Publications

2017

Doll S, Urisman A, Oses-Prieto JA, Arnott D, Burlingame AL. Quantitative Proteomics Reveals Fundamental Regulatory Differences in Oncogenic HRAS and Isocitrate Dehydrogenase (IDH1) Driven Astrocytoma. Mol Cell Proteomics. 2017 Jan; 16(1), 39-56 (2017). [Pubmed]

Lechler MC, Crawford ED, Groh N, Widmaier K, Jung R, Kirstein J, Trinidad JC, Burlingame AL, David DC. Reduced Insulin/IGF-1 Signaling Restores the Dynamic Properties of Key Stress Granule Proteins during Aging. Cell Rep. 2017 Jan 10; 18(2), 454-467 (2017). [Pubmed]

Zhao Q, Ouyang X, Wan X, Gajiwala KS, Kath JC, Jones LH, Burlingame AL, Taunton J.Broad-Spectrum Kinase Profiling in Live Cells with Lysine-Targeted Sulfonyl Fluoride Probes. 2017 Jan 18; 139(2), 680-685 (2017). [Pubmed]

2016

Barrette AM, Roberts JK, Chapin C, Egan EA, Segal MR, Oses-Prieto JA, Chand S, Burlingame AL, Ballard PL. Antiinflammatory Effects of Budesonide in Human Fetal Lung. Am J Respir Cell Mol Biol. 2016 Nov; 55(5), 623-632 (2016). [Pubmed]

Bu SL, Liu C, Liu N, Zhao JL, Ai LF, Chi H, Li KL, Chien CW, Burlingame AL, Zhang SW, Wang ZY. Immunopurification and Mass Spectrometry Identifies Protein Phosphatase 2A (PP2A) and BIN2/GSK3 as Regulators of AKS Transcription Factors in Arabidopsis. Mol Plant. 2016 Oct 18; pii, S1674-2052(16)30229-5 (2016). [Epub ahead of print] [Pubmed]

Burlingame AL. On Strengthening the MCP Editorial Leadership. Mol Cell Proteomics. 2016 Jul; 15(7),2214-6 (2016). [Pubmed]

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 (2016). [Pubmed]

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 (2016). [Pubmed]

Kim S, Maynard JC, Sasaki Y, Strickland A, Sherman DL, Brophy PJ, Burlingame AL, Milbrandt J. Schwann Cell O-GlcNAc Glycosylation Is Required for Myelin Maintenance and Axon Integrity. J Neurosci. 2016 Sep 14; 36(37),9633-46 (2016). [Pubmed]

Lee S, Shang Y, Redmond SA, Urisman A, Tang AA, Li KH, Burlingame AL, Pak RA, Jovičić A, Gitler AD, Wang J, Gray NS, Seeley WW, Siddique T, Bigio EH, Lee VM, Trojanowski JQ, Chan JR, Huang EJ. Activation of HIPK2 Promotes ER Stress-Mediated Neurodegeneration in Amyotrophic Lateral Sclerosis. Neuron. 2016 Jul 6; 91(1),41-55 (2016). [Pubmed]

Levin RS, Hertz NT, Burlingame AL, Shokat KM, Mukherjee S. 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 16;113(33),E4776-83 (2016). [Pubmed]

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 (2016). [Pubmed]

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 (2016). [Pubmed]

Li S, Yen L, Pastor WA, Johnston JB, Du J, Shew CJ, Liu W, Ho J, Stender B, Clark AT, Burlingame AL, Daxinger L, Patel DJ, Jacobsen SE. Mouse MORC3 is a GHKL ATPase that localizes to H3K4me3 marked chromatin. Proc Natl Acad Sci U S A. 2016 Aug 30; 113(35),E5108-16 (2016). [Pubmed]

Maynard JC, Burlingame AL, Medzihradszky KF. Cysteine S-linked N-acetylglucosamine (S-GlcNAcylation), A New Post-translational Modification in Mammals. Mol Cell Proteomics. 2016 Nov; 15(11),3405-3411 (2016). [Pubmed]

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 Mar 7; 5,e10647 (2016). [Pubmed]

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 (2016). [Pubmed]

Posch C, Sanlorenzo M, Vujic I, Oses-Prieto JA, Cholewa BD, Kim ST, Ma J, Lai K, Zekhtser M, Esteve-Puig R, Green G, Chand S, Burlingame AL, Panzer-Grümayer R, Rappersberger K, Ortiz-Urda S. Phosphoproteomic Analyses of NRAS(G12) and NRAS(Q61) Mutant Melanocytes Reveal Increased CK2α Kinase Levels in NRAS(Q61) Mutant Cells. J Invest Dermatol. 2016 Oct; 136(10),2041-8 (2016). [Pubmed]

