Al Burlingame, PhD
Professor
Pharmaceutical Chemistry
School of Pharmacy

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.

• Targeted suppression of mTORC2 reduces seizures across models of epilepsy.
  Nature communications 2023 Okoh J, Mays J, Bacq A, Oses-Prieto JA, Tyanova S, Chen CJ, Imanbeyev K, Doladilhe M, Zhou H, Jafar-Nejad P, Burlingame A, Noebels J, Baulac S, Costa-Mattioli M
• Antibody-directed extracellular proximity biotinylation reveals that Contactin-1 regulates axo-axonic innervation of axon initial segments.
  Nature communications 2023 Ogawa Y, Lim BC, George S, Oses-Prieto JA, Rasband JM, Eshed-Eisenbach Y, Hamdan H, Nair S, Boato F, Peles E, Burlingame AL, Van Aelst L, Rasband MN
• A Legionella toxin exhibits tRNA mimicry and glycosyl transferase activity to target the translation machinery and trigger a ribotoxic stress response.
  Nature cell biology 2023 Subramanian A, Wang L, Moss T, Voorhies M, Sangwan S, Stevenson E, Pulido EH, Kwok S, Chalkley RJ, Li KH, Krogan NJ, Swaney DL, Burlingame AL, Floor SN, Sil A, Walter P, Mukherjee S
• MCP's New Editorial Posture Moving Forward.
  Molecular & cellular proteomics : MCP 2023 Burlingame A
• Adaptor protein AP-3 produces synaptic vesicles that release at high frequency by recruiting phospholipid flippase ATP8A1.
  Nature neuroscience 2023 Xu H, Oses-Prieto JA, Khvotchev M, Jain S, Liang J, Burlingame A, Edwards RH
• The oncomodulin receptor ArmC10 enables axon regeneration in mice after nerve injury and neurite outgrowth in human iPSC-derived sensory neurons.
  Science translational medicine 2023 Xie L, Yin Y, Jayakar S, Kawaguchi R, Wang Q, Peterson S, Shi C, Turnes BL, Zhang Z, Oses-Prieto J, Li J, Burlingame A, Woolf CJ, Geschwind D, Rasband M, Benowitz LI
• PTBP1 regulates injury responses and sensory pathways in adult peripheral neurons.
  Science advances 2023 Alber S, Di Matteo P, Zdradzinski MD, Dalla Costa I, Medzihradszky KF, Kawaguchi R, Di Pizio A, Freund P, Panayotis N, Marvaldi L, Doron-Mandel E, Okladnikov N, Rishal I, Nevo R, Coppola G, Lee SJ, …
• Targeted high-throughput mutagenesis of the human spliceosome reveals its in vivo operating principles.
  Molecular cell 2023 Beusch I, Rao B, Studer MK, Luhovska T, Šukyte V, Lei S, Oses-Prieto J, SeGraves E, Burlingame A, Jonas S, Madhani HD
• Non-specific recognition of histone modifications by H3K9bhb antibody.
  iScience 2023 Tsusaka T, Oses-Prieto JA, Lee C, DeFelice BC, Burlingame AL, Goldberg EL
• Contrastsing synaptic roles of MDGA1 and MDGA2.
  bioRxiv : the preprint server for biology 2023 Bemben MA, Sandoval M, Le AA, Won S, Chau VN, Lauterborn JC, Incontro S, Li KH, Burlingame AL, Roche KW, Gall CM, Nicoll RA, Diaz-Alonso J
• Non-specific recognition of histone modifications by H3K9bhb antibody.
  bioRxiv : the preprint server for biology 2023 Tsusaka T, Oses-Prieto JA, Lee C, DeFelice BC, Burlingame AL, Goldberg E
• Capturing the hierarchically assorted modules of protein-protein interactions in the organized nucleome.
  Molecular plant 2023 Dai S, Liu S, Zhou C, Yu F, Zhu G, Zhang W, Deng H, Burlingame A, Yu W, Wang T, Li N
• Characterization of the Ciguatoxin Profile in Fish Samples from the Eastern Atlantic Ocean using Capillary Liquid Chromatography-High Resolution Mass Spectrometry.
  Food chemistry 2023 Estevez P, Oses Prieto J, Burlingame A, Gago Martinez A
• Mapping the signaling network of BIN2 kinase using TurboID-mediated biotin labeling and phosphoproteomics.
  The Plant cell 2023 Kim TW, Park CH, Hsu CC, Kim YW, Ko YW, Zhang Z, Zhu JY, Hsiao YC, Branon T, Kaasik K, Saldivar E, Li K, Pasha A, Provart NJ, Burlingame AL, Xu SL, Ting AY, Wang ZY
• Antibody-directed extracellular proximity biotinylation reveals Contactin-1 regulates axo-axonic innervation of axon initial segments.
  bioRxiv : the preprint server for biology 2023 Ogawa Y, Lim BC, George S, Oses-Prieto JA, Rasband JM, Eshed-Eisenbach Y, Nair S, Boato F, Peles E, Burlingame AL, Van Aelst L, Rasband MN
• O-GlcNAc glycosylation orchestrates fate decision and niche function of bone marrow stromal progenitors.
  eLife 2023 Zhang Z, Huang Z, Awad M, Elsalanty M, Cray J, Ball LE, Maynard JC, Burlingame AL, Zeng H, Mansky KC, Ruan HB
• Chemical Genetic Identification of PKC Epsilon Substrates in Mouse Brain.
  Molecular & cellular proteomics : MCP 2023 Dugan MP, Ferguson LB, Hertz NT, Chalkley RJ, Burlingame AL, Shokat KM, Parker PJ, Messing RO
• Capture, Release, and Identification of Newly Synthesized Proteins for Improved Profiling of Functional Translatomes.
  Molecular & cellular proteomics : MCP 2023 Phillips NJ, Vinaithirthan BM, Oses-Prieto JA, Chalkley RJ, Burlingame AL
• In-Cell Chemical Crosslinking Identifies Hotspots for SQSTM-1/p62-IκBα Interaction That Underscore a Critical Role of p62 in Limiting NF-κB Activation Through IκBα Stabilization.
  Molecular & cellular proteomics : MCP 2023 Liu Y, Trnka MJ, He L, Burlingame AL, Correia MA
• Regulation of eIF4E guides a unique translational program to control erythroid maturation.
  Science advances 2022 Forester CM, Oses-Prieto JA, Phillips NJ, Miglani S, Pang X, Byeon GW, DeMarco R, Burlingame A, Barna M, Ruggero D
• A New Monoclonal Antibody Enables BAR Analysis of Subcellular Importin β1 Interactomes.
  Molecular & cellular proteomics : MCP 2022 Song DA, Alber S, Doron-Mandel E, Schmid V, Albus CA, Leitner O, Hamawi H, Oses-Prieto JA, Dezorella N, Burlingame AL, Fainzilber M, Rishal I
• A stem cell roadmap of ribosome heterogeneity reveals a function for RPL10A in mesoderm production.
  Nature communications 2022 Genuth NR, Shi Z, Kunimoto K, Hung V, Xu AF, Kerr CH, Tiu GC, Oses-Prieto JA, Salomon-Shulman REA, Axelrod JD, Burlingame AL, Loh KM, Barna M
• Epithelial STAT6 O-GlcNAcylation drives a concerted anti-helminth alarmin response dependent on tuft cell hyperplasia and Gasdermin C.
  Immunity 2022 Zhao M, Ren K, Xiong X, Xin Y, Zou Y, Maynard JC, Kim A, Battist AP, Koneripalli N, Wang Y, Chen Q, Xin R, Yang C, Huang R, Yu J, Huang Z, Zhang Z, Wang H, Wang D, Xiao Y, Salgado OC, Jarjour NN, …
• Deconvoluting signals downstream of growth and immune receptor kinases by phosphocodes of the BSU1 family phosphatases.
  Nature plants 2022 Park CH, Bi Y, Youn JH, Kim SH, Kim JG, Xu NY, Shrestha R, Burlingame AL, Xu SL, Mudgett MB, Kim SK, Kim TW, Wang ZY
• Intra-axonal translation of Khsrp mRNA slows axon regeneration by destabilizing localized mRNAs.
  Nucleic acids research 2022 Patel P, Buchanan CN, Zdradzinski MD, Sahoo PK, Kar AN, Lee SJ, Vaughn LS, Urisman A, Oses-Prieto J, Dell'Orco M, Cassidy DE, Costa ID, Miller S, Thames E, Smith TP, Burlingame AL, Perrone-Bizzozero N…
• Reversible lysine-targeted probes reveal residence time-based kinase selectivity.
  Nature chemical biology 2022 Yang T, Cuesta A, Wan X, Craven GB, Hirakawa B, Khamphavong P, May JR, Kath JC, Lapek JD, Niessen S, Burlingame AL, Carelli JD, Taunton J
• Covalent labeling of a chromatin reader domain using proximity-reactive cyclic peptides.
  Chemical science 2022 Zhang MY, Yang H, Ortiz G, Trnka MJ, Petronikolou N, Burlingame AL, DeGrado WF, Fujimori DG
• Epithelial STAT6 O-GlcNAcylation drives a concerted anti-helminth alarmin response dependent on tuft cell hyperplasia and Gasdermin C.
  Immunity 2022 Zhao M, Ren K, Xiong X, Xin Y, Zou Y, Maynard JC, Kim A, Battist AP, Koneripalli N, Wang Y, Chen Q, Xin R, Yang C, Huang R, Yu J, Huang Z, Zhang Z, Wang H, Wang D, Xiao Y, Salgado OC, Jarjour NN, …
• Modulating environmental signals to reveal mechanisms and vulnerabilities of cancer persisters.
  Science advances 2022 Sun X, Bieber JM, Hammerlindl H, Chalkley RJ, Li KH, Burlingame AL, Jacobson MP, Wu LF, Altschuler SJ
• Disruption of MeCP2-TCF20 complex underlies distinct neurodevelopmental disorders.
  Proceedings of the National Academy of Sciences of the United States of America 2022 Zhou J, Hamdan H, Yalamanchili HK, Pang K, Pohodich AE, Lopez J, Shao Y, Oses-Prieto JA, Li L, Kim W, Durham MA, Bajikar SS, Palmer DJ, Ng P, Thompson ML, Bebin EM, Müller AJ, Kuechler A, Kampmeier A,…
• Comparative Proteomics of Coxiella like Endosymbionts (CLEs) in the Symbiotic Organs of Rhipicephalus sanguineus Ticks.
  Microbiology spectrum 2022 Cibichakravarthy B, Oses-Prieto JA, Ben-Yosef M, Burlingame AL, Karr TL, Gottlieb Y
• Hemin-Induced Death Models Hemorrhagic Stroke and Is a Variant of Classical Neuronal Ferroptosis.
  The Journal of neuroscience : the official journal of the Society for Neuroscience 2022 Zille M, Oses-Prieto JA, Savage SR, Karuppagounder SS, Chen Y, Kumar A, Morris JH, Scheidt KA, Burlingame AL, Ratan RR
• TSC1 loss increases risk for tauopathy by inducing tau acetylation and preventing tau clearance via chaperone-mediated autophagy.
  Science advances 2021 Alquezar C, Schoch KM, Geier EG, Ramos EM, Scrivo A, Li KH, Argouarch AR, Mlynarski EE, Dombroski B, DeTure M, Dickson DW, Yokoyama JS, Cuervo AM, Burlingame AL, Schellenberg GD, Miller TM, Miller BL,…
• Molecular Characterization of AMPA-Receptor-Containing Vesicles.
  Frontiers in molecular neuroscience 2021 Peters JJ, Leitz J, Oses-Prieto JA, Burlingame AL, Brunger AT
• Working Toward Reducing Bias in Peer Review.
  Molecular & cellular proteomics : MCP 2021 Rye KA, Davidson NO, Burlingame AL, Guengerich FP
• Working toward reducing bias in peer review.
  The Journal of biological chemistry 2021 Rye KA, Davidson NO, Burlingame AL, Guengerich FP
• Working toward reducing bias in peer review.
  Journal of lipid research 2021 Rye KA, Davidson NO, Burlingame AL, Guengerich FP
• ERα is an RNA-binding protein sustaining tumor cell survival and drug resistance.
  Cell 2021 Xu Y, Huangyang P, Wang Y, Xue L, Devericks E, Nguyen HG, Yu X, Oses-Prieto JA, Burlingame AL, Miglani S, Goodarzi H, Ruggero D
• The glycine arginine-rich domain of the RNA-binding protein nucleolin regulates its subcellular localization.
  The EMBO journal 2021 Doron-Mandel E, Koppel I, Abraham O, Rishal I, Smith TP, Buchanan CN, Sahoo PK, Kadlec J, Oses-Prieto JA, Kawaguchi R, Alber S, Zahavi EE, Di Matteo P, Di Pizio A, Song DA, Okladnikov N, Gordon D, Ben…
• Cell-cell adhesion regulates Merlin/NF2 interaction with the PAF complex.
  PloS one 2021 Roehrig AE, Klupsch K, Oses-Prieto JA, Chaib S, Henderson S, Emmett W, Young LC, Surinova S, Blees A, Pfeiffer A, Tijani M, Brunk F, Hartig N, Muñoz-Alegre M, Hergovich A, Jennings BH, Burlingame AL, …
• Isotopically Dimethyl Labeling-Based Quantitative Proteomic Analysis of Phosphoproteomes of Soybean Cultivars.
  Biomolecules 2021 Moradi A, Dai S, Wong EOY, Zhu G, Yu F, Lam HM, Wang Z, Burlingame A, Lin C, Afsharifar A, Yu W, Wang T, Li N
• Processing of progranulin into granulins involves multiple lysosomal proteases and is affected in frontotemporal lobar degeneration.
  Molecular neurodegeneration 2021 Mohan S, Sampognaro PJ, Argouarch AR, Maynard JC, Welch M, Patwardhan A, Courtney EC, Zhang J, Mason A, Li KH, Huang EJ, Seeley WW, Miller BL, Burlingame A, Jacobson MP, Kao AW
• Ankyrin-R regulates fast-spiking interneuron excitability through perineuronal nets and Kv3.1b K+ channels.
  eLife 2021 Stevens SR, Longley CM, Ogawa Y, Teliska LH, Arumanayagam AS, Nair S, Oses-Prieto JA, Burlingame AL, Cykowski MD, Xue M, Rasband MN
• Low-density lipoprotein receptor-related protein 1 (LRP1) is a novel receptor for apolipoprotein A4 (APOA4) in adipose tissue.
  Scientific reports 2021 Qu J, Fourman S, Fitzgerald M, Liu M, Nair S, Oses-Prieto J, Burlingame A, Morris JH, Davidson WS, Tso P, Bhargava A
• Native mass spectrometry analyses of chaperonin complex TRiC/CCT reveal subunit N-terminal processing and re-association patterns.
  Scientific reports 2021 Collier MP, Moreira KB, Li KH, Chen YC, Itzhak D, Samant R, Leitner A, Burlingame A, Frydman J
• Proteomic Analysis of Src Family Kinase Phosphorylation States in Cancer Cells Suggests Deregulation of the Unique Domain.
  Molecular cancer research : MCR 2021 Ruiz-Saenz A, Zahedi F, Peterson E, Yoo A, Dreyer CA, Spassov DS, Oses-Prieto J, Burlingame A, Moasser MM
• The major cap-binding protein eIF4E regulates lipid homeostasis and diet-induced obesity.
  Nature metabolism 2021 Conn CS, Yang H, Tom HJ, Ikeda K, Oses-Prieto JA, Vu H, Oguri Y, Nair S, Gill RM, Kajimura S, DeBerardinis RJ, Burlingame AL, Ruggero D
• Arabidopsis ACINUS is O-glycosylated and regulates transcription and alternative splicing of regulators of reproductive transitions.
  Nature communications 2021 Bi Y, Deng Z, Ni W, Shrestha R, Savage D, Hartwig T, Patil S, Hong SH, Zhang Z, Oses-Prieto JA, Li KH, Quail PH, Burlingame AL, Xu SL, Wang ZY
• Composition and origin of lung fluid proteome in premature infants and relationship to respiratory outcome.
