Publications

Found 1186 results
2008
Wilson J, Huynh C, Kennedy KA, Ward DM, Kaplan J, Aderem A, Andrews NW.  2008.  Control of parasitophorous vacuole expansion by LYST/Beige restricts the intracellular growth of Leishmania amazonensis. PLoS Pathog. 4:e1000179.
Ratushny AV, Ramsey SA, Roda O, Wan Y, Smith JJ, Aitchison JD.  2008.  Control of transcriptional variability by overlapping feed-forward regulatory motifs. Biophys J. 95:3715-23.
Brusniak MY, Bodenmiller B, Campbell D, Cooke K, Eddes J, Garbutt A, Lau H, Letarte S, Mueller LN, Sharma V et al..  2008.  Corra: Computational framework and tools for LC-MS discovery and targeted mass spectrometry-based proteomics. BMC Bioinformatics. 9:542.
Pascal LE, True LD, Campbell DS, Deutsch EW, Risk M, Coleman IM, Eichner LJ, Nelson PS, Liu AY.  2008.  Correlation of mRNA and protein levels: cell type-specific gene expression of cluster designation antigens in the prostate. BMC Genomics. 9:246.
Balleza E, Alvarez-Buylla ER, Chaos A, Kauffman S, Shmulevich I, Aldana M.  2008.  Critical dynamics in genetic regulatory networks: examples from four kingdoms. PLoS OnePLoS ONE. 3:e2456.
Nykter M, Price ND, Larjo A, Aho T, Kauffman SA, Yli-Harja O, Shmulevich I.  2008.  Critical networks exhibit maximal information diversity in structure-dynamics relationships. Phys Rev Lett. 100:058702.
Rubio ED, Reiss DJ, Welcsh PL, Disteche CM, Filippova GN, Baliga NS, Aebersold R, Ranish J, Krumm A.  2008.  CTCF physically links cohesin to chromatin. Proc Natl Acad Sci U S A. 105:8309-14.
Deutsch EW, Lam H, Aebersold R.  2008.  Data analysis and bioinformatics tools for tandem mass spectrometry in proteomics. Physiol Genomics. 33:18-25.
Picotti P, Lam H, Campbell D, Deutsch EW, Mirzaei H, Ranish J, Domon B, Aebersold R.  2008.  A database of mass spectrometric assays for the yeast proteome. Nat Methods. 5:913-4.
Letarte S, Brusniak MY, Campbell D, Eddes J, Kemp CJ, Lau H, Mueller L, Schmidt A, Shannon P, Kelly-Spratt KS et al..  2008.  Differential Plasma Glycoproteome of p19 Skin Cancer Mouse Model Using the Corra Label-Free LC-MS Proteomics Platform. Clin Proteomics. 4:105.
Geiss GK, Bumgarner RE, Birditt B, Dahl T, Dowidar N, Dunaway DL, Fell HP, Ferree S, George RD, Grogan T et al..  2008.  Direct multiplexed measurement of gene expression with color-coded probe pairs. Nat Biotechnol. 26:317-25.
Tabb DL, Ma ZQ, Martin DB, Ham AJ, Chambers MC.  2008.  DirecTag: accurate sequence tags from peptide MS/MS through statistical scoring. J Proteome Res. 7:3838-46.
Johanneson B, McDonnell SK, Karyadi DM, Hebbring SJ, Wang L, Deutsch K, McIntosh L, Kwon EM, Suuriniemi M, Stanford JL et al..  2008.  Fine mapping of familial prostate cancer families narrows the interval for a susceptibility locus on chromosome 22q12.3 to 1.36 Mb. Hum Genet. 123:65-75.
Nykter M, Price ND, Aldana M, Ramsey SA, Kauffman SA, Hood LE, Yli-Harja O, Shmulevich I.  2008.  Gene expression dynamics in the macrophage exhibit criticality. Proc Natl Acad Sci U S A. 105:1897-900.
Georgescu C, Longabaugh W, Scripture-Adams DD, David-Fung ES, Yui MA, Zarnegar MA, Bolouri H, Rothenberg EV.  2008.  A gene regulatory network armature for T lymphocyte specification. Proc Natl Acad Sci U S A. 105:20100-5.
Hood L.  2008.  Gene regulatory networks and embryonic specification. Proc Natl Acad Sci U S A. 105:5951-2.
Nurieva RI, Chung Y, Hwang D, Yang XO, Kang HS, Ma L, Wang YH, Watowich SS, Jetten AM, Tian Q et al..  2008.  Generation of T follicular helper cells is mediated by interleukin-21 but independent of T helper 1, 2, or 17 cell lineages. Immunity. 29:138-49.
