Publications

Found 1248 results
2008
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.
Chen M, Ha M, Lackey E, Wang J, Z Chen J.  2008.  RNAi of met1 reduces DNA methylation and induces genome-specific changes in gene expression and centromeric small RNA accumulation in Arabidopsis allopolyploids.. Genetics. 178(4):1845-58.
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.
Huertas-Vazquez A, Plaisier CL, Weissglas-Volkov D, Sinsheimer J, Canizales-Quinteros S, Cruz-Bautista I, Nikkola E, Herrera-Hernandez M, Davila-Cervantes A, Tusie-Luna T et al..  2008.  TCF7L2 is associated with high serum triacylglycerol and differentially expressed in adipose tissue in families with familial combined hyperlipidaemia.. Diabetologia. 51(1):62-9.
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.
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.

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