Publications

Found 312 results
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2008
Yan W, Hwang D, Aebersold R.  2008.  Quantitative proteomic analysis to profile dynamic changes in the spatial distribution of cellular proteins. Methods Mol Biol. 432:389-401.
Himeda CL, Ranish J, Hauschka SD.  2008.  Quantitative proteomic identification of MAZ as a transcriptional regulator of muscle-specific genes in skeletal and cardiac myocytes. Mol Cell Biol. 28:6521-35.
Lausted C, Hu Z, Hood L.  2008.  Quantitative serum proteomics from surface plasmon resonance imaging. Mol Cell Proteomics. 7:2464-74.
Price ND, Foltz G, Madan A, Hood L, Tian Q.  2008.  Systems biology and cancer stem cells. J Cell Mol Med. 12:97-110.
Hood L, Rowen L, Galas DJ, Aitchison JD.  2008.  Systems biology at the Institute for Systems Biology. Brief Funct Genomic Proteomic. 7:239-48.
Yang XO, Pappu BP, Nurieva R, Akimzhanov A, Kang HS, Chung Y, Ma L, Shah B, Panopoulos AD, Schluns KS et al..  2008.  T helper 17 lineage differentiation is programmed by orphan nuclear receptors ROR alpha and ROR gamma. Immunity. 28:29-39.
Aderem A, Shmulevich I.  2008.  Taming data. Cell Host Microbe. 4:312-3.
Pappu BP, Borodovsky A, Zheng TS, Yang X, Wu P, Dong X, Weng S, Browning B, Scott ML, Ma L et al..  2008.  TL1A-DR3 interaction regulates Th17 cell function and Th17-mediated autoimmune disease. J Exp Med. 205:1049-62.
Ramsey SA, Klemm SL, Zak DE, Kennedy KA, Thorsson V, Li B, Gilchrist M, Gold ES, Johnson CD, Litvak V et al..  2008.  Uncovering a macrophage transcriptional program by integrating evidence from motif scanning and expression dynamics. PLoS Comput Biol. 4:e1000021.
Lin B, Utleg AG, Gravdal K, White JT, Halvorsen OJ, Lu W, True LD, Vessella R, Lange PH, Nelson PS et al..  2008.  WDR19 expression is increased in prostate cancer compared with normal cells, but low-intensity expression in cancers is associated with shorter time to biochemical failures and local recurrence. Clin Cancer Res. 14:1397-406.
Hood LE.  2008.  Wu and Kabat 1970: a transforming view of antibody diversity. J Immunol. 180:7055-6.
2007
Lu Y, Bottari P, Aebersold R, Turecek F, Gelb MH.  2007.  Absolute quantification of specific proteins in complex mixtures using visible isotope-coded affinity tags. Methods Mol Biol. 359:159-76.
Demers C, Chaturvedi CP, Ranish J, Juban G, Lai P, Morle F, Aebersold R, Dilworth FJ, Groudine M, Brand M.  2007.  Activator-mediated recruitment of the MLL2 methyltransferase complex to the beta-globin locus. Mol Cell. 27:573-84.
Hawn TR, Berrington WR, Smith IA, Uematsu S, Akira S, Aderem A, Smith KD, Skerrett SJ.  2007.  Altered inflammatory responses in TLR5-deficient mice infected with Legionella pneumophila. J Immunol. 179:6981-7.
Gingras AC, Gstaiger M, Raught B, Aebersold R.  2007.  Analysis of protein complexes using mass spectrometry. Nat Rev Mol Cell Biol. 8:645-54.
Prakash A, Piening B, Whiteaker J, Zhang H, Shaffer SA, Martin D, Hohmann L, Cooke K, Olson JM, Hansen S et al..  2007.  Assessing bias in experiment design for large scale mass spectrometry-based quantitative proteomics. Mol Cell Proteomics. 6:1741-8.
Andersen-Nissen E, Smith KD, Bonneau R, Strong RK, Aderem A.  2007.  A conserved surface on Toll-like receptor 5 recognizes bacterial flagellin. J Exp Med. 204:393-403.
Andersen-Nissen E, Hawn TR, Smith KD, Nachman A, Lampano AE, Uematsu S, Akira S, Aderem A.  2007.  Cutting edge: Tlr5-/- mice are more susceptible to Escherichia coli urinary tract infection. J Immunol. 178:4717-20.