Robinson PJ, Trnka MJ, Bushnell DA, Davis RE, Mattei PJ, Burlingame AL, Kornberg RD. Structure of a Complete Mediator-RNA Polymerase II Pre-Initiation Complex. Cell. 2016 Sep 8; 166(6),1411-1422 (2016). [Pubmed]

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 (2016). [Pubmed]

Urisman A, Levin RS, Gordan JD, Webber JT, Hernandez H, Ishihama Y, Shokat KM, Burlingame AL. An optimized chromatographic strategy for multiplexing in parallel reaction monitoring mass spectrometry: Insights from quantitation of activated kinases. Mol Cell Proteomics. 2017 Feb; 16(2),265-277 (2016). [Pubmed]

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 (2016). [Pubmed]

Wei CQ, Chien CW, Ai LF, Zhao J, Zhang Z, Li KH, Burlingame AL, Sun Y, Wang ZY. The Arabidopsis B-box protein BZS1/BBX20 interacts with HY5 and mediates strigolactone regulation of photomorphogenesis. J Genet Genomics. 2016 Sep 20; 43(9),555-63 (2016). [Pubmed]

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 (2016). [Pubmed]

Yadav S, Oses-Prieto JA, Peters CJ, Zhou J, Pleasure SJ, Burlingame AL, Jan LY, Jan YN. TAOK2 Kinase Mediates PSD95 Stability and Dendritic Spine Maturation through Septin7 Phosphorylation. Neuron. 2016 Dec 29; 93(2),379-393 (2016). [Pubmed]

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 (2016). [Pubmed]

2015

Bradshaw RA, Burlingame AL. Minireviews revisited. Mol Cell Proteomics. 2015 Mar;14(3),455 (2015). [Pubmed]

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 (2015). [Pubmed]

Burlingame A, Carr SA, Bradshaw RA, Chalkley RJ. On Credibility, Clarity, and Compliance. Mol Cell Proteomics. 2015 Jul;14(7),1731-3 (2015). [Pubmed]

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 (2015). [Pubmed]

Doll S, Burlingame AL. Mass spectrometry-based detection and assignment of protein posttranslational modifications. ACS Chem Biol.2015 Jan 16; 10(1),63-71 (2015). [Pubmed]

Duong BH, Onizawa M, Oses-Prieto JA, Advincula R, Burlingame A, Malynn BA, Ma A. A20 Restricts Ubiquitination of Pro-Interleukin-1β Protein Complexes and Suppresses NLRP3 Inflammasome Activity. Immunity. 2015 Jan 20;42(1),55-67 (2015). [Pubmed]

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),8541-46 (2015). [Pubmed]

Lokappa SB, Chandrababu KB, Dutta K, Perovic I, Evans JS, Moradian-Oldak J. Interactions of amelogenin with phospholipids. Biopolymers. 2015 Feb; 103(2),96-108 (2015). [Pubmed]

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 (2015). [Pubmed]

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 (2015). [Pubmed]

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 12;11(5),e1004899 (2015). [Pubmed]

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 (2015). [Pubmed]

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 Sep 24;4,e08719 (2015). [Pubmed]

Rys JP, DuFort CC, Monteiro DA, Baird MA, Oses-Prieto JA, Chand S, Burlingame AL, Davidson MW, Alliston TN. Discrete spatial organization of TGFβ receptors couples receptor multimerization and signaling to cellular tension. Elife. 2015 Dec 104,e09300 (2015). [Pubmed]

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 (2015). [Pubmed]

2014

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 (2014). [Pubmed]

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. 4(2),200-15 (2014). [Pubmed]

Baker PR, Chalkley RJ. MS-viewer: a web-based spectral viewer for proteomics results. Mol Cell Proteomics. 2014 May;13(5), 1392-6 (2014). [Pubmed]

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. 2014 Nov 20. pii, S2212-4926(14)00062-1 (2014). [Pubmed]

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(2014). [Pubmed]

Chalkley RJ, Bandeira N, Chambers MC, Clauser KR, Cottrell JS, Deutsch EW, Kapp EA, Lam HH, McDonald WH, Neubert TA, Sun RX. Proteome Informatics Research Group (iPRG)_2012: A Study on Detecting Modified Peptides in a Complex Mixture. Mol Cell Proteomics. 13(1),360-71 (2014). [Pubmed]

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 (2014). [Pubmed]

Darula Z, Medzihradszky KF. Glycan side reaction may compromise ETD-based glycopeptide identification. J Am Soc Mass Spectrom. 2014 Jun;25(6), 977-87 (2014). [Pubmed]

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 (2014). [Pubmed]

