Publications

Found 1263 results
2007
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.
Rinner O, Mueller LN, Hubalek M, Muller M, Gstaiger M, Aebersold R.  2007.  An integrated mass spectrometric and computational framework for the analysis of protein interaction networks. Nat Biotechnol. 25:345-52.
Cline MS, Smoot M, Cerami E, Kuchinsky A, Landys N, Workman C, Christmas R, Avila-Campilo I, Creech M, Gross B et al..  2007.  Integration of biological networks and gene expression data using Cytoscape. Nat Protoc. 2:2366-82.
Heo K, Kim B, Kim K, Choi J, Kim H, Zhan Y, Ranish J, An W.  2007.  Isolation and characterization of proteins associated with histone H3 tails in vivo. J Biol Chem. 282:15476-83.
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.
Niemisto A, Korpelainen T, Saleem R, Yli-Harja O, Aitchison JD, Shmulevich I.  2007.  A K-means segmentation method for finding 2-D object areas based on 3-D image stacks obtained by confocal microscopy. Conf Proc IEEE Eng Med Biol Soc. 2007:5559-62.
Orellana MV, Petersen TW, Diercks AH, Donohue P, Verdugo P, van den Engh G.  2007.  Marine Microgels: Optical and Proteomic Fingerprint.. Marine Chemistry. 105:229-39.
Zhang H, Liu AY, Loriaux P, Wollscheid B, Zhou Y, Watts J, Aebersold R.  2007.  Mass spectrometric detection of tissue proteins in plasma. Mol Cell Proteomics. 6:64-71.
Taylor CF, Paton NW, Lilley KS, Binz PA, Julian, R. K. J., Jones AR, Zhu W, Apweiler R, Aebersold R, Deutsch EW et al..  2007.  The minimum information about a proteomics experiment (MIAPE). Nat Biotechnol. 25:887-93.
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.
Taylor RJ, Siegel AF, Galitski T.  2007.  Network motif analysis of a multi-mode genetic-interaction network. Genome Biol. 8:R160.
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.
Thuong NT, Hawn TR, Thwaites GE, Chau TT, Lan NT, Quy HT, Hieu NT, Aderem A, Hien TT, Farrar JJ et al..  2007.  A polymorphism in human TLR2 is associated with increased susceptibility to tuberculous meningitis. Genes Immun. 8:422-8.
Bochud PY, Magaret AS, Koelle DM, Aderem A, Wald A.  2007.  Polymorphisms in TLR2 are associated with increased viral shedding and lesional rate in patients with genital herpes simplex virus Type 2 infection. J Infect Dis. 196:505-9.
Bochud PY, Hersberger M, Taffe P, Bochud M, Stein CM, Rodrigues SD, Calandra T, Francioli P, Telenti A, Speck RF et al..  2007.  Polymorphisms in Toll-like receptor 9 influence the clinical course of HIV-1 infection. AIDS. 21:441-6.
Carter GW, Prinz S, Neou C, Shelby JP, Marzolf B, Thorsson V, Galitski T.  2007.  Prediction of phenotype and gene expression for combinations of mutations. Mol Syst Biol. 3:96.
Bonneau R, Facciotti MT, Reiss DJ, Schmid AK, Pan M, Kaur A, Thorsson V, Shannon P, Johnson MH, Bare JC et al..  2007.  A predictive model for transcriptional control of physiology in a free living cell. Cell. 131:1354-65.
Vencio RZ, Shmulevich I.  2007.  ProbCD: enrichment analysis accounting for categorization uncertainty. BMC Bioinformatics. 8:383.
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.
Tu LC, Yan X, Hood L, Lin B.  2007.  Proteomics analysis of the interactome of N-myc downstream regulated gene 1 and its interactions with the androgen response program in prostate cancer cells. Mol Cell Proteomics. 6:575-88.
Chen R, Pan S, Aebersold R, Brentnall TA.  2007.  Proteomics studies of pancreatic cancer. Proteomics Clin Appl. 1:1582-1591.
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.
Choi J, Kim B, Heo K, Kim K, Kim H, Zhan Y, Ranish J, An W.  2007.  Purification and characterization of cellular proteins associated with histone H4 tails. J Biol Chem. 282:21024-31.
Hu Z, Hood L, Tian Q.  2007.  Quantitative proteomic approaches for biomarker discovery. Proteomics Clin Appl. 1:1036-41.
Chen R, Brentnall TA, Pan S, Cooke K, Moyes KW, Lane Z, Crispin DA, Goodlett DR, Aebersold R, Bronner MP.  2007.  Quantitative proteomics analysis reveals that proteins differentially expressed in chronic pancreatitis are also frequently involved in pancreatic cancer. Mol Cell Proteomics. 6:1331-42.