Nurieva R, Yang XO, Martinez G, Zhang Y, Panopoulos AD, Ma L, Schluns K, Tian Q, Watowich SS, Jetten AM et al..  2007.  Essential autocrine regulation by IL-21 in the generation of inflammatory T cells. Nature. 448:480-3.
Lessard J, Wu JI, Ranish J, Wan M, Winslow MM, Staahl BT, Wu H, Aebersold R, Graef IA, Crabtree GR.  2007.  An essential switch in subunit composition of a chromatin remodeling complex during neural development. Neuron. 55:201-15.
Vokes SA, Ji H, McCuine S, Tenzen T, Giles S, Zhong S, Longabaugh W, Davidson EH, Wong WH, McMahon AP.  2007.  Genomic characterization of Gli-activator targets in sonic hedgehog-mediated neural patterning. Development. 134:1977-89.
Gagneux S, Small PM.  2007.  Global phylogeography of Mycobacterium tuberculosis and implications for tuberculosis product development. Lancet Infect Dis. 7:328-37.
Brunner E, Ahrens CH, Mohanty S, Baetschmann H, Loevenich S, Potthast F, Deutsch EW, Panse C, de Lichtenberg U, Rinner O et al..  2007.  A high-quality catalog of the Drosophila melanogaster proteome. Nat Biotechnol. 25:576-83.
Picotti P, Aebersold R, Domon B.  2007.  The implications of proteolytic background for shotgun proteomics. Mol Cell Proteomics. 6:1589-98.
Bodenmiller B, Mueller LN, Pedrioli PG, Pflieger D, Junger MA, Eng JK, Aebersold R, Tao WA.  2007.  An integrated chemical, mass spectrometric and computational strategy for (quantitative) phosphoproteomics: application to Drosophila melanogaster Kc167 cells. Mol Biosyst. 3:275-86.
Zhou Y, Aebersold R, Zhang H.  2007.  Isolation of N-linked glycopeptides from plasma. Anal Chem. 79:5826-37.
Ibrahim SF, Diercks AH, Petersen TW, van den Engh G.  2007.  Kinetic analyses as a critical parameter in defining the side population (SP) phenotype. Exp Cell Res. 313:1921-6.
Tydell CC, David-Fung ES, Moore JE, Rowen L, Taghon T, Rothenberg EV.  2007.  Molecular dissection of prethymic progenitor entry into the T lymphocyte developmental pathway. J Immunol. 179:421-38.
Ma L, Sun B, Hood L, Tian Q.  2007.  Molecular profiling of stem cells. Clin Chim Acta. 378:24-32.
Nakayama M, Underhill DM, Petersen TW, Li B, Kitamura T, Takai T, Aderem A.  2007.  Paired Ig-like receptors bind to bacteria and shape TLR-mediated cytokine production. J Immunol. 178:4250-9.
Ravetch J, Aderem A.  2007.  Phagocytic cells. Immunol Rev. 219:5-7.
Bodenmiller B, Malmstrom J, Gerrits B, Campbell D, Lam H, Schmidt A, Rinner O, Mueller LN, Shannon P, Pedrioli PG et al..  2007.  PhosphoPep--a phosphoproteome resource for systems biology research in Drosophila Kc167 cells. Mol Syst Biol. 3:139.
Ahrens CH, Brunner E, Hafen E, Aebersold R, Basler K.  2007.  A proteome catalog of Drosophila melanogaster: an essential resource for targeted quantitative proteomics. Fly (Austin). 1:182-6.
He XC, Yin T, Grindley JC, Tian Q, Sato T, Tao WA, Dirisina R, Porter-Westpfahl KS, Hembree M, Johnson T et al..  2007.  PTEN-deficient intestinal stem cells initiate intestinal polyposis. Nat Genet. 39:189-98.
Djouder N, Metzler SC, Schmidt A, Wirbelauer C, Gstaiger M, Aebersold R, Hess D, Krek W.  2007.  S6K1-mediated disassembly of mitochondrial URI/PP1gamma complexes activates a negative feedback program that counters S6K1 survival signaling. Mol Cell. 28:28-40.