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 Mar 25;18(2), R50 (2014). [Pubmed]

Julien O, Kampmann M, Bassik MC, Zorn JA, Venditto VJ, Shimbo K, Agard NJ, Shimada K, Rheingold AL, Stockwell BR, Weissman JS, Wells JA. Unraveling the mechanism of cell death induced by chemical fibrils. Nat Chem Biol. 2014 Nov;10(11),969-76 (2014). [Pubmed]

Kido-Nakahara M, Buddenkotte J, Kempkes C, Ikoma A, Cevikbas F, Akiyama T, Nunes F, Seeliger S, Hasdemir B, Mess C, Buhl T, Sulk M, Müller FU, Metze D, Bunnett NW, Bhargava A, Carstens E, Furue M, Steinhoff M. Neural peptidase endothelin-converting enzyme 1 regulates endothelin 1-induced pruritus. J Clin Invest. 2014 Jun 2;124(6),2683-95 (2014). [Pubmed]

Krishnan S, Miller RM, Tian B, Mullins RD, Jacobson MP, Taunton J. Design of reversible, cysteine-targeted Michael acceptors guided by kinetic and computational analysis. J Am Chem Soc. 2014 Sep 10;136(36), 12624-30 (2014). [Pubmed]

Martins MM, Zhou AY, Corella A, Horiuchi D, Yau C, Rakshandehroo T, Gordan JD, Levin RS, Johnson J, Jascur J, Shales M, Sorrentino A, Cheah J, Clemons PA, Shamji AF, Schreiber SL, Krogan NJ, Shokat KM, McCormick F, Goga A, Bandyopadhyay S. Linking Tumor Mutations to Drug Responses via a Quantitative Chemical-Genetic Interaction Map. Cancer Discov. 2014 Dec 12. [Epub ahead of print] [Pubmed]

Medzihradszky KF. Noncovalent dimer formation in liquid chromatography-mass spectrometry analysis. Anal Chem. 2014 Sep 16;86(18), 8906-9 (2014). [Pubmed]

Morris JH, Knudsen GM, Verschueren E, Johnson JR, Cimermancic P, Greninger AL, Pico AR. Affinity purification-mass spectrometry and network analysis to understand protein-protein interactions. Nat Protoc. 2014 Nov;9(11), 2539-54 (2014). [Pubmed]

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 (2014). [Pubmed]

Seymour SL, Farrah T, Binz PA, Chalkley RJ, Cottrell JS, Searle BC, Tabb DL, Vizcaíno JA, Prieto G, Uszkoreit J, Eisenacher M, Martínez-Bartolomé S, Ghali F, Jones AR. A standardized framing for reporting protein identifications in mzIdentML 1.2. Proteomics. 2014 Nov;14(21-22), 2389-99 (2014). [Pubmed]

Skorobogatko Y, Landicho A, Chalkley RJ, Kossenkov AV, Gallo G, Vosseller K. O-Linked β-N-Acetylglucosamine (O-GlcNAc) site Thr87 regulates synapsin I localization to synapses and size of the reserve pool of synaptic vesicles. J Biol Chem. 289(6), 3602-12 (2014). [Pubmed]

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 (2014). [Pubmed]

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. 13(2),420-34 (2014). [Pubmed]

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 (2014). [Pubmed]

Vizcaíno JA, Deutsch EW, Wang R, Csordas A, Reisinger F, Ríos D, Dianes JA, Sun Z, Farrah T, Bandeira N, Binz PA, Xenarios I, Eisenacher M, Mayer G, Gatto L, Campos A, Chalkley RJ, Kraus HJ, Albar JP, Martinez-Bartolomé S, Apweiler R, Omenn GS, Martens L, Jones AR, Hermjakob H. ProteomeXchange provides globally coordinated proteomics data submission and dissemination. Nat Biotechnol. 2014 Mar;32(3), 223-6 (2014). [Pubmed]

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 (AMFR) and UbcH5a/C-terminus of Hsc70-interacting Protein (CHIP)/Hsc70/Hsp40 E2/E3 Ubiquitin Ligase Complexes. J Biol Chem. 2014 Dec 1. pii: jbc.M114.611525. [Epub ahead of print] [Pubmed]

Wiita AP, Hsu GW, Lu CM, Esensten JH, Wells JA. Circulating proteolytic signatures of chemotherapy-induced cell death in humans discovered by N-terminal labeling. Proc Natl Acad Sci U S A. 2014 May 27;111(21), 7594-9 (2014). [Pubmed]

Wiita AP, Seaman JE, Wells JA. Global analysis of cellular proteolysis by selective enzymatic labeling of protein N-termini. Methods Enzymol. 2014;544, 327-58 (2014). [Pubmed]