Saleem RA, Knoblach B, Mast FD, Smith JJ, Boyle J, Dobson CM, Long-O'Donnell R, Rachubinski RA, Aitchison JD.  2008.  Genome-wide analysis of signaling networks regulating fatty acid-induced gene expression and organelle biogenesis. J Cell Biol. 181:281-92.
Dishaw LJ, Mueller MG, Gwatney N, Cannon JP, Haire RN, Litman RT, Amemiya CT, Ota T, Rowen L, Glusman G et al..  2008.  Genomic complexity of the variable region-containing chitin-binding proteins in amphioxus. BMC Genet. 9:78.
Taylor CF, Binz PA, Aebersold R, Affolter M, Barkovich R, Deutsch EW, Horn DM, Huhmer A, Kussmann M, Lilley K et al..  2008.  Guidelines for reporting the use of mass spectrometry in proteomics. Nat Biotechnol. 26:860-1.
Van PT, Schmid AK, King NL, Kaur A, Pan M, Whitehead K, Koide T, Facciotti MT, Goo YA, Deutsch EW et al..  2008.  Halobacterium salinarum NRC-1 PeptideAtlas: toward strategies for targeted proteomics and improved proteome coverage. J Proteome Res. 7:3755-64.
Hershberg R, Lipatov M, Small PM, Sheffer H, Niemann S, Homolka S, Roach J, Kremer K, Petrov DA, Feldman MW et al..  2008.  High functional diversity in Mycobacterium tuberculosis driven by genetic drift and human demography. PLoS Biol. 6:e311.
Mathivanan S, Ahmed M, Ahn NG, Alexandre H, Amanchy R, Andrews PC, Bader JS, Balgley BM, Bantscheff M, Bennett KL et al..  2008.  Human Proteinpedia enables sharing of human protein data. Nat Biotechnol. 26:164-7.
Tischkowitz MD, Yilmaz A, Chen LQ, Karyadi DM, Novak D, Kirchhoff T, Hamel N, Tavtigian SV, Kolb S, Bismar TA et al..  2008.  Identification and characterization of novel SNPs in CHEK2 in Ashkenazi Jewish men with prostate cancer. Cancer Lett. 270:173-80.
Chi Y, Welcker M, Hizli AA, Posakony JJ, Aebersold R, Clurman BE.  2008.  Identification of CDK2 substrates in human cell lysates. Genome Biol. 9:R149.
Rinner O, Seebacher J, Walzthoeni T, Mueller LN, Beck M, Schmidt A, Mueller M, Aebersold R.  2008.  Identification of cross-linked peptides from large sequence databases. Nat Methods. 5:315-8.
Thuong NT, Dunstan SJ, Chau TT, Thorsson V, Simmons CP, Quyen NT, Thwaites GE, Thi Ngoc Lan N, Hibberd M, Teo YY et al..  2008.  Identification of tuberculosis susceptibility genes with human macrophage gene expression profiles. PLoS Pathog. 4:e1000229.
Marelli M, Nesvizhskii AI, Aitchison JD.  2008.  Identifying bona fide components of an organelle by isotope-coded labeling of subcellular fractions : an example in peroxisomes. Methods Mol Biol. 432:357-71.
E P, B D, C F, O D, T V, Am DG.  2008.  The Inactivation of a New Peptidoglycan Hydrolase Pmp23 Leads to Abnormal Septum Formation in Streptococcus pneumoniae. Open Microbiol J. 2:107-14.
Liu W, Lahdesmaki H, Dougherty ER, Shmulevich I.  2008.  Inference of Boolean networks using sensitivity regularization. EURASIP J Bioinform Syst Biol. :780541.
Korb M, Rust AG, Thorsson V, Battail C, Li B, Hwang D, Kennedy KA, Roach J, Rosenberger CM, Gilchrist M et al..  2008.  The Innate Immune Database (IIDB). BMC Immunol. 9:7.
Charles JF, Humphrey MB, Zhao X, Quarles E, Nakamura MC, Aderem A, Seaman WE, Smith KD.  2008.  The innate immune response to Salmonella enterica serovar Typhimurium by macrophages is dependent on TREM2-DAP12. Infect Immun. 76:2439-47.
Fan R, Vermesh O, Srivastava A, Yen BK, Qin L, Ahmad H, Kwong GA, Liu CC, Gould J, Hood L et al..  2008.  Integrated barcode chips for rapid, multiplexed analysis of proteins in microliter quantities of blood. Nat Biotechnol. 26:1373-8.
