Publications

Found 1195 results
2006
Deutsch EW, Ball CA, Bova GS, Brazma A, Bumgarner RE, Campbell D, Causton HC, Christiansen J, Davidson D, Eichner LJ et al..  2006.  Development of the Minimum Information Specification for In Situ Hybridization and Immunohistochemistry Experiments (MISFISHIE). OMICS. 10:205-8.
Carter GW, Rupp S, Fink GR, Galitski T.  2006.  Disentangling information flow in the Ras-cAMP signaling network. Genome Res. 16:520-6.
Ramsey SA, Smith JJ, Orrell D, Marelli M, Petersen TW, de Atauri P, Bolouri H, Aitchison JD.  2006.  Dual feedback loops in the GAL regulon suppress cellular heterogeneity in yeast. Nat Genet. 38:1082-7.
Nesvizhskii AI, Roos FF, Grossmann J, Vogelzang M, Eddes JS, Gruissem W, Baginsky S, Aebersold R.  2006.  Dynamic spectrum quality assessment and iterative computational analysis of shotgun proteomic data: toward more efficient identification of post-translational modifications, sequence polymorphisms, and novel peptides. Mol Cell Proteomics. 5:652-70.
Vizeacoumar FJ, Vreden WN, Fagarasanu M, Eitzen GA, Aitchison JD, Rachubinski RA.  2006.  The dynamin-like protein Vps1p of the yeast Saccharomyces cerevisiae associates with peroxisomes in a Pex19p-dependent manner. J Biol Chem. 281:12817-23.
Rundle NT, Nelson J, Flory MR, Joseph J, Th'ng J, Aebersold R, Dasso M, Andersen RJ, Roberge M.  2006.  An ent-kaurene that inhibits mitotic chromosome movement and binds the kinetochore protein ran-binding protein 2. ACS Chem Biol. 1:443-50.
Smith JJ, Sydorskyy Y, Marelli M, Hwang D, Bolouri H, Rachubinski RA, Aitchison JD.  2006.  Expression and functional profiling reveal distinct gene classes involved in fatty acid metabolism. Mol Syst Biol. 2:20060009.
Chung Y, Yang X, Chang SH, Ma L, Tian Q, Dong C.  2006.  Expression and regulation of IL-22 in the IL-17-producing CD4+ T lymphocytes. Cell Res. 16:902-7.
Niemisto A, Selinummi J, Saleem R, Shmulevich I, Aitchison JD, Yli-Harja O.  2006.  Extraction of the number of peroxisomes in yeast cells by automated image analysis. Conf Proc IEEE Eng Med Biol Soc. 1:2353-6.
de Orrell, D. R M S P A A BSMJ.  2006.  Feedback control of stochastic noise in the yeast galactose utilization pathway. Physica D. 217:64-76.
Shannon P, Reiss DJ, Bonneau R, Baliga NS.  2006.  The Gaggle: an open-source software system for integrating bioinformatics software and data sources. BMC Bioinformatics. 7:176.
Jimenez-Corona ME, Garcia-Garcia L, Deriemer K, Ferreyra-Reyes L, Bobadilla-del-Valle M, Cano-Arellano B, Canizales-Quintero S, Martinez-Gamboa A, Small PM, Sifuentes-Osornio J et al..  2006.  Gender differentials of pulmonary tuberculosis transmission and reactivation in an endemic area. Thorax. 61:348-53.
Roach J, Deutsch K, Li S, Siegel AF, Bekris LM, Einhaus DC, Sheridan CM, Glusman G, Hood L, Lernmark A et al..  2006.  Genetic mapping at 3-kilobase resolution reveals inositol 1,4,5-triphosphate receptor 3 as a risk factor for type 1 diabetes in Sweden. Am J Hum Genet. 79:614-27.
Foltz G, Ryu GY, Yoon JG, Nelson T, Fahey J, Frakes A, Lee H, Field L, Zander K, Sibenaller Z et al..  2006.  Genome-wide analysis of epigenetic silencing identifies BEX1 and BEX2 as candidate tumor suppressor genes in malignant glioma. Cancer Res. 66:6665-74.
