Publications

Found 1248 results
2000
Chaudhary PM, Eby MT, Jasmin A, Kumar A, Liu L, Hood L.  2000.  Activation of the NF-kappaB pathway by caspase 8 and its homologs. Oncogene. 19:4451-60.
Gold ES, Morrissette NS, Underhill DM, Guo J, Bassetti M, Aderem A.  2000.  Amphiphysin IIm, a novel amphiphysin II isoform, is required for macrophage phagocytosis. Immunity. 12:285-92.
Allen EE, Hood L.  2000.  Biotechnology, inquiry, and public education. Trends Biotechnol. 18:329-30.
Mikheev AM, Mikheev SA, Zhang Y, Aebersold R, Zarbl H.  2000.  CArG binding factor A (CBF-A) is involved in transcriptional regulation of the rat Ha-ras promoter. Nucleic Acids Res. 28:3762-70.
Deng Y, Madan A, Banta AB, Friedman C, Trask BJ, Hood L, Li L.  2000.  Characterization, chromosomal localization, and the complete 30-kb DNA sequence of the human Jagged2 (JAG2) gene. Genomics. 63:133-8.
Rampazzo A, Pivotto F, Occhi G, Tiso N, Bortoluzzi S, Rowen L, Hood L, Nava A, Danieli GA.  2000.  Characterization of C14orf4, a novel intronless human gene containing a polyglutamine repeat, mapped to the ARVD1 critical region. Biochem Biophys Res Commun. 278:766-74.
Nelson PS, Han D, Rochon Y, Corthals GL, Lin B, Monson A, Nguyen V, Franza BR, Plymate SR, Aebersold R et al..  2000.  Comprehensive analyses of prostate gene expression: convergence of expressed sequence tag databases, transcript profiling and proteomics. Electrophoresis. 21:1823-31.
Heller M, Goodlett DR, Watts J, Aebersold R.  2000.  A comprehensive characterization of the T-cell antigen receptor complex composition by microcapillary liquid chromatography-tandem mass spectrometry. Electrophoresis. 21:2180-95.
Brewster JL, Martin SL, Toms J, Goss D, Wang K, Zachrone K, Davis A, Carlson G, Hood L, Coffin JD.  2000.  Deletion of Dad1 in mice induces an apoptosis-associated embryonic death. Genesis. 26:271-8.
Ideker TE, Thorsson V, Karp RM.  2000.  Discovery of regulatory interactions through perturbation: inference and experimental design. Pac Symp Biocomput. :305-16.
Aebersold R, Hood LE, Watts J.  2000.  Equipping scientists for the new biology. Nat Biotechnol. 18:359.
Gygi SP, Corthals GL, Zhang Y, Rochon Y, Aebersold R.  2000.  Evaluation of two-dimensional gel electrophoresis-based proteome analysis technology. Proc Natl Acad Sci U S A. 97:9390-5.
Baliga NS, Goo YA, Ng WV, Hood L, Daniels CJ, DasSarma S.  2000.  Is gene expression in Halobacterium NRC-1 regulated by multiple TBP and TFB transcription factors? Mol Microbiol. 36:1184-5.
Livak F, Burtrum DB, Rowen L, Schatz DG, Petrie HT.  2000.  Genetic modulation of T cell receptor gene segment usage during somatic recombination. J Exp Med. 192:1191-6.
Ng WV, Kennedy SP, Mahairas GG, Berquist B, Pan M, Shukla HD, Lasky SR, Baliga NS, Thorsson V, Sbrogna J et al..  2000.  Genome sequence of Halobacterium species NRC-1. Proc Natl Acad Sci U S A. 97:12176-81.
Gibbs M, Stanford JL, Jarvik GP, Janer M, Badzioch M, Peters MA, Goode EL, Kolb S, Chakrabarti L, Shook M et al..  2000.  A genomic scan of families with prostate cancer identifies multiple regions of interest. Am J Hum Genet. 67:100-9.
Aderem A, Hume DA.  2000.  How do you see CG? Cell. 103:993-6.
Hood L.  2000.  The human genome project–launch pad for human genetic engineering. Engineering the Human Germline (1st Edition). :17-24.
Rowen L, Wong GK, Lane RP, Hood L.  2000.  Intellectual property. Publication rights in the era of open data release policies. Science. 289:1881.