  PloS one 2020 Ballard PL, Oses-Prieto J, Chapin C, Segal MR, Ballard RA, Burlingame AL
• Reactivity-Based Probe of the Iron(II)-Dependent Interactome Identifies New Cellular Modulators of Ferroptosis.
  Journal of the American Chemical Society 2020 Chen YC, Oses-Prieto JA, Pope LE, Burlingame AL, Dixon SJ, Renslo AR
• A Novel Mechanism for NF-κB-activation via IκB-aggregation: Implications for Hepatic Mallory-Denk-Body Induced Inflammation.
  Molecular & cellular proteomics : MCP 2020 Liu Y, Trnka MJ, Guan S, Kwon D, Kim DH, Chen JJ, Greer PA, Burlingame AL, Correia MA
• Age-related loss of neural stem cell O-GlcNAc promotes a glial fate switch through STAT3 activation.
  Proceedings of the National Academy of Sciences of the United States of America 2020 White CW, Fan X, Maynard JC, Wheatley EG, Bieri G, Couthouis J, Burlingame AL, Villeda SA
• An ER translocon for multi-pass membrane protein biogenesis.
  eLife 2020 McGilvray PT, Anghel SA, Sundaram A, Zhong F, Trnka MJ, Fuller JR, Hu H, Burlingame AL, Keenan RJ
• Cytosolic N-GlcNAc proteins are formed by the action of endo-β-N-acetylglucosaminidase.
  Biochemical and biophysical research communications 2020 Maynard JC, Fujihira H, Dolgonos GE, Suzuki T, Burlingame AL
• TMEM16K is an interorganelle regulator of endosomal sorting.
  Nature communications 2020 Petkovic M, Oses-Prieto J, Burlingame A, Jan LY, Jan YN
• Opening ASBMB publications freely to all.
  Journal of lipid research 2020 Gierasch LM, Davidson NO, Rye KA, Burlingame AL
• Opening ASBMB publications freely to all.
  Molecular & cellular proteomics : MCP 2020 Gierasch LM, Davidson NO, Rye KA, Burlingame AL
• TRIPP Is a Plant-Specific Component of the Arabidopsis TRAPPII Membrane Trafficking Complex with Important Roles in Plant Development.
  The Plant cell 2020 Garcia VJ, Xu SL, Ravikumar R, Wang W, Elliott L, Gonzalez E, Fesenko M, Altmann M, Brunschweiger B, Falter-Braun P, Moore I, Burlingame A, Assaad FF, Wang ZY
• LEM2 phase separation promotes ESCRT-mediated nuclear envelope reformation.
  Nature 2020 von Appen A, LaJoie D, Johnson IE, Trnka MJ, Pick SM, Burlingame AL, Ullman KS, Frost A
• Characterization of Prenylated C-terminal Peptides Using a Thiopropyl-based Capture Technique and LC-MS/MS.
  Molecular & cellular proteomics : MCP 2020 Wilkins JA, Kaasik K, Chalkley RJ, Burlingame AL
• Virtual Issue: Technological Innovations.
  Molecular & cellular proteomics : MCP 2020 Gingras AC, Carr SA, Burlingame AL
• Compliance Checklists No Longer Required at Initial Manuscript Submission.
  Molecular & cellular proteomics : MCP 2020 Burlingame AL, Carr S, Gingras AC
• The change of gravity vector induces short-term phosphoproteomic alterations in Arabidopsis.
  Journal of proteomics 2020 Yang Z, Guo G, Yang N, Pun SS, Ho TKL, Ji L, Hu I, Zhang J, Burlingame AL, Li N
• The Data Must Be Accessible to All.
  Molecular & cellular proteomics : MCP 2020 Gierasch LM, Davidson NO, Rye KA, Burlingame AL
• The data must be accessible to all.
  The Journal of biological chemistry 2020 Gierasch LM, Davidson NO, Rye KA, Burlingame AL
• The data must be accessible to all.
  Journal of lipid research 2020 Gierasch LM, Davidson NO, Rye KA, Burlingame AL
• Ligand Conformational Bias Drives Enantioselective Modification of a Surface-Exposed Lysine on Hsp90.
  Journal of the American Chemical Society 2020 Cuesta A, Wan X, Burlingame AL, Taunton J
• NuMA1 promotes axon initial segment assembly through inhibition of endocytosis.
  The Journal of cell biology 2020 Torii T, Ogawa Y, Liu CH, Ho TS, Hamdan H, Wang CC, Oses-Prieto JA, Burlingame AL, Rasband MN
• Mapping axon initial segment structure and function by multiplexed proximity biotinylation.
  Nature communications 2020 Hamdan H, Lim BC, Torii T, Joshi A, Konning M, Smith C, Palmer DJ, Ng P, Leterrier C, Oses-Prieto JA, Burlingame AL, Rasband MN
• p38γ MAPK contributes to left ventricular remodeling after pathologic stress and disinhibits calpain through phosphorylation of calpastatin.
  FASEB journal : official publication of the Federation of American Societies for Experimental Biology 2019 Loonat AA, Martin ED, Sarafraz-Shekary N, Tilgner K, Hertz NT, Levin R, Shokat KM, Burlingame AL, Arabacilar P, Uddin S, Thomas M, Marber MS, Clark JE
• HP1 reshapes nucleosome core to promote phase separation of heterochromatin.
  Nature 2019 Sanulli S, Trnka MJ, Dharmarajan V, Tibble RW, Pascal BD, Burlingame AL, Griffin PR, Gross JD, Narlikar GJ
• Quantitative proteomic analysis reveals high interference on protein expression of H9c2 cells activated with glucose and cardiotonic steroids.
  Journal of proteomics 2019 Meneses-Romero E, Hernández-Orihuela L, Pando-Robles V, López TD, Oses-Prieto JA, Burlingame AL, Batista CVF
• The Golgi Outpost Protein TPPP Nucleates Microtubules and Is Critical for Myelination.
  Cell 2019 Fu MM, McAlear TS, Nguyen H, Oses-Prieto JA, Valenzuela A, Shi RD, Perrino JJ, Huang TT, Burlingame AL, Bechstedt S, Barres BA
• The Gene-Silencing Protein MORC-1 Topologically Entraps DNA and Forms Multimeric Assemblies to Cause DNA Compaction.
  Molecular cell 2019 Kim H, Yen L, Wongpalee SP, Kirshner JA, Mehta N, Xue Y, Johnston JB, Burlingame AL, Kim JK, Loparo JJ, Jacobsen SE
• A two-step probing method to compare lysine accessibility across macromolecular complex conformations.
  RNA biology 2019 MacRae AJ, Coltri P, Hrabeta-Robinson E, Chalkley RJ, Burlingame AL, Jurica MS
• Mutual Regulation of Receptor-Like Kinase SIT1 and B'κ-PP2A Shapes the Early Response of Rice to Salt Stress.
  The Plant cell 2019 Zhao JL, Zhang LQ, Liu N, Xu SL, Yue ZL, Zhang LL, Deng ZP, Burlingame AL, Sun DY, Wang ZY, Sun Y, Zhang SW
• Tau/MAPT disease-associated variant A152T alters tau function and toxicity via impaired retrograde axonal transport.
  Human molecular genetics 2019 Butler VJ, Salazar DA, Soriano-Castell D, Alves-Ferreira M, Dennissen FJA, Vohra M, Oses-Prieto JA, Li KH, Wang AL, Jing B, Li B, Groisman A, Gutierrez E, Mooney S, Burlingame AL, Ashrafi K, Mandelkow…
• Phosphoregulation of the oncogenic protein regulator of cytokinesis 1 (PRC1) by the atypical CDK16/CCNY complex.
  Experimental & molecular medicine 2019 Hernández-Ortega S, Sánchez-Botet A, Quandt E, Masip N, Gasa L, Verde G, Jiménez J, Levin RS, Rutaganira FU, Burlingame AL, Wolfgeher D, Ribeiro MPC, Kron SJ, Shokat KM, Clotet J
• Phosphorylation at distinct subcellular locations underlies specificity in mTORC2-mediated activation of SGK1 and Akt.
  Journal of cell science 2019 Gleason CE, Oses-Prieto JA, Li KH, Saha B, Situ G, Burlingame AL, Pearce D
• Mechanisms underlying the synaptic trafficking of the glutamate delta receptor GluD1.
  Molecular psychiatry 2019 Tao W, Ma C, Bemben MA, Li KH, Burlingame AL, Zhang M, Nicoll RA
• For the Sake of Science.
  Molecular & cellular proteomics : MCP 2019 Gierasch LM, Davidson NO, Rye KA, Burlingame AL
• For the sake of science.
  The Journal of biological chemistry 2019 Gierasch LM, Davidson NO, Rye KA, Burlingame AL
• For the sake of science.
  Journal of lipid research 2019 Gierasch LM, Davidson NO, Rye KA, Burlingame AL
• Chemically reprogramming the phospho-transfer reaction to crosslink protein kinases to their substrates.
  Protein science : a publication of the Protein Society 2019 Wong AW, Urisman A, Burlingame AL, Shokat KM
• The lineage stability and suppressive program of regulatory T cells require protein O-GlcNAcylation.
  Nature communications 2019 Liu B, Salgado OC, Singh S, Hippen KL, Maynard JC, Burlingame AL, Ball LE, Blazar BR, Farrar MA, Hogquist KA, Ruan HB
• Histone H3 binding to the PHD1 domain of histone demethylase KDM5A enables active site remodeling.
  Nature communications 2019 Longbotham JE, Chio CM, Dharmarajan V, Trnka MJ, Torres IO, Goswami D, Ruiz K, Burlingame AL, Griffin PR, Fujimori DG
• Chemically induced vesiculation as a platform for studying TMEM16F activity.
  Proceedings of the National Academy of Sciences of the United States of America 2019 Han TW, Ye W, Bethel NP, Zubia M, Kim A, Li KH, Burlingame AL, Grabe M, Jan YN, Jan LY
• Probing the Interactome of Corticotropin-Releasing Factor Receptor Heteromers Using Mass Spectrometry.
  Methods in molecular biology (Clifton, N.J.) 2019 Hasdemir B, Oses-Prieto JA, Burlingame A, Bhargava A
• A Viral Protein Restricts Drosophila RNAi Immunity by Regulating Argonaute Activity and Stability.
  Cell host & microbe 2018 Nayak A, Kim DY, Trnka MJ, Kerr CH, Lidsky PV, Stanley DJ, Rivera BM, Li KH, Burlingame AL, Jan E, Frydman J, Gross JD, Andino R
• Targeting CD46 for both adenocarcinoma and neuroendocrine prostate cancer.
  JCI insight 2018 Su Y, Liu Y, Behrens CR, Bidlingmaier S, Lee NK, Aggarwal R, Sherbenou DW, Burlingame AL, Hann BC, Simko JP, Premasekharan G, Paris PL, Shuman MA, Seo Y, Small EJ, Liu B
• Axonal G3BP1 stress granule protein limits axonal mRNA translation and nerve regeneration.
  Nature communications 2018 Sahoo PK, Lee SJ, Jaiswal PB, Alber S, Kar AN, Miller-Randolph S, Taylor EE, Smith T, Singh B, Ho TS, Urisman A, Chand S, Pena EA, Burlingame AL, Woolf CJ, Fainzilber M, English AW, Twiss JL
• hnRNPs Interacting with mRNA Localization Motifs Define Axonal RNA Regulons.
  Molecular & cellular proteomics : MCP 2018 Lee SJ, Oses-Prieto JA, Kawaguchi R, Sahoo PK, Kar AN, Rozenbaum M, Oliver D, Chand S, Ji H, Shtutman M, Miller-Randolph S, Taylor RJ, Fainzilber M, Coppola G, Burlingame AL, Twiss JL
• The lincRNA MIRAT binds to IQGAP1 and modulates the MAPK pathway in NRAS mutant melanoma.
  Scientific reports 2018 Sanlorenzo M, Vujic I, Esteve-Puig R, Lai K, Vujic M, Lin K, Posch C, Dimon M, Moy A, Zekhtser M, Johnston K, Gho D, Ho W, Gajjala A, Oses Prieto J, Burlingame A, Daud A, Rappersberger K, Ortiz-Urda S
• Schwann cell O-GlcNAcylation promotes peripheral nerve remyelination via attenuation of the AP-1 transcription factor JUN.
  Proceedings of the National Academy of Sciences of the United States of America 2018 Kim S, Maynard JC, Strickland A, Burlingame AL, Milbrandt J
• Gaining an Easy Visual Grasp on MCP Content.
  Molecular & cellular proteomics : MCP 2018 Burlingame A, Carr S, Gingras AC
• Arginine methylation of SMAD7 by PRMT1 in TGF-β-induced epithelial-mesenchymal transition and epithelial stem-cell generation.
  The Journal of biological chemistry 2018 Katsuno Y, Qin J, Oses-Prieto J, Wang H, Jackson-Weaver O, Zhang T, Lamouille S, Wu J, Burlingame A, Xu J, Derynck R
• The ER membrane protein complex interacts cotranslationally to enable biogenesis of multipass membrane proteins.
  eLife 2018 Shurtleff MJ, Itzhak DN, Hussmann JA, Schirle Oakdale NT, Costa EA, Jonikas M, Weibezahn J, Popova KD, Jan CH, Sinitcyn P, Vembar SS, Hernandez H, Cox J, Burlingame AL, Brodsky JL, Frost A, Borner GH,…
• A molecular cascade modulates MAP1B and confers resistance to mTOR inhibition in human glioblastoma.
  Neuro-oncology 2018 Laks DR, Oses-Prieto JA, Alvarado AG, Nakashima J, Chand S, Azzam DB, Gholkar AA, Sperry J, Ludwig K, Condro MC, Nazarian S, Cardenas A, Shih MYS, Damoiseaux R, France B, Orozco N, Visnyei K, Crisman …
• Translatome Regulation in Neuronal Injury and Axon Regrowth.
  eNeuro 2018 Rozenbaum M, Rajman M, Rishal I, Koppel I, Koley S, Medzihradszky KF, Oses-Prieto JA, Kawaguchi R, Amieux PS, Burlingame AL, Coppola G, Fainzilber M
• The nucleosomal acidic patch relieves auto-inhibition by the ISWI remodeler SNF2h.
  eLife 2018 Gamarra N, Johnson SL, Trnka MJ, Burlingame AL, Narlikar GJ
• Locally translated mTOR controls axonal local translation in nerve injury.
  Science (New York, N.Y.) 2018 Terenzio M, Koley S, Samra N, Rishal I, Zhao Q, Sahoo PK, Urisman A, Marvaldi L, Oses-Prieto JA, Forester C, Gomes C, Kalinski AL, Di Pizio A, Doron-Mandel E, Perry RB, Koppel I, Twiss JL, Burlingame …
• The Transcriptionally Permissive Chromatin State of Embryonic Stem Cells Is Acutely Tuned to Translational Output.
  Cell stem cell 2018 Bulut-Karslioglu A, Macrae TA, Oses-Prieto JA, Covarrubias S, Percharde M, Ku G, Diaz A, McManus MT, Burlingame AL, Ramalho-Santos M
• Prp8 positioning of U5 snRNA is linked to 5' splice site recognition.
  RNA (New York, N.Y.) 2018 MacRae AJ, Mayerle M, Hrabeta-Robinson E, Chalkley RJ, Guthrie C, Burlingame AL, Jurica MS
• Revealing nascent proteomics in signaling pathways and cell differentiation.
  Proceedings of the National Academy of Sciences of the United States of America 2018 Forester CM, Zhao Q, Phillips NJ, Urisman A, Chalkley RJ, Oses-Prieto JA, Zhang L, Ruggero D, Burlingame AL
• αII Spectrin Forms a Periodic Cytoskeleton at the Axon Initial Segment and Is Required for Nervous System Function.
  The Journal of neuroscience : the official journal of the Society for Neuroscience 2017 Huang CY, Zhang C, Ho TS, Oses-Prieto J, Burlingame AL, Lalonde J, Noebels JL, Leterrier C, Rasband MN
• Hypoxia-ischemia modifies postsynaptic GluN2B-containing NMDA receptor complexes in the neonatal mouse brain.