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. 7(2), 441-4 (2014). [Pubmed]

Zeng-Elmore X, Gao XZ, Pellarin R, Schneidman-Duhovny D, Zhang XJ, Kozacka KA, Tang Y, Sali A, Chalkley RJ, Cote RH, Chu F. Molecular architecture of photoreceptor phosphodiesterase elucidated by chemical cross-linking and integrative modeling. J Mol Biol. 2014 Nov 11;426(22), 3713-28 (2014). [Pubmed]

2013

Aebersold R, Burlingame AL, Bradshaw RA. Western blots versus selected reaction monitoring assays: time to turn the tables? Mol Cell Proteomics. 12(9), 2381-2 (2013). [Pubmed]

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. 3(5), 1493-502 (2013). [Pubmed]

Bessat M, Knudsen G, Burlingame AL, Wang CC. A minimal anaphase promoting complex/cyclosome (APC/C) in Trypanosoma brucei. PLoS One. 8(3), e59258 (2013). [Pubmed]

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. 288(23),16606-18 (2013). [Pubmed]

Bradshaw RA, Chalkley RJ, Biarc J, Burlingame AL. Receptor tyrosine kinase signaling mechanisms: Devolving TrkA responses with phosphoproteomics. Adv BiolRegul. 53(1),87-96 (2013). [Pubmed]

Chalkley RJ. Improving Peptide identification using empirical scoring systems. Methods Mol Biol. 1007,173-82 (2013). [Pubmed]

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. 9,15-25 (2013). [Pubmed]

Crawford ED, Seaman JE, Agard N, Hsu GW, Julien O, Mahrus S, Nguyen H, Shimbo K, Yoshihara HA, Zhuang M, Chalkley RJ, Wells JA. The DegraBase: a database of proteolysis in healthy and apoptotic human cells. Mol Cell Proteomics. 12(3), 813-24 (2013). [Pubmed]

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. 74, 96-107(2013). [Pubmed]

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. M Bio. 4(2), e00098-13 (2013). [Pubmed]

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. 154(4), 737-47 (2013). [Pubmed]

Ilagan JO, Chalkley RJ, Burlingame AL, Jurica MS. Rearrangements within human spliceosomes captured after exon ligation. RNA. 19(3), 400-12 (2013). [Pubmed]

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. 83(3),633-9 (2013). [Pubmed]

Kaasik K, Kivimäe S, Allen JJ, Chalkley RJ, Huang Y, Baer K, Kissel H, Burlingame AL, Shokat KM, Ptáček LJ, Fu YH. Glucose sensor O-GlcNAcylation coordinates with phosphorylation to regulate circadian clock. Cell Metab. 17(2),291-302 (2013). [Pubmed]

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. 135(8), 2879-82 (2013). [Pubmed]

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. 48(12), 1343-52 (2013). [Pubmed]

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. 13(6), 982-91 (2013). [Pubmed]

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. 25(7),2679-98 (2013). [Pubmed]

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. 2, e00712 (2013). [Pubmed]

O'Donoghue AJ, Jin Y, Knudsen GM, Perera NC, Jenne DE, Murphy JE, Craik CS, Hermiston TW. Global substrate profiling of proteases in human neutrophil extracellular traps reveals consensus motif predominantly contributed by elastase. PLoS One. 8(9), e75141 (2013). [Pubmed]

Sanchez LM, Knudsen GM, Helbig C, De Muylder G, Mascuch SM, Mackey ZB, Gerwick L, Clayton C, McKerrow JH, Linington RG. Examination of the mode of action of the almiramide family of natural products against the kinetoplastid parasite Trypanosoma brucei. J Nat Prod. 76(4),630-41 (2013). [Pubmed]

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. 20(4), 494-9 (2013). [Pubmed]

Small JL, O'Donoghue AJ, Boritsch EC, Tsodikov OV, Knudsen GM, Vandal O, Craik CS, Ehrt S. Substrate specificity of MarP, a periplasmic protease required for resistance to acid and oxidative stress in Mycobacterium tuberculosis. J Biol Chem. 288(18),12489-99 (2013). [Pubmed]

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. 78(3),469-82 (2013). [Pubmed]

Trinidad JC, Schoepfer R, Burlingame AL, Medzihradszky KF. N- and O-glycosylation in the murine synaptosome. Mol Cell Proteomics. 12(12),3474-88 (2013). [Pubmed]

Trinidad JC, Thalhammer A, Burlingame AL, Schoepfer R. Activity-dependent protein dynamics define interconnected cores of co-regulated postsynaptic proteins. Mol Cell Proteomics. 12(1), 29-41 (2013). [Pubmed]