Bodenmiller B, Mueller LN, Mueller M, Domon B, Aebersold R.  2007.  Reproducible isolation of distinct, overlapping segments of the phosphoproteome. Nat Methods. 4:231-7.
Fu E, Ramsey SA, Chen J, Chinowsky TM, Wiley B, Xia Y, Yager P.  2007.  Resonance wavelength-dependent signal of absorptive particles in surface plasmon resonance-based detection. Sens Actuators B Chem. 123:606-613.
Ahdesmaki M, Lahdesmaki H, Gracey A, Shmulevich I, Yli-Harja O.  2007.  Robust regression for periodicity detection in non-uniformly sampled time-course gene expression data. BMC Bioinformatics. 8:233.
Makhnevych T, Ptak C, Lusk CP, Aitchison JD, Wozniak RW.  2007.  The role of karyopherins in the regulated sumoylation of septins. J Cell Biol. 177:39-49.
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.
Vencio RZ, Varuzza L, de PBCA, Brentani H, Shmulevich I.  2007.  Simcluster: clustering enumeration gene expression data on the simplex space. BMC Bioinformatics. 8:246.
Tian Y, Zhou Y, Elliott S, Aebersold R, Zhang H.  2007.  Solid-phase extraction of N-linked glycopeptides. Nat Protoc. 2:334-9.
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.
Johanneson B, Deutsch K, McIntosh L, Friedrichsen-Karyadi DM, Janer M, Kwon EM, Iwasaki L, Hood L, Ostrander EA, Stanford JL.  2007.  Suggestive genetic linkage to chromosome 11p11.2-q12.2 in hereditary prostate cancer families with primary kidney cancer. Prostate. 67:732-42.
Aderem A.  2007.  Systems biology. Current Opinion in Biotechnology. 18:331-332.
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.
Zosso D, Podvinec M, Muller M, Aebersold R, Peitsch MC, Schwede T.  2007.  Tandem mass spectrometry protein identification on a PC grid. Stud Health Technol Inform. 126:3-12.
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.
Kim B, Nesvizhskii AI, Rani PG, Hahn S, Aebersold R, Ranish J.  2007.  The transcription elongation factor TFIIS is a component of RNA polymerase II preinitiation complexes. Proc Natl Acad Sci U S A. 104:16068-73.
Roach J, Smith KD, Strobe KL, Nissen SM, Haudenschild CD, Zhou D, Vasicek TJ, Held GA, Stolovitzky GA, Hood LE et al..  2007.  Transcription factor expression in lipopolysaccharide-activated peripheral-blood-derived mononuclear cells. Proc Natl Acad Sci U S A. 104:16245-50.
Smith JJ, Ramsey SA, Marelli M, Marzolf B, Hwang D, Saleem RA, Rachubinski RA, Aitchison JD.  2007.  Transcriptional responses to fatty acid are coordinated by combinatorial control. Mol Syst Biol. 3:115.
Li X, Zhang Y, Shen X, Shen G, Gui X, Sun B, Mei J, Deriemer K, Small PM, Gao Q.  2007.  Transmission of drug-resistant tuberculosis among treated patients in Shanghai, China. J Infect Dis. 195:864-9.
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.
Kyttala M., Plaisier CL, Aouizerat B., de Bruin T., Schadt E.E., van der Kallen C., Pajukanta P..  2007.  WO7OR4 IDENTIFICATION OF A GENE ON CHROMOSOME 11P REGULATING PLASMA TRIGLYCERIDE LEVELS. Atherosclerosis Supplements.
2006
Perkins MD, Small PM.  2006.  Admitting defeat. Int J Tuberc Lung Dis. 10:1.
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.
King NL, Deutsch EW, Ranish J, Nesvizhskii AI, Eddes JS, Mallick P, Eng J, Desiere F, Flory M, Martin DB et al..  2006.  Analysis of the Saccharomyces cerevisiae proteome with PeptideAtlas. Genome Biol. 7:R106.
Hongay CF, Grisafi PL, Galitski T, Fink GR.  2006.  Antisense transcription controls cell fate in Saccharomyces cerevisiae. Cell. 127:735-45.
Pedrioli PG, Raught B, Zhang XD, Rogers R, Aitchison JD, Matunis M, Aebersold R.  2006.  Automated identification of SUMOylation sites using mass spectrometry and SUMmOn pattern recognition software. Nat Methods. 3:533-9.