  Experimental neurology 2017 Lu F, Shao G, Wang Y, Guan S, Burlingame AL, Liu X, Liang X, Knox R, Ferriero DM, Jiang X
• Peripheral Elevation of a Klotho Fragment Enhances Brain Function and Resilience in Young, Aging, and α-Synuclein Transgenic Mice.
  Cell reports 2017 Leon J, Moreno AJ, Garay BI, Chalkley RJ, Burlingame AL, Wang D, Dubal DB
• Actin cytoskeleton-dependent regulation of corticotropin-releasing factor receptor heteromers.
  Molecular biology of the cell 2017 Hasdemir B, Mahajan S, Oses-Prieto J, Chand S, Woolley M, Burlingame A, Grammatopoulos DK, Bhargava A
• Liquid droplet formation by HP1α suggests a role for phase separation in heterochromatin.
  Nature 2017 Larson AG, Elnatan D, Keenen MM, Trnka MJ, Johnston JB, Burlingame AL, Agard DA, Redding S, Narlikar GJ
• Regulation of Rvb1/Rvb2 by a Domain within the INO80 Chromatin Remodeling Complex Implicates the Yeast Rvbs as Protein Assembly Chaperones.
  Cell reports 2017 Zhou CY, Stoddard CI, Johnston JB, Trnka MJ, Echeverria I, Palovcak E, Sali A, Burlingame AL, Cheng Y, Narlikar GJ
• PPKs mediate direct signal transfer from phytochrome photoreceptors to transcription factor PIF3.
  Nature communications 2017 Ni W, Xu SL, González-Grandío E, Chalkley RJ, Huhmer AFR, Burlingame AL, Wang ZY, Quail PH
• Proteomic Analysis of Mouse Cortex Postsynaptic Density following Neonatal Brain Hypoxia-Ischemia.
  Developmental neuroscience 2017 Shao G, Wang Y, Guan S, Burlingame AL, Lu F, Knox R, Ferriero DM, Jiang X
• Proteomic analysis reveals O-GlcNAc modification on proteins with key regulatory functions in Arabidopsis.
  Proceedings of the National Academy of Sciences of the United States of America 2017 Xu SL, Chalkley RJ, Maynard JC, Wang W, Ni W, Jiang X, Shin K, Cheng L, Savage D, Hühmer AF, Burlingame AL, Wang ZY
• Reduced Insulin/IGF-1 Signaling Restores the Dynamic Properties of Key Stress Granule Proteins during Aging.
  Cell reports 2017 Lechler MC, Crawford ED, Groh N, Widmaier K, Jung R, Kirstein J, Trinidad JC, Burlingame AL, David DC
• TAOK2 Kinase Mediates PSD95 Stability and Dendritic Spine Maturation through Septin7 Phosphorylation.
  Neuron 2017 Yadav S, Oses-Prieto JA, Peters CJ, Zhou J, Pleasure SJ, Burlingame AL, Jan LY, Jan YN
• Broad-Spectrum Kinase Profiling in Live Cells with Lysine-Targeted Sulfonyl Fluoride Probes.
  Journal of the American Chemical Society 2017 Zhao Q, Ouyang X, Wan X, Gajiwala KS, Kath JC, Jones LH, Burlingame AL, Taunton J
• An Optimized Chromatographic Strategy for Multiplexing In Parallel Reaction Monitoring Mass Spectrometry: Insights from Quantitation of Activated Kinases.
  Molecular & cellular proteomics : MCP 2016 Urisman A, Levin RS, Gordan JD, Webber JT, Hernandez H, Ishihama Y, Shokat KM, Burlingame AL
• Quantitative Proteomics Reveals Fundamental Regulatory Differences in Oncogenic HRAS and Isocitrate Dehydrogenase (IDH1) Driven Astrocytoma.
  Molecular & cellular proteomics : MCP 2016 Doll S, Urisman A, Oses-Prieto JA, Arnott D, Burlingame AL
• Antiinflammatory Effects of Budesonide in Human Fetal Lung.
  American journal of respiratory cell and molecular biology 2016 Barrette AM, Roberts JK, Chapin C, Egan EA, Segal MR, Oses-Prieto JA, Chand S, Burlingame AL, Ballard PL
• Immunopurification and Mass Spectrometry Identifies Protein Phosphatase 2A (PP2A) and BIN2/GSK3 as Regulators of AKS Transcription Factors in Arabidopsis.
  Molecular plant 2016 Bu SL, Liu C, Liu N, Zhao JL, Ai LF, Chi H, Li KL, Chien CW, Burlingame AL, Zhang SW, Wang ZY
• Schwann Cell O-GlcNAc Glycosylation Is Required for Myelin Maintenance and Axon Integrity.
  The Journal of neuroscience : the official journal of the Society for Neuroscience 2016 Kim S, Maynard JC, Sasaki Y, Strickland A, Sherman DL, Brophy PJ, Burlingame AL, Milbrandt J
• Structure of a Complete Mediator-RNA Polymerase II Pre-Initiation Complex.
  Cell 2016 Robinson PJ, Trnka MJ, Bushnell DA, Davis RE, Mattei PJ, Burlingame AL, Kornberg RD
• Cysteine S-linked N-acetylglucosamine (S-GlcNAcylation), A New Post-translational Modification in Mammals.
  Molecular & cellular proteomics : MCP 2016 Maynard JC, Burlingame AL, Medzihradszky KF
• Mouse MORC3 is a GHKL ATPase that localizes to H3K4me3 marked chromatin.
  Proceedings of the National Academy of Sciences of the United States of America 2016 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
• Innate immunity kinase TAK1 phosphorylates Rab1 on a hotspot for posttranslational modifications by host and pathogen.
  Proceedings of the National Academy of Sciences of the United States of America 2016 Levin RS, Hertz NT, Burlingame AL, Shokat KM, Mukherjee S
• Nucleolin-Mediated RNA Localization Regulates Neuron Growth and Cycling Cell Size.
  Cell reports 2016 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, …
• Activation of HIPK2 Promotes ER Stress-Mediated Neurodegeneration in Amyotrophic Lateral Sclerosis.
  Neuron 2016 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
• On Strengthening the MCP Editorial Leadership.
  Molecular & cellular proteomics : MCP 2016 Burlingame AL
• The Arabidopsis B-box protein BZS1/BBX20 interacts with HY5 and mediates strigolactone regulation of photomorphogenesis.
  Journal of genetics and genomics = Yi chuan xue bao 2016 Wei CQ, Chien CW, Ai LF, Zhao J, Zhang Z, Li KH, Burlingame AL, Sun Y, Wang ZY
• Phosphoproteomic Analyses of NRAS(G12) and NRAS(Q61) Mutant Melanocytes Reveal Increased CK2α Kinase Levels in NRAS(Q61) Mutant Cells.
  The Journal of investigative dermatology 2016 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
• Oncogenic KIT mutations in different exons lead to specific changes in melanocyte phospho-proteome.
  Journal of proteomics 2016 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
• Photoactivatable protein labeling by singlet oxygen mediated reactions.
  Bioorganic & medicinal chemistry letters 2016 To TL, Medzihradszky KF, Burlingame AL, DeGrado WF, Jo H, Shu X
• Human RNA Polymerase II Promoter Recruitment in Vitro Is Regulated by O-Linked N-Acetylglucosaminyltransferase (OGT).
  The Journal of biological chemistry 2016 Lewis BA, Burlingame AL, Myers SA
• Concerted genomic targeting of H3K27 demethylase REF6 and chromatin-remodeling ATPase BRM in Arabidopsis.
  Nature genetics 2016 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
• N-Glycopeptide Profiling in Arabidopsis Inflorescence.
  Molecular & cellular proteomics : MCP 2016 Xu SL, Medzihradszky KF, Wang ZY, Burlingame AL, Chalkley RJ
• SOX2 O-GlcNAcylation alters its protein-protein interactions and genomic occupancy to modulate gene expression in pluripotent cells.
  eLife 2016 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
• saRNA-guided Ago2 targets the RITA complex to promoters to stimulate transcription.
  Cell research 2016 Portnoy V, Lin SH, Li KH, Burlingame A, Hu ZH, Li H, Li LC
• Chaperonin TRiC/CCT Modulates the Folding and Activity of Leukemogenic Fusion Oncoprotein AML1-ETO.
  The Journal of biological chemistry 2015 Roh SH, Kasembeli M, Galaz-Montoya JG, Trnka M, Lau WC, Burlingame A, Chiu W, Tweardy DJ
• OsBRI1 Activates BR Signaling by Preventing Binding between the TPR and Kinase Domains of OsBSK3 via Phosphorylation.
  Plant physiology 2015 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
• Discrete spatial organization of TGFβ receptors couples receptor multimerization and signaling to cellular tension.
  eLife 2015 Rys JP, DuFort CC, Monteiro DA, Baird MA, Oses-Prieto JA, Chand S, Burlingame AL, Davidson MW, Alliston TN
• The Brassinosteroid-Activated BRI1 Receptor Kinase Is Switched off by Dephosphorylation Mediated by Cytoplasm-Localized PP2A B' Subunits.
  Molecular plant 2015 Wang R, Liu M, Yuan M, Oses-Prieto JA, Cai X, Sun Y, Burlingame AL, Wang ZY, Tang W
• A non-synonymous single-nucleotide polymorphism associated with multiple sclerosis risk affects the EVI5 interactome.
  Human molecular genetics 2015 Didonna A, Isobe N, Caillier SJ, Li KH, Burlingame AL, Hauser SL, Baranzini SE, Patsopoulos NA, Oksenberg JR
• Oligomerization between BSU1 Family Members Potentiates Brassinosteroid Signaling in Arabidopsis.
  Molecular plant 2015 Kim EJ, Youn JH, Park CH, Kim TW, Guan S, Xu S, Burlingame AL, Kim YP, Kim SK, Wang ZY, Kim TW
• Molecular architecture of the yeast Mediator complex.
  eLife 2015 Robinson PJ, Trnka MJ, Pellarin R, Greenberg CH, Bushnell DA, Davis R, Burlingame AL, Sali A, Kornberg RD
• Isolation and analyses of axonal ribonucleoprotein complexes.
  Methods in cell biology 2015 Doron-Mandel E, Alber S, Oses JA, Medzihradszky KF, Burlingame AL, Fainzilber M, Twiss JL, Lee SJ
• Improved Peak Detection and Deconvolution of Native Electrospray Mass Spectra from Large Protein Complexes.
  Journal of the American Society for Mass Spectrometry 2015 Lu J, Trnka MJ, Roh SH, Robinson PJ, Shiau C, Fujimori DG, Chiu W, Burlingame AL, Guan S
• Deconvolution method for specific and nonspecific binding of ligand to multiprotein complex by native mass spectrometry.
  Analytical chemistry 2015 Guan S, Trnka MJ, Bushnell DA, Robinson PJ, Gestwicki JE, Burlingame AL
• Tau post-translational modifications in wild-type and human amyloid precursor protein transgenic mice.
  Nature neuroscience 2015 Morris M, Knudsen GM, Maeda S, Trinidad JC, Ioanoviciu A, Burlingame AL, Mucke L
• Erratum: The ubiquitin-modifying enzyme A20 restricts ubiquitination of the kinase RIPK3 and protects cells from necroptosis.
  Nature immunology 2015 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
• On Credibility, Clarity, and Compliance.
  Molecular & cellular proteomics : MCP 2015 Burlingame A, Carr SA, Bradshaw RA, Chalkley RJ
• A ribonucleoprotein complex protects the interleukin-6 mRNA from degradation by distinct herpesviral endonucleases.
  PLoS pathogens 2015 Muller M, Hutin S, Marigold O, Li KH, Burlingame A, Glaunsinger BA
• The ubiquitin-modifying enzyme A20 restricts ubiquitination of the kinase RIPK3 and protects cells from necroptosis.
  Nature immunology 2015 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
• Minireviews revisited.
  Molecular & cellular proteomics : MCP 2015 Bradshaw RA, Burlingame AL
• A20 restricts ubiquitination of pro-interleukin-1β protein complexes and suppresses NLRP3 inflammasome activity.
  Immunity 2015 Duong BH, Onizawa M, Oses-Prieto JA, Advincula R, Burlingame A, Malynn BA, Ma A
• Mass spectrometry-based detection and assignment of protein posttranslational modifications.
  ACS chemical biology 2015 Doll S, Burlingame AL
• 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.
  The Journal of biological chemistry 2014 Wang Y, Kim SM, Trnka MJ, Liu Y, Burlingame AL, Correia MA
• NGF and ProNGF: Regulation of neuronal and neoplastic responses through receptor signaling.
  Advances in biological regulation 2014 Bradshaw RA, Pundavela J, Biarc J, Chalkley RJ, Burlingame AL, Hondermarck H
• MST3 kinase phosphorylates TAO1/2 to enable Myosin Va function in promoting spine synapse development.
  Neuron 2014 Ultanir SK, Yadav S, Hertz NT, Oses-Prieto JA, Claxton S, Burlingame AL, Shokat KM, Jan LY, Jan YN
• Oncogene mimicry as a mechanism of primary resistance to BRAF inhibitors.
  Cell reports 2014 Sos ML, Levin RS, Gordan JD, Oses-Prieto JA, Webber JT, Salt M, Hann B, Burlingame AL, McCormick F, Bandyopadhyay S, Shokat KM
• Quantitative proteomic analysis of Huh-7 cells infected with Dengue virus by label-free LC-MS.
  Journal of proteomics 2014 Pando-Robles V, Oses-Prieto JA, Rodríguez-Gandarilla M, Meneses-Romero E, Burlingame AL, Batista CV
• A mutually assured destruction mechanism attenuates light signaling in Arabidopsis.
  Science (New York, N.Y.) 2014 Ni W, Xu SL, Tepperman JM, Stanley DJ, Maltby DA, Gross JD, Burlingame AL, Wang ZY, Quail PH
• Blue light-induced proteomic changes in etiolated Arabidopsis seedlings.
  Journal of proteome research 2014 Deng Z, Oses-Prieto JA, Kutschera U, Tseng TS, Hao L, Burlingame AL, Wang ZY, Briggs WR
• Syntaxin13 expression is regulated by mammalian target of rapamycin (mTOR) in injured neurons to promote axon regeneration.
  The Journal of biological chemistry 2014 Cho Y, Di Liberto V, Carlin D, Abe N, Li KH, Burlingame AL, Guan S, Michaelevski I, Cavalli V
• Double impact of cigarette smoke and mechanical ventilation on the alveolar epithelial type II cell.
  Critical care (London, England) 2014 Hirsch J, Chalkley RJ, Bentley T, Burlingame AL, Frank JA
• Targeted peptide measurements in biology and medicine: best practices for mass spectrometry-based assay development using a fit-for-purpose approach.
  Molecular & cellular proteomics : MCP 2014 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, …
• Gammaherpesviral gene expression and virion composition are broadly controlled by accelerated mRNA degradation.
  PLoS pathogens 2014 Abernathy E, Clyde K, Yeasmin R, Krug LT, Burlingame A, Coscoy L, Glaunsinger B
• MEK-dependent negative feedback underlies BCR-ABL-mediated oncogene addiction.
  Cancer discovery 2013 Asmussen J, Lasater EA, Tajon C, Oses-Prieto J, Jun YW, Taylor BS, Burlingame A, Craik CS, Shah NP
• Matching cross-linked peptide spectra: only as good as the worse identification.
  Molecular & cellular proteomics : MCP 2013 Trnka MJ, Baker PR, Robinson PJ, Burlingame AL, Chalkley RJ
• An MRAS, SHOC2, and SCRIB complex coordinates ERK pathway activation with polarity and tumorigenic growth.
  Molecular cell 2013 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
• Global cellular response to chemotherapy-induced apoptosis.
  eLife 2013 Wiita AP, Ziv E, Wiita PJ, Urisman A, Julien O, Burlingame AL, Weissman JS, Wells JA
• A brassinosteroid-signaling kinase interacts with multiple receptor-like kinases in Arabidopsis.