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. 12(12), 3653-65 (2013). [Pubmed]

Wiita AP, Ziv E, Wiita PJ, Urisman A, Julien O, Burlingame AL, Weissman JS, Wells JA. Global cellular response to chemotherapy-induced apoptosis. Elife. 2, e01236 (2013). [Pubmed]

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. 51(1),5-19 (2013). [Pubmed]

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. 52(5),679-92 (2013). [Pubmed]

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. 49(2),273-82 (2013). [Pubmed]

2012

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. 109(6),1913-8 (2012). [Pubmed]

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. 150(2),413-25 (2012). [Pubmed]

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. 303(1),L12-9 (2012). [Pubmed]

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. 11(5),15-30 (2012). [Pubmed]

Crawford ED, Seaman JE, Barber AE 2nd, 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. 19(12), 2040-8 (2012). [Pubmed]

Darula Z, Sherman J, Medzihradszky KF. How to dig deeper? Improved enrichment methods for mucin core-1 type glycopeptides. Mol Cell Proteomics. 11(7), O111.016774 (2012). [Pubmed]

Demont Y, Corbet C, Page A, Ataman-Önal Y, Choquet-Kastylevsky G, Fliniaux I, Le Bourhis X, Toillon RA, Bradshaw RA, Hondermarck H. Pro-nerve growth factor induces autocrine stimulation of breast cancer cell invasion through tropomyosin-related kinase A (TrkA) and sortilin protein. J Biol Chem. 287(3), 1923-31 (2012). [Pubmed]

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). 14(3), 420-7(2012). [Pubmed]

Greninger AL, Knudsen GM, Betegon M, Burlingame AL, Derisi JL. The 3A protein from multiple picornaviruses utilizes the golgi adaptor protein ACBD3 to recruit PI4KIIIβ. J Virol. 86(7),3605-16(2012). [Pubmed]

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. 11(5),47-59 (2012). [Pubmed]

Kinsinger CR, Apffel J, Baker M, Bian X, Borchers CH, Bradshaw R, Brusniak MY, Chan DW, Deutsch EW, Domon B, Gorman J, Grimm R, Hancock W, Hermjakob H, Horn D, Hunter C, Kolar P, Kraus HJ, Langen H, Linding R, Moritz RL, Omenn GS, Orlando R, Pandey A, Ping P, Rahbar A, Rivers R, Seymour SL, Simpson RJ, Slotta D, Smith RD, Stein SE, Tabb DL, Tagle D, Yates JR, Rodriguez H. Recommendations for mass spectrometry data quality metrics for open access data (corollary to the Amsterdam Principles). J Proteome Res. 11(2),1412-9 (2012). [Pubmed]

Kinsinger CR, Apffel J, Baker M, Bian X, Borchers CH, Bradshaw R, Brusniak MY, Chan DW, Deutsch EW, Domon B, Gorman J, Grimm R, Hancock W, Hermjakob H, Horn D, Hunter C, Kolar P, Kraus HJ, Langen H, Linding R, Moritz RL, Omenn GS, Orlando R, Pandey A, Ping P, Rahbar A, Rivers R, Seymour SL, Simpson RJ, Slotta D, Smith RD, Stein SE, Tabb DL, Tagle D, Yates JR, Rodriguez H. Recommendations for mass spectrometry data quality metrics for open access data (corollary to the Amsterdam principles). Proteomics. 12(1),11-20 (2012). [Pubmed]

Medzihradszky KF, Trinidad JC. Unusual fragmentation of Pro-Ser/Thr-containing peptides detected in collision-induced dissociation spectra. J Am Soc Mass Spectrom. 23(4),602-7(2012). [Pubmed]

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. 11(12), 1690-708 (2012). [Pubmed]

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. 9(11),1095-100 (2012). [Pubmed]

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. 109(44),17931-5 (2012). [Pubmed]

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. 11(5),171-86 (2012). [Pubmed]

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. 109(31),12432-7 (2012). [Pubmed]

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. 26(13),1421-6 (2012). [Pubmed]

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. 11(8),215-29(2012). [Pubmed]

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. 73(6),1127-42 (2012). [Pubmed]

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. 11(2), M111.010132 (2012). [Pubmed]

2011

Baker PR, Trinidad JC, Chalkley RJ. Modification site localization scoring integrated into a search engine. Mol Cell Proteomics. 10(7),M111.008078 (2011). [Pubmed]

Banko MR, Allen JJ, Schaffer BE, Wilker EW, Tsou P, White JL, Villén J, WangB, Kim SR, Sakamoto K, Gygi SP, Cantley LC, Yaffe MB, Shokat KM, Brunet A.Chemical genetic screen for AMPKα2 substrates uncovers a network of proteinsinvolved in mitosis. Mol Cell. 44(6),878-92 (2011). [Pubmed]