Schmidt A, Gehlenborg N, Bodenmiller B, Mueller LN, Campbell D, Mueller M, Aebersold R, Domon B.  2008.  An integrated, directed mass spectrometric approach for in-depth characterization of complex peptide mixtures. Mol Cell Proteomics. 7:2138-50.
Carter GW, Thorsson V, Galitski T.  2008.  Integrated Network Modeling of Molecular and Genetic Interactions. Sourcebook of Models for Biomedical Research. :67-74.
Ulintz PJ, Bodenmiller B, Andrews PC, Aebersold R, Nesvizhskii AI.  2008.  Investigating MS2/MS3 matching statistics: a model for coupling consecutive stage mass spectrometry data for increased peptide identification confidence. Mol Cell Proteomics. 7:71-87.
Lähdesmäki H, Shmulevich I.  2008.  Learning the structure of dynamic Bayesian networks from time series and steady state measurements. Machine Learning. 71:185-217.
Leng X, Lin H, Ding T, Wang Y, Wu Y, Klumpp S, Sun T, Zhou Y, Monaco P, Belmont J et al..  2008.  Lipocalin 2 is required for BCR-ABL-induced tumorigenesis. Oncogene. 27:6110-9.
Gavin AC, Aebersold R, Heck AJ.  2008.  Meeting report on the 7th World Congress of the Human Proteome Organization (HUPO) in Amsterdam: Proteome Biology. Mol Cell Proteomics. 7:2288-91.
Wu Z, Jia X, de la Cruz L, Su XC, Marzolf B, Troisch P, Zak D, Hamilton A, Whittle B, Yu D et al..  2008.  Memory T cell RNA rearrangement programmed by heterogeneous nuclear ribonucleoprotein hnRNPLL. Immunity. 29:863-75.
Deutsch EW, Ball CA, Berman JJ, Bova GS, Brazma A, Bumgarner RE, Campbell D, Causton HC, Christiansen JH, Daian F et al..  2008.  Minimum information specification for in situ hybridization and immunohistochemistry experiments (MISFISHIE). Nat Biotechnol. 26:305-12.
Reiss DJ, Facciotti MT, Baliga NS.  2008.  Model-based deconvolution of genome-wide DNA binding. Bioinformatics. 24:396-403.
Snitkin ES, Dudley AM, Janse DM, Wong K, Church GM, Segre D.  2008.  Model-driven analysis of experimentally determined growth phenotypes for 465 yeast gene deletion mutants under 16 different conditions. Genome Biol. 9:R140.
Zhang Q, Menon R, Deutsch EW, Pitteri SJ, Faca VM, Wang H, Newcomb LF, Depinho RA, Bardeesy N, Dinulescu D et al..  2008.  A mouse plasma peptide atlas as a resource for disease proteomics. Genome Biol. 9:R93.
Martin DB, Holzman T, May D, Peterson A, Eastham A, Eng J, McIntosh M.  2008.  MRMer, an interactive open source and cross-platform system for data extraction and visualization of multiple reaction monitoring experiments. Mol Cell Proteomics. 7:2270-8.
Hwang D, Zhang N, Lee H, Yi E, Zhang H, Lee I, Hood L, Aebersold R.  2008.  MS-BID: a Java package for label-free LC-MS-based comparative proteomic analysis. Bioinformatics. 24:2641-2.
Warren SE, Mao DP, Rodriguez AE, Miao EA, Aderem A.  2008.  Multiple Nod-like receptors activate caspase 1 during Listeria monocytogenes infection. J Immunol. 180:7558-64.
Soltermann A, Ossola R, Kilgus-Hawelski S, von Eckardstein A, Suter T, Aebersold R, Moch H.  2008.  N-glycoprotein profiling of lung adenocarcinoma pleural effusions by shotgun proteomics. Cancer. 114:124-33.
Deutsch EW, Lam H, Aebersold R.  2008.  PeptideAtlas: a resource for target selection for emerging targeted proteomics workflows. EMBO Rep. 9:429-34.
Hood L.  2008.  A personal journey of discovery: developing technology and changing biology. Annu Rev Anal Chem (Palo Alto Calif). 1:1-43.
Bodenmiller B, Campbell D, Gerrits B, Lam H, Jovanovic M, Picotti P, Schlapbach R, Aebersold R.  2008.  PhosphoPep--a database of protein phosphorylation sites in model organisms. Nat Biotechnol. 26:1339-40.
Lahdesmaki H, Rust AG, Shmulevich I.  2008.  Probabilistic inference of transcription factor binding from multiple data sources. PLoS OnePLoS ONE. 3:e1820.
