Publications

Found 1263 results
2005
Dilworth DJ, Tackett AJ, Rogers RS, Yi EC, Christmas RH, Smith JJ, Siegel AF, Chait BT, Wozniak RW, Aitchison JD.  2005.  The mobile nucleoporin Nup2p and chromatin-bound Prp20p function in endogenous NPC-mediated transcriptional control. J Cell Biol. 171:955-65.
Aebersold R.  2005.  Molecular Systems Biology: a new journal for a new biology? Mol Syst Biol. 1:20050005.
de Jong BC, Hill PC, Brookes RH, Otu JK, Peterson KL, Small PM, Adegbola RA.  2005.  Mycobacterium africanum: a new opportunistic pathogen in HIV infection? AIDS. 19:1714-5.
Toulouse T, Ao P, Shmulevich I, Kauffman S.  2005.  Noise in a Small Genetic Circuit that Undergoes Bifurcation. Complexity. 11:45-51.
Sydorskyy Y, Dilworth DJ, Halloran B, Yi EC, Makhnevych T, Wozniak RW, Aitchison JD.  2005.  Nop53p is a novel nucleolar 60S ribosomal subunit biogenesis protein. Biochem J. 388:819-26.
Gingras AC, Caballero M, Zarske M, Sanchez A, Hazbun TR, Fields S, Sonenberg N, Hafen E, Raught B, Aebersold R.  2005.  A novel, evolutionarily conserved protein phosphatase complex involved in cisplatin sensitivity. Mol Cell Proteomics. 4:1725-40.
Omenn GS, States DJ, Adamski M, Blackwell TW, Menon R, Hermjakob H, Apweiler R, Haab BB, Simpson RJ, Eddes JS et al..  2005.  Overview of the HUPO Plasma Proteome Project: results from the pilot phase with 35 collaborating laboratories and multiple analytical groups, generating a core dataset of 3020 proteins and a publicly-available database. Proteomics. 5:3226-45.
Chen R, Yi EC, Donohoe S, Pan S, Eng J, Cooke K, Crispin DA, Lane Z, Goodlett DR, Bronner MP et al..  2005.  Pancreatic cancer proteome: the proteins that underlie invasion, metastasis, and immunologic escape. Gastroenterology. 129:1187-97.
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.
Bradshaw RA, Burlingame AL, Carr S, Aebersold R.  2005.  Protein identification: the good, the bad, and the ugly. Mol Cell Proteomics. 4:1221-2.
Tackett AJ, Dilworth DJ, Davey MJ, O'Donnell M, Aitchison JD, Rout MP, Chait BT.  2005.  Proteomic and genomic characterization of chromatin complexes at a boundary. J Cell Biol. 169:35-47.
Chen R, Pan S, Brentnall TA, Aebersold R.  2005.  Proteomic profiling of pancreatic cancer for biomarker discovery. Mol Cell Proteomics. 4:523-33.
Tao WA, Wollscheid B, O'Brien R, Eng JK, Li XJ, Bodenmiller B, Watts J, Hood L, Aebersold R.  2005.  Quantitative phosphoproteome analysis using a dendrimer conjugation chemistry and tandem mass spectrometry. Nat Methods. 2:591-8.
Zhang J, Goodlett DR, Peskind ER, Quinn JF, Zhou Y, Wang Q, Pan C, Yi E, Eng J, Aebersold R et al..  2005.  Quantitative proteomic analysis of age-related changes in human cerebrospinal fluid. Neurobiol Aging. 26:207-27.
Zhang J, Goodlett DR, Quinn JF, Peskind E, Kaye JA, Zhou Y, Pan C, Yi E, Eng J, Wang Q et al..  2005.  Quantitative proteomics of cerebrospinal fluid from patients with Alzheimer disease. J Alzheimers Dis. 7:125-33;discussion173-80.
de Atauri P, Orrell D, Ramsey S, Bolouri H.  2005.  Is the regulation of galactose 1-phosphate tuned against gene expression noise? Biochem J. 387:77-84.
Knudsen BS, Lucas JM, Fazli L, Hawley S, Falcon S, Coleman IM, Martin DB, Xu C, True LD, Gleave ME et al..  2005.  Regulation of hepatocyte activator inhibitor-1 expression by androgen and oncogenic transformation in the prostate. Am J Pathol. 167:255-66.
Thorsson V, Hornquist M, Siegel AF, Hood L.  2005.  Reverse engineering galactose regulation in yeast through model selection. Stat Appl Genet Mol Biol. 4:Article28.
Gershenson C, Kauffman SA, Shmulevich I.  2005.  The role of redundancy in the robustness of random Boolean networks. Arxiv preprint nlin/0511018.
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.
