Publications

Found 1195 results
2004
Mayer ML, Pot I, Chang M, Xu H, Aneliunas V, Kwok T, Newitt R, Aebersold R, Boone C, Brown GW et al..  2004.  Identification of protein complexes required for efficient sister chromatid cohesion. Mol Biol Cell. 15:1736-45.
Ranish J, Hahn S, Lu Y, Yi EC, Li XJ, Eng J, Aebersold R.  2004.  Identification of TFB5, a new component of general transcription and DNA repair factor IIH. Nat Genet. 36:707-13.
Hood L, Perlmutter RM.  2004.  The impact of systems approaches on biological problems in drug discovery. Nat Biotechnol. 22:1215-7.
Raghunathan A., Price ND, Galperin MY, Makarova KS, Purvine S, Picone AF, Cherny T, Xie T, Reilly TJ, Munson, Jr. R. et al..  2004.  In Silico Metabolic Model and Protein Expression of Haemophilus influenzae Strain Rd KW20 in Rich Medium. Omics : a journal of integrative biology. 8:25-41.
Tian Q, Stepaniants SB, Mao M, Weng L, Feetham MC, Doyle MJ, Yi EC, Dai H, Thorsson V, Eng J et al..  2004.  Integrated genomic and proteomic analyses of gene expression in Mammalian cells. Mol Cell Proteomics. 3:960-9.
Lefkir Y, Malbouyres M, Gotthardt D, Ozinsky A, Cornillon S, Bruckert F, Aderem A, Soldati T, Cosson P, Letourneur F.  2004.  Involvement of the AP-1 adaptor complex in early steps of phagocytosis and macropinocytosis. Mol Biol Cell. 15:861-9.
Liu AY, Brubaker KD, Goo YA, Quinn JE, Kral S, Sorensen CM, Vessella RL, Belldegrun AS, Hood LE.  2004.  Lineage relationship between LNCaP and LNCaP-derived prostate cancer cell lines. Prostate. 60:98-108.
Wollscheid B, von Haller PD, Yi E, Donohoe S, Vaughn K, Keller A, Nesvizhskii AI, Eng J, Li XJ, Goodlett DR et al..  2004.  Lipid raft proteins and their identification in T lymphocytes. Subcell Biochem. 37:121-52.
Flo TH, Smith KD, Sato S, Rodriguez DJ, Holmes MA, Strong RK, Akira S, Aderem A.  2004.  Lipocalin 2 mediates an innate immune response to bacterial infection by sequestrating iron. Nature. 432:917-21.
Goo YA, Roach J, Glusman G, Baliga NS, Deutsch K, Pan M, Kennedy S, DasSarma S, Ng WV, Hood L.  2004.  Low-pass sequencing for microbial comparative genomics. BMC Genomics. 5:3.
Shumaker-Parry JS, Zareie MH, Aebersold R, Campbell CT.  2004.  Microspotting streptavidin and double-stranded DNA arrays on gold for high-throughput studies of protein-DNA interactions by surface plasmon resonance microscopy. Anal Chem. 76:918-29.
Galitski T.  2004.  Molecular networks in model systems. Annu Rev Genomics Hum Genet. 5:177-87.
Trushina E, Dyer RB, Badger, J. D. 2nd, Ure D, Eide L, Tran DD, Vrieze BT, Legendre-Guillemin V, McPherson PS, Mandavilli BS et al..  2004.  Mutant huntingtin impairs axonal trafficking in mammalian neurons in vivo and in vitro. Mol Cell Biol. 24:8195-209.
Chen X, Chi Y, Bloecher A, Aebersold R, Clurman BE, Roberts JM.  2004.  N-acetylation and ubiquitin-independent proteasomal degradation of p21(Cip1). Mol Cell. 16:839-47.
Carr S, Aebersold R, Baldwin M, Burlingame A, Clauser K, Nesvizhskii A, Working Group on Publication Guidelines for P, Protein Identification D.  2004.  The need for guidelines in publication of peptide and protein identification data: Working Group on Publication Guidelines for Peptide and Protein Identification Data. Mol Cell Proteomics. 3:531-3.
