Found 1274 results
Wan Y, Chiang JH, Lin CH, Arens CE, Saleem RA, Smith JJ, Aitchison JD.  2010.  Histone chaperone Chz1p regulates H2B ubiquitination and subtelomeric anti-silencing. Nucleic Acids Res. 38:1431-40.
Eddy JA, Hood L, Price ND, Geman D.  2010.  Identifying tightly regulated and variably expressed networks by Differential Rank Conservation (DIRAC). PLoS Comput Biol. 6:e1000792.
Munson MS, Spotts JM, Niemisto A, Selinummi J, Kralj JG, Salit ML, Ozinsky A.  2010.  Image-based feedback control for real-time sorting of microspheres in a microfluidic device. Lab Chip. 10:2402-10.
Edelman L.B, Eddy JA, Price ND.  2010.  In silico models of cancer. Wiley interdisciplinary reviews. Systems biology and medicine. 2:438-59.
Miao EA, Warren SE.  2010.  Innate immune detection of bacterial virulence factors via the NLRC4 inflammasome. J Clin Immunol. 30:502-6.
Miao EA, Mao DP, Yudkovsky N, Bonneau R, Lorang CG, Warren SE, Leaf IA, Aderem A.  2010.  Innate immune detection of the type III secretion apparatus through the NLRC4 inflammasome. Proc Natl Acad Sci U S A. 107:3076-80.
Saleem RA, Rogers RS, Ratushny AV, Dilworth DJ, Shannon P, Shteynberg D, Wan Y, Moritz RL, Nesvizhskii AI, Rachubinski RA et al..  2010.  Integrated phosphoproteomics analysis of a signaling network governing nutrient response and peroxisome induction. Mol Cell Proteomics. 9:2076-88.
Yang J, Eddy JA, Pan Y., Hategan A., Tabus I, Wang Y, Cogdell D, Price ND, Pollock RE, Lazar A.J et al..  2010.  Integrated proteomics and genomics analysis reveals a novel mesenchymal to epithelial reverting transition in leiomyosarcoma through regulation of slug. Molecular & cellular proteomics : MCP. 9:2405-13.
Yang D, Ylipaa A, Yang J, Hunt K, Pollock R, Trent J, Yli-Harja O, Shmulevich I, Nykter M, Zhang W.  2010.  An integrated study of aberrant gene copy number and gene expression in GIST and LMS. Technol Cancer Res Treat. 9:171-8.
Bare JC, Koide T, Reiss DJ, Tenenbaum D, Baliga NS.  2010.  Integration and visualization of systems biology data in context of the genome. BMC Bioinformatics. 11:382.
Amon LM, Law W, Fitzgibbon MP, Gross JA, O'Briant K, Peterson A, Drescher C, Martin DB, McIntosh M.  2010.  Integrative proteomic analysis of serum and peritoneal fluids helps identify proteins that are up-regulated in serum of women with ovarian cancer. PLoS OnePLoS ONE. 5:e11137.
Gilchrist M, Henderson, W. R. J., Morotti A, Johnson CD, Nachman A, Schmitz F, Smith KD, Aderem A.  2010.  A key role for ATF3 in regulating mast cell survival and mediator release. Blood. 115:4734-41.
Himeda CL, Ranish J, Pearson RC, Crossley M, Hauschka SD.  2010.  KLF3 regulates muscle-specific gene expression and synergizes with serum response factor on KLF binding sites. Mol Cell Biol. 30:3430-43.
Facciotti MT, Pang WL, Lo FY, Whitehead K, Koide T, Masumura K, Pan M, Kaur A, Larsen DJ, Reiss DJ et al..  2010.  Large scale physiological readjustment during growth enables rapid, comprehensive and inexpensive systems analysis. BMC Syst Biol. 4:64.
Youn A, Reiss DJ, Stuetzle W.  2010.  Learning transcriptional networks from the integration of ChIP-chip and expression data in a non-parametric model. Bioinformatics. 26:1879-86.
Kim P.J, Price ND.  2010.  Macroscopic kinetic effect of cell-to-cell variation in biochemical reactions. Physical review letters. 104:148103.
Sakhanenko NA, Galas DJ.  2010.  Markov Logic Networks in the Analysis of Genetic Data. J Comput Biol.