Schmidt A, Aebersold R.  2006.  High-accuracy proteome maps of human body fluids. Genome Biol. 7:242.
Shiio Y, Rose DW, Aur R, Donohoe S, Aebersold R, Eisenman RN.  2006.  Identification and characterization of SAP25, a novel component of the mSin3 corepressor complex. Mol Cell Biol. 26:1386-97.
Lee SI, Pe'er D, Dudley AM, Church GM, Koller D.  2006.  Identifying regulatory mechanisms using individual variation reveals key role for chromatin modification. Proc Natl Acad Sci U S A. 103:14062-7.
Gagneux S, Burgos MV, Deriemer K, Encisco A, Munoz S, Hopewell PC, Small PM, Pym AS.  2006.  Impact of bacterial genetics on the transmission of isoniazid-resistant Mycobacterium tuberculosis. PLoS Pathog. 2:e61.
Bonneau R, Reiss DJ, Shannon P, Facciotti M, Hood L, Baliga NS, Thorsson V.  2006.  The Inferelator: an algorithm for learning parsimonious regulatory networks from systems-biology data sets de novo. Genome Biol. 7:R36.
Reiss DJ, Baliga NS, Bonneau R.  2006.  Integrated biclustering of heterogeneous genome-wide datasets for the inference of global regulatory networks. BMC Bioinformatics. 7:280.
Whitehead K, Kish A, Pan M, Kaur A, Reiss DJ, King N, Hohmann L, DiRuggiero J, Baliga NS.  2006.  An integrated systems approach for understanding cellular responses to gamma radiation. Mol Syst Biol. 2:47.
Zhang H, Aebersold R.  2006.  Isolation of glycoproteins and identification of their N-linked glycosylation sites. Methods Mol Biol. 328:177-85.
Lu W, Zhou D, Glusman G, Utleg AG, White JT, Nelson PS, Vasicek TJ, Hood L, Lin B.  2006.  KLK31P is a novel androgen regulated and transcribed pseudogene of kallikreins that is expressed at lower levels in prostate cancer cells than in normal prostate cells. Prostate. 66:936-44.
Guo Z, Hood L, Malkki M, Petersdorf EW.  2006.  Long-range multilocus haplotype phasing of the MHC. Proc Natl Acad Sci U S A. 103:6964-9.
Allen T.E, Price ND, Joyce A.R, Palsson BO.  2006.  Long-range periodic patterns in microbial genomes indicate significant multi-scale chromosomal organization. PLoS computational biology. 2:e2.
Subramanian N, Qadri A.  2006.  Lysophospholipid sensing triggers secretion of flagellin from pathogenic salmonella.. Nat Immunol. 7(6):583-9.
Domon B, Aebersold R.  2006.  Mass spectrometry and protein analysis. Science. 312:212-7.
Gianchandani E.P, Papin JA, Price ND, Joyce A.R, Palsson BO.  2006.  Matrix formalism to describe functional states of transcriptional regulatory systems. PLoS computational biology. 2:e101.
Kowalewska J, Smith KD, Hudkins KL, Chang A, Fogo AB, Houghton D, Leslie D, Aitchison JD, Nicosia RF, Alpers CE.  2006.  Membranous glomerulopathy with spherules: an uncommon variant with obscure pathogenesis. Am J Kidney Dis. 47:983-92.
Becker S.A, Price ND, Palsson BO.  2006.  Metabolite coupling in genome-scale metabolic networks. BMC bioinformatics. 7:111.
Aga RS, Fair E, Abernethy NF, Deriemer K, Paz EA, Kawamura LM, Small PM, Kato-Maeda M.  2006.  Microevolution of the direct repeat locus of Mycobacterium tuberculosis in a strain prevalent in San Francisco. J Clin Microbiol. 44:1558-60.
True L, Coleman I, Hawley S, Huang CY, Gifford D, Coleman R, Beer TM, Gelmann E, Datta M, Mostaghel E et al..  2006.  A molecular correlate to the Gleason grading system for prostate adenocarcinoma. Proc Natl Acad Sci U S A. 103:10991-6.
Pym A, Small PM.  2006.  Mycobacterial Evolution: Insights from genomics and bacterial ecology.
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.

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