Giglia-Mari G, Coin F, Ranish J, Hoogstraten D, Theil A, Wijgers N, Jaspers NG, Raams A, Argentini M, van der Spek PJ et al..  2004.  A new, tenth subunit of TFIIH is responsible for the DNA repair syndrome trichothiodystrophy group A. Nat Genet. 36:714-9.
Lee H, Yi EC, Wen B, Reily TP, Pohl L, Nelson S, Aebersold R, Goodlett DR.  2004.  Optimization of reversed-phase microcapillary liquid chromatography for quantitative proteomics. J Chromatogr B Analyt Technol Biomed Life Sci. 803:101-10.
Graveley BR, Kaur A, Gunning D, Zipursky SL, Rowen L, Clemens JC.  2004.  The organization and evolution of the dipteran and hymenopteran Down syndrome cell adhesion molecule (Dscam) genes. RNA. 10:1499-506.
Shumaker-Parry JS, Aebersold R, Campbell CT.  2004.  Parallel, quantitative measurement of protein binding to a 120-element double-stranded DNA array in real time using surface plasmon resonance microscopy. Anal Chem. 76:2071-82.
Vizeacoumar FJ, Torres-Guzman JC, Bouard D, Aitchison JD, Rachubinski RA.  2004.  Pex30p, Pex31p, and Pex32p form a family of peroxisomal integral membrane proteins regulating peroxisome size and number in Saccharomyces cerevisiae. Mol Biol Cell. 15:665-77.
Lausted C, Dahl T, Warren C, King K, Smith K, Johnson M, Saleem R, Aitchison JD, Hood L, Lasky SR.  2004.  POSaM: a fast, flexible, open-source, inkjet oligonucleotide synthesizer and microarrayer. Genome Biol. 5:R58.
Warfield L, Ranish J, Hahn S.  2004.  Positive and negative functions of the SAGA complex mediated through interaction of Spt8 with TBP and the N-terminal domain of TFIIA. Genes Dev. 18:1022-34.
Reiss DJ, Schwikowski B.  2004.  Predicting protein-peptide interactions via a network-based motif sampler. Bioinformatics. 20 Suppl 1:i274-82.
Tian Q, Feetham MC, Tao WA, He XC, Li L, Aebersold R, Hood L.  2004.  Proteomic analysis identifies that 14-3-3zeta interacts with beta-catenin and facilitates its activation by Akt. Proc Natl Acad Sci U S A. 101:15370-5.
Hardwidge PR, Rodriguez-Escudero I, Goode D, Donohoe S, Eng J, Goodlett DR, Aebersold R, Finlay BB.  2004.  Proteomic analysis of the intestinal epithelial cell response to enteropathogenic Escherichia coli. J Biol Chem. 279:20127-36.
Wollscheid B, Watts J, Aebersold R.  2004.  Proteomics/genomics and signaling in lymphocytes. Curr Opin Immunol. 16:337-44.
Sozio MS, Mathis MA, Young JA, Walchli S, Pitcher LA, Wrage PC, Bartok B, Campbell A, Watts J, Aebersold R et al..  2004.  PTPH1 is a predominant protein-tyrosine phosphatase capable of interacting with and dephosphorylating the T cell receptor zeta subunit. J Biol Chem. 279:7760-9.
Marelli M, Smith JJ, Jung S, Yi E, Nesvizhskii AI, Christmas RH, Saleem RA, Tam YY, Fagarasanu A, Goodlett DR et al..  2004.  Quantitative mass spectrometry reveals a role for the GTPase Rho1p in actin organization on the peroxisome membrane. J Cell Biol. 167:1099-112.
Zhou H, Boyle R, Aebersold R.  2004.  Quantitative protein analysis by solid phase isotope tagging and mass spectrometry. Methods Mol Biol. 261:511-8.