Biarc J, Chalkley RJ, Burlingame AL, Bradshaw RA. Receptor tyrosine kinase signaling--a proteomic perspective. Adv Enzyme Regul. 51(1),293-305(2011). [Pubmed]

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. 479(7373),410-4 (2011). [Pubmed]

Bromley KM, Kiss AS, Lokappa SB, Lakshminarayanan R, Fan D, Ndao M, Evans JS, Moradian-Oldak J. Dissecting amelogenin protein nanospheres: characterization of metastable oligomers. J Biol Chem. 286(40),34643-53 (2011). [Pubmed]

Brown CM, Ray M, Eroy-Reveles AA, Egea P, Tajon C, Craik CS. Peptide length and leaving-group sterics influence potency of peptide phosphonate protease inhibitors. Chem Biol. 18(1),48-57 (2011). [Pubmed]

Chandran S, Li H, Dong W, Krasinska K, Adams C, Alexandrova L, Chien A,Hallows KR, Bhalla V. Neural precursor cell-expressed developmentallydown-regulated protein 4-2 (Nedd4-2) regulation by 14-3-3 protein binding atcanonical serum and glucocorticoid kinase 1 (SGK1) phosphorylation sites. J Biol Chem. 286(43),37830-40 (2011). [Pubmed]

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. 108(26), 10620-5 (2011). [Pubmed]

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. 6(4), e19061 (2011). [Pubmed]

Darula Z, Chalkley RJ, Lynn A, Baker PR, Medzihradszky KF. Improved identification of O-linked glycopeptides from ETD data with optimized scoring for different charge states and cleavage specificities. Amino Acids. 41(2), 321-8 (2011). [Pubmed]

Fahey ME, Bennett MJ, Mahon C, Jäger S, Pache L, Kumar D, Shapiro A, Rao K,Chanda SK, Craik CS, Frankel AD, Krogan NJ. GPS-Prot: a web-based visualizationplatform for integrating host-pathogen interaction data. BMC Bioinformatics. 12, 298 (2011). [Pubmed]

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 themurine procollagen C-proteinase enhancer 2 gene causes accumulation of pro-apoA-Iand increased HDL levels. J Lipid Res. 52(11), 1974-83 (2011). [Pubmed]

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. 1814(12),1964-73 (2011). [Pubmed]

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. 10(12), M111.010728 (2011). [Pubmed]

Ingram J, Knudsen G, Lim KC, Hansell E, Sakanari J, McKerrow J. Proteomic analysis of human skin treated with larval schistosome peptidases reveals distinct invasion strategies among species of blood flukes. PLoS Negl Trop Dis. 5(9), e1337 (2011). [Pubmed]

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. 481(7381),365-70 (2011). [Pubmed]

Jäger S, Gulbahce N, Cimermancic P, Kane J, He N, Chou S, D'Orso I, Fernandes J, Jang G, Frankel AD, Alber T, Zhou Q, Krogan NJ. Purification and characterization of HIV-human protein complexes. Methods. 53(1), 13-9 (2011). [Pubmed]

Kao A, Chiu CL, Vellucci D, Yang Y, Patel VR, Guan S, Randall A, Baldi P, Rychnovsky SD, Huang L. Development of a novel cross-linking strategy for fast and accurate identification of cross-linked peptides of protein complexes. Mol Cell Proteomics. 10(1),M110.002212 (2011). [Pubmed]

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. 43(4),561-71 (2011). [Pubmed]

Kinsinger CR, Apffel J, Baker M, Bian X, Borchers CH, Bradshaw R, Brusniak MY, Chan DW, Deutsch EW, Domon B, Gorman J, Grimm R, Hancock W, Hermjakob H, Horn D, Hunter C, Kolar P, Kraus HJ, Langen H, Linding R, Moritz RL, Omenn GS, Orlando R, Pandey A, Ping P, Rahbar A, Rivers R, Seymour SL, Simpson RJ, Slotta D, Smith RD, Stein SE, Tabb DL, Tagle D, Yates JR 3rd, Rodriguez H. Recommendations for mass spectrometry data quality metrics for open access data (corollary to the Amsterdam principles). Proteomics Clin Appl. 5(11-12),580-9 (2011). [Pubmed]

Knudsen GM, Chalkley RJ. The effect of using an inappropriate protein database for proteomic data analysis. PLoS One. 6(6), e20873 (2011). [Pubmed]

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. 4(185), ra52 (2011). [Pubmed]

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. 4(2),361-74 (2011). [Pubmed]

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. 108(23),9490-5 (2011). [Pubmed]

