Publications

Found 1263 results
2006
de Jong BC, Hill PC, Brookes RH, Gagneux S, Jeffries DJ, Otu JK, Donkor SA, Fox A, McAdam KP, Small PM et al..  2006.  Mycobacterium africanum elicits an attenuated T cell response to early secreted antigenic target, 6 kDa, in patients with tuberculosis and their household contacts. J Infect Dis. 193:1279-86.
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.
Barrett C.L, Price ND, Palsson BO.  2006.  Network-level analysis of metabolic regulation in the human red blood cell using random sampling and singular value decomposition. BMC bioinformatics. 7:132.
Fu E, Ramsey S, Thariani R, Yager P.  2006.  One-dimensional surface plasmon resonance imaging system using wavelength interrogation. Review of Scientific Instruments. 77:076106.
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.
Perkins MD, Small PM.  2006.  Partnering for better microbial diagnostics. Nat Biotechnol. 24:919-21.
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.
Jiang R, Mircean C, Shmulevich I, Cogdell D, Jia Y, Tabus I, Aldape K, Sawaya R, Bruner JM, Fuller GN et al..  2006.  Pathway alterations during glioma progression revealed by reverse phase protein lysate arrays. Proteomics. 6:2964-71.
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.
Fagarasanu A, Fagarasanu M, Eitzen GA, Aitchison JD, Rachubinski RA.  2006.  The peroxisomal membrane protein Inp2p is the peroxisome-specific receptor for the myosin V motor Myo2p of Saccharomyces cerevisiae. Dev Cell. 10:587-600.
Vizeacoumar FJ, Vreden WN, Aitchison JD, Rachubinski RA.  2006.  Pex19p binds Pex30p and Pex32p at regions required for their peroxisomal localization but separate from their peroxisomal targeting signals. J Biol Chem. 281:14805-12.
Hawn TR, Dunstan SJ, Thwaites GE, Simmons CP, Thuong NT, Lan NT, Quy HT, Chau TT, Hieu NT, Rodrigues S et al..  2006.  A polymorphism in Toll-interleukin 1 receptor domain containing adaptor protein is associated with susceptibility to meningeal tuberculosis. J Infect Dis. 194:1127-34.
Schaid DJ, McDonnell SK, Zarfas KE, Cunningham JM, Hebbring S, Thibodeau SN, Eeles RA, Easton DF, Foulkes WD, Simard J et al..  2006.  Pooled genome linkage scan of aggressive prostate cancer: results from the International Consortium for Prostate Cancer Genetics. Hum Genet. 120:471-85.
Lausted C, Warren CB, Hood LE, Lasky SR.  2006.  Printing your own inkjet microarrays. Methods Enzymol. 410:168-89.
Schmid A, Baliga NS.  2006.  Prokaryotic Systems Biology. Cell Engineering. 5
Stanford JL, McDonnell SK, Friedrichsen DM, Carlson EE, Kolb S, Deutsch K, Janer M, Hood L, Ostrander EA, Schaid DJ.  2006.  Prostate cancer and genetic susceptibility: a genome scan incorporating disease aggressiveness. Prostate. 66:317-25.
Seebacher J, Mallick P, Zhang N, Eddes JS, Aebersold R, Gelb MH.  2006.  Protein cross-linking analysis using mass spectrometry, isotope-coded cross-linkers, and integrated computational data processing. J Proteome Res. 5:2270-82.
Stewart JJ, White JT, Yan X, Collins S, Drescher CW, Urban ND, Hood L, Lin B.  2006.  Proteins associated with Cisplatin resistance in ovarian cancer cells identified by quantitative proteomic technology and integrated with mRNA expression levels. Mol Cell Proteomics. 5:433-43.
Gan RR, Yi EC, Chiu Y, Lee H, Kao YC, Wu TH, Aebersold R, Goodlett DR, Ng WV.  2006.  Proteome analysis of Halobacterium sp. NRC-1 facilitated by the biomodule analysis tool BMSorter. Mol Cell Proteomics. 5:987-97.
Hardwidge PR, Donohoe S, Aebersold R, Finlay BB.  2006.  Proteomic analysis of the binding partners to enteropathogenic Escherichia coli virulence proteins expressed in Saccharomyces cerevisiae. Proteomics. 6:2174-9.
Tian Q.  2006.  Proteomic exploration of the Wnt/beta-catenin pathway. Curr Opin Mol Ther. 8:191-7.