Kao WC, Chen YR, Yi EC, Lee H, Tian Q, Wu KM, Tsai SF, Yu SS, Chen YJ, Aebersold R et al..  2004.  Quantitative proteomic analysis of metabolic regulation by copper ions in Methylococcus capsulatus (Bath). J Biol Chem. 279:51554-60.
Martin DB, Gifford DR, Wright ME, Keller A, Yi E, Goodlett DR, Aebersold R, Nelson PS.  2004.  Quantitative proteomic analysis of proteins released by neoplastic prostate epithelium. Cancer Res. 64:347-55.
Himeda CL, Ranish J, Angello JC, Maire P, Aebersold R, Hauschka SD.  2004.  Quantitative proteomic identification of six4 as the trex-binding factor in the muscle creatine kinase enhancer. Mol Cell Biol. 24:2132-43.
Ranish J, Hahn S, Lu H, Yi EC, Li XJ, Eng J, Aebersold R.  2004.  Quantitative proteomics analysis of an RNA polymerase II transcription complex identifies TFB5, a new component of general transcription factor IIH. Mol Cell Biol. 24:1709-20.
Rani PG, Ranish J, Hahn S.  2004.  RNA polymerase II (Pol II)-TFIIF and Pol II-mediator complexes: the major stable Pol II complexes and their activity in transcription initiation and reinitiation. Mol Cell Biol. 24:1709-20.
Zhu XM, Yin L, Hood L, Ao P.  2004.  Robustness, stability and efficiency of phage lambda genetic switch: dynamical structure analysis. J Bioinform Comput Biol. 2:785-817.
Chin WC, Orellana MV, Quesada I, Verdugo P.  2004.  Secretion in unicellular marine phytoplankton: demonstration of regulated exocytosis in Phaeocystis globosa. Plant Cell Physiol. 45:535-42.
Matsumoto M, Einhaus D, Gold ES, Aderem A.  2004.  Simvastatin augments lipopolysaccharide-induced proinflammatory responses in macrophages by differential regulation of the c-Fos and c-Jun transcription factors. J Immunol. 172:7377-84.
Flory MR, Carson AR, Muller EG, Aebersold R.  2004.  An SMC-domain protein in fission yeast links telomeres to the meiotic centrosome. Mol Cell. 16:619-30.
Facciotti MT, Cheung VS, Lunde CS, Rouhani S, Baliga NS, Glaeser RM.  2004.  Specificity of anion binding in the substrate pocket of bacteriorhodopsin. Biochemistry. 43:4934-43.
Yan W, Lee H, Yi EC, Reiss D, Shannon P, Kwieciszewski BK, Coito C, Li XJ, Keller A, Eng J et al..  2004.  System-based proteomic analysis of the interferon response in human liver cells. Genome Biol. 5:R54.
Aderem A, Smith KD.  2004.  A systems approach to dissecting immunity and inflammation. Semin Immunol. 16:55-67.
Hood L, Heath JR, Phelps ME, Lin B.  2004.  Systems biology and new technologies enable predictive and preventative medicine. Science. 306:640-3.
Facciotti MT, Bonneau R, Hood L, Baliga NS.  2004.  Systems Biology Experimental Design - Considerations for Building Predictive Gene Regulatory Network Models for Prokaryotic Systems. Current Genomics. 5:527-544(18).
Weston AD, Hood L.  2004.  Systems biology, proteomics, and the future of health care: toward predictive, preventative, and personalized medicine. J Proteome Res. 3:179-96.
Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J.  2004.  Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1. Genome Res. 14:1025-35.
Eng J, Martin D, Aebersold R.  2004.  Tandem mass spectrometry database searching. Encyclopedia of Genetics, Genomics, Proteomics and Bioinformatics.
Li XJ, Pedrioli PG, Eng J, Martin D, Yi EC, Lee H, Aebersold R.  2004.  A tool to visualize and evaluate data obtained by liquid chromatography-electrospray ionization-mass spectrometry. Anal Chem. 76:3856-60.
Camacho-Carvajal MM, Wollscheid B, Aebersold R, Steimle V, Schamel WW.  2004.  Two-dimensional Blue native/SDS gel electrophoresis of multi-protein complexes from whole cellular lysates: a proteomics approach. Mol Cell Proteomics. 3:176-82.