Ndao M, Dutta K, Bromley KM, Lakshminarayanan R, Sun Z, Rewari G, Moradian-Oldak J, Evans JS. Probing the self-association, intermolecular contacts, and folding propensity of amelogenin. Protein Sci. 20(4),724-34 (2011). [Pubmed]

Sivaramakrishnan S, Ouellet H, Jing D, McLean KJ, Medzihradszky KF, Dawson JH, Munro AW, Ortiz de Montellano PR. A Novel Intermediate in the Reaction of Seleno CYP119 with m-Chloroperbenzoic Acid. Biochemistry. 50(14), 3014-24 (2011). [Pubmed]

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. 74(7),1045-67 (2011). [Pubmed]

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. 13(41),18288-96 (2011). [Pubmed]

Swenerton RK, Zhang S, Sajid M, Medzihradszky KF, Craik CS, Kelly BL, McKerrow JH. The oligopeptidase B of Leishmania regulates parasite enolase and immune evasion. J Biol Chem. 286(1), 429-40 (2011). [Pubmed]

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. 13(2),124-31 (2011). [Pubmed]

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. 286(11), 9443-56 (2011). [Pubmed]

Yan F, Fujimori DG. RNA methylation by radical SAM enzymes RlmN and Cfr proceeds via methylene transfer and hydride shift. Proc Natl Acad Sci U S A. 108(10),3930-4 (2011). [Pubmed]

Yang X, Sun Z, Ma R, Fan D, Moradian-Oldak J. Amelogenin "nanorods" formation during proteolysis by Mmp-20. J Struct Biol. 176(2),220-8 (2011). [Pubmed]

2010

Agard NJ, Maltby D, Wells JA. Inflammatory stimuli regulate caspase substrate profiles. Mol Cell Proteomics. 9(5),880-93 (2010). [Pubmed]

An S, Kyoung M, Allen JJ, Shokat KM, Benkovic SJ. Dynamic regulation of a metabolic multi-enzyme complex by protein kinase CK2. J Biol Chem. 285(15),11093-9 (2010). [Pubmed]

Baker PR, Medzihradszky KF, Chalkley RJ. Improving software performance for peptide electron transfer dissociation data analysis by implementation of charge state- and sequence-dependent scoring. Mol Cell Proteomics. 9(9),1795-803 (2010). [Pubmed]

Barkan DT, Hostetter DR, Mahrus S, Pieper U, Wells JA, Craik CS, Sali A. Prediction of protease substrates using sequence and structure features. Bioinformatics. 26(14),1714-22 (2010). [Pubmed]

Berndt A, Miller S, Williams O, Le DD, Houseman BT, Pacold JI, Gorrec F, Hon WC, Liu Y, Rommel C, Gaillard P, Rückle T, Schwarz MK, Shokat KM, Shaw JP, Williams RL. The p110 delta structure: mechanisms for selectivity and potency of new PI(3)K inhibitors. Nat Chem Biol. 6(2),117-24 (2010). [Pubmed]

Bradshaw RA, Burlingame AL. Technological innovation revisited. Mol Cell Proteomics. 9(11),2335-6 (2010). [Pubmed]

Bradshaw RA, Medzihradszky KF, Chalkley RJ. Protein PTMs: post-translational modifications or pesky trouble makers? J Mass Spectrom. 45(10),1095-7 (2010). [Pubmed]

Brak K, Kerr ID, Barrett KT, Fuchi N, Debnath M, Ang K, Engel JC, McKerrow JH, Doyle PS, Brinen LS, Ellman JA. Nonpeptidic tetrafluorophenoxymethyl ketone cruzain inhibitors as promising new leads for Chagas disease chemotherapy. J Med Chem 53(4), 1763-73 (2010). [Pubmed]

Burlingame AL, Stults JT. Mass spectrometry and the evolution of proteomics. Mol Cell Proteomics. 9(5), 753 (2010). [Pubmed]

Cade CE, Dlouhy AC, Medzihradszky KF, Salas-Castillo SP, Ghiladi RA. Isoniazid-resistance conferring mutations in Mycobacterium tuberculosis KatG: catalase, peroxidase, and INH-NADH adduct formation activities. Protein Sci.19(3),458-74 (2010). [Pubmed]

Camerer E, Barker A, Duong DN, Ganesan R, Kataoka H, Cornelissen I, Darragh MR, Hussain A, Zheng YW, Srinivasan Y, Brown C, Xu SM, Regard JB, Lin CY, Craik CS, Kirchhofer D, Coughlin SR. Local protease signaling contributes to neural tube closure in the mouse embryo. Dev Cell. 18(1),25-38 (2010). [Pubmed]