Stolovitzky GA, Kundaje A, Held GA, Duggar KH, Haudenschild CD, Zhou D, Vasicek TJ, Smith KD, Aderem A, Roach J.  2005.  Statistical analysis of MPSS measurements: application to the study of LPS-activated macrophage gene expression. Proc Natl Acad Sci U S A. 102:1402-7.
Brun M, Dougherty ER, Shmulevich I.  2005.  Steady-state probabilities for attractors in probabilistic Boolean networks. Signal Processing. 85:1993-2013.
Hawn TR, Wu H, Grossman JM, Hahn BH, Tsao BP, Aderem A.  2005.  A stop codon polymorphism of Toll-like receptor 5 is associated with resistance to systemic lupus erythematosus. Proc Natl Acad Sci U S A. 102:10593-7.
Cieslewicz MJ, Chaffin D, Glusman G, Kasper D, Madan A, Rodrigues S, Fahey J, Wessels MR, Rubens CE.  2005.  Structural and genetic diversity of group B streptococcus capsular polysaccharides. Infect Immun. 73:3096-103.
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.
Hawn TR, Verbon A, Janer M, Zhao LP, Beutler B, Aderem A.  2005.  Toll-like receptor 4 polymorphisms are associated with resistance to Legionnaires' disease. Proc Natl Acad Sci U S A. 102:2487-9.
Reiss DJ, Avila-Campillo I, Thorsson V, Schwikowski B, Galitski T.  2005.  Tools enabling the elucidation of molecular pathways active in human disease: application to Hepatitis C virus infection. BMC Bioinformatics. 6:154.
Keller A, Eng J, Zhang N, Li XJ, Aebersold R.  2005.  A uniform proteomics MS/MS analysis platform utilizing open XML file formats. Mol Syst Biol. 1:20050017.
Freeman R, Kato-Maeda M, Hauge KA, Horan KL, Oren E, Narita M, Wallis CK, Cave D, Nolan CM, Small PM et al..  2005.  Use of rapid genomic deletion typing to monitor a tuberculosis outbreak within an urban homeless population. J Clin Microbiol. 43:5550-4.
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.
Nesvizhskii AI, Aebersold R.  2004.  Analysis, statistical validation and dissemination of large-scale proteomics datasets generated by tandem MS. Drug Discov Today. 9:173-81.
Hood L.  2004.  Bioinformatics: A Practical Guide to the Analysis of Genes and Proteins. :Foreword.
Hood L.  2004.  Biotechnology Annual Review. :Preface.
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.
Zhu XM, Yin L, Hood L, Ao P.  2004.  Calculating biological behaviors of epigenetic states in the phage lambda life cycle. Funct Integr Genomics. 4:188-95.
Leslie DM, Zhang W, Timney BL, Chait BT, Rout MP, Wozniak RW, Aitchison JD.  2004.  Characterization of karyopherin cargoes reveals unique mechanisms of Kap121p-mediated nuclear import. Mol Cell Biol. 24:8487-503.
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.
Pedrioli PG, Eng JK, Hubley R, Vogelzang M, Deutsch EW, Raught B, Pratt B, Nilsson E, Angeletti RH, Apweiler R et al..  2004.  A common open representation of mass spectrometry data and its application to proteomics research. Nat Biotechnol. 22:1459-66.
Papin JA, Stelling J., Price ND, Klamt S., Schuster S., Palsson BO.  2004.  Comparison of network-based pathway analysis methods. Trends in biotechnology. 22:400-5.
Schmidt F, Donahoe S, Hagens K, Mattow J, Schaible UE, Kaufmann SH, Aebersold R, Jungblut PR.  2004.  Complementary analysis of the Mycobacterium tuberculosis proteome by two-dimensional electrophoresis and isotope-coded affinity tag technology. Mol Cell Proteomics. 3:24-42.
Bonneau R, Baliga NS, Deutsch EW, Shannon P, Hood L.  2004.  Comprehensive de novo structure prediction in a systems-biology context for the archaea Halobacterium sp. NRC-1. Genome Biol. 5:R52.
Prinz S, Avila-Campillo I, Aldridge C, Srinivasan A, Dimitrov K, Siegel AF, Galitski T.  2004.  Control of yeast filamentous-form growth by modules in an integrated molecular network. Genome Res. 14:380-90.
Yan W, Lee H, Deutsch EW, Lazaro CA, Tang W, Chen E, Fausto N, Katze MG, Aebersold R.  2004.  A dataset of human liver proteins identified by protein profiling via isotope-coded affinity tag (ICAT) and tandem mass spectrometry. Mol Cell Proteomics. 3:1039-41.
Andalis AA, Storchova Z, Styles C, Galitski T, Pellman D, Fink GR.  2004.  Defects arising from whole-genome duplications in Saccharomyces cerevisiae. Genetics. 167:1109-21.
Bottari P, Aebersold R, Turecek F, Gelb MH.  2004.  Design and synthesis of visible isotope-coded affinity tags for the absolute quantification of specific proteins in complex mixtures. Bioconjug Chem. 15:380-8.