Taylor CF, Field D, Sansone SA, Aerts J, Apweiler R, Ashburner M, Ball CA, Binz PA, Bogue M, Booth T et al..  2008.  Promoting coherent minimum reporting guidelines for biological and biomedical investigations: the MIBBI project. Nat Biotechnol. 26:889-96.
Kauffman S, Logan RK, Este R, Goebel R, Hobill D, Shmulevich I.  2008.  Propagating organization: an enquiry. Biology and Philosophy. 23:27-45.
Ramos H, Shannon P, Aebersold R.  2008.  The protein information and property explorer: an easy-to-use, rich-client web application for the management and functional analysis of proteomic data. Bioinformatics. 24:2110-1.
Li R, Guo Y, Han BM, Yan X, Utleg AG, Li W, Tu LC, Wang J, Hood L, Xia S et al..  2008.  Proteomics cataloging analysis of human expressed prostatic secretions reveals rich source of biomarker candidates. Proteomics Clin Appl. 2:543-555.
Tress ML, Bodenmiller B, Aebersold R, Valencia A.  2008.  Proteomics studies confirm the presence of alternative protein isoforms on a large scale. Genome Biol. 9:R162.
Miao EA, Ernst RK, Dors M, Mao DP, Aderem A.  2008.  Pseudomonas aeruginosa activates caspase 1 through Ipaf. Proc Natl Acad Sci U S A. 105:2562-7.
Hohmann LJ, Eng JK, Gemmill A, Klimek J, Vitek O, Reid GE, Martin DB.  2008.  Quantification of the compositional information provided by immonium ions on a quadrupole-time-of-flight mass spectrometer. Anal Chem. 80:5596-606.
Pflieger D, Junger MA, Muller M, Rinner O, Lee H, Gehrig PM, Gstaiger M, Aebersold R.  2008.  Quantitative proteomic analysis of protein complexes: concurrent identification of interactors and their state of phosphorylation. Mol Cell Proteomics. 7:326-46.
Yan W, Hwang D, Aebersold R.  2008.  Quantitative proteomic analysis to profile dynamic changes in the spatial distribution of cellular proteins. Methods Mol Biol. 432:389-401.
Himeda CL, Ranish J, Hauschka SD.  2008.  Quantitative proteomic identification of MAZ as a transcriptional regulator of muscle-specific genes in skeletal and cardiac myocytes. Mol Cell Biol. 28:6521-35.
Lausted C, Hu Z, Hood L.  2008.  Quantitative serum proteomics from surface plasmon resonance imaging. Mol Cell Proteomics. 7:2464-74.
Gradolatto A, Rogers RS, Lavender H, Taverna SD, Allis CD, Aitchison JD, Tackett AJ.  2008.  Saccharomyces cerevisiae Yta7 regulates histone gene expression. Genetics. 179:291-304.
Lange V, Picotti P, Domon B, Aebersold R.  2008.  Selected reaction monitoring for quantitative proteomics: a tutorial. Mol Syst Biol. 4:222.
Klimek J, Eddes JS, Hohmann L, Jackson J, Peterson A, Letarte S, Gafken PR, Katz JE, Mallick P, Lee H et al..  2008.  The standard protein mix database: a diverse data set to assist in the production of improved Peptide and protein identification software tools. J Proteome Res. 7:96-103.
Zou Z, Ibisate M, Zhou Y, Aebersold R, Xia Y, Zhang H.  2008.  Synthesis and evaluation of superparamagnetic silica particles for extraction of glycopeptides in the microtiter plate format. Anal Chem. 80:1228-34.
Price ND, Foltz G, Madan A, Hood L, Tian Q.  2008.  Systems biology and cancer stem cells. J Cell Mol Med. 12:97-110.
Hood L, Rowen L, Galas DJ, Aitchison JD.  2008.  Systems biology at the Institute for Systems Biology. Brief Funct Genomic Proteomic. 7:239-48.
Boyle J, Cavnor C, Killcoyne S, Shmulevich I.  2008.  Systems biology driven software design for the research enterprise. BMC Bioinformatics. 9:295.
Baliga NS.  2008.  Systems biology. The scale of prediction. Science. 320:1297-8.
Ludwig C, Baliga NS.  2008.  Systems Concepts Effectively Taught Using Systems Practices. Science Scope. 31:16-20.
Yang XO, Pappu BP, Nurieva R, Akimzhanov A, Kang HS, Chung Y, Ma L, Shah B, Panopoulos AD, Schluns KS et al..  2008.  T helper 17 lineage differentiation is programmed by orphan nuclear receptors ROR alpha and ROR gamma. Immunity. 28:29-39.