  Molecular plant 2013 Xu P, Xu SL, Li ZJ, Tang W, Burlingame AL, Wang ZY
• Identification of BZR1-interacting proteins as potential components of the brassinosteroid signaling pathway in Arabidopsis through tandem affinity purification.
  Molecular & cellular proteomics : MCP 2013 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
• A neo-substrate that amplifies catalytic activity of parkinson's-disease-related kinase PINK1.
  Cell 2013 Hertz NT, Berthet A, Sos ML, Thorn KS, Burlingame AL, Nakamura K, Shokat KM
• 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.
  The Plant cell 2013 Ni W, Xu SL, Chalkley RJ, Pham TN, Guan S, Maltby DA, Burlingame AL, Wang ZY, Quail PH
• Hypothemycin, a fungal natural product, identifies therapeutic targets in Trypanosoma brucei [corrected].
  eLife 2013 Nishino M, Choy JW, Gushwa NN, Oses-Prieto JA, Koupparis K, Burlingame AL, Renslo AR, McKerrow JH, Taunton J
• N- and O-glycosylation in the murine synaptosome.
  Molecular & cellular proteomics : MCP 2013 Trinidad JC, Schoepfer R, Burlingame AL, Medzihradszky KF
• Western blots versus selected reaction monitoring assays: time to turn the tables?
  Molecular & cellular proteomics : MCP 2013 Aebersold R, Burlingame AL, Bradshaw RA
• Arginine Methylation Initiates BMP-Induced Smad Signaling.
  Molecular cell 2013 Xu J, Wang AH, Oses-Prieto J, Makhijani K, Katsuno Y, Pei M, Yan L, Zheng YG, Burlingame A, Brückner K, Derynck R
• H/ACA small RNA dysfunctions in disease reveal key roles for noncoding RNA modifications in hematopoietic stem cell differentiation.
  Cell reports 2013 Bellodi C, McMahon M, Contreras A, Juliano D, Kopmar N, Nakamura T, Maltby D, Burlingame A, Savage SA, Shimamura A, Ruggero D
• Three mechanisms assemble central nervous system nodes of Ranvier.
  Neuron 2013 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
• Nedd4 is a specific E3 ubiquitin ligase for the NMDA receptor subunit GluN2D.
  Neuropharmacology 2013 Gautam V, Trinidad JC, Rimerman RA, Costa BM, Burlingame AL, Monaghan DT
• Reconstitution of nucleosome demethylation and catalytic properties of a Jumonji histone demethylase.
  Chemistry & biology 2013 Shiau C, Trnka MJ, Bozicevic A, Ortiz Torres I, Al-Sady B, Burlingame AL, Narlikar GJ, Fujimori DG
• Dissecting the roles of tyrosines 490 and 785 of TrkA protein in the induction of downstream protein phosphorylation using chimeric receptors.
  The Journal of biological chemistry 2013 Biarc J, Chalkley RJ, Burlingame AL, Bradshaw RA
• ACBD3 interaction with TBC1 domain 22 protein is differentially affected by enteroviral and kobuviral 3A protein binding.
  mBio 2013 Greninger AL, Knudsen GM, Betegon M, Burlingame AL, DeRisi JL
• A minimal anaphase promoting complex/cyclosome (APC/C) in Trypanosoma brucei.
  PloS one 2013 Bessat M, Knudsen G, Burlingame AL, Wang CC
• Inhibition of lysosomal enzyme activities by proton pump inhibitors.
  Journal of gastroenterology 2013 Liu W, Baker SS, Trinidad J, Burlingame AL, Baker RD, Forte JG, Virtuoso LP, Egilmez NK, Zhu L
• 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 Myers SA, Daou S, Affar el B, Burlingame A
• Site-specific and regiospecific installation of methylarginine analogues into recombinant histones and insights into effector protein binding.
  Journal of the American Chemical Society 2013 Le DD, Cortesi AT, Myers SA, Burlingame AL, Fujimori DG
• Glucose sensor O-GlcNAcylation coordinates with phosphorylation to regulate circadian clock.
  Cell metabolism 2013 Kaasik K, Kivimäe S, Allen JJ, Chalkley RJ, Huang Y, Baer K, Kissel H, Burlingame AL, Shokat KM, Ptácek LJ, Fu YH
• Rearrangements within human spliceosomes captured after exon ligation.
  RNA (New York, N.Y.) 2013 Ilagan JO, Chalkley RJ, Burlingame AL, Jurica MS
• Chemical-biological characterization of a cruzain inhibitor reveals a second target and a mammalian off-target.
  Beilstein journal of organic chemistry 2013 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
• Genetic and mass spectrometric tools for elucidating the physiological function(s) of cytochrome P450 enzymes from Mycobacterium tuberculosis.
  Methods in molecular biology (Clifton, N.J.) 2013 Ouellet H, Chow ED, Guan S, Cox JS, Burlingame AL, de Montellano PR
• Differentiation of opioid drug effects by hierarchical multi-site phosphorylation.
  Molecular pharmacology 2012 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
• Substrates of IAP ubiquitin ligases identified with a designed orthogonal E3 ligase, the NEDDylator.
  Molecular cell 2012 Zhuang M, Guan S, Wang H, Burlingame AL, Wells JA
• Receptor tyrosine kinase signaling mechanisms: Devolving TrkA responses with phosphoproteomics.
  Advances in biological regulation 2012 Bradshaw RA, Chalkley RJ, Biarc J, Burlingame AL
• Structure of the mediator head module bound to the carboxy-terminal domain of RNA polymerase II.
  Proceedings of the National Academy of Sciences of the United States of America 2012 Robinson PJ, Bushnell DA, Trnka MJ, Burlingame AL, Kornberg RD
• Activity-dependent protein dynamics define interconnected cores of co-regulated postsynaptic proteins.
  Molecular & cellular proteomics : MCP 2012 Trinidad JC, Thalhammer A, Burlingame AL, Schoepfer R
• Global identification of peptidase specificity by multiplex substrate profiling.
  Nature methods 2012 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
• Functional proteomic analysis of long-term growth factor stimulation and receptor tyrosine kinase coactivation in Swiss 3T3 fibroblasts.
  Molecular & cellular proteomics : MCP 2012 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
• Conservation of caspase substrates across metazoans suggests hierarchical importance of signaling pathways over specific targets and cleavage site motifs in apoptosis.
  Cell death and differentiation 2012 Crawford ED, Seaman JE, Barber AE, David DC, Babbitt PC, Burlingame AL, Wells JA
• Systematic functional prioritization of protein posttranslational modifications.
  Cell 2012 Beltrao P, Albanèse V, Kenner LR, Swaney DL, Burlingame A, Villén J, Lim WA, Fraser JS, Frydman J, Krogan NJ
• Quantitative profiling of caspase-cleaved substrates reveals different drug-induced and cell-type patterns in apoptosis.
  Proceedings of the National Academy of Sciences of the United States of America 2012 Shimbo K, Hsu GW, Nguyen H, Mahrus S, Trinidad JC, Burlingame AL, Wells JA
• A shared molecular mechanism underlies the human rasopathies Legius syndrome and Neurofibromatosis-1.
  Genes & development 2012 Stowe IB, Mercado EL, Stowe TR, Bell EL, Oses-Prieto JA, Hernández H, Burlingame AL, McCormick F
• Global identification and characterization of both O-GlcNAcylation and phosphorylation at the murine synapse.
  Molecular & cellular proteomics : MCP 2012 Trinidad JC, Barkan DT, Gulledge BF, Thalhammer A, Sali A, Schoepfer R, Burlingame AL
• IQGAP1 is necessary for pulmonary vascular barrier protection in murine acute lung injury and pneumonia.
  American journal of physiology. Lung cellular and molecular physiology 2012 Bhattacharya M, Su G, Su X, Oses-Prieto JA, Li JT, Huang X, Hernandez H, Atakilit A, Burlingame AL, Matthay MA, Sheppard D
• Compartment modeling for mammalian protein turnover studies by stable isotope metabolic labeling.
  Analytical chemistry 2012 Guan S, Price JC, Ghaemmaghami S, Prusiner SB, Burlingame AL
• Mass spectrometry: reconnaissance at the Frontiers of biology.
  Molecular & cellular proteomics : MCP 2012 Burlingame AL, Stults JT
• 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.
  Molecular & cellular proteomics : MCP 2012 Ruperez P, Gago-Martinez A, Burlingame AL, Oses-Prieto JA
• Proximal ligand electron donation and reactivity of the cytochrome P450 ferric-peroxo anion.
  Journal of the American Chemical Society 2012 Sivaramakrishnan S, Ouellet H, Matsumura H, Guan S, Moënne-Loccoz P, Burlingame AL, Ortiz de Montellano PR
• Why complexity and entropy matter: information, posttranslational modifications, and assay fidelity.
  Proteomics 2012 Sherman J, Molloy MP, Burlingame AL
• Chemical genetic identification of NDR1/2 kinase substrates AAK1 and Rabin8 Uncovers their roles in dendrite arborization and spine development.
  Neuron 2012 Ultanir SK, Hertz NT, Li G, Ge WP, Burlingame AL, Pleasure SJ, Shokat KM, Jan LY, Jan YN
• Global kinetic analysis of proteolysis via quantitative targeted proteomics.
  Proceedings of the National Academy of Sciences of the United States of America 2012 Agard NJ, Mahrus S, Trinidad JC, Lynn A, Burlingame AL, Wells JA
• Development of a chemical genetic approach for human aurora B kinase identifies novel substrates of the chromosomal passenger complex.
  Molecular & cellular proteomics : MCP 2012 Hengeveld RC, Hertz NT, Vromans MJ, Zhang C, Burlingame AL, Shokat KM, Lens SM
• The 3A protein from multiple picornaviruses utilizes the golgi adaptor protein ACBD3 to recruit PI4KIIIβ.
  Journal of virology 2012 Greninger AL, Knudsen GM, Betegon M, Burlingame AL, Derisi JL
• Identification of O-linked β-D-N-acetylglucosamine-modified proteins from Arabidopsis.
  Methods in molecular biology (Clifton, N.J.) 2012 Xu SL, Chalkley RJ, Wang ZY, Burlingame AL
• Global landscape of HIV-human protein complexes.
  Nature 2011 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…
• Vif hijacks CBF-β to degrade APOBEC3G and promote HIV-1 infection.
  Nature 2011 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, …
• Rapid auxin-mediated changes in the proteome of the epidermal cells in rye coleoptiles: implications for the initiation of growth.
  Plant biology (Stuttgart, Germany) 2011 Deng Z, Xu S, Chalkley RJ, Oses-Prieto JA, Burlingame AL, Wang ZY, Kutschera U
• 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.
  Molecular & cellular proteomics : MCP 2011 Wang Y, Guan S, Acharya P, Liu Y, Thirumaran RK, Brandman R, Schuetz EG, Burlingame AL, Correia MA
• A heteromeric Texas coral snake toxin targets acid-sensing ion channels to produce pain.
  Nature 2011 Bohlen CJ, Chesler AT, Sharif-Naeini R, Medzihradszky KF, Zhou S, King D, Sánchez EE, Burlingame AL, Basbaum AI, Julius D
• The induction of serine/threonine protein phosphorylations by a PDGFR/TrkA chimera in stably transfected PC12 cells.
  Molecular & cellular proteomics : MCP 2011 Biarc J, Chalkley RJ, Burlingame AL, Bradshaw RA
• A data processing pipeline for mammalian proteome dynamics studies using stable isotope metabolic labeling.
  Molecular & cellular proteomics : MCP 2011 Guan S, Price JC, Prusiner SB, Ghaemmaghami S, Burlingame AL
• The CDG1 kinase mediates brassinosteroid signal transduction from BRI1 receptor kinase to BSU1 phosphatase and GSK3-like kinase BIN2.
  Molecular cell 2011 Kim TW, Guan S, Burlingame AL, Wang ZY
• Quantitative encoding of the effect of a partial agonist on individual opioid receptors by multisite phosphorylation and threshold detection.
  Science signaling 2011 Lau EK, Trester-Zedlitz M, Trinidad JC, Kotowski SJ, Krutchinsky AN, Burlingame AL, von Zastrow M
• Proteomic analyses of apoplastic proteins from germinating Arabidopsis thaliana pollen.
  Biochimica et biophysica acta 2011 Ge W, Song Y, Zhang C, Zhang Y, Burlingame AL, Guo Y
• Disruption of the murine procollagen C-proteinase enhancer 2 gene causes accumulation of pro-apoA-I and increased HDL levels.
  Journal of lipid research 2011 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
• Site-specific acetylation mark on an essential chromatin-remodeling complex promotes resistance to replication stress.
  Proceedings of the National Academy of Sciences of the United States of America 2011 Charles GM, Chen C, Shih SC, Collins SR, Beltrao P, Zhang X, Sharma T, Tan S, Burlingame AL, Krogan NJ, Madhani HD, Narlikar GJ
• Polycomb repressive complex 2 is necessary for the normal site-specific O-GlcNAc distribution in mouse embryonic stem cells.
  Proceedings of the National Academy of Sciences of the United States of America 2011 Myers SA, Panning B, Burlingame AL
• Breaking up the C complex spliceosome shows stable association of proteins with the lariat intron intermediate.
  PloS one 2011 Coltri P, Effenberger K, Chalkley RJ, Burlingame AL, Jurica MS
• A Raf-induced allosteric transition of KSR stimulates phosphorylation of MEK.
  Nature 2011 Brennan DF, Dar AC, Hertz NT, Chao WC, Burlingame AL, Shokat KM, Barford D
• Identification of NaCl stress-responsive apoplastic proteins in rice shoot stems by 2D-DIGE.
  Journal of proteomics 2011 Song Y, Zhang C, Ge W, Zhang Y, Burlingame AL, Guo Y
• The role of conformational flexibility on protein supercharging in native electrospray ionization.
  Physical chemistry chemical physics : PCCP 2011 Sterling HJ, Cassou CA, Trnka MJ, Burlingame AL, Krantz BA, Williams ER
• PP2A activates brassinosteroid-responsive gene expression and plant growth by dephosphorylating BZR1.
  Nature cell biology 2011 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
• Proteomics analysis reveals post-translational mechanisms for cold-induced metabolic changes in Arabidopsis.
  Molecular plant 2011 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
• Ubiquitin-dependent proteasomal degradation of human liver cytochrome P450 2E1: identification of sites targeted for phosphorylation and ubiquitination.
  The Journal of biological chemistry 2011 Wang Y, Guan S, Acharya P, Koop DR, Liu Y, Liao M, Burlingame AL, Correia MA
• Quantitative mass spectrometry reveals the epigenome as a target of arsenic.
  Chemico-biological interactions 2010 Chu F, Ren X, Chasse A, Hickman T, Zhang L, Yuh J, Smith MT, Burlingame AL
• Receptor tyrosine kinase signaling--a proteomic perspective.
  Advances in enzyme regulation 2010 Biarc J, Chalkley RJ, Burlingame AL, Bradshaw RA
• A kinase cascade leading to Rab11-FIP5 controls transcytosis of the polymeric immunoglobulin receptor.
  Nature cell biology 2010 Su T, Bryant DM, Luton F, Vergés M, Ulrich SM, Hansen KC, Datta A, Eastburn DJ, Burlingame AL, Shokat KM, Mostov KE
• Proteomic study identifies proteins involved in brassinosteroid regulation of rice growth.
  Journal of integrative plant biology 2010 Wang F, Bai MY, Deng Z, Oses-Prieto JA, Burlingame AL, Lu T, Chong K, Wang ZY
• Technological innovation revisited.
  Molecular & cellular proteomics : MCP 2010 Bradshaw RA, Burlingame AL
• Arabidopsis L10 ribosomal proteins in UV-B responses.
  Plant signaling & behavior 2010 Ferreyra ML, Biarc J, Burlingame AL, Casati P
• 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.
  Molecular & cellular proteomics : MCP 2010 Trnka MJ, Burlingame AL
• The male sterile 8 mutation of maize disrupts the temporal progression of the transcriptome and results in the mis-regulation of metabolic functions.