Z Chen J, Wang J, Tian L, Lee H-S, Wang JJ, Chen M, Lee JJ, Josefsson C, Madlung A, Watson B et al..  2004.  The development of an Arabidopsis model system for genome-wide analysis of polyploidy effects.. Biol J Linn Soc Lond. 82(4):689-700.
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.
Bunimovich YL, Ge G, Beverly KC, Ries RS, Hood L, Heath JR.  2004.  Electrochemically programmed, spatially selective biofunctionalization of silicon wires. Langmuir. 20:10630-8.
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.
Croteau GA, Martin DB, Camp J, Yost M, Conrad C, Zeitlin PL, Heald AE.  2004.  Evaluation of exposure and health care worker response to nebulized administration of tgAAVCF to patients with cystic fibrosis. Ann Occup Hyg. 48:673-81.
de Atauri P, Orrell D, Ramsey S, Bolouri H.  2004.  Evolution of 'design' principles in biochemical networks. Syst Biol (Stevenage). 1:28-40.
Smith KD, Thorsson V.  2004.  Exploring Toll-Like Receptor Regulation of Innate Immunity with the Tools of Systems Biology. Current Genomics. 5:545-557.
International Human Genome Sequencing C.  2004.  Finishing the euchromatic sequence of the human genome. Nature. 431:931-45.
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.
MacKay VL, Li X, Flory MR, Turcott E, Law GL, Serikawa KA, Xu XL, Lee H, Goodlett DR, Aebersold R et al..  2004.  Gene expression analyzed by high-resolution state array analysis and quantitative proteomics: response of yeast to mating pheromone. Mol Cell Proteomics. 3:478-89.
Moises H, Zoega T, Li L, Hood L.  2004.  Genes and Neurodevelopment in Schizophrenia. Behavior Genetics Principles: Perspectives in Development, Personality, and Psycophathology. :145-157.
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.
Hartwell L, Hood L, Goldberg ML, Reynolds AE, Silver LM, Veres RC.  2004.  Genetics: from genes to genomes.
Baliga NS, Bonneau R, Facciotti MT, Pan M, Glusman G, Deutsch EW, Shannon P, Chiu Y, Weng RS, Gan RR et al..  2004.  Genome sequence of Haloarcula marismortui: a halophilic archaeon from the Dead Sea. Genome Res. 14:2221-34.
Price ND, Reed J.L, Palsson BO.  2004.  Genome-scale models of microbial cells: evaluating the consequences of constraints. Nature reviews. Microbiology. 2:886-97.
Roginski RS, Mohan Raj BK, Birditt B, Rowen L.  2004.  The human GRINL1A gene defines a complex transcription unit, an unusual form of gene organization in eukaryotes. Genomics. 84:265-76.
Friedrichsen DM, Stanford JL, Isaacs SD, Janer M, Chang BL, Deutsch K, Gillanders E, Kolb S, Wiley KE, Badzioch MD et al..  2004.  Identification of a prostate cancer susceptibility locus on chromosome 7q11-21 in Jewish families. Proc Natl Acad Sci U S A. 101:1939-44.
Mayer ML, Pot I, Chang M, Xu H, Aneliunas V, Kwok T, Newitt R, Aebersold R, Boone C, Brown GW et al..  2004.  Identification of protein complexes required for efficient sister chromatid cohesion. Mol Biol Cell. 15:1736-45.
Ranish J, Hahn S, Lu Y, Yi EC, Li XJ, Eng J, Aebersold R.  2004.  Identification of TFB5, a new component of general transcription and DNA repair factor IIH. Nat Genet. 36:707-13.
Hood L, Perlmutter RM.  2004.  The impact of systems approaches on biological problems in drug discovery. Nat Biotechnol. 22:1215-7.
Raghunathan A., Price ND, Galperin MY, Makarova KS, Purvine S, Picone AF, Cherny T, Xie T, Reilly TJ, Munson, Jr. R. et al..  2004.  In Silico Metabolic Model and Protein Expression of Haemophilus influenzae Strain Rd KW20 in Rich Medium. Omics : a journal of integrative biology. 8:25-41.
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.
Liu AY, Brubaker KD, Goo YA, Quinn JE, Kral S, Sorensen CM, Vessella RL, Belldegrun AS, Hood LE.  2004.  Lineage relationship between LNCaP and LNCaP-derived prostate cancer cell lines. Prostate. 60:98-108.
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.
Goo YA, Roach J, Glusman G, Baliga NS, Deutsch K, Pan M, Kennedy S, DasSarma S, Ng WV, Hood L.  2004.  Low-pass sequencing for microbial comparative genomics. BMC Genomics. 5:3.