Deutsch EW.  2010.  Mass spectrometer output file format mzML. Methods Mol Biol. 604:319-31.
Lin B, Madan A, Yoon JG, Fang X, Yan X, Kim TK, Hwang D, Hood L, Foltz G.  2010.  Massively parallel signature sequencing and bioinformatics analysis identifies up-regulation of TGFBI and SOX4 in human glioblastoma. PLoS OnePLoS ONE. 5:e10210.
Weber JA, Baxter DH, Zhang S, Huang DY, How Huang K, Jen Lee M, Galas DJ, Wang K.  2010.  The MicroRNA Spectrum in 12 Body Fluids. Clin Chem. 56:1733-41.
Handcock J, Deutsch EW, Boyle J.  2010.  mspecLINE: bridging knowledge of human disease with the proteome. BMC Med Genomics. 3:7.
Walker CB, de la Torre JR, Klotz MG, Urakawa H, Pinel N, Arp DJ, Brochier-Armanet C, Chain PSG, Chan PP, Gollabgir A et al..  2010.  Nitrosopumilus maritimus genome reveals unique mechanisms for nitrification and autotrophy in globally distributed marine crenarchaea.. Proc Natl Acad Sci U S A. 107(19):8818-23.
Ouellet E, Lausted C, Lin T, Yang CW, Hood L, Lagally ET.  2010.  Parallel microfluidic surface plasmon resonance imaging arrays. Lab Chip. 10:581-8.
Deutsch EW.  2010.  The PeptideAtlas Project. Methods Mol Biol. 604:285-96.
Bodenmiller B, Wanka S, Kraft C, Urban J, Campbell D, Pedrioli PG, Gerrits B, Picotti P, Lam H, Vitek O et al..  2010.  Phosphoproteomic analysis reveals interconnected system-wide responses to perturbations of kinases and phosphatases in yeast. Sci Signal. 3:rs4.
Erkkila T, Lehmusvaara S, Ruusuvuori P, Visakorpi T, Shmulevich I, Lahdesmaki H.  2010.  Probabilistic analysis of gene expression measurements from heterogeneous tissues. Bioinformatics. 26:2571-7.
Chandrasekaran S, Price ND.  2010.  Probabilistic integrative modeling of genome-scale metabolic and regulatory networks in Escherichia coli and Mycobacterium tuberculosis. Proceedings of the National Academy of Sciences of the United States of America. 107:17845-50.
Dilworth DJ, Saleem RA, Rogers RS, Mirzaei H, Boyle J, Aitchison JD.  2010.  QTIPS: a novel method of unsupervised determination of isotopic amino acid distribution in SILAC experiments. J Am Soc Mass Spectrom. 21:1417-22.
Eddy JA, Sung J, Geman D, Price ND.  2010.  Relative expression analysis for molecular cancer diagnosis and prognosis. Technology in cancer research & treatment. 9:149-59.
Burdick DB, Cavnor CC, Handcock J, Killcoyne S, Lin J, Marzolf B, Ramsey SA, Rovira H, Bressler R, Shmulevich I et al..  2010.  SEQADAPT: an adaptable system for the tracking, storage and analysis of high throughput sequencing experiments. BMC Bioinformatics. 11:377.
Shimada T, Park BG, Wolf AJ, Brikos C, Goodridge HS, Becker CA, Reyes CN, Miao EA, Aderem A, Gotz F et al..  2010.  Staphylococcus aureus evades lysozyme-based peptidoglycan digestion that links phagocytosis, inflammasome activation, and IL-1beta secretion. Cell Host Microbe. 7:38-49.
Arpanaei A, Winther-Jensen B, Theodosiou E, Kingshott P, Hobley TJ, Thomas OR.  2010.  Surface modification of chromatography adsorbents by low temperature low pressure plasma. J Chromatogr A. 1217:6905-16.
Sipova H, Zhang S, Dudley AM, Galas DJ, Wang K, Homola J.  2010.  Surface plasmon resonance biosensor for rapid label-free detection of microribonucleic acid at subfemtomole level. Anal Chem. 82:10110-5.
Ma S, Funk C.C, Price ND.  2010.  Systems approaches to molecular cancer diagnostics. Discovery medicine. 10:531-42.