Orchard S, Hermjakob H, Taylor C, Binz PA, Hoogland C, Julian R, Garavelli JS, Aebersold R, Apweiler R.  2006.  Autumn 2005 Workshop of the Human Proteome Organisation Proteomics Standards Initiative (HUPO-PSI) Geneva, September, 4-6, 2005. Proteomics. 6:738-41.
Brown V, Brown RA, Ozinsky A, Hesselberth JR, Fields S.  2006.  Binding specificity of Toll-like receptor cytoplasmic domains. Eur J Immunol. 36:742-53.
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.
Price ND, Thiele I, Palsson BO.  2006.  Candidate states of Helicobacter pylori's genome-scale metabolic network upon application of "loop law" thermodynamic constraints. Biophysical journal. 90:3919-28.
Domon B, Aebersold R.  2006.  Challenges and opportunities in proteomics data analysis. Mol Cell Proteomics. 5:1921-6.
Gagneux S, Long CD, Small PM, Van T, Schoolnik GK, Bohannan BJ.  2006.  The competitive cost of antibiotic resistance in Mycobacterium tuberculosis. Science. 312:1944-6.
Purcell MK, Smith KD, Hood L, Winton JR, Roach J.  2006.  Conservation of Toll-Like Receptor Signaling Pathways in Teleost Fish. Comp Biochem Physiol Part D Genomics Proteomics. 1:77-88.
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.
Deutsch EW, Ball CA, Bova GS, Brazma A, Bumgarner RE, Campbell D, Causton HC, Christiansen J, Davidson D, Eichner LJ et al..  2006.  Development of the Minimum Information Specification for In Situ Hybridization and Immunohistochemistry Experiments (MISFISHIE). OMICS. 10:205-8.
Carter GW, Rupp S, Fink GR, Galitski T.  2006.  Disentangling information flow in the Ras-cAMP signaling network. Genome Res. 16:520-6.
Ramsey SA, Smith JJ, Orrell D, Marelli M, Petersen TW, de Atauri P, Bolouri H, Aitchison JD.  2006.  Dual feedback loops in the GAL regulon suppress cellular heterogeneity in yeast. Nat Genet. 38:1082-7.
Nesvizhskii AI, Roos FF, Grossmann J, Vogelzang M, Eddes JS, Gruissem W, Baginsky S, Aebersold R.  2006.  Dynamic spectrum quality assessment and iterative computational analysis of shotgun proteomic data: toward more efficient identification of post-translational modifications, sequence polymorphisms, and novel peptides. Mol Cell Proteomics. 5:652-70.
Vizeacoumar FJ, Vreden WN, Fagarasanu M, Eitzen GA, Aitchison JD, Rachubinski RA.  2006.  The dynamin-like protein Vps1p of the yeast Saccharomyces cerevisiae associates with peroxisomes in a Pex19p-dependent manner. J Biol Chem. 281:12817-23.
Rundle NT, Nelson J, Flory MR, Joseph J, Th'ng J, Aebersold R, Dasso M, Andersen RJ, Roberge M.  2006.  An ent-kaurene that inhibits mitotic chromosome movement and binds the kinetochore protein ran-binding protein 2. ACS Chem Biol. 1:443-50.
Smith JJ, Sydorskyy Y, Marelli M, Hwang D, Bolouri H, Rachubinski RA, Aitchison JD.  2006.  Expression and functional profiling reveal distinct gene classes involved in fatty acid metabolism. Mol Syst Biol. 2:20060009.
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.
Niemisto A, Selinummi J, Saleem R, Shmulevich I, Aitchison JD, Yli-Harja O.  2006.  Extraction of the number of peroxisomes in yeast cells by automated image analysis. Conf Proc IEEE Eng Med Biol Soc. 1:2353-6.
de Orrell, D. R M S P A A BSMJ.  2006.  Feedback control of stochastic noise in the yeast galactose utilization pathway. Physica D. 217:64-76.
Shannon P, Reiss DJ, Bonneau R, Baliga NS.  2006.  The Gaggle: an open-source software system for integrating bioinformatics software and data sources. BMC Bioinformatics. 7:176.
Jimenez-Corona ME, Garcia-Garcia L, Deriemer K, Ferreyra-Reyes L, Bobadilla-del-Valle M, Cano-Arellano B, Canizales-Quintero S, Martinez-Gamboa A, Small PM, Sifuentes-Osornio J et al..  2006.  Gender differentials of pulmonary tuberculosis transmission and reactivation in an endemic area. Thorax. 61:348-53.