  The Plant journal : for cell and molecular biology 2010 Wang D, Oses-Prieto JA, Li KH, Fernandes JF, Burlingame AL, Walbot V
• Analysis of proteome dynamics in the mouse brain.
  Proceedings of the National Academy of Sciences of the United States of America 2010 Price JC, Guan S, Burlingame A, Prusiner SB, Ghaemmaghami S
• Widespread protein aggregation as an inherent part of aging in C. elegans.
  PLoS biology 2010 David DC, Ollikainen N, Trinidad JC, Cary MP, Burlingame AL, Kenyon C
• Signaling to transcription networks in the neuronal retrograde injury response.
  Science signaling 2010 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
• Mycobacterium tuberculosis CYP125A1, a steroid C27 monooxygenase that detoxifies intracellularly generated cholest-4-en-3-one.
  Molecular microbiology 2010 Ouellet H, Guan S, Johnston JB, Chow ED, Kells PM, Burlingame AL, Cox JS, Podust LM, de Montellano PR
• The transcriptional coactivator DRIP/mediator complex is involved in vitamin D receptor function and regulates keratinocyte proliferation and differentiation.
  The Journal of investigative dermatology 2010 Oda Y, Chalkley RJ, Burlingame AL, Bikle DD
• Plant L10 ribosomal proteins have different roles during development and translation under ultraviolet-B stress.
  Plant physiology 2010 Falcone Ferreyra ML, Pezza A, Biarc J, Burlingame AL, Casati P
• HIV-1 Tat and host AFF4 recruit two transcription elongation factors into a bifunctional complex for coordinated activation of HIV-1 transcription.
  Molecular cell 2010 He N, Liu M, Hsu J, Xue Y, Chou S, Burlingame A, Krogan NJ, Alber T, Zhou Q
• Phosphopeptide screen uncovers novel phosphorylation sites of Nedd4-2 that potentiate its inhibition of the epithelial Na+ channel.
  The Journal of biological chemistry 2010 Hallows KR, Bhalla V, Oyster NM, Wijngaarden MA, Lee JK, Li H, Chandran S, Xia X, Huang Z, Chalkley RJ, Burlingame AL, Pearce D
• Mass spectrometry and the evolution of proteomics.
  Molecular & cellular proteomics : MCP 2010 Burlingame AL, Stults JT
• Cessation of coleoptile elongation and loss of auxin sensitivity in developing rye seedlings: a quantitative proteomic analysis.
  Plant signaling & behavior 2010 Kutschera U, Deng Z, Oses-Prieto JA, Burlingame AL, Wang ZY
• Chemical genetic approach for kinase-substrate mapping by covalent capture of thiophosphopeptides and analysis by mass spectrometry.
  Current protocols in chemical biology 2010 Hertz NT, Wang BT, Allen JJ, Zhang C, Dar AC, Burlingame AL, Shokat KM
• The RasGAP proteins Ira2 and neurofibromin are negatively regulated by Gpb1 in yeast and ETEA in humans.
  Molecular and cellular biology 2010 Phan VT, Ding VW, Li F, Chalkley RJ, Burlingame A, McCormick F
• 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.
  Molecular & cellular proteomics : MCP 2010 Eliuk SM, Maltby D, Panning B, Burlingame AL
• Axoplasm isolation from peripheral nerve.
  Developmental neurobiology 2010 Rishal I, Michaelevski I, Rozenbaum M, Shinder V, Medzihradszky KF, Burlingame AL, Fainzilber M
• ADAM22, a Kv1 channel-interacting protein, recruits membrane-associated guanylate kinases to juxtaparanodes of myelinated axons.
  The Journal of neuroscience : the official journal of the Society for Neuroscience 2010 Ogawa Y, Oses-Prieto J, Kim MY, Horresh I, Peles E, Burlingame AL, Trimmer JS, Meijer D, Rasband MN
• Statistical analysis of Peptide electron transfer dissociation fragmentation mass spectrometry.
  Analytical chemistry 2010 Chalkley RJ, Medzihradszky KF, Lynn AJ, Baker PR, Burlingame AL
• Mass spectrometric analysis, automated identification and complete annotation of O-linked glycopeptides.
  European journal of mass spectrometry (Chichester, England) 2010 Darula Z, Chalkley RJ, Baker P, Burlingame AL, Medzihradszky KF
• High mass selectivity for top-down proteomics by application of SWIFT technology.
  Journal of the American Society for Mass Spectrometry 2009 Guan S, Burlingame AL
• Data processing algorithms for analysis of high resolution MSMS spectra of peptides with complex patterns of posttranslational modifications.
  Molecular & cellular proteomics : MCP 2009 Guan S, Burlingame AL
• Axonal transport proteomics reveals mobilization of translation machinery to the lesion site in injured sciatic nerve.
  Molecular & cellular proteomics : MCP 2009 Michaelevski I, Medzihradszky KF, Lynn A, Burlingame AL, Fainzilber M
• Finding chimeras: a bioinformatics strategy for identification of cross-linked peptides.
  Molecular & cellular proteomics : MCP 2009 Chu F, Baker PR, Burlingame AL, Chalkley RJ
• The role of exon sequences in C complex spliceosome structure.
  Journal of molecular biology 2009 Ilagan J, Yuh P, Chalkley RJ, Burlingame AL, Jurica MS
• Brassinosteroid signal transduction from cell-surface receptor kinases to nuclear transcription factors.
  Nature cell biology 2009 Kim TW, Guan S, Sun Y, Deng Z, Tang W, Shang JX, Sun Y, Burlingame AL, Wang ZY
• Acetylated H4K16 by MYST1 protects UROtsa cells from arsenic toxicity and is decreased following chronic arsenic exposure.
  Toxicology and applied pharmacology 2009 Jo WJ, Ren X, Chu F, Aleshin M, Wintz H, Burlingame A, Smith MT, Vulpe CD, Zhang L
• Nicotinic agonist binding site mapped by methionine- and tyrosine-scanning coupled with azidochloropyridinyl photoaffinity labeling.
  Journal of medicinal chemistry 2009 Tomizawa M, Talley TT, Park JF, Maltby D, Medzihradszky KF, Durkin KA, Cornejo-Bravo JM, Burlingame AL, Casida JE, Taylor P
• Evolution of phosphoregulation: comparison of phosphorylation patterns across yeast species.
  PLoS biology 2009 Beltrao P, Trinidad JC, Fiedler D, Roguev A, Lim WA, Shokat KM, Burlingame AL, Krogan NJ
• Identification of protein O-GlcNAcylation sites using electron transfer dissociation mass spectrometry on native peptides.
  Proceedings of the National Academy of Sciences of the United States of America 2009 Chalkley RJ, Thalhammer A, Schoepfer R, Burlingame AL
• HDL antielastase activity prevents smooth muscle cell anoikis, a potential new antiatherogenic property.
  FASEB journal : official publication of the Federation of American Societies for Experimental Biology 2009 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
• Mutator transposon activity reprograms the transcriptomes and proteomes of developing maize anthers.
  The Plant journal : for cell and molecular biology 2009 Skibbe DS, Fernandes JF, Medzihradszky KF, Burlingame AL, Walbot V
• Normal protein composition of synapses in Ts65Dn mice: a mouse model of Down syndrome.
  Journal of neurochemistry 2009 Fernandez F, Trinidad JC, Blank M, Feng DD, Burlingame AL, Garner CC
• Promiscuous aggregate-based inhibitors promote enzyme unfolding.
  Journal of medicinal chemistry 2009 Coan KE, Maltby DA, Burlingame AL, Shoichet BK
• 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.
  Journal of molecular medicine (Berlin, Germany) 2009 Conrad F, Zhu X, Zhang X, Chalkley RJ, Burlingame AL, Marks JD, Liu B
• A transmembrane accessory subunit that modulates kainate-type glutamate receptors.
  Neuron 2009 Zhang W, St-Gelais F, Grabner CP, Trinidad JC, Sumioka A, Morimoto-Tomita M, Kim KS, Straub C, Burlingame AL, Howe JR, Tomita S
• Densin-180: revised membrane topology, domain structure and phosphorylation status.
  Journal of neurochemistry 2009 Thalhammer A, Trinidad JC, Burlingame AL, Schoepfer R
• Identification of new p53 acetylation sites in COS-1 cells.
  Molecular & cellular proteomics : MCP 2009 Joubel A, Chalkley RJ, Medzihradszky KF, Hondermarck H, Burlingame AL
• SIRT6 stabilizes DNA-dependent protein kinase at chromatin for DNA double-strand break repair.
  Aging 2009 McCord RA, Michishita E, Hong T, Berber E, Boxer LD, Kusumoto R, Guan S, Shi X, Gozani O, Burlingame AL, Bohr VA, Chua KF
• Defining the TRiC/CCT interactome links chaperonin function to stabilization of newly made proteins with complex topologies.
  Nature structural & molecular biology 2008 Yam AY, Xia Y, Lin HT, Burlingame A, Gerstein M, Frydman J
• Tpr directly binds to Mad1 and Mad2 and is important for the Mad1-Mad2-mediated mitotic spindle checkpoint.
  Genes & development 2008 Lee SH, Sterling H, Burlingame A, McCormick F
• Microtubule interfering agents and KSP inhibitors induce the phosphorylation of the nuclear protein p54(nrb), an event linked to G2/M arrest.
  Journal of proteomics 2008 Casado P, Prado MA, Zuazua-Villar P, Del Valle E, Artime N, Cabal-Hierro L, Rupérez P, Burlingame AL, Lazo PS, Ramos S
• Global sequencing of proteolytic cleavage sites in apoptosis by specific labeling of protein N termini.
  Cell 2008 Mahrus S, Trinidad JC, Barkan DT, Sali A, Burlingame AL, Wells JA
• BSKs mediate signal transduction from the receptor kinase BRI1 in Arabidopsis.
  Science (New York, N.Y.) 2008 Tang W, Kim TW, Oses-Prieto JA, Sun Y, Deng Z, Zhu S, Wang R, Burlingame AL, Wang ZY
• In-depth analysis of tandem mass spectrometry data from disparate instrument types.
  Molecular & cellular proteomics : MCP 2008 Chalkley RJ, Baker PR, Medzihradszky KF, Lynn AJ, Burlingame AL
• Cell cycle-dependent phosphorylation of human CDC5 regulates RNA processing.
  Cell cycle (Georgetown, Tex.) 2008 Gräub R, Lancero H, Pedersen A, Chu M, Padmanabhan K, Xu XQ, Spitz P, Chalkley R, Burlingame AL, Stokoe D, Bernstein HS
• Identification of a novel chromosomal passenger complex and its unique localization during cytokinesis in Trypanosoma brucei.
  PloS one 2008 Li Z, Lee JH, Chu F, Burlingame AL, Günzl A, Wang CC
• Alterations in the proteome of pulmonary alveolar type II cells in the rat after hepatic ischemia-reperfusion.
  Critical care medicine 2008 Hirsch J, Niemann CU, Hansen KC, Choi S, Su X, Frank JA, Fang X, Hirose R, Theodore P, Sapru A, Burlingame AL, Matthay MA
• Histone acetylation and chromatin remodeling are required for UV-B-dependent transcriptional activation of regulated genes in maize.
  The Plant cell 2008 Casati P, Campi M, Chu F, Suzuki N, Maltby D, Guan S, Burlingame AL, Walbot V
• Atypical nicotinic agonist bound conformations conferring subtype selectivity.
  Proceedings of the National Academy of Sciences of the United States of America 2008 Tomizawa M, Maltby D, Talley TT, Durkin KA, Medzihradszky KF, Burlingame AL, Taylor P, Casida JE
• Proteomics studies of brassinosteroid signal transduction using prefractionation and two-dimensional DIGE.
  Molecular & cellular proteomics : MCP 2008 Tang W, Deng Z, Oses-Prieto JA, Suzuki N, Zhu S, Zhang X, Burlingame AL, Wang ZY
• Quantitative analysis of synaptic phosphorylation and protein expression.
  Molecular & cellular proteomics : MCP 2007 Trinidad JC, Thalhammer A, Specht CG, Lynn AJ, Baker PR, Schoepfer R, Burlingame AL
• Pkh-kinases control eisosome assembly and organization.
  The EMBO journal 2007 Walther TC, Aguilar PS, Fröhlich F, Chu F, Moreira K, Burlingame AL, Walter P
• Renal defects associated with improper polarization of the CRB and DLG polarity complexes in MALS-3 knockout mice.
  The Journal of cell biology 2007 Olsen O, Funke L, Long JF, Fukata M, Kazuta T, Trinidad JC, Moore KA, Misawa H, Welling PA, Burlingame AL, Zhang M, Bredt DS
• A proteomics study of brassinosteroid response in Arabidopsis.
  Molecular & cellular proteomics : MCP 2007 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
• Critical role for arginine methylation in adenovirus-infected cells.
  Journal of virology 2007 Iacovides DC, O'Shea CC, Oses-Prieto J, Burlingame A, McCormick F
• An essential role for 14-3-3 proteins in brassinosteroid signal transduction in Arabidopsis.
  Developmental cell 2007 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
• Defining nicotinic agonist binding surfaces through photoaffinity labeling.
  Biochemistry 2007 Tomizawa M, Maltby D, Medzihradszky KF, Zhang N, Durkin KA, Presley J, Talley TT, Taylor P, Burlingame AL, Casida JE
• Sulfopeptide fragmentation in electron-capture and electron-transfer dissociation.
  Journal of the American Society for Mass Spectrometry 2007 Medzihradszky KF, Guan S, Maltby DA, Burlingame AL
• A semisynthetic epitope for kinase substrates.
  Nature methods 2007 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
• Mapping the elusive neonicotinoid binding site.
  Proceedings of the National Academy of Sciences of the United States of America 2007 Tomizawa M, Talley TT, Maltby D, Durkin KA, Medzihradszky KF, Burlingame AL, Taylor P, Casida JE
• Gene and protein expression profiling of human ovarian cancer cells treated with the heat shock protein 90 inhibitor 17-allylamino-17-demethoxygeldanamycin.
  Cancer research 2007 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, …
• Impact of low and high tidal volumes on the rat alveolar epithelial type II cell proteome.
  American journal of respiratory and critical care medicine 2007 Hirsch J, Hansen KC, Sapru A, Frank JA, Chalkley RJ, Fang X, Trinidad JC, Baker P, Burlingame AL, Matthay MA
• The site-specific installation of methyl-lysine analogs into recombinant histones.
  Cell 2007 Simon MD, Chu F, Racki LR, de la Cruz CC, Burlingame AL, Panning B, Narlikar GJ, Shokat KM
• Formation of epsilon-formyllysine on silver-stained proteins: implications for assignment of isobaric dimethylation sites by tandem mass spectrometry.
  Molecular & cellular proteomics : MCP 2006 Osés-Prieto JA, Zhang X, Burlingame AL
• Isotope-coded and affinity-tagged cross-linking (ICATXL): an efficient strategy to probe protein interaction surfaces.
  Journal of the American Chemical Society 2006 Chu F, Mahrus S, Craik CS, Burlingame AL
• Side-chain fragmentation of alkylated cysteine residues in electron capture dissociation mass spectrometry.
  Journal of the American Society for Mass Spectrometry 2006 Chalkley RJ, Brinkworth CS, Burlingame AL
• Identification of novel quaternary domain interactions in the Hsp90 chaperone, GRP94.
  Protein science : a publication of the Protein Society 2006 Chu F, Maynard JC, Chiosis G, Nicchitta CV, Burlingame AL
• Electrospray mass spectrometry of NeuAc oligomers associated with the C fragment of the tetanus toxin.
  Journal of the American Society for Mass Spectrometry 2006 Conway MCP, Whittal RM, Baldwin MA, Burlingame AL, Balhorn R
• Reporting protein identification data: the next generation of guidelines.
  Molecular & cellular proteomics : MCP 2006 Bradshaw RA, Burlingame AL, Carr S, Aebersold R
• A phosphatase holoenzyme comprised of Shoc2/Sur8 and the catalytic subunit of PP1 functions as an M-Ras effector to modulate Raf activity.