Sun B, Ranish J, Utleg AG, White JT, Yan X, Lin B, Hood L.  2007.  Shotgun glycopeptide capture approach coupled with mass spectrometry for comprehensive glycoproteomics. Mol Cell Proteomics. 6:141-9.
Au E, Richter MW, Vincent AJ, Tetzlaff W, Aebersold R, Sage EH, Roskams AJ.  2007.  SPARC from olfactory ensheathing cells stimulates Schwann cells to promote neurite outgrowth and enhances spinal cord repair. J Neurosci. 27:7208-21.
Wang P, Tang H, Fitzgibbon MP, McIntosh M, Coram M, Zhang H, Yi E, Aebersold R.  2007.  A statistical method for chromatographic alignment of LC-MS data. Biostatistics. 8:357-67.
Hulbert EM, Smink LJ, Adlem EC, Allen JE, Burdick DB, Burren OS, Cassen VM, Cavnor CC, Dolman GE, Flamez D et al..  2007.  T1DBase: integration and presentation of complex data for type 1 diabetes research. Nucleic Acids Res. 35:D742-6.
Miao EA, Andersen-Nissen E, Warren SE, Aderem A.  2007.  TLR5 and Ipaf: dual sensors of bacterial flagellin in the innate immune system. Semin Immunopathol. 29:275-88.
Noll H, Alcedo J, Daube M, Frei E, Schiltz E, Hunt J, Humphries T, Matranga V, Hochstrasser M, Aebersold R et al..  2007.  The toposome, essential for sea urchin cell adhesion and development, is a modified iron-less calcium-binding transferrin. Dev Biol. 310:54-70.
Pascal LE, Deutsch EW, Campbell DS, Korb M, True LD, Liu AY.  2007.  The urologic epithelial stem cell database (UESC) - a web tool for cell type-specific gene expression and immunohistochemistry images of the prostate and bladder. BMC Urol. 7:19.
Ranish J, Brand M, Aebersold R.  2007.  Using stable isotope tagging and mass spectrometry to characterize protein complexes and to detect changes in their composition. Methods Mol Biol. 359:17-35.
Reed MB, Gagneux S, Deriemer K, Small PM, Barry, C. E. 3rd.  2007.  The W-Beijing lineage of Mycobacterium tuberculosis overproduces triglycerides and has the DosR dormancy regulon constitutively upregulated. J Bacteriol. 189:2583-9.
2006
Burrage K, Hood L, Ragan MA.  2006.  Advanced computing for systems biology. Brief Bioinform. 7:390-8.
Zody MC, Garber M, Sharpe T, Young SK, Rowen L, O'Neill K, Whittaker CA, Kamal M, Chang JL, Cuomo CA et al..  2006.  Analysis of the DNA sequence and duplication history of human chromosome 15. Nature. 440:671-5.
Maccarana M, Olander B, Malmstrom J, Tiedemann K, Aebersold R, Lindahl U, Li JP, Malmstrom A.  2006.  Biosynthesis of dermatan sulfate: chondroitin-glucuronate C5-epimerase is identical to SART2. J Biol Chem. 281:11560-8.
Miao EA, Alpuche-Aranda CM, Dors M, Clark AE, Bader MW, Miller SI, Aderem A.  2006.  Cytoplasmic flagellin activates caspase-1 and secretion of interleukin 1beta via Ipaf. Nat Immunol. 7:569-75.
Chung Y, Yang X, Chang SH, Ma L, Tian Q, Dong C.  2006.  Expression and regulation of IL-22 in the IL-17-producing CD4+ T lymphocytes. Cell Res. 16:902-7.
Shiio Y, Rose DW, Aur R, Donohoe S, Aebersold R, Eisenman RN.  2006.  Identification and characterization of SAP25, a novel component of the mSin3 corepressor complex. Mol Cell Biol. 26:1386-97.
Zhang H, Aebersold R.  2006.  Isolation of glycoproteins and identification of their N-linked glycosylation sites. Methods Mol Biol. 328:177-85.
Hawn TR, Smith KD, Aderem A, Skerrett SJ.  2006.  Myeloid differentiation primary response gene (88)- and toll-like receptor 2-deficient mice are susceptible to infection with aerosolized Legionella pneumophila. J Infect Dis. 193:1693-702.