Shumaker-Parry JS, Zareie MH, Aebersold R, Campbell CT.  2004.  Microspotting streptavidin and double-stranded DNA arrays on gold for high-throughput studies of protein-DNA interactions by surface plasmon resonance microscopy. Anal Chem. 76:918-29.
Galitski T.  2004.  Molecular networks in model systems. Annu Rev Genomics Hum Genet. 5:177-87.
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.
Carr S, Aebersold R, Baldwin M, Burlingame A, Clauser K, Nesvizhskii A, Working Group on Publication Guidelines for P, Protein Identification D.  2004.  The need for guidelines in publication of peptide and protein identification data: Working Group on Publication Guidelines for Peptide and Protein Identification Data. Mol Cell Proteomics. 3:531-3.
Giglia-Mari G, Coin F, Ranish J, Hoogstraten D, Theil A, Wijgers N, Jaspers NG, Raams A, Argentini M, van der Spek PJ et al..  2004.  A new, tenth subunit of TFIIH is responsible for the DNA repair syndrome trichothiodystrophy group A. Nat Genet. 36:714-9.
Lee H, Yi EC, Wen B, Reily TP, Pohl L, Nelson S, Aebersold R, Goodlett DR.  2004.  Optimization of reversed-phase microcapillary liquid chromatography for quantitative proteomics. J Chromatogr B Analyt Technol Biomed Life Sci. 803:101-10.
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.
Vizeacoumar FJ, Torres-Guzman JC, Bouard D, Aitchison JD, Rachubinski RA.  2004.  Pex30p, Pex31p, and Pex32p form a family of peroxisomal integral membrane proteins regulating peroxisome size and number in Saccharomyces cerevisiae. Mol Biol Cell. 15:665-77.
Lausted C, Dahl T, Warren C, King K, Smith K, Johnson M, Saleem R, Aitchison JD, Hood L, Lasky SR.  2004.  POSaM: a fast, flexible, open-source, inkjet oligonucleotide synthesizer and microarrayer. Genome Biol. 5:R58.
Warfield L, Ranish J, Hahn S.  2004.  Positive and negative functions of the SAGA complex mediated through interaction of Spt8 with TBP and the N-terminal domain of TFIIA. Genes Dev. 18:1022-34.
Reiss DJ, Schwikowski B.  2004.  Predicting protein-peptide interactions via a network-based motif sampler. Bioinformatics. 20 Suppl 1:i274-82.
Tian Q, Feetham MC, Tao WA, He XC, Li L, Aebersold R, Hood L.  2004.  Proteomic analysis identifies that 14-3-3zeta interacts with beta-catenin and facilitates its activation by Akt. Proc Natl Acad Sci U S A. 101:15370-5.
Hardwidge PR, Rodriguez-Escudero I, Goode D, Donohoe S, Eng J, Goodlett DR, Aebersold R, Finlay BB.  2004.  Proteomic analysis of the intestinal epithelial cell response to enteropathogenic Escherichia coli. J Biol Chem. 279:20127-36.
Wollscheid B, Watts J, Aebersold R.  2004.  Proteomics/genomics and signaling in lymphocytes. Curr Opin Immunol. 16:337-44.
Sozio MS, Mathis MA, Young JA, Walchli S, Pitcher LA, Wrage PC, Bartok B, Campbell A, Watts J, Aebersold R et al..  2004.  PTPH1 is a predominant protein-tyrosine phosphatase capable of interacting with and dephosphorylating the T cell receptor zeta subunit. J Biol Chem. 279:7760-9.
Marelli M, Smith JJ, Jung S, Yi E, Nesvizhskii AI, Christmas RH, Saleem RA, Tam YY, Fagarasanu A, Goodlett DR et al..  2004.  Quantitative mass spectrometry reveals a role for the GTPase Rho1p in actin organization on the peroxisome membrane. J Cell Biol. 167:1099-112.
Zhou H, Boyle R, Aebersold R.  2004.  Quantitative protein analysis by solid phase isotope tagging and mass spectrometry. Methods Mol Biol. 261:511-8.
Kao WC, Chen YR, Yi EC, Lee H, Tian Q, Wu KM, Tsai SF, Yu SS, Chen YJ, Aebersold R et al..  2004.  Quantitative proteomic analysis of metabolic regulation by copper ions in Methylococcus capsulatus (Bath). J Biol Chem. 279:51554-60.
Martin DB, Gifford DR, Wright ME, Keller A, Yi E, Goodlett DR, Aebersold R, Nelson PS.  2004.  Quantitative proteomic analysis of proteins released by neoplastic prostate epithelium. Cancer Res. 64:347-55.
Himeda CL, Ranish J, Angello JC, Maire P, Aebersold R, Hauschka SD.  2004.  Quantitative proteomic identification of six4 as the trex-binding factor in the muscle creatine kinase enhancer. Mol Cell Biol. 24:2132-43.

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