  Molecular cell 2006 Rodriguez-Viciana P, Oses-Prieto J, Burlingame A, Fried M, McCormick F
• Histone chaperone Asf1 is required for histone H3 lysine 56 acetylation, a modification associated with S phase in mitosis and meiosis.
  Proceedings of the National Academy of Sciences of the United States of America 2006 Recht J, Tsubota T, Tanny JC, Diaz RL, Berger JM, Zhang X, Garcia BA, Shabanowitz J, Burlingame AL, Hunt DF, Kaufman PD, Allis CD
• Keratin 20 serine 13 phosphorylation is a stress and intestinal goblet cell marker.
  The Journal of biological chemistry 2006 Zhou Q, Cadrin M, Herrmann H, Chen CH, Chalkley RJ, Burlingame AL, Omary MB
• Warm ischemia-induced alterations in oxidative and inflammatory proteins in hepatic Kupffer cells in rats.
  Molecular & cellular proteomics : MCP 2006 Hirsch J, Hansen KC, Choi S, Noh J, Hirose R, Roberts JP, Matthay MA, Burlingame AL, Maher JJ, Niemann CU
• Comprehensive identification of phosphorylation sites in postsynaptic density preparations.
  Molecular & cellular proteomics : MCP 2006 Trinidad JC, Specht CG, Thalhammer A, Schoepfer R, Burlingame AL
• O-linked N-acetylglucosamine proteomics of postsynaptic density preparations using lectin weak affinity chromatography and mass spectrometry.
  Molecular & cellular proteomics : MCP 2006 Vosseller K, Trinidad JC, Chalkley RJ, Specht CG, Thalhammer A, Lynn AJ, Snedecor JO, Guan S, Medzihradszky KF, Maltby DA, Schoepfer R, Burlingame AL
• Peptidomics of a single identified neuron reveals diversity of multiple neuropeptides with convergent actions on cellular excitability.
  The Journal of neuroscience : the official journal of the Society for Neuroscience 2006 Jiménez CR, Spijker S, de Schipper S, Lodder JC, Janse CK, Geraerts WP, van Minnen J, Syed NI, Burlingame AL, Smit AB, Li K
• Mapping post-translational modifications of the histone variant MacroH2A1 using tandem mass spectrometry.
  Molecular & cellular proteomics : MCP 2005 Chu F, Nusinow DA, Chalkley RJ, Plath K, Panning B, Burlingame AL
• Atg19p ubiquitination and the cytoplasm to vacuole trafficking pathway in yeast.
  The Journal of biological chemistry 2005 Baxter BK, Abeliovich H, Zhang X, Stirling AG, Burlingame AL, Goldfarb DS
• Neurotransmitter release regulated by a MALS-liprin-alpha presynaptic complex.
  The Journal of cell biology 2005 Olsen O, Moore KA, Fukata M, Kazuta T, Trinidad JC, Kauer FW, Streuli M, Misawa H, Burlingame AL, Nicoll RA, Bredt DS
• Protein identification: the good, the bad, and the ugly.
  Molecular & cellular proteomics : MCP 2005 Bradshaw RA, Burlingame AL, Carr S, Aebersold R
• Mass spectrometric analysis of histone posttranslational modifications.
  Methods (San Diego, Calif.) 2005 Burlingame AL, Zhang X, Chalkley RJ
• Analysis of leaf proteome after UV-B irradiation in maize lines differing in sensitivity.
  Molecular & cellular proteomics : MCP 2005 Casati P, Zhang X, Burlingame AL, Walbot V
• WDR5 associates with histone H3 methylated at K4 and is essential for H3 K4 methylation and vertebrate development.
  Cell 2005 Wysocka J, Swigut T, Milne TA, Dou Y, Zhang X, Burlingame AL, Roeder RG, Brivanlou AH, Allis CD
• 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.
  Molecular & cellular proteomics : MCP 2005 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: I. How much of the data is theoretically interpretable by search engines?
  Molecular & cellular proteomics : MCP 2005 Chalkley RJ, Baker PR, Hansen KC, Medzihradszky KF, Allen NP, Rexach M, Burlingame AL
• Molecular constituents of neuronal AMPA receptors.
  The Journal of cell biology 2005 Fukata Y, Tzingounis AV, Trinidad JC, Fukata M, Burlingame AL, Nicoll RA, Bredt DS
• Mass spectrometric analysis of agonist effects on posttranslational modifications of the beta-2 adrenoceptor in mammalian cells.
  Biochemistry 2005 Trester-Zedlitz M, Burlingame A, Kobilka B, von Zastrow M
• An unbiased cell morphology-based screen for new, biologically active small molecules.
  PLoS biology 2005 Tanaka M, Bateman R, Rauh D, Vaisberg E, Ramachandani S, Zhang C, Hansen KC, Burlingame AL, Trautman JK, Shokat KM, Adams CL
• From proteins to proteomics.
  IUBMB life 2005 Bradshaw RA, Burlingame AL
• Phosphorylation state of postsynaptic density proteins.
  Journal of neurochemistry 2005 Trinidad JC, Thalhammer A, Specht CG, Schoepfer R, Burlingame AL
• Quantitative analysis of both protein expression and serine / threonine post-translational modifications through stable isotope labeling with dithiothreitol.
  Proteomics 2005 Vosseller K, Hansen KC, Chalkley RJ, Trinidad JC, Wells L, Hart GW, Burlingame AL
• Comprehensive mass spectrometric analysis of the 20S proteasome complex.
  Methods in enzymology 2005 Huang L, Burlingame AL
• Proteomic analysis of plasma membrane vesicles isolated from the rat renal cortex.
  Proteomics 2005 Cutillas PR, Biber J, Marks J, Jacob R, Stieger B, Cramer R, Waterfield M, Burlingame AL, Unwin RJ
• Proteome changes in ovarian epithelial cells derived from women with BRCA1 mutations and family histories of cancer.
  Molecular & cellular proteomics : MCP 2004 Smith-Beckerman DM, Fung KW, Williams KE, Auersperg N, Godwin AK, Burlingame AL
• Unraveling the interface of signal recognition particle and its receptor by using chemical cross-linking and tandem mass spectrometry.
  Proceedings of the National Academy of Sciences of the United States of America 2004 Chu F, Shan SO, Moustakas DT, Alber F, Egea PF, Stroud RM, Walter P, Burlingame AL
• Victor L. Talroze: 1922-2004.
  Journal of the American Society for Mass Spectrometry 2004 Baldwin MA, Burlingame AL, Nikolaev E
• The mammalian retromer regulates transcytosis of the polymeric immunoglobulin receptor.
  Nature cell biology 2004 Vergés M, Luton F, Gruber C, Tiemann F, Reinders LG, Huang L, Burlingame AL, Haft CR, Mostov KE
• Proteomics: current techniques and potential applications to lung disease.
  American journal of physiology. Lung cellular and molecular physiology 2004 Hirsch J, Hansen KC, Burlingame AL, Matthay MA
• Characterization of Tetrahymena histone H2B variants and posttranslational populations by electron capture dissociation (ECD) Fourier transform ion cyclotron mass spectrometry (FT-ICR MS).
  Molecular & cellular proteomics : MCP 2004 Medzihradszky KF, Zhang X, Chalkley RJ, Guan S, McFarland MA, Chalmers MJ, Marshall AG, Diaz RL, Allis CD, Burlingame AL
• Proteomic strategies and their application in studies of renal function.
  News in physiological sciences : an international journal of physiology produced jointly by the International Union of Physiological Sciences and the American Physiological Society 2004 Cutillas P, Burlingame A, Unwin R
• The urinary proteome in Fanconi syndrome implies specificity in the reabsorption of proteins by renal proximal tubule cells.
  American journal of physiology. Renal physiology 2004 Cutillas PR, Chalkley RJ, Hansen KC, Cramer R, Norden AG, Waterfield MD, Burlingame AL, Unwin RJ
• Spatio-temporal dynamics of the egg-laying-inducing peptides during an egg-laying cycle: a semiquantitative matrix-assisted laser desorption/ionization mass spectrometry approach.
  Journal of neurochemistry 2004 Jiménez CR, ter Maat A, Pieneman A, Burlingame AL, Smit AB, Li KW
• Two distinct coactivators, DRIP/mediator and SRC/p160, are differentially involved in VDR transactivation during keratinocyte differentiation.
  The Journal of steroid biochemistry and molecular biology 2004 Oda Y, Sihlbom C, Chalkley RJ, Huang L, Rachez C, Chang CP, Burlingame AL, Freedman LP, Bikle DD
• The need for guidelines in publication of peptide and protein identification data: Working Group on Publication Guidelines for Peptide and Protein Identification Data.
  Molecular & cellular proteomics : MCP 2004 Carr S, Aebersold R, Baldwin M, Burlingame A, Clauser K, Nesvizhskii A, Working Group on Publication Guidelines for Peptide and Protein Identification Data
• Differential proteomics reveals multiple components in retrogradely transported axoplasm after nerve injury.
  Molecular & cellular proteomics : MCP 2004 Perlson E, Medzihradszky KF, Darula Z, Munno DW, Syed NI, Burlingame AL, Fainzilber M
• From snails to sciatic nerve: Retrograde injury signaling from axon to soma in lesioned neurons.
  Journal of neurobiology 2004 Perlson E, Hanz S, Medzihradszky KF, Burlingame AL, Fainzilber M
• O-sulfonation of serine and threonine: mass spectrometric detection and characterization of a new posttranslational modification in diverse proteins throughout the eukaryotes.
  Molecular & cellular proteomics : MCP 2004 Medzihradszky KF, Darula Z, Perlson E, Fainzilber M, Chalkley RJ, Ball H, Greenbaum D, Bogyo M, Tyson DR, Bradshaw RA, Burlingame AL
• Identification of a novel protein regulating microtubule stability through a chemical approach.
  Chemistry & biology 2004 Wignall SM, Gray NS, Chang YT, Juarez L, Jacob R, Burlingame A, Schultz PG, Heald R
• Urinary proteomics of renal Fanconi syndrome.
  Contributions to nephrology 2004 Cutillas PR, Norden AG, Cramer R, Burlingame AL, Unwin RJ
• Regulated expression of apolipoprotein E by human retinal pigment epithelial cells.
  Journal of lipid research 2003 Ishida BY, Bailey KR, Duncan KG, Chalkley RJ, Burlingame AL, Kane JP, Schwartz DM
• Two distinct coactivators, DRIP/mediator and SRC/p160, are differentially involved in vitamin D receptor transactivation during keratinocyte differentiation.
  Molecular endocrinology (Baltimore, Md.) 2003 Oda Y, Sihlbom C, Chalkley RJ, Huang L, Rachez C, Chang CP, Burlingame AL, Freedman LP, Bikle DD
• Toward deciphering the knowledge encrypted in large datasets.
  Molecular & cellular proteomics : MCP 2003 Burlingame AL
• Mass spectrometric analysis of protein mixtures at low levels using cleavable 13C-isotope-coded affinity tag and multidimensional chromatography.
  Molecular & cellular proteomics : MCP 2003 Hansen KC, Schmitt-Ulms G, Chalkley RJ, Hirsch J, Baldwin MA, Burlingame AL
• Detection and analysis of urinary peptides by on-line liquid chromatography and mass spectrometry: application to patients with renal Fanconi syndrome.
  Clinical science (London, England : 1979) 2003 Cutillas PR, Norden AG, Cramer R, Burlingame AL, Unwin RJ
• Human apoC-IV: isolation, characterization, and immunochemical quantification in plasma and plasma lipoproteins.
  Journal of lipid research 2003 Kotite L, Zhang LH, Yu Z, Burlingame AL, Havel RJ
• Identification of novel sites of O-N-acetylglucosamine modification of serum response factor using quadrupole time-of-flight mass spectrometry.
  Molecular & cellular proteomics : MCP 2003 Chalkley RJ, Burlingame AL
• Deciphering networks of protein interactions at the nuclear pore complex.
  Molecular & cellular proteomics : MCP 2002 Allen NP, Patel SS, Huang L, Chalkley RJ, Burlingame A, Lutzmann M, Hurt EC, Rexach M
• Attomole detection of in vivo protein targets of benzene in mice: evidence for a highly reactive metabolite.
  Molecular & cellular proteomics : MCP 2002 Williams KE, Carver TA, Miranda JJ, Kautiainen A, Vogel JS, Dingley K, Baldwin MA, Turteltaub KW, 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.
  Analytical biochemistry 2002 Zhang K, Tang H, Huang L, Blankenship JW, Jones PR, Xiang F, Yau PM, Burlingame AL
• Histone acetylation and deacetylation: identification of acetylation and methylation sites of HeLa histone H4 by mass spectrometry.
  Molecular & cellular proteomics : MCP 2002 Zhang K, Williams KE, Huang L, Yau P, Siino JS, Bradbury EM, Jones PR, Minch MJ, Burlingame AL
• Stress-inducible protein 1 is a cell surface ligand for cellular prion that triggers neuroprotection.
  The EMBO journal 2002 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
• Structure and functional characterization of the periplasmic N-terminal polypeptide domain of the sugar-specific ion channel protein (ScrY porin).
  Protein science : a publication of the Protein Society 2002 Michels J, Geyer A, Mocanu V, Welte W, Burlingame AL, Przybylski M
• 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.
  Molecular & cellular proteomics : MCP 2002 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
• Cytochrome P450(cin) (CYP176A), isolation, expression, and characterization.
  The Journal of biological chemistry 2002 Hawkes DB, Adams GW, Burlingame AL, Ortiz de Montellano PR, De Voss JJ
• Differential proteome analysis of replicative senescence in rat embryo fibroblasts.
  Molecular & cellular proteomics : MCP 2002 Benvenuti S, Cramer R, Quinn CC, Bruce J, Zvelebil M, Corless S, Bond J, Yang A, Hockfield S, Burlingame AL, Waterfield MD, Jat PS
• Towards proteome-wide production of monoclonal antibody by phage display.
  Journal of molecular biology 2002 Liu B, Huang L, Sihlbom C, Burlingame A, Marks JD
• Chemical approaches for functionally probing the proteome.
  Molecular & cellular proteomics : MCP 2002 Greenbaum D, Baruch A, Hayrapetian L, Darula Z, Burlingame A, Medzihradszky KF, Bogyo M
• Identification of GlcNAcylation sites of peptides and alpha-crystallin using Q-TOF mass spectrometry.
  Journal of the American Society for Mass Spectrometry 2001 Chalkley RJ, Burlingame AL
• Novel inter-protein cross-link identified in the GGH-ecotin D137Y dimer.
  Protein science : a publication of the Protein Society 2001 Person MD, Brown KC, Mahrus S, Craik CS, Burlingame AL
• Enzymatic approaches for obtaining amino acid sequence: on-target ladder sequencing.
  Current protocols in protein science 2001 Jiménez CR, Huang L, Qiu Y, Burlingame AL
• In-gel digestion of proteins for MALDI-MS fingerprint mapping.
  Current protocols in protein science 2001 Jiménez CR, Huang L, Qiu Y, Burlingame AL
• Sample preparation for MALDI mass analysis of peptides and proteins.
  Current protocols in protein science 2001 Jiménez CR, Huang L, Qiu Y, Burlingame AL
• Searching sequence databases over the internet: protein identification using MS-Fit.
  Current protocols in protein science 2001 Jiménez CR, Huang L, Qiu Y, Burlingame AL
• Searching sequence databases over the internet: protein identification using MS-tag.
  Current protocols in protein science 2001 Jiménez CR, Huang L, Qiu Y, Burlingame AL
• Functional assignment of the 20 S proteasome from Trypanosoma brucei using mass spectrometry and new bioinformatics approaches.
  The Journal of biological chemistry 2001 Huang L, Jacob RJ, Pegg SC, Baldwin MA, Wang CC, Burlingame AL, Babbitt PC
• Matrix-assisted laser desorption/ionization coupled with quadrupole/orthogonal acceleration time-of-flight mass spectrometry for protein discovery, identification, and structural analysis.
  Analytical chemistry 2001 Baldwin MA, Medzihradszky KF, Lock CM, Fisher B, Settineri TA, Burlingame AL
• Functional proteomics: examining the effects of hypoxia on the cytotrophoblast protein repertoire.
