Publications

Found 1195 results
2007
Price ND, Shmulevich I.  2007.  Biochemical and statistical network models for systems biology. Curr Opin Biotechnol. 18:365-70.
Avila-Campillo I, Drew K, Lin J, Reiss DJ, Bonneau R.  2007.  BioNetBuilder: automatic integration of biological networks. Bioinformatics. 23:392-3.
Aitchison JD, Wozniak RW.  2007.  Cell biology: pore puzzle. Nature. 450:621-2.
de Jong BC, Hill PC, Aiken A, Jeffries DJ, Onipede A, Small PM, Adegbola RA, Corrah TP.  2007.  Clinical presentation and outcome of tuberculosis patients infected by M. africanum versus M. tuberculosis. Int J Tuberc Lung Dis. 11:450-6.
Hawn TR, Misch EA, Dunstan SJ, Thwaites GE, Lan NT, Quy HT, Chau TT, Rodrigues S, Nachman A, Janer M et al..  2007.  A common human TLR1 polymorphism regulates the innate immune response to lipopeptides. Eur J Immunol. 37:2280-9.
Chen R, Pan S, Cooke K, Moyes KW, Bronner MP, Goodlett DR, Aebersold R, Brentnall TA.  2007.  Comparison of pancreas juice proteins from cancer versus pancreatitis using quantitative proteomic analysis. Pancreas. 34:70-9.
Camp NJ, Cannon-Albright LA, Farnham JM, Baffoe-Bonnie AB, George A, Powell I, Bailey-Wilson JE, Carpten JD, Giles GG, Hopper JL et al..  2007.  Compelling evidence for a prostate cancer gene at 22q12.3 by the International Consortium for Prostate Cancer Genetics. Hum Mol Genet. 16:1271-8.
Oeffinger M, Wei KE, Rogers R, DeGrasse JA, Chait BT, Aitchison JD, Rout MP.  2007.  Comprehensive analysis of diverse ribonucleoprotein complexes. Nat Methods. 4:951-6.
Mallick P, Schirle M, Chen SS, Flory MR, Lee H, Martin D, Ranish J, Raught B, Schmitt R, Werner T et al..  2007.  Computational prediction of proteotypic peptides for quantitative proteomics. Nat Biotechnol. 25:125-31.
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.
Prinz S, Aldridge C, Ramsey SA, Taylor RJ, Galitski T.  2007.  Control of signaling in a MAP-kinase pathway by an RNA-binding protein. PLoS OnePLoS ONE. 2:e249.
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.
Fu E, Ramsey SA, Yager P.  2007.  Dependence of the signal amplification potential of colloidal gold nanoparticles on resonance wavelength in surface plasmon resonance-based detection. Anal Chim Acta. 599:118-23.
Lam H, Deutsch EW, Eddes JS, Eng JK, King N, Stein SE, Aebersold R.  2007.  Development and validation of a spectral library searching method for peptide identification from MS/MS. Proteomics. 7:655-67.
Zhu X-M, Yin L, Hood L, Galas DJ, Ao P.  2007.  Efficiency, Robustness, and Stochasticity of Gene Regulatory Networks in Systems Biology: λ Switch as a Working Example. Introduction to Systems Biology. :336-371.
Krawitz P, Shmulevich I.  2007.  Entropy of complex relevant components of Boolean networks. Phys Rev E Stat Nonlin Soft Matter Phys. 76:036115.
Rostad K, Mannelqvist M, Halvorsen OJ, Oyan AM, Bo TH, Stordrange L, Olsen S, Haukaas SA, Lin B, Hood L et al..  2007.  ERG upregulation and related ETS transcription factors in prostate cancer. Int J Oncol. 30:19-32.
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.
Bare JC, Shannon P, Schmid AK, Baliga NS.  2007.  The Firegoose: two-way integration of diverse data from different bioinformatics web resources with desktop applications. BMC Bioinformatics. 8:456.
Jones AR, Miller M, Aebersold R, Apweiler R, Ball CA, Brazma A, Degreef J, Hardy N, Hermjakob H, Hubbard SJ et al..  2007.  The Functional Genomics Experiment model (FuGE): an extensible framework for standards in functional genomics. Nat Biotechnol. 25:1127-33.
Facciotti MT, Reiss DJ, Pan M, Kaur A, Vuthoori M, Bonneau R, Shannon P, Srivastava A, Donohoe SM, Hood LE et al..  2007.  General transcription factor specified global gene regulation in archaea. Proc Natl Acad Sci U S A. 104:4630-5.
Schaid DJ, Stanford JL, McDonnell SK, Suuriniemi M, McIntosh L, Karyadi DM, Carlson EE, Deutsch K, Janer M, Hood L et al..  2007.  Genome-wide linkage scan of prostate cancer Gleason score and confirmation of chromosome 19q. Hum Genet. 121:729-35.
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.
Pierce BL, Friedrichsen-Karyadi DM, McIntosh L, Deutsch K, Hood L, Ostrander EA, Austin MA, Stanford JL.  2007.  Genomic scan of 12 hereditary prostate cancer families having an occurrence of pancreas cancer. Prostate. 67:410-5.
Gagneux S, Small PM.  2007.  Global phylogeography of Mycobacterium tuberculosis and implications for tuberculosis product development. Lancet Infect Dis. 7:328-37.
Bekris LM, Shephard C, Janer M, Graham J, McNeney B, Shin J, Zarghami M, Griffith W, Farin F, Kavanagh TJ et al..  2007.  Glutamate cysteine ligase catalytic subunit promoter polymorphisms and associations with type 1 diabetes age-at-onset and GAD65 autoantibody levels. Exp Clin Endocrinol Diabetes. 115:221-8.
Whiteaker JR, Zhang H, Eng JK, Fang R, Piening BD, Feng LC, Lorentzen TD, Schoenherr RM, Keane JF, Holzman T et al..  2007.  Head-to-head comparison of serum fractionation techniques. J Proteome Res. 6:828-36.
Price ND, Trent J, El-Naggar AK, Cogdell D, Taylor E, Hunt KK, Pollock RE, Hood L, Shmulevich I, Zhang W.  2007.  Highly accurate two-gene classifier for differentiating gastrointestinal stromal tumors and leiomyosarcomas. Proc Natl Acad Sci U S A. 104:3414-9.
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.
Dall'Era MA, Oudes A, Martin DB, Liu AY.  2007.  HSP27 and HSP70 interact with CD10 in C4-2 prostate cancer cells. Prostate. 67:714-21.
Shin JH, Janer M, McNeney B, Blay S, Deutsch K, Sanjeevi CB, Kockum I, Lernmark A, Graham J, Arnqvist H et al..  2007.  IA-2 autoantibodies in incident type I diabetes patients are associated with a polyadenylation signal polymorphism in GIMAP5. Genes Immun. 8:503-12.
Jasavala R, Martinez H, Thumar J, Andaya A, Gingras AC, Eng JK, Aebersold R, Han DK, Wright ME.  2007.  Identification of putative androgen receptor interaction protein modules: cytoskeleton and endosomes modulate androgen receptor signaling in prostate cancer cells. Mol Cell Proteomics. 6:252-71.
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.
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.
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.

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