Price ND, Schellenberger J., Palsson BO.  2004.  Uniform sampling of steady-state flux spaces: means to design experiments and to interpret enzymopathies. Biophysical journal. 87:2172-86.
Orellana MV, Petersen TW, van den Engh G.  2004.  UV-excited blue autoflourescence of Pseudo-nitzschia multiseries.. J. Phycology. 40:705-10.
Marzolf B, Johnson MH.  2004.  Validation of microarray image analysis accuracy. Biotechniques. 36:304-8.
2003
Griffin TJ, Lock CM, Li XJ, Patel A, Chervetsova I, Lee H, Wright ME, Ranish J, Chen SS, Aebersold R.  2003.  Abundance ratio-dependent proteomic analysis by mass spectrometry. Anal Chem. 75:867-74.
Xie T, Hood L.  2003.  ACGT-a comparative genomics tool. Bioinformatics. 19:1039-40.
Tao WA, Aebersold R.  2003.  Advances in quantitative proteomics via stable isotope tagging and mass spectrometry. Curr Opin Biotechnol. 14:110-8.
Price ND, Reed J.L, Papin JA, Famili I., Palsson BO.  2003.  Analysis of metabolic capabilities using singular value decomposition of extreme pathway matrices. Biophysical journal. 84:794-804.
Xie T, Rowen L, Aguado B, Ahearn ME, Madan A, Qin S, Campbell RD, Hood L.  2003.  Analysis of the gene-dense major histocompatibility complex class III region and its comparison to mouse. Genome Res. 13:2621-36.
Wright ME, Tsai MJ, Aebersold R.  2003.  Androgen receptor represses the neuroendocrine transdifferentiation process in prostate cancer cells. Mol Endocrinol. 17:1726-37.
von Haller PD, Yi E, Donohoe S, Vaughn K, Keller A, Nesvizhskii AI, Eng J, Li XJ, Goodlett DR, Aebersold R et al..  2003.  The application of new software tools to quantitative protein profiling via isotope-coded affinity tag (ICAT) and tandem mass spectrometry: II. Evaluation of tandem mass spectrometry methodologies for large-scale protein analysis, and the application of s. Mol Cell Proteomics. 2:428-42.
von Haller PD, Yi E, Donohoe S, Vaughn K, Keller A, Nesvizhskii AI, Eng J, Li XJ, Goodlett DR, Aebersold R et al..  2003.  The application of new software tools to quantitative protein profiling via isotope-coded affinity tag (ICAT) and tandem mass spectrometry: I. Statistically annotated datasets for peptide sequences and proteins identified via the application of ICAT and t. Mol Cell Proteomics. 2:426-7.
Li XJ, Zhang H, Ranish J, Aebersold R.  2003.  Automated statistical analysis of protein abundance ratios from data generated by stable-isotope dilution and tandem mass spectrometry. Anal Chem. 75:6648-57.
Makhnevych T, Lusk CP, Anderson AM, Aitchison JD, Wozniak RW.  2003.  Cell cycle regulated transport controlled by alterations in the nuclear pore complex. Cell. 115:813-23.
Hawn TR, Verbon A, Lettinga KD, Zhao LP, Li SS, Laws RJ, Skerrett SJ, Beutler B, Schroeder L, Nachman A et al..  2003.  A common dominant TLR5 stop codon polymorphism abolishes flagellin signaling and is associated with susceptibility to legionnaires' disease. J Exp Med. 198:1563-72.
Aebersold R.  2003.  Constellations in a cellular universe. Nature. 422:115-6.
Bochud PY, Hawn TR, Aderem A.  2003.  Cutting edge: a Toll-like receptor 2 polymorphism that is associated with lepromatous leprosy is unable to mediate mycobacterial signaling. J Immunol. 170:3451-4.
Shannon P, Markiel A, Ozier O, Baliga NS, Wang JT, Ramage D, Amin N, Schwikowski B, Ideker T.  2003.  Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res. 13:2498-504.