  Biochemistry 2001 Hoang VM, Foulk R, Clauser K, Burlingame A, Gibson BW, Fisher SJ
• Kaposi's sarcoma-associated herpesvirus K-bZIP protein is phosphorylated by cyclin-dependent kinases.
  Journal of virology 2001 Polson AG, Huang L, Lukac DM, Blethrow JD, Morgan DO, Burlingame AL, Ganem D
• Identification of new JNK substrate using ATP pocket mutant JNK and a corresponding ATP analogue.
  The Journal of biological chemistry 2001 Habelhah H, Shah K, Huang L, Burlingame AL, Shokat KM, Ronai Z
• ERK phosphorylation drives cytoplasmic accumulation of hnRNP-K and inhibition of mRNA translation.
  Nature cell biology 2001 Habelhah H, Shah K, Huang L, Ostareck-Lederer A, Burlingame AL, Shokat KM, Hentze MW, Ronai Z
• Protein identification by in-gel digestion, high-performance liquid chromatography, and mass spectrometry: peptide analysis by complementary ionization techniques.
  Journal of the American Society for Mass Spectrometry 2001 Medzihradszky KF, Leffler H, Baldwin MA, 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.
  Advances in experimental medicine and biology 2001 Qiu Y, Benet LZ, Burlingame AL
• Epoxide electrophiles as activity-dependent cysteine protease profiling and discovery tools.
  Chemistry & biology 2000 Greenbaum D, Medzihradszky KF, Burlingame A, Bogyo M
• Preferential oxidation of zinc finger 2 in estrogen receptor DNA-binding domain prevents dimerization and, hence, DNA binding.
  Biochemistry 2000 Whittal RM, Benz CC, Scott G, Semyonov J, Burlingame AL, Baldwin MA
• Toxicity of ALS-linked SOD1 mutants.
  Science (New York, N.Y.) 2000 Williamson TL, Corson LB, Huang L, Burlingame A, Liu J, Bruijn LI, Cleveland DW
• Atmospheric pressure matrix-assisted laser desorption/ionization mass spectrometry.
  Analytical chemistry 2000 Laiko VV, Baldwin MA, Burlingame AL
• Copper binding to octarepeat peptides of the prion protein monitored by mass spectrometry.
  Protein science : a publication of the Protein Society 2000 Whittal RM, Ball HL, Cohen FE, Burlingame AL, Prusiner SB, Baldwin MA
• 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 physiology 2000 Chang WW, Huang L, Shen M, Webster C, Burlingame AL, Roberts JK
• The characteristics of peptide collision-induced dissociation using a high-performance MALDI-TOF/TOF tandem mass spectrometer.
  Analytical chemistry 2000 Medzihradszky KF, Campbell JM, Baldwin MA, Falick AM, Juhasz P, Vestal ML, Burlingame AL
• Employing target modifications for the investigation of liquid infrared matrix-assisted laser desorption/ionization mass spectrometry.
  Rapid communications in mass spectrometry : RCM 2000 Cramer R, Burlingame AL
• alpha5 subunit in Trypanosoma brucei proteasome can self-assemble to form a cylinder of four stacked heptamer rings.
  The Biochemical journal 1999 Yao Y, Toth CR, Huang L, Wong ML, Dias P, Burlingame AL, Coffino P, Wang CC
• Structural and functional characterizations of the proteasome-activating protein PA26 from Trypanosoma brucei.
  The Journal of biological chemistry 1999 Yao Y, Huang L, Krutchinsky A, Wong ML, Standing KG, Burlingame AL, Wang CC
• Analysis of cross-linked human hemoglobin by conventional isoelectric focusing, immobilized pH gradients, capillary electrophoresis, and mass spectrometry.
  Electrophoresis 1999 Bossi A, Patel MJ, Webb EJ, Baldwin MA, Jacob RJ, Burlingame AL, Righetti PG
• Identification and isolation of three proteasome subunits and their encoding genes from Trypanosoma brucei.
  Molecular and biochemical parasitology 1999 Huang L, Shen M, Chernushevich I, Burlingame AL, Wang CC, Robertson CD
• Role of accurate mass measurement (+/- 10 ppm) in protein identification strategies employing MS or MS/MS and database searching.
  Analytical chemistry 1999 Clauser KR, Baker P, 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 Stimson E, Hope J, Chong A, 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.
  Journal of mass spectrometry : JMS 1999 Wolfender JL, Chu F, Ball H, Wolfender F, Fainzilber M, Baldwin MA, Burlingame AL
• Transcription factor phosphorylation by pp90(rsk2). Identification of Fos kinase and NGFI-B kinase I as pp90(rsk2).
  The Journal of biological chemistry 1999 Swanson KD, Taylor LK, Haung L, Burlingame AL, Landreth GE
• Insight into absorption of radiation/energy transfer in infrared matrix-assisted laser desorption/ionization: the roles of matrices, water and metal substrates.
  Rapid communications in mass spectrometry : RCM 1999 Talrose VL, Person MD, Whittal RM, Walls FC, Burlingame AL, Baldwin MA
• Analysis of phospho- and glycopolypeptides with infrared matrix-assisted laser desorption and ionization.
  Analytical chemistry 1998 Cramer R, Richter WJ, Stimson E, Burlingame AL
• Ultramicroanalysis of peptide profiles in biological samples using MALDI mass spectrometry.
  Experimental nephrology 1998 Jiménez CR, Burlingame AL
• Mass spectrometry.
  Analytical chemistry 1998 Burlingame AL, Boyd RK, Gaskell SJ
• Identification of the hepatic protein targets of reactive metabolites of acetaminophen in vivo in mice using two-dimensional gel electrophoresis and mass spectrometry.
  The Journal of biological chemistry 1998 Qiu Y, Benet LZ, Burlingame AL
• Human low-molecular-weight salivary mucin expresses the sialyl lewisx determinant and has L-selectin ligand activity.
  Biochemistry 1998 Prakobphol A, Thomsson KA, Hansson GC, Rosen SD, Singer MS, Phillips NJ, Medzihradszky KF, Burlingame AL, Leffler H, Fisher SJ
• Determining protein-protein interactions by oxidative cross-linking of a glycine-glycine-histidine fusion protein.
  Biochemistry 1998 Brown KC, Yu Z, Burlingame AL, Craik CS
• Mechanisms for covalent binding of benoxaprofen glucuronide to human serum albumin. Studies By tandem mass spectrometry.
  Drug metabolism and disposition: the biological fate of chemicals 1998 Qiu Y, Burlingame AL, Benet LZ
• Direct mass spectrometric peptide profiling and sequencing of single neurons reveals differential peptide patterns in a small neuronal network.
  Biochemistry 1998 Jiménez CR, Li KW, Dreisewerd K, Spijker S, Kingston R, Bateman RH, Burlingame AL, Smit AB, van Minnen J, Geraerts WP
• gamma-Conotoxin-PnVIIA, a gamma-carboxyglutamate-containing peptide agonist of neuronal pacemaker cation currents.
  Biochemistry 1998 Fainzilber M, Nakamura T, Lodder JC, Zlotkin E, Kits KS, 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 communications in mass spectrometry : RCM 1998 Medzihradszky KF, Besman MJ, Burlingame AL
• Cytosolic phox proteins interact with and regulate the assembly of coronin in neutrophils.
  Journal of cell science 1997 Grogan A, Reeves E, Keep N, Wientjes F, Totty NF, Burlingame AL, Hsuan JJ, Segal AW
• Structural characterization of human hemoglobin crosslinked by bis(3,5-dibromosalicyl) fumarate using mass spectrometric techniques.
  Protein science : a publication of the Protein Society 1997 Yu Z, Friso G, Miranda JJ, Patel MJ, Lo-Tseng T, Moore EG, Burlingame AL
• Mammalian actin-related protein 2/3 complex localizes to regions of lamellipodial protrusion and is composed of evolutionarily conserved proteins.
  The Biochemical journal 1997 Machesky LM, Reeves E, Wientjes F, Mattheyse FJ, Grogan A, Totty NF, Burlingame AL, Hsuan JJ, Segal AW
• Alkylation of a catalytic aspartate group of the SIV protease by an epoxide inhibitor.
  Bioorganic & medicinal chemistry 1997 Caldera PS, Yu Z, Knegtel RM, McPhee F, Burlingame AL, Craik CS, Kuntz ID, Ortiz de Montellano PR
• Structural characterization of site-specific N-glycosylation of recombinant human factor VIII by reversed-phase high-performance liquid chromatography-electrospray ionization mass spectrometry.
  Analytical chemistry 1997 Medzihradszky KF, Besman MJ, Burlingame AL
• A low molecular weight substance purified from human placenta inhibits cAMP-dependent protein kinase and activates protein kinase C.
  Molecular and cellular biochemistry 1997 Talwar N, Pilz RB, Yu Z, Burlingame A, Boss GR
• Identification of constitutive and gamma-interferon- and interleukin 4-regulated proteins in the human renal carcinoma cell line ACHN.
  Cancer research 1997 Sullivan CM, Smith DM, Matsui NM, Andrews LE, Clauser KR, Chapeaurouge A, 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 Matsui NM, Smith DM, Clauser KR, Fichmann J, Andrews LE, Sullivan CM, Burlingame AL, Epstein LB
• 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 Epstein LB, Smith DM, Matsui NM, Tran HM, Sullivan C, Raineri I, Burlingame AL, Clauser KR, Hall SC, Andrews LE
• Search of sequence databases with uninterpreted high-energy collision-induced dissociation spectra of peptides.
  Journal of the American Society for Mass Spectrometry 1996 Yates JR, Eng JK, Clauser KR, Burlingame AL
• A crosslinked cofactor in lysyl oxidase: redox function for amino acid side chains.
  Science (New York, N.Y.) 1996 Wang SX, Mure M, Medzihradszky KF, Burlingame AL, Brown DE, Dooley DM, Smith AJ, Kagan HM, Klinman JP
• A novel hydrophobic omega-conotoxin blocks molluscan dihydropyridine-sensitive calcium channels.
  Biochemistry 1996 Fainzilber M, Lodder JC, van der Schors RC, Li KW, Yu Z, Burlingame AL, Geraerts WP, Kits KS
• Mass spectrometry.
  Analytical chemistry 1996 Burlingame AL, Boyd RK, Gaskell SJ
• Reactions of Charged Substrates. 4. The Gas-Phase Dissociation of (4-Substituted benzyl)dimethylsulfoniums and -pyridiniums.
  The Journal of organic chemistry 1996 Buckley N, Maltby D, Burlingame AL, Oppenheimer NJ
• 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 science : a publication of the Protein Society 1996 Nakamura T, Yu Z, Fainzilber M, Burlingame AL
• Characterization of protein glycosylation by mass spectrometry.
  Current opinion in biotechnology 1996 Burlingame AL
• High-energy collision-induced dissociation mass spectrometry of synthetic mannose-6-phosphate oligosaccharides.
  Journal of the American Society for Mass Spectrometry 1996 Lipniunas PH, Townsend RR, Burlingame AL, Hindsgaul O
• Peptide sequence determination by matrix-assisted laser desorption ionization employing a tandem double focusing magnetic-Orthogonal acceleration time-of-flight mass spectrometer.
  Journal of the American Society for Mass Spectrometry 1996 Medzihradszky KF, Adams GW, Burlingame AL, Bateman RH, Green MR
• Structural characterization of protein glycosylation using HPLC/electrospray ionization mass spectrometry and glycosidase digestion.
  Methods in molecular biology (Clifton, N.J.) 1996 Settineri CA, Burlingame AL
• Determination of in vivo phosphorylation sites in protein kinase C.
  The Journal of biological chemistry 1995 Tsutakawa SE, Medzihradszky KF, Flint AJ, Burlingame AL, Koshland DE
• Purification, characterization, and cloning of a heme-binding protein (23 kDa) in rat liver cytosol.
  Biochemistry 1995 Iwahara S, Satoh H, Song DX, Webb J, Burlingame AL, Nagae Y, Muller-Eberhard U
• Synthesis and mass-spectrometric characterization of human serum albumins modified by covalent binding of two non-steroidal anti-inflammatory drugs: tolmetin and zomepirac.
  The Biochemical journal 1995 Zia-Amirhosseini P, Ding A, Burlingame AL, McDonagh AF, Benet LZ
• Activation of the tamoxifen derivative metabolite E to form DNA adducts: comparison with the adducts formed by microsomal activation of tamoxifen.
  Cancer research 1995 Pongracz K, Pathak DN, Nakamura T, Burlingame AL, Bodell WJ
• A new cysteine framework in sodium channel blocking conotoxins.
  Biochemistry 1995 Fainzilber M, Nakamura T, Gaathon A, Lodder JC, Kits KS, Burlingame AL, Zlotkin E
• Rapid mass spectrometric peptide sequencing and mass matching for characterization of human melanoma proteins isolated by two-dimensional PAGE.
  Proceedings of the National Academy of Sciences of the United States of America 1995 Clauser KR, Hall SC, Smith DM, Webb JW, Andrews LE, Tran HM, Epstein LB, 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 science : a publication of the Protein Society 1995 Schindler PA, Settineri CA, Collet X, Fielding CJ, Burlingame AL
• Reactivity of tolmetin glucuronide with human serum albumin. Identification of binding sites and mechanisms of reaction by tandem mass spectrometry.
  Drug metabolism and disposition: the biological fate of chemicals 1995 Ding A, Zia-Amirhosseini P, McDonagh AF, Burlingame AL, Benet LZ
• Mass spectrometric studies of the primary sequence and structure of bovine liver and serum amine oxidase.
  Methods in enzymology 1995 Adams GW, Mayer P, Medzihradszky KF, Burlingame AL
• Complete assignment of disulfide bonds in bovine dopamine beta-hydroxylase.
  Biochemistry 1994 Robertson JG, Adams GW, Medzihradszky KF, Burlingame AL, Villafranca JJ
• Subunits of the Saccharomyces cerevisiae signal recognition particle required for its functional expression.
  The EMBO journal 1994 Brown JD, Hann BC, Medzihradszky KF, Niwa M, Burlingame AL, Walter P
• New mollusc-specific alpha-conotoxins block Aplysia neuronal acetylcholine receptors.
  Biochemistry 1994 Fainzilber M, Hasson A, Oren R, Burlingame AL, Gordon D, Spira ME, Zlotkin E
• Mass spectrometry.
  Analytical chemistry 1994 Burlingame AL, Boyd RK, Gaskell SJ
• Characterization of protein iv-glycosylation by reversed-phase microbore liquid chromatography / electrospray mass spectrometry, complementary mobile phases, and sequential exoglycosidase digestion.
  Journal of the American Society for Mass Spectrometry 1994 Medzihradszky KF, Maltby DA, Hall SC, Settineri CA, Burlingame AL
• In vitro characterization of nonpeptide irreversible inhibitors of HIV proteases.
  The Journal of biological chemistry 1994 Salto R, Babé LM, Li J, Rosé JR, Yu Z, Burlingame A, De Voss JJ, Sui Z, Ortiz de Montellano P, Craik CS
• Primary structures for a mammalian cellular and serum copper amine oxidase.
  The Journal of biological chemistry 1994 Mu D, Medzihradszky KF, Adams GW, Mayer P, Hines WM, Burlingame AL, Smith AJ, Cai D, Klinman JP
• 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.
  The Journal of biological chemistry 1993 Herrmann J, Turck CW, Atchison RE, Huflejt ME, Poulter L, Gitt MA, Burlingame AL, Barondes SH, Leffler H
• Mapping a membrane-associated conformation of colicin Ia.
  Biochemistry 1993 Mel SF, Falick AM, Burlingame AL, Stroud RM
• Evidence for covalent binding of acyl glucuronides to serum albumin via an imine mechanism as revealed by tandem mass spectrometry.
  Proceedings of the National Academy of Sciences of the United States of America 1993 Ding A, Ojingwa JC, McDonagh AF, Burlingame AL, Benet LZ
• Soluble lactose-binding lectin from rat intestine with two different carbohydrate-binding domains in the same peptide chain.