Wang K, Lee I, Carlson G, Hood L, Galas DJ.  2010.  Systems biology and the discovery of diagnostic biomarkers. Dis Markers. 28:199-207.
Ramsey SA, Gold ES, Aderem A.  2010.  A systems biology approach to understanding atherosclerosis. EMBO Mol Med. 2:79-89.
Edelman L.B, Chandrasekaran S, Price ND.  2010.  Systems biology of embryogenesis. Reproduction, fertility, and development. 22:98-105.
Saleem RA, Aitchison JD.  2010.  Systems cell biology of the mitotic spindle. J Cell Biol. 188:7-9.
Carter GW, Rush CG, Uygun F, Sakhanenko NA, Galas DJ, Galitski T.  2010.  A systems-biology approach to modular genetic complexity. Chaos. 20:026102.
Ao P, Galas DJ, Hood L, Yin L, Zhu XM.  2010.  Towards predictive stochastic dynamical modeling of cancer genesis and progression. Interdiscip Sci. 2:140-4.
Deutsch EW, Shteynberg D, Lam H, Sun Z, Eng JK, Carapito C, von Haller PD, Tasman N, Mendoza L, Farrah T et al..  2010.  Trans-Proteomic Pipeline supports and improves analysis of electron transfer dissociation data sets. Proteomics. 10:1190-5.
Schmid AK, Pan M, Sharma K, Baliga NS.  2010.  Two transcription factors are necessary for iron homeostasis in a salt-dwelling archaeon. Nucleic Acids Res.
Gehlenborg N, O'Donoghue SI, Baliga NS, Goesmann A, Hibbs MA, Kitano H, Kohlbacher O, Neuweger H, Schneider R, Tenenbaum D et al..  2010.  Visualization of omics data for systems biology. Nat Methods. 7:S56-68.
Mo F, Mo Q, Chen Y, Goodlett DR, Hood L, Omenn GS, Li S, Lin B.  2010.  WaveletQuant, an improved quantification software based on wavelet signal threshold de-noising for labeled quantitative proteomic analysis. BMC Bioinformatics. 11:219.
Omenn GS, Aebersold R, Paik YK.  2009.  7(th) HUPO World Congress of Proteomics: launching the second phase of the HUPOPlasma Proteome Project (PPP-2) 16-20 August 2008, Amsterdam, The Netherlands. Proteomics. 9:4-6.
Milne C.B, Kim P.J, Eddy JA, Price ND.  2009.  Accomplishments in genome-scale in silico modeling for industrial and medical biotechnology. Biotechnology journal. 4:1653-70.
Boyle J, Rovira H, Cavnor C, Burdick D, Killcoyne S, Shmulevich I.  2009.  Adaptable data management for systems biology investigations. BMC Bioinformatics. 10:79.
Schiess R, Mueller LN, Schmidt A, Mueller M, Wollscheid B, Aebersold R.  2009.  Analysis of cell surface proteome changes via label-free, quantitative mass spectrometry. Mol Cell Proteomics. 8:624-38.
Akiyoshi B, Nelson CR, Ranish J, Biggins S.  2009.  Analysis of Ipl1-mediated phosphorylation of the Ndc80 kinetochore protein in Saccharomyces cerevisiae. Genetics. 183:1591-5.
Peterson A, Hohmann L, Huang L, Kim B, Eng JK, Martin DB.  2009.  Analysis of RP-HPLC loading conditions for maximizing peptide identifications in shotgun proteomics. J Proteome Res. 8:4161-8.
Gstaiger M, Aebersold R.  2009.  Applying mass spectrometry-based proteomics to genetics, genomics and network biology. Nat Rev Genet. 10:617-27.
Jeong SK, Kwon MS, Lee EY, Lee HJ, Cho SY, Kim H, Yoo JS, Omenn GS, Aebersold R, Hanash S et al..  2009.  BiomarkerDigger: a versatile disease proteome database and analysis platform for the identification of plasma cancer biomarkers. Proteomics. 9:3729-40.
Selinummi J, Ruusuvuori P, Podolsky I, Ozinsky A, Gold E, Yli-Harja O, Aderem A, Shmulevich I.  2009.  Bright field microscopy as an alternative to whole cell fluorescence in automated analysis of macrophage images. PLoS OnePLoS ONE. 4:e7497.