Palsson BO, Price ND, Papin JA.  2003.  Development of network-based pathway definitions: the need to analyze real metabolic networks. Trends in biotechnology. 21:195-8.
Marr KA, Balajee SA, Hawn TR, Ozinsky A, Pham U, Akira S, Aderem A, Liles WC.  2003.  Differential role of MyD88 in macrophage-mediated responses to opportunistic fungal pathogens. Infect Immun. 71:5280-6.
Hood L, Galas DJ.  2003.  The digital code of DNA. Nature. 421:444-8.
McBride CM, Pollak KI, Garst J, Keefe F, Lyna P, Fish L, Hood L.  2003.  Distress and motivation for smoking cessation among lung cancer patients' relatives who smoke. J Cancer Educ. 18:150-6.
Heilig R, Eckenberg R, Petit JL, Fonknechten N, Da Silva C, Cattolico L, Levy M, Barbe V, de Berardinis V, Ureta-Vidal A et al..  2003.  The DNA sequence and analysis of human chromosome 14. Nature. 421:601-7.
Hubley RM, Zitzler E, Roach J.  2003.  Evolutionary algorithms for the selection of single nucleotide polymorphisms. BMC Bioinformatics. 4:30.
Auffray C, Chen Z, Hood L, Soares B, Sugano S.  2003.  Foreword: from the TRANSCRIPTOME conferences to the SYSTEMOSCOPE international consortium. C R Biol. 326:867-75.
Auffray C, Imbeaud S, Roux-Rouquie M, Hood L.  2003.  From functional genomics to systems biology: concepts and practices. C R Biol. 326:879-92.
Price ND, Papin JA, Schilling C.H, Palsson BO.  2003.  Genome-scale microbial in silico models: the constraints-based approach. Trends in biotechnology. 21:162-9.
Janer M, Friedrichsen DM, Stanford JL, Badzioch MD, Kolb S, Deutsch K, Peters MA, Goode EL, Welti R, DeFrance HB et al..  2003.  Genomic scan of 254 hereditary prostate cancer families. Prostate. 57:309-19.
Haendeler J, Yin G, Hojo Y, Saito Y, Melaragno M, Yan C, Sharma VK, Heller M, Aebersold R, Berk BC.  2003.  GIT1 mediates Src-dependent activation of phospholipase Cgamma by angiotensin II and epidermal growth factor. J Biol Chem. 278:49936-44.
Lin F, Cordes K, Li L, Hood L, Couser WG, Shankland SJ, Igarashi P.  2003.  Hematopoietic stem cells contribute to the regeneration of renal tubules after renal ischemia-reperfusion injury in mice. J Am Soc Nephrol. 14:1188-99.
Rolandsson O, Hagg E, Janer M, Rutledge E, Gaur LK, Nilsson M, Hallmans G, Lernmark A.  2003.  High GAD65 autoantibody levels in nondiabetic adults are associated with HLA but not with CTLA-4 or INS VNTR. J Intern Med. 253:447-53.
Zhang H, Li XJ, Martin DB, Aebersold R.  2003.  Identification and quantification of N-linked glycoproteins using hydrazide chemistry, stable isotope labeling and mass spectrometry. Nat Biotechnol. 21:660-6.
Wright ME, Eng J, Sherman J, Hockenbery DM, Nelson PS, Galitski T, Aebersold R.  2003.  Identification of androgen-coregulated protein networks from the microsomes of human prostate cancer cells. Genome Biol. 5:R4.
Hu S, Le Z, Newitt R, Aebersold R, Kraly JR, Jones M, Dovichi NJ.  2003.  Identification of proteins in single-cell capillary electrophoresis fingerprints based on comigration with standard proteins. Anal Chem. 75:3502-5.
Kolker E, Purvine S, Galperin MY, Stolyar S, Goodlett DR, Nesvizhskii AI, Keller A, Xie T, Eng JK, Yi E et al..  2003.  Initial proteome analysis of model microorganism Haemophilus influenzae strain Rd KW20. J Bacteriol. 185:4593-602.