Saleem RA, Smith JJ, Aitchison JD.  2006.  Proteomics of the peroxisome. Biochim Biophys Acta. 1763:1541-51.
Gessler D, Dye C, Farmer P, Murray M, Navin T, Reves R, Shinnick T, Small PM, Yates T, Simpson G.  2006.  Public health. A National Tuberculosis Archive. Science. 311:1245-6.
Shiio Y, Aebersold R.  2006.  Quantitative proteome analysis using isotope-coded affinity tags and mass spectrometry. Nat Protoc. 1:139-45.
Gupta N, Wollscheid B, Watts J, Scheer B, Aebersold R, DeFranco AL.  2006.  Quantitative proteomic analysis of B cell lipid rafts reveals that ezrin regulates antigen receptor-mediated lipid raft dynamics. Nat Immunol. 7:625-33.
Shiio Y, Suh KS, Lee H, Yuspa SH, Eisenman RN, Aebersold R.  2006.  Quantitative proteomic analysis of myc-induced apoptosis: a direct role for Myc induction of the mitochondrial chloride ion channel, mtCLIC/CLIC4. J Biol Chem. 281:2750-6.
Flory MR, Lee H, Bonneau R, Mallick P, Serikawa K, Morris DR, Aebersold R.  2006.  Quantitative proteomic analysis of the budding yeast cell cycle using acid-cleavable isotope-coded affinity tag reagents. Proteomics. 6:6146-57.
Chen R, Pan S, Yi EC, Donohoe S, Bronner MP, Potter JD, Goodlett DR, Aebersold R, Brentnall TA.  2006.  Quantitative proteomic profiling of pancreatic cancer juice. Proteomics. 6:3871-9.
Lahdesmaki H, Hautaniemi S, Shmulevich I, Yli-Harja O.  2006.  Relationships between probabilistic Boolean networks and dynamic Bayesian networks as models of gene regulatory networks. Signal Processing. 86:814-834.
Bradshaw RA, Burlingame AL, Carr S, Aebersold R.  2006.  Reporting protein identification data: the next generation of guidelines. Mol Cell Proteomics. 5:787-8.
Marzolf B, Deutsch EW, Moss P, Campbell D, Johnson MH, Galitski T.  2006.  SBEAMS-Microarray: database software supporting genomic expression analyses for systems biology. BMC Bioinformatics. 7:286.
Prakash A, Mallick P, Whiteaker J, Zhang H, Paulovich A, Flory M, Lee H, Aebersold R, Schwikowski B.  2006.  Signal maps for mass spectrometry-based comparative proteomics. Mol Cell Proteomics. 5:423-32.
Marzolf B, Troisch P.  2006.  SLIMarray: lightweight software for microarray facility management. Source Code Biol Med. 1:5.
Leslie DM, Timney B, Rout MP, Aitchison JD.  2006.  Studying nuclear protein import in yeast. Methods. 39:291-308.
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.
Kaur A, Pan M, Meislin M, Facciotti MT, El-Geweley R, Baliga NS.  2006.  A systems view of haloarchaeal strategies to withstand stress from transition metals. Genome Res. 16:841-854.
Glusman G, Qin S, El-Gewely MR, Siegel AF, Roach J, Hood L, Smit A.  2006.  A third approach to gene prediction suggests thousands of additional human transcribed regions. PLoS Comput Biol. 2:e18.
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.
Longabaugh W, Bolouri H.  2006.  Understanding the dynamic behavior of genetic regulatory networks by functional decomposition. Curr Genomics. 7:333-41.
Zhang H, Loriaux P, Eng J, Campbell D, Keller A, Moss P, Bonneau R, Zhang N, Zhou Y, Wollscheid B et al..  2006.  UniPep--a database for human N-linked glycosites: a resource for biomarker discovery. Genome Biol. 7:R73.
Nykter M, Hunt KK, Pollock RE, El-Naggar AK, Taylor E, Shmulevich I, Yli-Harja O, Zhang W.  2006.  Unsupervised analysis uncovers changes in histopathologic diagnosis in supervised genomic studies. Technol Cancer Res Treat. 5:177-82.
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.
Gagneux S, Deriemer K, Van T, Kato-Maeda M, de Jong BC, Narayanan S, Nicol M, Niemann S, Kremer K, Gutierrez MC et al..  2006.  Variable host-pathogen compatibility in Mycobacterium tuberculosis. Proc Natl Acad Sci U S A. 103:2869-73.