Malmstrom J, Lee H, Nesvizhskii AI, Shteynberg D, Mohanty S, Brunner E, Ye M, Weber G, Eckerskorn C, Aebersold R.  2006.  Optimized peptide separation and identification for mass spectrometry based proteomics via free-flow electrophoresis. J Proteome Res. 5:2241-9.
Fischbach MA, Lin H, Zhou L, Yu Y, Abergel RJ, Liu DR, Raymond KN, Wanner BL, Strong RK, Walsh CT et al..  2006.  The pathogen-associated iroA gene cluster mediates bacterial evasion of lipocalin 2. Proc Natl Acad Sci U S A. 103:16502-7.
Desiere F, Deutsch EW, King NL, Nesvizhskii AI, Mallick P, Eng J, Chen S, Eddes J, Loevenich SN, Aebersold R.  2006.  The PeptideAtlas project. Nucleic Acids Res. 34:D655-8.
Tian Q.  2006.  Proteomic exploration of the Wnt/beta-catenin pathway. Curr Opin Mol Ther. 8:191-7.
Gilchrist M, Thorsson V, Li B, Rust AG, Korb M, Roach J, Kennedy K, Hai T, Bolouri H, Aderem A.  2006.  Systems biology approaches identify ATF3 as a negative regulator of Toll-like receptor 4. Nature. 441:173-8.
Ehlers M, Fukuyama H, McGaha TL, Aderem A, Ravetch JV.  2006.  TLR9/MyD88 signaling is required for class switching to pathogenic IgG2a and 2b autoantibodies in SLE. J Exp Med. 203:553-61.
Ramsey S, Ozinsky A, Clark A, Smith KD, de Atauri P, Thorsson V, Orrell D, Bolouri H.  2006.  Transcriptional noise and cellular heterogeneity in mammalian macrophages. Philos Trans R Soc Lond B Biol Sci. 361:495-506.
Cameron RA, Rowen L, Nesbitt R, Bloom S, Rast JP, Berney K, Arenas-Mena C, Martinez P, Lucas S, Richardson PM et al..  2006.  Unusual gene order and organization of the sea urchin hox cluster. J Exp Zool B Mol Dev Evol. 306:45-58.
2005
Heller M, Ye M, Michel PE, Morier P, Stalder D, Junger MA, Aebersold R, Reymond F, Rossier JS.  2005.  Added value for tandem mass spectrometry shotgun proteomics data validation through isoelectric focusing of peptides. J Proteome Res. 4:2273-82.
Gingras AC, Aebersold R, Raught B.  2005.  Advances in protein complex analysis using mass spectrometry. J Physiol. 563:11-21.
Niemisto A, Dunmire V, Yli-Harja O, Zhang W, Shmulevich I.  2005.  Analysis of angiogenesis using in vitro experiments and stochastic growth models. Phys Rev E Stat Nonlin Soft Matter Phys. 72:062902.
Tian Q, He XC, Hood L, Li L.  2005.  Bridging the BMP and Wnt pathways by PI3 kinase/Akt and 14-3-3zeta. Cell Cycle. 4:215-6.
Iyer R, Baliga NS, Camilli A.  2005.  Catabolite control protein A (CcpA) contributes to virulence and regulation of sugar metabolism in Streptococcus pneumoniae. J Bacteriol. 187:8340-9.
Bergman MA, Cummings LA, Barrett SL, Smith KD, Lara JC, Aderem A, Cookson BT.  2005.  CD4+ T cells and toll-like receptors recognize Salmonella antigens expressed in bacterial surface organelles. Infect Immun. 73:1350-6.
Gilad Y, Man O, Glusman G.  2005.  A comparison of the human and chimpanzee olfactory receptor gene repertoires. Genome Res. 15:224-30.
Park H, Li Z, Yang XO, Chang SH, Nurieva R, Wang YH, Wang Y, Hood L, Zhu Z, Tian Q et al..  2005.  A distinct lineage of CD4 T cells regulates tissue inflammation by producing interleukin 17. Nat Immunol. 6:1133-41.
Iliev DB, Roach J, Mackenzie S, Planas JV, Goetz FW.  2005.  Endotoxin recognition: in fish or not in fish? FEBS Lett. 579:6519-28.