Chalkley RJ, Medzihradszky KF, Lynn AJ, Baker PR and Burlingame AL. Statistical analysis of peptide electron transfer dissociation fragmentation mass spectrometry. Anal Chem. 82(2), 579-84 (2010). [Pubmed]

Chen YT, Brinen LS, Kerr ID, Hansell E, Doyle PS, McKerrow JH, Roush WR. In vitro and in vivo studies of the trypanocidal properties of WRR-483 against Trypanosoma cruzi. PLoS Negl Trop Dis 4(9), pii: e825 (2010). [Pubmed]

Chu F, Baker PR, Burlingame AL and Chalkley RJ. Finding Chimeras: A bioinformatic strategy for identification of cross-linked peptides. Mol Cell Proteomics. 9(1), 25-31 (2010). [Pubmed]

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). 16(3),421-8 (2010). [Pubmed]

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. 8(8),e1000450 (2010). [Pubmed]

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. 9(5), 824-37 (2010). [Pubmed]

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. 153(4),1878-94 (2010). [Pubmed]

Ferreira RS, Simeonov A, Jadhav A, Eidam O, Mott BT, Keiser MJ, McKerrow JH, Maloney DJ, Irwin JJ, Shoichet BK. Complementarity between a docking and a high-throughput screen in discovering new cruzain inhibitors. J Med Chem 53(13),4891-905 (2010). [Pubmed]

Ferreyra ML, Biarc J, Burlingame AL, Casati P. Arabidopsis L10 ribosomal proteins in UV-B responses. Plant Signal Behav. 5(10), 1222-5 (2010). [Pubmed]

Gray DC, Mahrus S, Wells JA. Activation of specific apoptotic caspases with an engineered small-molecule-activated protease. Cell. 142(4),637-46 (2010). [Pubmed]

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. 9(5),804-10 (2010). [Pubmed]

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. 285(28),21671-8 (2010). [Pubmed]

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. 38(3),428-38 (2010). [Pubmed]

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. 2(1), 15-36 (2010). [Pubmed]

Hong B, Nauss R, Harwood IM, Miller SM. Direct Measurement of Hg(II) Removal from Organomercurial Lyase (MerB) by Tryptophan Fluorescence: NmerA Domain of Co-evolved g-Proteobacterial Mercuric Reductase (MerA) Is More Efficient than MerA Catalytic Core or Glutathione. Biochemistry. 49(37), 8187-96 (2010). [Pubmed]

Klement E, Lipinszki Z, Kupihár Z, Udvardy A, Medzihradszky KF. Enrichment of O-GlcNAc modified proteins by the periodate oxidation – hydrazide resin capture approach. J Proteome Res. 9(5), 2200-6 (2010). [Pubmed]

Lenassi M, Cagney G, Liao M, Vaupotic T, Cheng Y, Krogan NJ, Plemenitas A, Matija Peterlin B. HIV Nef is secreted in exosomes and triggers apoptosis in bystander CD4+ cells. Traffic. 11(1), 110-22 (2010). [Pubmed]

Lim WA, Pawson T. Phosphotyrosine signaling: evolving a new cellular communication system. Cell. 142(5), 661-7 (2010). [Pubmed]

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. 9(5), 976-87 (2010). [Pubmed]

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. 3(130),ra53 (2010). [Pubmed]

Mott BT, Ferreira RS, Simeonov A, Jadhav A, Ang KK, Leister W, Shen M, Silveira JT, Doyle PS, Arkin MR, McKerrow JH, Inglese J, Austin CP, Thomas CJ, Shoichet BK, Maloney DJ. Identification and optimization of inhibitors of Trypanosomal cysteine proteases: cruzain, rhodesain, and TbCatB. J Med Chem 53(1),52-60 (2010). [Pubmed]

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. 130(10),2377-88(2010). [Pubmed]

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 MAGUKs to juxtaparanodes of myelinated axons. J Neurosci. 30(3),1038-48 (2010). [Pubmed]

Ohol YM, Goetz DH, Chan K, Shiloh MU, Craik CS, Cox JS. Mycobacterium tuberculosis MycP1 protease plays a dual role in regulation of ESX-1 secretion and virulence. Cell Host Microbe. 7(3),210-20 (2010). [Pubmed]

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. 77(3), 730-42 (2010). [Pubmed]

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. 30(9), 2264-79 (2010). [Pubmed]

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. 107(32),14508-13 (2010). [Pubmed]

Rishal I, Michaelevski I, Rozenbaum M, Shinder V, Medzihradszky KF, Burlingame AL, Fainzilber M. Axoplasm isolation from peripheral nerve. Dev Neurobiol. 70(2), 126-33 (2010). [Pubmed]

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