Kao SC, Wu H, Xie J, Chang CP, Ranish J, Graef IA, Crabtree GR.  2009.  Calcineurin/NFAT signaling is required for neuregulin-regulated Schwann cell differentiation. Science. 323:651-4.
Huber A, Bodenmiller B, Uotila A, Stahl M, Wanka S, Gerrits B, Aebersold R, Loewith R.  2009.  Characterization of the rapamycin-sensitive phosphoproteome reveals that Sch9 is a central coordinator of protein synthesis. Genes Dev. 23:1929-43.
Wang K, Zhang S, Marzolf B, Troisch P, Brightman A, Hu Z, Hood LE, Galas DJ.  2009.  Circulating microRNAs, potential biomarkers for drug-induced liver injury. Proc Natl Acad Sci U S A. 106:4402-7.
Tan CS, Bodenmiller B, Pasculescu A, Jovanovic M, Hengartner MO, Jorgensen C, Bader GD, Aebersold R, Pawson T, Linding R.  2009.  Comparative analysis reveals conserved protein phosphorylation networks implicated in multiple diseases. Sci Signal. 2:ra39.
Schrimpf SP, Weiss M, Reiter L, Ahrens CH, Jovanovic M, Malmstrom J, Brunner E, Mohanty S, Lercher MJ, Hunziker PE et al..  2009.  Comparative functional analysis of the Caenorhabditis elegans and Drosophila melanogaster proteomes. PLoS Biol. 7:e48.
Theis M, Slabicki M, Junqueira M, Paszkowski-Rogacz M, Sontheimer J, Kittler R, Heninger AK, Glatter T, Kruusmaa K, Poser I et al..  2009.  Comparative profiling identifies C13orf3 as a component of the Ska complex required for mammalian cell division. EMBO J. 28:1453-65.
Ulintz PJ, Yocum AK, Bodenmiller B, Aebersold R, Andrews PC, Nesvizhskii AI.  2009.  Comparison of MS(2)-only, MSA, and MS(2)/MS(3) methodologies for phosphopeptide identification. J Proteome Res. 8:887-99.
Sherwood CA, Eastham A, Lee LW, Risler J, Vitek O, Martin DB.  2009.  Correlation between y-type ions observed in ion trap and triple quadrupole mass spectrometers. J Proteome Res. 8:4243-51.
Chung Y, Chang SH, Martinez GJ, Yang XO, Nurieva R, Kang HS, Ma L, Watowich SS, Jetten AM, Tian Q et al..  2009.  Critical regulation of early Th17 cell differentiation by interleukin-1 signaling. Immunity. 30:576-87.
Liu X, Alexiou M, Martin-Orozco N, Chung Y, Nurieva RI, Ma L, Tian Q, Kollias G, Lu S, Graf D et al..  2009.  Cutting edge: A critical role of B and T lymphocyte attenuator in peripheral T cell tolerance induction. J Immunol. 182:4516-20.
Killcoyne S, Carter GW, Smith J, Boyle J.  2009.  Cytoscape: a community-based framework for network modeling. Methods Mol Biol. 563:219-39.
Nykter M, Lahdesmaki H, Rust A, Thorsson V, Shmulevich I.  2009.  A data integration framework for prediction of transcription factor targets. Ann N Y Acad Sci. 1158:205-14.
Lin B, White JT, Wu J, Lele S, Old LJ, Hood L, Odunsi K.  2009.  Deep depletion of abundant serum proteins reveals low-abundant proteins as potential biomarkers for human ovarian cancer. Proteomics Clin Appl. 3:853-861.
Portis JL, Askovich P, Austin J, Gutierrez-Cotto Y, McAtee FJ.  2009.  The degree of folding instability of the envelope protein of a neurovirulent murine retrovirus correlates with the severity of the neurological disease. J Virol. 83:6079-86.
Stanford JL, Fitzgerald LM, McDonnell SK, Carlson EE, McIntosh LM, Deutsch K, Hood L, Ostrander EA, Schaid DJ.  2009.  Dense genome-wide SNP linkage scan in 301 hereditary prostate cancer families identifies multiple regions with suggestive evidence for linkage. Hum Mol Genet. 18:1839-48.