Andersen-Nissen E, Smith KD, Strobe KL, Barrett SL, Cookson BT, Logan SM, Aderem A.  2005.  Evasion of Toll-like receptor 5 by flagellated bacteria. Proc Natl Acad Sci U S A. 102:9247-52.
Roach J, Glusman G, Rowen L, Kaur A, Purcell MK, Smith KD, Hood LE, Aderem A.  2005.  The evolution of vertebrate Toll-like receptors. Proc Natl Acad Sci U S A. 102:9577-82.
Zhang H, Yi EC, Li XJ, Mallick P, Kelly-Spratt KS, Masselon CD, Camp, D. G. 2nd, Smith RD, Kemp CJ, Aebersold R.  2005.  High throughput quantitative analysis of serum proteins using glycopeptide capture and liquid chromatography mass spectrometry. Mol Cell Proteomics. 4:144-55.
Toigo M, Donohoe S, Sperrazzo G, Jarrold B, Wang F, Hinkle R, Dolan E, Isfort RJ, Aebersold R.  2005.  ICAT-MS-MS time course analysis of atrophying mouse skeletal muscle cytosolic subproteome. Mol Biosyst. 1:229-41.
Avila GE, Zheng X, Cui XX, Ryan AD, Hansson A, Suh J, Rabson AB, Chang RL, Shih WJ, Lin Y et al..  2005.  Inhibitory effects of 12-O-tetradecanoylphorbol-13-acetate alone or in combination with all-trans retinoic acid on the growth of cultured human pancreas cancer cells and pancreas tumor xenografts in immunodeficient mice. J Pharmacol Exp Ther. 315:170-87.
Desiere F, Deutsch EW, Nesvizhskii AI, Mallick P, King NL, Eng JK, Aderem A, Boyle R, Brunner E, Donohoe S et al..  2005.  Integration with the human genome of peptide sequences obtained by high-throughput mass spectrometry. Genome Biol. 6:R9.
Alsam S, Sissons J, Dudley R, Khan NA.  2005.  Mechanisms associated with Acanthamoeba castellanii (T4) phagocytosis. Parasitol Res. 96:402-9.
Aebersold R, Anderson L, Caprioli R, Druker B, Hartwell L, Smith R.  2005.  Perspective: a program to improve protein biomarker discovery for cancer. J Proteome Res. 4:1104-9.
Zhang N, Li XJ, Ye M, Pan S, Schwikowski B, Aebersold R.  2005.  ProbIDtree: an automated software program capable of identifying multiple peptides from a single collision-induced dissociation spectrum collected by a tandem mass spectrometer. Proteomics. 5:4096-106.
Kuster B, Schirle M, Mallick P, Aebersold R.  2005.  Scoring proteomes with proteotypic peptide probes. Nat Rev Mol Cell Biol. 6:577-83.
Li XJ, Yi EC, Kemp CJ, Zhang H, Aebersold R.  2005.  A software suite for the generation and comparison of peptide arrays from sets of data collected by liquid chromatography-mass spectrometry. Mol Cell Proteomics. 4:1328-40.
Aderem A.  2005.  Systems biology: its practice and challenges. Cell. 121:511-3.
Smink LJ, Helton EM, Healy BC, Cavnor CC, Lam AC, Flamez D, Burren OS, Wang Y, Dolman GE, Burdick DB et al..  2005.  T1DBase, a community web-based resource for type 1 diabetes research. Nucleic Acids Res. 33:D544-9.
2004
Gold ES, Simmons RM, Petersen TW, Campbell LA, Kuo CC, Aderem A.  2004.  Amphiphysin IIm is required for survival of Chlamydia pneumoniae in macrophages. J Exp Med. 200:581-6.
Zhou Y, Gu G, Goodlett DR, Zhang T, Pan C, Montine TJ, Montine KS, Aebersold R, Zhang J.  2004.  Analysis of alpha-synuclein-associated proteins by quantitative proteomics. J Biol Chem. 279:39155-64.
He XC, Zhang J, Tong WG, Tawfik O, Ross J, Scoville DH, Tian Q, Zeng X, He X, Wiedemann LM et al..  2004.  BMP signaling inhibits intestinal stem cell self-renewal through suppression of Wnt-beta-catenin signaling. Nat Genet. 36:1117-21.