Roach J, Deutsch K, Li S, Siegel AF, Bekris LM, Einhaus DC, Sheridan CM, Glusman G, Hood L, Lernmark A et al..  2006.  Genetic mapping at 3-kilobase resolution reveals inositol 1,4,5-triphosphate receptor 3 as a risk factor for type 1 diabetes in Sweden. Am J Hum Genet. 79:614-27.
Foltz G, Ryu GY, Yoon JG, Nelson T, Fahey J, Frakes A, Lee H, Field L, Zander K, Sibenaller Z et al..  2006.  Genome-wide analysis of epigenetic silencing identifies BEX1 and BEX2 as candidate tumor suppressor genes in malignant glioma. Cancer Res. 66:6665-74.
Schmidt A, Aebersold R.  2006.  High-accuracy proteome maps of human body fluids. Genome Biol. 7:242.
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.
Lee SI, Pe'er D, Dudley AM, Church GM, Koller D.  2006.  Identifying regulatory mechanisms using individual variation reveals key role for chromatin modification. Proc Natl Acad Sci U S A. 103:14062-7.
Gagneux S, Burgos MV, Deriemer K, Encisco A, Munoz S, Hopewell PC, Small PM, Pym AS.  2006.  Impact of bacterial genetics on the transmission of isoniazid-resistant Mycobacterium tuberculosis. PLoS Pathog. 2:e61.
Bonneau R, Reiss DJ, Shannon P, Facciotti M, Hood L, Baliga NS, Thorsson V.  2006.  The Inferelator: an algorithm for learning parsimonious regulatory networks from systems-biology data sets de novo. Genome Biol. 7:R36.
Reiss DJ, Baliga NS, Bonneau R.  2006.  Integrated biclustering of heterogeneous genome-wide datasets for the inference of global regulatory networks. BMC Bioinformatics. 7:280.
Whitehead K, Kish A, Pan M, Kaur A, Reiss DJ, King N, Hohmann L, DiRuggiero J, Baliga NS.  2006.  An integrated systems approach for understanding cellular responses to gamma radiation. Mol Syst Biol. 2:47.
Zhang H, Aebersold R.  2006.  Isolation of glycoproteins and identification of their N-linked glycosylation sites. Methods Mol Biol. 328:177-85.
Lu W, Zhou D, Glusman G, Utleg AG, White JT, Nelson PS, Vasicek TJ, Hood L, Lin B.  2006.  KLK31P is a novel androgen regulated and transcribed pseudogene of kallikreins that is expressed at lower levels in prostate cancer cells than in normal prostate cells. Prostate. 66:936-44.
Guo Z, Hood L, Malkki M, Petersdorf EW.  2006.  Long-range multilocus haplotype phasing of the MHC. Proc Natl Acad Sci U S A. 103:6964-9.
Allen T.E, Price ND, Joyce A.R, Palsson BO.  2006.  Long-range periodic patterns in microbial genomes indicate significant multi-scale chromosomal organization. PLoS computational biology. 2:e2.
Subramanian N, Qadri A.  2006.  Lysophospholipid sensing triggers secretion of flagellin from pathogenic salmonella.. Nat Immunol. 7(6):583-9.
Domon B, Aebersold R.  2006.  Mass spectrometry and protein analysis. Science. 312:212-7.
Gianchandani E.P, Papin JA, Price ND, Joyce A.R, Palsson BO.  2006.  Matrix formalism to describe functional states of transcriptional regulatory systems. PLoS computational biology. 2:e101.
Kowalewska J, Smith KD, Hudkins KL, Chang A, Fogo AB, Houghton D, Leslie D, Aitchison JD, Nicosia RF, Alpers CE.  2006.  Membranous glomerulopathy with spherules: an uncommon variant with obscure pathogenesis. Am J Kidney Dis. 47:983-92.
Becker S.A, Price ND, Palsson BO.  2006.  Metabolite coupling in genome-scale metabolic networks. BMC bioinformatics. 7:111.
Aga RS, Fair E, Abernethy NF, Deriemer K, Paz EA, Kawamura LM, Small PM, Kato-Maeda M.  2006.  Microevolution of the direct repeat locus of Mycobacterium tuberculosis in a strain prevalent in San Francisco. J Clin Microbiol. 44:1558-60.
True L, Coleman I, Hawley S, Huang CY, Gifford D, Coleman R, Beer TM, Gelmann E, Datta M, Mostaghel E et al..  2006.  A molecular correlate to the Gleason grading system for prostate adenocarcinoma. Proc Natl Acad Sci U S A. 103:10991-6.
Pym A, Small PM.  2006.  Mycobacterial Evolution: Insights from genomics and bacterial ecology.

Pages