; 89(26):7150-1. PMID: 6064361.
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      396. Haug P, Schnoes HK, Burlingame AL. Isoprenoid and dicarboxylic acids isolated from colorado green river shale (eocene). Science. 1967 Nov 10; 158(3802):772-3. PMID: 17732625.
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      397. Kupchan SM, Davies AP, Barboutis SJ, Schnoes HK, Burlingame AL. The isolation, structural elucidation, and synthesis of solapalmitine and solapalmitenine, two novel alkaloid tumor inhibitors from Solanum tripartitum. J Am Chem Soc. 1967 Oct 25; 89(22):5718-9. PMID: 5622365.
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      398. Urey HC, Lewis JS, Burlingame AL, Schnoes HK, Studier MH, Hayatsu R, Anders E. Organic matter in carbonaceous chondrites. Science. 1966 Apr 1; 152(3718):102-7. PMID: 17830238.
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      399. Burlingame AL, Haug P, Belsky T, Calvin M. OCCURRENCE OF BIOGENIC STERANES AND PENTACYCLIC TRITERPANES IN AN EOCENE SHALE (52 MILLION YEARS) AND IN AN EARLY PRECAMBRIAN SHALE (2.7 BILLION YEARS): A PRELIMINARY REPORT. Proc Natl Acad Sci U S A. 1965 Nov; 54(5):1406-12. PMID: 16591314; PMCID: PMC219916.
      400. Eglinton G, Scott PM, Belsky T, Burlingame AL, Calvin M. Hydrocarbons of Biological Origin from a One-Billion-Year-Old Sediment. Science. 1964 Jul 17; 145(3629):263-4. PMID: 17833034.
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