Kutlu B, Burdick D, Baxter D, Rasschaert J, Flamez D, Eizirik DL, Welsh N, Goodman N, Hood L.  2009.  Detailed transcriptome atlas of the pancreatic beta cell. BMC Med Genomics. 2:3.
Shmulevich I, Aitchison JD.  2009.  Deterministic and stochastic models of genetic regulatory networks. Methods Enzymol. 467:335-56.
Chan TM, Longabaugh W, Bolouri H, Chen HL, Tseng WF, Chao CH, Jang TH, Lin YI, Hung SC, Wang HD et al..  2009.  Developmental gene regulatory networks in the zebrafish embryo. Biochim Biophys Acta. 1789:279-98.
Schmidt A, Claassen M, Aebersold R.  2009.  Directed mass spectrometry: towards hypothesis-driven proteomics. Curr Opin Chem Biol. 13:510-7.
Whitehead K, Pan M, Masumura K, Bonneau R, Baliga NS.  2009.  Diurnally entrained anticipatory behavior in archaea. PLoS ONEPLoS ONE. 4:e5485.
Foltz G, Yoon JG, Lee H, Ryken TC, Sibenaller Z, Ehrich M, Hood L, Madan A.  2009.  DNA methyltransferase-mediated transcriptional silencing in malignant glioma: a combined whole-genome microarray and promoter array analysis. Oncogene. 28:2667-77.
Loevenich SN, Brunner E, King NL, Deutsch EW, Stein SE, FlyBase C, Aebersold R, Hafen E.  2009.  The Drosophila melanogaster PeptideAtlas facilitates the use of peptide data for improved fly proteomics and genome annotation. BMC Bioinformatics. 10:59.
Chaturvedi CP, Hosey AM, Palii C, Perez-Iratxeta C, Nakatani Y, Ranish J, Dilworth FJ, Brand M.  2009.  Dual role for the methyltransferase G9a in the maintenance of beta-globin gene transcription in adult erythroid cells. Proc Natl Acad Sci U S A. 106:18303-8.
Taylor RJ, Falconnet D, Niemisto A, Ramsey SA, Prinz S, Shmulevich I, Galitski T, Hansen CL.  2009.  Dynamic analysis of MAPK signaling using a high-throughput microfluidic single-cell imaging platform. Proc Natl Acad Sci U S A. 106:3758-63.
Majeti R, Becker MW, Tian Q, Lee TL, Yan X, Liu R, Chiang JH, Hood L, Clarke MF, Weissman IL.  2009.  Dysregulated gene expression networks in human acute myelogenous leukemia stem cells. Proc Natl Acad Sci U S A. 106:3396-401.
Domon B, Bodenmiller B, Carapito C, Hao Z, Huehmer A, Aebersold R.  2009.  Electron transfer dissociation in conjunction with collision activation to investigate the Drosophila melanogaster phosphoproteome. J Proteome Res. 8:2633-9.
Hertz AL, Bender AT, Smith KC, Gilchrist M, Amieux PS, Aderem A, Beavo JA.  2009.  Elevated cyclic AMP and PDE4 inhibition induce chemokine expression in human monocyte-derived macrophages. Proc Natl Acad Sci U S A. 106:21978-83.
Yu B, Yang X, Xu Y, Yao G, Shu H, Lin B, Hood L, Wang H, Yang S, Gu J et al..  2009.  Elevated expression of DKK1 is associated with cytoplasmic/nuclear beta-catenin accumulation and poor prognosis in hepatocellular carcinomas. J Hepatol. 50:948-57.
Fedorov VB, Goropashnaya AV, Toien O, Stewart NC, Gracey AY, Chang C, Qin S, Pertea G, Quackenbush J, Showe LC et al..  2009.  Elevated expression of protein biosynthesis genes in liver and muscle of hibernating black bears (Ursus americanus). Physiol Genomics. 37:108-18.
Ho L, Ronan JL, Wu J, Staahl BT, Chen L, Kuo A, Lessard J, Nesvizhskii AI, Ranish J, Crabtree GR.  2009.  An embryonic stem cell chromatin remodeling complex, esBAF, is essential for embryonic stem cell self-renewal and pluripotency. Proc Natl Acad Sci U S A. 106:5181-6.