Aderem A, Shmulevich I.  2008.  Taming data. Cell Host Microbe. 4:312-3.
Lange V, Malmstrom JA, Didion J, King NL, Johansson BP, Schafer J, Rameseder J, Wong CH, Deutsch EW, Brusniak MY et al..  2008.  Targeted quantitative analysis of Streptococcus pyogenes virulence factors by multiple reaction monitoring. Mol Cell Proteomics. 7:1489-500.
Pappu BP, Borodovsky A, Zheng TS, Yang X, Wu P, Dong X, Weng S, Browning B, Scott ML, Ma L et al..  2008.  TL1A-DR3 interaction regulates Th17 cell function and Th17-mediated autoimmune disease. J Exp Med. 205:1049-62.
Bochud PY, Hawn TR, Siddiqui MR, Saunderson P, Britton S, Abraham I, Argaw AT, Janer M, Zhao LP, Kaplan G et al..  2008.  Toll-like receptor 2 (TLR2) polymorphisms are associated with reversal reaction in leprosy. J Infect Dis. 197:253-61.
Bochud PY, Chien JW, Marr KA, Leisenring WM, Upton A, Janer M, Rodrigues SD, Li S, Hansen JA, Zhao LP et al..  2008.  Toll-like receptor 4 polymorphisms and aspergillosis in stem-cell transplantation. N Engl J Med. 359:1766-77.
Ramsey SA, Klemm SL, Zak DE, Kennedy KA, Thorsson V, Li B, Gilchrist M, Gold ES, Johnson CD, Litvak V et al..  2008.  Uncovering a macrophage transcriptional program by integrating evidence from motif scanning and expression dynamics. PLoS Comput Biol. 4:e1000021.
Lin B, Utleg AG, Gravdal K, White JT, Halvorsen OJ, Lu W, True LD, Vessella R, Lange PH, Nelson PS et al..  2008.  WDR19 expression is increased in prostate cancer compared with normal cells, but low-intensity expression in cancers is associated with shorter time to biochemical failures and local recurrence. Clin Cancer Res. 14:1397-406.
Hood LE.  2008.  Wu and Kabat 1970: a transforming view of antibody diversity. J Immunol. 180:7055-6.
2007
Lu Y, Bottari P, Aebersold R, Turecek F, Gelb MH.  2007.  Absolute quantification of specific proteins in complex mixtures using visible isotope-coded affinity tags. Methods Mol Biol. 359:159-76.
Demers C, Chaturvedi CP, Ranish J, Juban G, Lai P, Morle F, Aebersold R, Dilworth FJ, Groudine M, Brand M.  2007.  Activator-mediated recruitment of the MLL2 methyltransferase complex to the beta-globin locus. Mol Cell. 27:573-84.
Malmstrom J, Lee H, Aebersold R.  2007.  Advances in proteomic workflows for systems biology. Curr Opin Biotechnol. 18:378-84.
Hawn TR, Berrington WR, Smith IA, Uematsu S, Akira S, Aderem A, Smith KD, Skerrett SJ.  2007.  Altered inflammatory responses in TLR5-deficient mice infected with Legionella pneumophila. J Immunol. 179:6981-7.
Nesvizhskii AI, Vitek O, Aebersold R.  2007.  Analysis and validation of proteomic data generated by tandem mass spectrometry. Nat Methods. 4:787-97.
Gingras AC, Gstaiger M, Raught B, Aebersold R.  2007.  Analysis of protein complexes using mass spectrometry. Nat Rev Mol Cell Biol. 8:645-54.
Schmid AK, Reiss DJ, Kaur A, Pan M, King N, Van PT, Hohmann L, Martin DB, Baliga NS.  2007.  The anatomy of microbial cell state transitions in response to oxygen. Genome Res. 17:1399-1413.
Prakash A, Piening B, Whiteaker J, Zhang H, Shaffer SA, Martin D, Hohmann L, Cooke K, Olson JM, Hansen S et al..  2007.  Assessing bias in experiment design for large scale mass spectrometry-based quantitative proteomics. Mol Cell Proteomics. 6:1741-8.
Krawitz P, Shmulevich I.  2007.  Basin entropy in Boolean network ensembles. Phys Rev Lett. 98:158701.
Iyer S, Deutsch K, Yan X, Lin B.  2007.  Batch RNAi selector: a standalone program to predict specific siRNA candidates in batches with enhanced sensitivity. Comput Methods Programs Biomed. 85:203-9.
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.

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