Publications

Found 1195 results
2005
Iliev DB, Roach J, Mackenzie S, Planas JV, Goetz FW.  2005.  Endotoxin recognition: in fish or not in fish? FEBS Lett. 579:6519-28.
Shmulevich I, Kauffman SA, Aldana M.  2005.  Eukaryotic cells are dynamically ordered or critical but not chaotic. Proc Natl Acad Sci U S A. 102:13439-44.
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.
Lin B, White JT, Lu W, Xie T, Utleg AG, Yan X, Yi EC, Shannon P, Khrebtukova I, Lange PH et al..  2005.  Evidence for the presence of disease-perturbed networks in prostate cancer cells by genomic and proteomic analyses: a systems approach to disease. Cancer Res. 65:3081-91.
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.
Thiele I, Vo T.D, Price ND, Palsson BO.  2005.  Expanded metabolic reconstruction of Helicobacter pylori (iIT341 GSM/GPR): an in silico genome-scale characterization of single- and double-deletion mutants. Journal of bacteriology. 187:5818-30.
Gao Q, Kripke KE, Saldanha AJ, Yan W, Holmes S, Small PM.  2005.  Gene expression diversity among Mycobacterium tuberculosis clinical isolates. Microbiology. 151:5-14.
Tsolaki AG, Gagneux S, Pym AS, Goguet de la Salmoniere YO, Kreiswirth BN, Van Soolingen D, Small PM.  2005.  Genomic deletions classify the Beijing/W strains as a distinct genetic lineage of Mycobacterium tuberculosis. J Clin Microbiol. 43:3185-91.
Whittle AE, Garcia-Garcia L, Orozco S, Ferreyra-Reyes L, Bobadilla M, Small PM, Gomex-Perez F, Cano B, Sifuentes-Osornio J, Ponce-de-Leon A.  2005.  Glucose Tolerance and Progression to Type 2 Diabetes in Tuberculosis Patients. Diabetes Care.
Pan S, Zhang H, Rush J, Eng J, Zhang N, Patterson D, Comb MJ, Aebersold R.  2005.  High throughput proteome screening for biomarker detection. Mol Cell Proteomics. 4:182-90.
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.
Dunstan SJ, Hawn TR, Hue NT, Parry CP, Ho VA, Vinh H, Diep TS, House D, Wain J, Aderem A et al..  2005.  Host susceptibility and clinical outcomes in toll-like receptor 5-deficient patients with typhoid fever in Vietnam. J Infect Dis. 191:1068-71.
Deutsch EW, Eng JK, Zhang H, King NL, Nesvizhskii AI, Lin B, Lee H, Yi EC, Ossola R, Aebersold R.  2005.  Human Plasma PeptideAtlas. Proteomics. 5:3497-500.
Orchard S, Hermjakob H, Taylor C, Aebersold R, Apweiler R.  2005.  Human Proteome Organisation Proteomics Standards Initiative. Pre-Congress Initiative. Proteomics. 5:4651-2.
Yang K, Puel A, Zhang S, Eidenschenk C, Ku CL, Casrouge A, Picard C, von Bernuth H, Senechal B, Plancoulaine S et al..  2005.  Human TLR-7-, -8-, and -9-mediated induction of IFN-alpha/beta and -lambda Is IRAK-4 dependent and redundant for protective immunity to viruses. Immunity. 23:465-78.
Hawn TR, Ozinsky A, Williams LM, Rodrigues S, Clark A, Pham U, Hill HR, Ochs H, Aderem A, Liles WC.  2005.  Hyper-IgE syndrome is not associated with defects in several candidate toll-like receptor pathway genes. Hum Immunol. 66:842-7.
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.
Corthals GL, Aebersold R, Goodlett DR.  2005.  Identification of phosphorylation sites using microimmobilized metal affinity chromatography. Methods Enzymol. 405:66-81.
Chen SS, Deutsch EW, Yi EC, Li XJ, Goodlett DR, Aebersold R.  2005.  Improving mass and liquid chromatography based identification of proteins using bayesian scoring. J Proteome Res. 4:2174-84.
Yi EC, Li XJ, Cooke K, Lee H, Raught B, Page A, Aneliunas V, Hieter P, Goodlett DR, Aebersold R.  2005.  Increased quantitative proteome coverage with (13)C/(12)C-based, acid-cleavable isotope-coded affinity tag reagent and modified data acquisition scheme. Proteomics. 5:380-7.
Carter GW.  2005.  Inferring network interactions within a cell. Brief Bioinform. 6:380-9.
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.
Fagarasanu M, Fagarasanu A, Tam YY, Aitchison JD, Rachubinski RA.  2005.  Inp1p is a peroxisomal membrane protein required for peroxisome inheritance in Saccharomyces cerevisiae. J Cell Biol. 169:765-75.
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.
Scott RJ, Lusk CP, Dilworth DJ, Aitchison JD, Wozniak RW.  2005.  Interactions between Mad1p and the nuclear transport machinery in the yeast Saccharomyces cerevisiae. Mol Biol Cell. 16:4362-74.
Rowen L, Williams E, Glusman G, Linardopoulou E, Friedman C, Ahearn ME, Seto J, Boysen C, Qin S, Wang K et al..  2005.  Interchromosomal segmental duplications explain the unusual structure of PRSS3, the gene for an inhibitor-resistant trypsinogen. Mol Biol Evol. 22:1712-20.
Nesvizhskii AI, Aebersold R.  2005.  Interpretation of shotgun proteomic data: the protein inference problem. Mol Cell Proteomics. 4:1419-40.
Martin DB, Eng JK, Nesvizhskii AI, Gemmill A, Aebersold R.  2005.  Investigation of neutral loss during collision-induced dissociation of peptide ions. Anal Chem. 77:4870-82.
Chen SS, Aebersold R.  2005.  LC-MS solvent composition monitoring and chromatography alignment using mobile phase tracer molecules. J Chromatogr B Analyt Technol Biomed Life Sci. 829:107-14.
Wright ME, Han DK, Aebersold R.  2005.  Mass spectrometry-based expression profiling of clinical prostate cancer. Mol Cell Proteomics. 4:545-54.
Yan W, Chen SS.  2005.  Mass spectrometry-based quantitative proteomic profiling. Brief Funct Genomic Proteomic. 4:27-38.
Alsam S, Sissons J, Dudley R, Khan NA.  2005.  Mechanisms associated with Acanthamoeba castellanii (T4) phagocytosis. Parasitol Res. 96:402-9.
Orrell D, Ramsey S, de Atauri P, Bolouri H.  2005.  A method for estimating stochastic noise in large genetic regulatory networks. Bioinformatics. 21:208-17.
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.
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.

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