J C, G G.  2009.  Enhancing gene detection with computer generated intergenic regions. IEEE International Workshop on Genomic Signal Processing and Statistics, 2009. GENSIPS 2009. . :1-4.
Yan W, Aebersold R, Raines EW.  2009.  Evolution of organelle-associated protein profiling. J Proteomics. 72:4-11.
Knijnenburg TA, Wessels LF, Reinders MJ, Shmulevich I.  2009.  Fewer permutations, more accurate P-values. Bioinformatics. 25:i161-8.
Picotti P, Bodenmiller B, Mueller LN, Domon B, Aebersold R.  2009.  Full dynamic range proteome analysis of S. cerevisiae by targeted proteomics. Cell. 138:795-806.
Litvak V, Ramsey SA, Rust AG, Zak DE, Kennedy KA, Lampano AE, Nykter M, Shmulevich I, Aderem A.  2009.  Function of C/EBPdelta in a regulatory circuit that discriminates between transient and persistent TLR4-induced signals. Nat Immunol. 10:437-43.
Pascal LE, Goo YA, Vencio RZ, Page LS, Chambers AA, Liebeskind ES, Takayama TK, True LD, Liu AY.  2009.  Gene expression down-regulation in CD90+ prostate tumor-associated stromal cells involves potential organ-specific genes. BMC Cancer. 9:317.
Pascal LE, Vencio RZ, Page LS, Liebeskind ES, Shadle CP, Troisch P, Marzolf B, True LD, Hood LE, Liu AY.  2009.  Gene expression relationship between prostate cancer cells of Gleason 3, 4 and normal epithelial cells as revealed by cell type-specific transcriptomes. BMC Cancer. 9:452.
Ghosh D, Yan X, Tian Q.  2009.  Gene regulatory networks in embryonic stem cells and brain development. Birth Defects Res C Embryo Today. 87:182-91.
Hawn TR, Scholes D, Wang H, Li SS, Stapleton AE, Janer M, Aderem A, Stamm WE, Zhao LP, Hooton TM.  2009.  Genetic variation of the human urinary tract innate immune response and asymptomatic bacteriuria in women. PLoS OnePLoS ONE. 4:e8300.
Glusman G, Smit A.  2009.  Genome organization. Encyclopedia of Complexity and Systems Science. 4:4160-4178.
Eisenacher M, Martens L, Hardt T, Kohl M, Barsnes H, Helsens K, Hakkinen J, Levander F, Aebersold R, Vandekerckhove J et al..  2009.  Getting a grip on proteomics data - Proteomics Data Collection (ProDaC). Proteomics. 9:3928-33.
Mirzaei H, Brusniak MY, Mueller LN, Letarte S, Watts J, Aebersold R.  2009.  Halogenated peptides as internal standards (H-PINS): introduction of an MS-based internal standard set for liquid chromatography-mass spectrometry. Mol Cell Proteomics. 8:1934-46.
Anderson NL, Anderson NG, Pearson TW, Borchers CH, Paulovich AG, Patterson SD, Gillette M, Aebersold R, Carr SA.  2009.  A human proteome detection and quantitation project. Mol Cell Proteomics. 8:883-6.
Bell AW, Deutsch EW, Au CE, Kearney RE, Beavis R, Sechi S, Nilsson T, Bergeron JJ.  2009.  A HUPO test sample study reveals common problems in mass spectrometry-based proteomics. Nat Methods. 6:423-30.
Goetze S, Qeli E, Mosimann C, Staes A, Gerrits B, Roschitzki B, Mohanty S, Niederer EM, Laczko E, Timmerman E et al..  2009.  Identification and functional characterization of N-terminally acetylated proteins in Drosophila melanogaster. PLoS Biol. 7:e1000236.
Lin B, Wang J, Hong X, Yan X, Hwang D, Cho JH, Yi D, Utleg AG, Fang X, Schones DE et al..  2009.  Integrated expression profiling and ChIP-seq analyses of the growth inhibition response program of the androgen receptor. PLoS OnePLoS ONE. 4:e6589.
Glatter T, Wepf A, Aebersold R, Gstaiger M.  2009.  An integrated workflow for charting the human interaction proteome: insights into the PP2A system. Mol Syst Biol. 5:237.