  The Journal of biological chemistry 1993 Oda Y, Herrmann J, Gitt MA, Turck CW, Burlingame AL, Barondes SH, Leffler H
• Structural studies of the scrapie prion protein using mass spectrometry and amino acid sequencing.
  Biochemistry 1993 Stahl N, Baldwin MA, Teplow DB, Hood L, Gibson BW, Burlingame AL, Prusiner SB
• Mass spectrometric and Edman sequencing of lipocortin I isolated by two-dimensional SDS/PAGE of human melanoma lysates.
  Proceedings of the National Academy of Sciences of the United States of America 1993 Hall SC, Smith DM, Masiarz FR, Soo VW, Tran HM, Epstein LB, 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.
  Chemical research in toxicology 1993 Kaur S, Pongracz K, Bodell WJ, Burlingame AL
• 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.
  The Journal of biological chemistry 1992 Wen DX, Livingston BD, Medzihradszky KF, Kelm S, Burlingame AL, Paulson JC
• Phosphorylation site of NtrC, a protein phosphatase whose covalent intermediate activates transcription.
  Journal of bacteriology 1992 Sanders DA, Gillece-Castro BL, Burlingame AL, Koshland DE
• Mass spectrometry.
  Analytical chemistry 1992 Burlingame AL, Baillie TA, Russell DH
• Glycosylinositol phospholipid anchors of the scrapie and cellular prion proteins contain sialic acid.
  Biochemistry 1992 Stahl N, Baldwin MA, Hecker R, Pan KM, Burlingame AL, Prusiner SB
• Pattern-based algorithm for peptide sequencing from tandem high energy collision-induced dissociation mass spectra.
  Journal of the American Society for Mass Spectrometry 1992 Hines WM, Falick AM, Burlingame AL, Gibson BW
• Identification of N2-substituted 2'-deoxyguanosine-3'-phosphate adducts detected by 32P-postlabeling of styrene-oxide-treated DNA.
  Carcinogenesis 1992 Pongracz K, Kaur S, Burlingame AL, Bodell WJ
• The active site of creatine kinase. Affinity labeling of cysteine 282 with N-(2,3-epoxypropyl)-N-amidinoglycine.
  The Journal of biological chemistry 1992 Buechter DD, Medzihradszky KF, Burlingame AL, Kenyon GL
• The primary structure of fatty-acid-binding protein from nurse shark liver. Structural and evolutionary relationship to the mammalian fatty-acid-binding protein family.
  European journal of biochemistry 1992 Medzihradszky KF, Gibson BW, Kaur S, Yu ZH, Medzihradszky D, Burlingame AL, Bass NM
• Structure and bacterial receptor activity of a human salivary proline-rich glycoprotein.
  The Journal of biological chemistry 1991 Gillece-Castro BL, Prakobphol A, Burlingame AL, Leffler H, Fisher SJ
• n-Alkyl p-aminobenzoates as derivatizing agents in the isolation, separation, and characterization of submicrogram quantities of oligosaccharides by liquid secondary ion mass spectrometry.
  Analytical biochemistry 1991 Poulter L, Karrer R, Burlingame AL
• Strategies for identification of covalent xenobiotic modifications in proteins by mass spectrometry.
  Progress in clinical and biological research 1991 Kaur S, Hall SC, Burlingame AL
• Structure determination of O-linked glycopeptides by tandem mass spectrometry.
  Biomedical & environmental mass spectrometry 1990 Medzihradszky KF, Gillece-Castro BL, Settineri CA, Townsend RR, Masiarz FR, Burlingame AL
• Permethylation and tandem mass spectrometry of oligosaccharides having free hexosamine: analysis of the glycoinositol phospholipid anchor glycan from the scrapie prion protein.
  Analytical biochemistry 1990 Baldwin MA, Stahl N, Reinders LG, Gibson BW, Prusiner SB, Burlingame AL
• 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.
  Biomedical & environmental mass spectrometry 1990 Settineri CA, Medzihradszky KF, Masiarz FR, Burlingame AL, Chu C, George-Nascimento C
• Identification of glycoinositol phospholipid linked and truncated forms of the scrapie prion protein.
  Biochemistry 1990 Stahl N, Baldwin MA, Burlingame AL, Prusiner SB
• Detection of (3'-hydroxy)-3,N4-benzetheno-2'-deoxycytidine-3'-phosphate by 32P-postlabeling of DNA reacted with p-benzoquinone.
  Carcinogenesis 1990 Pongracz K, Kaur S, Burlingame AL, Bodell WJ
• Mass spectrometry.
  Analytical chemistry 1990 Burlingame AL, Millington DS, Norwood DL, Russell DH
• A new redox cofactor in eukaryotic enzymes: 6-hydroxydopa at the active site of bovine serum amine oxidase.
  Science (New York, N.Y.) 1990 Janes SM, Mu D, Wemmer D, Smith AJ, Kaur S, Maltby D, Burlingame AL, Klinman JP
• Desorption mass spectrometry of oligosaccharides coupled with hydrophobic chromophores.
  Methods in enzymology 1990 Poulter L, Burlingame AL
• Investigation of styrene oxide-DNA adducts and their detection in workers exposed to styrene.
  Progress in clinical and biological research 1990 Bodell WJ, Pongracz K, Kaur S, Burlingame AL, Liu SF, Rappaport SM
• Oligosaccharide characterization with high-energy collision-induced dissociation mass spectrometry.
  Methods in enzymology 1990 Gillece-Castro BL, Burlingame AL
• Identification of the site of phosphorylation of the chemotaxis response regulator protein, CheY.
  The Journal of biological chemistry 1989 Sanders DA, Gillece-Castro BL, Stock AM, Burlingame AL, Koshland DE
• Characterization of structural xenobiotic modifications in proteins by high sensitivity tandem mass spectrometry. Human hemoglobin treated in vitro with styrene 7,8-oxide.
  The Journal of biological chemistry 1989 Kaur S, Hollander D, Haas R, Burlingame AL
• Asparagine-linked glycosylation of the scrapie and cellular prion proteins.
  Archives of biochemistry and biophysics 1989 Haraguchi T, Fisher S, Olofsson S, Endo T, Groth D, Tarentino A, Borchelt DR, Teplow D, Hood L, Burlingame A
• Structure, oligosaccharide structures, and posttranslationally modified sites of the nicotinic acetylcholine receptor.
  Proceedings of the National Academy of Sciences of the United States of America 1989 Poulter L, Earnest JP, Stroud RM, Burlingame AL
• A new Saccharomyces cerevisiae mnn mutant N-linked oligosaccharide structure.
  The Journal of biological chemistry 1989 Hernández LM, Ballou L, Alvarado E, Gillece-Castro BL, Burlingame AL, Ballou CE
• O6-substituted-2'-deoxyguanosine-3'-phosphate adducts detected by 32P post-labeling of styrene oxide treated DNA.
  Carcinogenesis 1989 Pongracz K, Kaur S, Burlingame AL, Bodell WJ
• Structure and heterogeneity of the oligosaccharides from the lipopolysaccharides of a pyocin-resistant Neisseria gonorrhoeae.
  Proceedings of the National Academy of Sciences of the United States of America 1989 Gibson BW, Webb JW, Yamasaki R, Fisher SJ, Burlingame AL, Mandrell RE, Schneider H, Griffiss JM
• Cesium ion liquid secondary ion mass spectrometry of membrane-bound glycoproteins: structural and topological considerations of acetylcholine receptor from Torpedo californica.
  Biomedical & environmental mass spectrometry 1988 Poulter L, Earnest JP, Stroud RM, Burlingame AL
• Environmental applications of organic mass spectrometry in China.
  Biomedical and environmental sciences : BES 1988 Xu XB, 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.
  Analytical chemistry 1988 Aberth WH, Burlingame AL
• Mass spectrometry.
  Analytical chemistry 1988 Burlingame AL, Maltby D, Russell DH, Holland PT
• Revision of the blocked N terminus of rat heart fatty acid-binding protein by liquid secondary ion mass spectrometry.
  The Journal of biological chemistry 1988 Gibson BW, Yu ZG, Aberth W, Burlingame AL, Bass NM
• Structural characterization of intact, branched oligosaccharides by high performance liquid chromatography and liquid secondary ion mass spectrometry.
  Analytical biochemistry 1988 Webb JW, Jiang K, Gillece-Castro BL, Tarentino AL, Plummer TH, Byrd JC, Fisher SJ, Burlingame AL
• Structure of the oligosaccharide portion of human hepatitis B surface antigen.
  Archives of biochemistry and biophysics 1987 Gillece-Castro BL, Fisher SJ, Tarentino AL, Peterson DL, Burlingame AL
• Mass spectrometry.
  Analytical chemistry 1986 Burlingame AL, Baillie TA, Derrick PJ
• Positive and negative liquid secondary ion mass spectrometry of chloro- and nitrophenylglucuronides.
  Biomedical mass spectrometry 1985 Wickramanayake PP, Deinzer ML, Burlingame AL
• Comparison of three geometries for a cesium primary beam liquid secondary ion mass spectrometry source.
  Analytical chemistry 1984 Aberth W, Burlingame AL
• High-performance liquid chromatographic isolation and fast atom bombardment mass spectrometric identification of Di-N-desethylamiodarone, a new metabolite of amiodarone in the dog.
  Biomedical mass spectrometry 1984 Latini R, Reginato R, Burlingame AL, Kates RE
• Human stratum corneum lipids: characterization and regional variations.
  Journal of lipid research 1983 Lampe MA, Burlingame AL, Whitney J, Williams ML, Brown BE, Roitman E, Elias PM
• Carcinogen binding to DNA.
  Biomedical mass spectrometry 1981 Straub KM, Burlingame AL
• Identification of 2-nitrofluorene in diesel exhaust particulates.
  Journal of applied toxicology : JAT 1981 Xu XB, Nachtman JP, Rappaport SM, Wei ET, Lewis S, Burlingame AL
• Structural identification of autoinducer of Photobacterium fischeri luciferase.
  Biochemistry 1981 Eberhard A, Burlingame AL, Eberhard C, Kenyon GL, Nealson KH, Oppenheimer NJ
• Field desorption mass spectrometry of oligosaccharides.
  Proceedings of the National Academy of Sciences of the United States of America 1981 Linscheid M, D'Angona J, Burlingame AL, Dell A, Ballou CE
• Exchange of methyl hydrogens in ethanol during incorporation in bile acids in vivo.
  Biochimica et biophysica acta 1979 Cronholm T, Sjövall J, Wilson DM, Burlingame AL
• High resolution gas chromatographic/real-time high resolution mass spectrometric identification of organic acids in human urine.
  Analytical chemistry 1979 Lewis S, Kenyon CN, Meili J, Burlingame AL
• Identification of the major adducts formed by reaction of benzo(a)pyrene diol epoxide with DNA in vitro.
  Proceedings of the National Academy of Sciences of the United States of America 1977 Straub KM, Meehan T, Burlingame AL, Calvin M
• 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.
  Ecotoxicology and environmental safety 1977 Burlingame AL
• Identification of chlorinated dibenzofurans in American polychlorinated biphenyls.
  Nature 1975 Bowes CW, Mulvihill MJ, Simoneit BR, Burlingame AL, Risebrough RW
• Utilization of the carbon and hydrogen atoms of ethanol in the biosynthesis of steroids and bile acids.
  European journal of biochemistry 1974 Cronholm T, Burlingame AL, Sjövall J
• Deuterium and carbon-13 tracer studies of ethanol metabolism in the rat by 2H, 1H-decoupled 13C nuclear magnetic resonance.
  Biochemical and biophysical research communications 1974 Wilson DM, Burlingame AL
• Nonheuristic computer determination of molecular structure based upon carbon-13 nuclear magnetic resonance data: branched alkanes.
  Proceedings of the National Academy of Sciences of the United States of America 1973 Burlingame AL, McPherron RV, Wilson DM
• Application of real-time mass spectrometric techniques to environmental organic geochemistry. II. Organic matter in San Francisco Bay area water.
  Archives of environmental contamination and toxicology 1973 Simoneit BR, Smith DH, Eglinton G, Burlingame AL
• The search for chlorinated dibenzofurans and chlorinated dibenzodioxins in wildlife populations showing elevated levels of embryonic death.
  Environmental health perspectives 1973 Bowes GW, Simoneit BR, Burlingame AL, de Lappe BW, Risebrough RW
• Very long-chain fatty acids in yeast.
  Journal of bacteriology 1973 Welch JW, Burlingame AL
• Study of carbon compounds in Apollo 12 and 14 lunar samples.
  Space life sciences 1972 Holland PT, Simoneit BR, Wszolek PC, Burlingame AL
• Mass spectrometry.
  Analytical chemistry 1972 Burlingame AL, Johanson GA
• Carbon-13 NMR study of the stereochemistry of steranes from oil shale of the Green River formation (Eocene).
  Nature 1971 Balogh B, Wilson DM, Burlingame AL
• Minimal substrate structural requirements for lanosterol-squalene 2,3-oxide cyclase action. 10'-norsqualene 2,3-oxide.
  Journal of the American Chemical Society 1970 van Tamelen EE, Hanzlik RP, Clayton RB, Burlingame AL
• Nitrogenous compounds of the Colorado Green River Formation oil shale: a preliminary analysis by mass spectrometry.
  Nature 1970 Simoneit BR, Schnoes HK, Haug P, Burlingame AL
• Lunar organic compounds: search and characterization.
  Science (New York, N.Y.) 1970 Burlingame AL, Calvin M, Han J, Henderson W, Reed W, Simoneit BR
• Tumor inhibitors XL. The isolation and structural elucidation of elephantin and elephantopin, two novel sesquiterpenoid tumor inhibitors from Elephantopus elatus.
  The Journal of organic chemistry 1969 Kupchan SM, Aynehchi Y, Cassady JM, Schnoes HK, Burlingame AL
• Tumor inhibitors. 43. Solapalmitine and solapalmitenine, two novel alkaloid tumor inhibitors from Solanum tripartitium.
  The Journal of organic chemistry 1969 Kupchan SM, Davies AP, Barboutis SJ, Schnoes HK, Burlingame AL
• Tumor inhibitors. XXXIX. Active principles of Acnistus arborescens. Isolation and structural and spectral studies of withaferin A and withacnistin.
  The Journal of organic chemistry 1969 Kupchan SM, Anderson WK, Bollinger P, Doskotch RW, Smith RM, Renauld JA, Schnoes HK, Burlingame AL, Smith DH
• Apollo lunar module engine exhaust products.
  Science (New York, N.Y.) 1969 Simoneit BR, Burlingame AL, Flory DA, Smith ID
• Isoprenoid Fatty acids isolated from the kerogen matrix of the green river formation (eocene).
  Science (New York, N.Y.) 1968 Burlingame AL, Simoneit BR
• Enzymic cyclization of trans,trans,trans-18,19-dihydrosqualene 2,3-oxide.
  Journal of the American Chemical Society 1967 van Tamelen EE, Sharpless KB, Hanzlik R, Clayton RB, Burlingame AL, Wszolek PC
• Isoprenoid and dicarboxylic acids isolated from colorado green river shale (eocene).
  Science (New York, N.Y.) 1967 Haug P, Schnoes HK, Burlingame AL
• The isolation, structural elucidation, and synthesis of solapalmitine and solapalmitenine, two novel alkaloid tumor inhibitors from Solanum tripartitum.
  Journal of the American Chemical Society 1967 Kupchan SM, Davies AP, Barboutis SJ, Schnoes HK, Burlingame AL
• Organic matter in carbonaceous chondrites.
  Science (New York, N.Y.) 1966 Urey HC, Lewis JS, Burlingame AL, Schnoes HK, Studier MH, Hayatsu R, Anders E
• 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.
  Proceedings of the National Academy of Sciences of the United States of America 1965 Burlingame AL, Haug P, Belsky T, Calvin M
• Hydrocarbons of Biological Origin from a One-Billion-Year-Old Sediment.
  Science (New York, N.Y.) 1964 Eglinton G, Scott PM, Belsky T, Burlingame AL, Calvin M