Sydorskyy Y, Dilworth DJ, Yi EC, Goodlett DR, Wozniak RW, Aitchison JD.  2003.  Intersection of the Kap123p-mediated nuclear import and ribosome export pathways. Mol Cell Biol. 23:2042-54.
Aitchison JD, Galitski T.  2003.  Inventories to insights. J Cell Biol. 161:465-9.
Lin B, White JT, Utleg AG, Wang S, Ferguson C, True LD, Vessella R, Hood L, Nelson PS.  2003.  Isolation and characterization of human and mouse WDR19,a novel WD-repeat protein exhibiting androgen-regulated expression in prostate epithelium. Genomics. 82:331-42.
Hood L.  2003.  Leroy Hood expounds the principles, practice and future of systems biology. Drug Discov Today. 8:436-8.
Britten RJ, Rowen L, Williams J, Cameron RA.  2003.  Majority of divergence between closely related DNA samples is due to indels. Proc Natl Acad Sci U S A. 100:4661-5.
Aebersold R.  2003.  A mass spectrometric journey into protein and proteome research. J Am Soc Mass Spectrom. 14:685-95.
Aebersold R, Mann M.  2003.  Mass spectrometry-based proteomics. Nature. 422:198-207.
Papin JA, Price ND, Wiback S.J, Fell D.A, Palsson BO.  2003.  Metabolic pathways in the post-genome era. Trends in biochemical sciences. 28:250-8.
Yi EC, Lee H, Aebersold R, Goodlett DR.  2003.  A microcapillary trap cartridge-microcapillary high-performance liquid chromatography electrospray ionization emitter device capable of peptide tandem mass spectrometry at the attomole level on an ion trap mass spectrometer with automated routine operatio. Rapid Commun Mass Spectrom. 17:2093-8.
Rives AW, Galitski T.  2003.  Modular organization of cellular networks. Proc Natl Acad Sci U S A. 100:1128-33.
Heath JR, Phelps ME, Hood L.  2003.  NanoSystems biology. Mol Imaging Biol. 5:312-25.
Price ND, Reed J.L, Papin JA, Wiback S.J, Palsson BO.  2003.  Network-based analysis of metabolic regulation in the human red blood cell. Journal of theoretical biology. 225:185-94.
Conlon EM, Goode EL, Gibbs M, Stanford JL, Badzioch M, Janer M, Kolb S, Hood L, Ostrander EA, Jarvik GP et al..  2003.  Oligogenic segregation analysis of hereditary prostate cancer pedigrees: evidence for multiple loci affecting age at onset. Int J Cancer. 105:630-5.
Tam YY, Torres-Guzman JC, Vizeacoumar FJ, Smith JJ, Marelli M, Aitchison JD, Rachubinski RA.  2003.  Pex11-related proteins in peroxisome dynamics: a role for the novel peroxin Pex27p in controlling peroxisome size and number in Saccharomyces cerevisiae. Mol Biol Cell. 14:4089-102.
Aderem A.  2003.  Phagocytosis and the inflammatory response. J Infect Dis. 187 Suppl 2:S340-5.
Chikamori K, Grabowski DR, Kinter M, Willard BB, Yadav S, Aebersold R, Bukowski RM, Hickson ID, Andersen AH, Ganapathi R et al..  2003.  Phosphorylation of serine 1106 in the catalytic domain of topoisomerase II alpha regulates enzymatic activity and drug sensitivity. J Biol Chem. 278:12696-702.
Seward RJ, von Haller PD, Aebersold R, Huber BT.  2003.  Phosphorylation of the pro-apoptotic protein Bim in lymphocytes is associated with protection from apoptosis. Mol Immunol. 39:983-93.
Anderson JP, Learn GH, Rodrigo AG, He X, Wang Y, Weinstock H, Kalish ML, Robbins KE, Hood L, Mullins JI.  2003.  Predicting demographic group structures based on DNA sequence data. Mol Biol Evol. 20:1168-80.

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