Zhang H, Yan W, Aebersold R.  2004.  Chemical probes and tandem mass spectrometry: a strategy for the quantitative analysis of proteomes and subproteomes. Curr Opin Chem Biol. 8:66-75.
Petersen TW, Ibrahim SF, Diercks AH, van den Engh G.  2004.  Chromatic shifts in the fluorescence emitted by murine thymocytes stained with Hoechst 33342. Cytometry A. 60:173-81.
Brand M, Ranish J, Kummer NT, Hamilton J, Igarashi K, Francastel C, Chi TH, Crabtree GR, Aebersold R, Groudine M.  2004.  Dynamic changes in transcription factor complexes during erythroid differentiation revealed by quantitative proteomics. Nat Struct Mol Biol. 11:73-80.
Glusman G, Kaur A, Hood L, Rowen L.  2004.  An enigmatic fourth runt domain gene in the fugu genome: ancestral gene loss versus accelerated evolution. BMC Evol Biol. 4:43.
Nakamura K, Aebersold R, Bairoch A, Dunn M, Celis J, Hanash S, Hochstrasser D, Humphrey-Smith I, James P, Klose J et al..  2004.  [From genome to proteome--aim of human proteomics]. Seikagaku. 76:1271-4.
Ogushi K, Wada A, Niidome T, Okuda T, Llanes R, Nakayama M, Nishi Y, Kurazono H, Smith KD, Aderem A et al..  2004.  Gangliosides act as co-receptors for Salmonella enteritidis FliC and promote FliC induction of human beta-defensin-2 expression in Caco-2 cells. J Biol Chem. 279:12213-9.
Daza-Vamenta R, Glusman G, Rowen L, Guthrie B, Geraghty DE.  2004.  Genetic divergence of the rhesus macaque major histocompatibility complex. Genome Res. 14:1501-15.
Tian Q, Stepaniants SB, Mao M, Weng L, Feetham MC, Doyle MJ, Yi EC, Dai H, Thorsson V, Eng J et al..  2004.  Integrated genomic and proteomic analyses of gene expression in Mammalian cells. Mol Cell Proteomics. 3:960-9.
Lefkir Y, Malbouyres M, Gotthardt D, Ozinsky A, Cornillon S, Bruckert F, Aderem A, Soldati T, Cosson P, Letourneur F.  2004.  Involvement of the AP-1 adaptor complex in early steps of phagocytosis and macropinocytosis. Mol Biol Cell. 15:861-9.
Wollscheid B, von Haller PD, Yi E, Donohoe S, Vaughn K, Keller A, Nesvizhskii AI, Eng J, Li XJ, Goodlett DR et al..  2004.  Lipid raft proteins and their identification in T lymphocytes. Subcell Biochem. 37:121-52.
Flo TH, Smith KD, Sato S, Rodriguez DJ, Holmes MA, Strong RK, Akira S, Aderem A.  2004.  Lipocalin 2 mediates an innate immune response to bacterial infection by sequestrating iron. Nature. 432:917-21.
Trushina E, Dyer RB, Badger, J. D. 2nd, Ure D, Eide L, Tran DD, Vrieze BT, Legendre-Guillemin V, McPherson PS, Mandavilli BS et al..  2004.  Mutant huntingtin impairs axonal trafficking in mammalian neurons in vivo and in vitro. Mol Cell Biol. 24:8195-209.
Chen X, Chi Y, Bloecher A, Aebersold R, Clurman BE, Roberts JM.  2004.  N-acetylation and ubiquitin-independent proteasomal degradation of p21(Cip1). Mol Cell. 16:839-47.
Graveley BR, Kaur A, Gunning D, Zipursky SL, Rowen L, Clemens JC.  2004.  The organization and evolution of the dipteran and hymenopteran Down syndrome cell adhesion molecule (Dscam) genes. RNA. 10:1499-506.
Shumaker-Parry JS, Aebersold R, Campbell CT.  2004.  Parallel, quantitative measurement of protein binding to a 120-element double-stranded DNA array in real time using surface plasmon resonance microscopy. Anal Chem. 76:2071-82.

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