Taylor CF, Hermjakob H, Julian, R. K. J., Garavelli JS, Aebersold R, Apweiler R.  2006.  The work of the Human Proteome Organisation's Proteomics Standards Initiative (HUPO PSI). OMICS. 10:145-51.
Taverna SD, Ilin S, Rogers RS, Tanny JC, Lavender H, Li H, Baker L, Boyle J, Blair LP, Chait BT et al..  2006.  Yng1 PHD finger binding to H3 trimethylated at K4 promotes NuA3 HAT activity at K14 of H3 and transcription at a subset of targeted ORFs. Mol Cell. 24:785-96.
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.
Oudes AJ, Roach J, Walashek LS, Eichner LJ, True LD, Vessella RL, Liu AY.  2005.  Application of Affymetrix array and Massively Parallel Signature Sequencing for identification of genes involved in prostate cancer progression. BMC Cancer. 5:86.
Niemisto A, Shmulevich I, Yli-Harja O, Chirieac LR, Hamilton SR.  2005.  Automated quantification of lymph node size and number in surgical specimens of stage II colorectal cancer. Conf Proc IEEE Eng Med Biol Soc. 6:6313-6.
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.
Thiele I, Price ND, Vo T.D, Palsson BO.  2005.  Candidate metabolic network states in human mitochondria. Impact of diabetes, ischemia, and diet. The Journal of biological chemistry. 280:11683-95.
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.
Shih JL, Reck-Peterson SL, Newitt R, Mooseker MS, Aebersold R, Herskowitz I.  2005.  Cell polarity protein Spa2P associates with proteins involved in actin function in Saccharomyces cerevisiae. Mol Biol Cell. 16:4595-608.
Jacobson LM, de Lourdes Garcia-Garcia M, Hernandez-Avila JE, Cano-Arellano B, Small PM, Sifuentes-Osornio J, Ponce-de-Leon A.  2005.  Changes in the geographical distribution of tuberculosis patients in Veracruz, Mexico, after reinforcement of a tuberculosis control programme. Trop Med Int Health. 10:305-11.
Xu J, Dimitrov L, Chang BL, Adams TS, Turner AR, Meyers DA, Eeles RA, Easton DF, Foulkes WD, Simard J et al..  2005.  A combined genomewide linkage scan of 1,233 families for prostate cancer-susceptibility genes conducted by the international consortium for prostate cancer genetics. Am J Hum Genet. 77:219-29.
Gilad Y, Man O, Glusman G.  2005.  A comparison of the human and chimpanzee olfactory receptor gene repertoires. Genome Res. 15:224-30.
Longabaugh W, Davidson EH, Bolouri H.  2005.  Computational representation of developmental genetic regulatory networks. Dev Biol. 283:1-16.
Hwang D, Rust AG, Ramsey S, Smith JJ, Leslie DM, Weston AD, de Atauri P, Aitchison JD, Hood L, Siegel AF et al..  2005.  A data integration methodology for systems biology. Proc Natl Acad Sci U S A. 102:17296-301.
Hwang D, Smith JJ, Leslie DM, Weston AD, Rust AG, Ramsey S, de Atauri P, Siegel AF, Bolouri H, Aitchison JD et al..  2005.  A data integration methodology for systems biology: experimental verification. Proc Natl Acad Sci U S A. 102:17302-7.
Drees BL, Thorsson V, Carter GW, Rives AW, Raymond MZ, Avila-Campillo I, Shannon P, Galitski T.  2005.  Derivation of genetic interaction networks from quantitative phenotype data. Genome Biol. 6:R38.
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.
Ramsey S, Orrell D, Bolouri H.  2005.  Dizzy: stochastic simulation of large-scale genetic regulatory networks (supplementary material). J Bioinform Comput Biol. 3:437-54.
Deriemer K, Garcia-Garcia L, Bobadilla-del-Valle M, Palacios-Martinez M, Martinez-Gamboa A, Small PM, Sifuentes-Osornio J, Ponce-de-Leon A.  2005.  Does DOTS work in populations with drug-resistant tuberculosis? Lancet. 365:1239-45.
de Jong BC, Onipede A, Pym AS, Gagneux S, Aga RS, Deriemer K, Small PM.  2005.  Does resistance to pyrazinamide accurately indicate the presence of Mycobacterium bovis? J Clin Microbiol. 43:3530-2.
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.

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