Goode EL, Stanford JL, Chakrabarti L, Gibbs M, Kolb S, McIndoe RA, Buckley VA, Schuster EF, Neal CL, Miller EL et al..  2000.  Linkage analysis of 150 high-risk prostate cancer families at 1q24-25. Genet Epidemiol. 18:251-75.
Gygi SP, Aebersold R.  2000.  Mass spectrometry and proteomics. Curr Opin Chem Biol. 4:489-94.
Gygi SP, Rist B, Aebersold R.  2000.  Measuring gene expression by quantitative proteome analysis. Curr Opin Biotechnol. 11:396-401.
Siegel AF, van den Engh G, Hood L, Trask B, Roach J.  2000.  Modeling the feasibility of whole genome shotgun sequencing using a pairwise end strategy. Genomics. 68:237-46.
Yu G, Nishimura M, Arawaka S, Levitan D, Zhang L, Tandon A, Song YQ, Rogaeva E, Chen F, Kawarai T et al..  2000.  Nicastrin modulates presenilin-mediated notch/glp-1 signal transduction and betaAPP processing. Nature. 407:48-54.
Roach J, Thorsson V, Siegel AF.  2000.  Parking strategies for genome sequencing. Genome Res. 10:1020-30.
Lin B, White JT, Ferguson C, Bumgarner R, Friedman C, Trask B, Ellis W, Lange P, Hood L, Nelson PS.  2000.  PART-1: a novel human prostate-specific, androgen-regulated gene that maps to chromosome 5q12. Cancer Res. 60:858-63.
Timperman AT, Aebersold R.  2000.  Peptide electroextraction for direct coupling of in-gel digests with capillary LC-MS/MS for protein identification and sequencing. Anal Chem. 72:4115-21.
Nelson PS, Clegg N, Eroglu B, Hawkins V, Bumgarner R, Smith T, Hood L.  2000.  The prostate expression database (PEDB): status and enhancements in 2000. Nucleic Acids Res. 28:212-3.
Goodlett DR, Bruce JE, Anderson GA, Rist B, Pasa-Tolic L, Fiehn O, Smith RD, Aebersold R.  2000.  Protein identification with a single accurate mass of a cysteine-containing peptide and constrained database searching. Anal Chem. 72:1112-8.
Ebrini I, Agnello D, Miller I, Villa P, Fratelli M, Ghezzi P, Gemeiner M, Chan J, Aebersold R, Gianazza E.  2000.  Proteins of rat serum V: adjuvant arthritis and its modulation by nonsteroidal anti-inflammatory drugs. Electrophoresis. 21:2170-9.
Liao DF, Jin ZG, Baas AS, Daum G, Gygi SP, Aebersold R, Berk BC.  2000.  Purification and identification of secreted oxidative stress-induced factors from vascular smooth muscle cells. J Biol Chem. 275:189-96.
Goodlett DR, Aebersold R, Watts J.  2000.  Quantitative in vitro kinase reaction as a guide for phosphoprotein analysis by mass spectrometry. Rapid Commun Mass Spectrom. 14:344-8.
Morrison DL, Yee A, Paddon HB, Vilimek D, Aebersold R, Pelech SL.  2000.  Regulation of the meiosis-inhibited protein kinase, a p38(MAPK) isoform, during meiosis and following fertilization of seastar oocytes. J Biol Chem. 275:34236-44.
Ozinsky A, Underhill DM, Fontenot JD, Hajjar AM, Smith KD, Wilson CB, Schroeder L, Aderem A.  2000.  The repertoire for pattern recognition of pathogens by the innate immune system is defined by cooperation between toll-like receptors. Proc Natl Acad Sci U S A. 97:13766-71.
Aitchison JD, Rout MP.  2000.  The road to ribosomes. Filling potholes in the export pathway. J Cell Biol. 151:F23-6.
Ostrowski J, Schullery DS, Denisenko ON, Higaki Y, Watts J, Aebersold R, Stempka L, Gschwendt M, Bomsztyk K.  2000.  Role of tyrosine phosphorylation in the regulation of the interaction of heterogenous nuclear ribonucleoprotein K protein with its protein and RNA partners. J Biol Chem. 275:3619-28.
Cameron RA, Mahairas G, Rast JP, Martinez P, Biondi TR, Swartzell S, Wallace JC, Poustka AJ, Livingston BT, Wray GA et al..  2000.  A sea urchin genome project: sequence scan, virtual map, and additional resources. Proc Natl Acad Sci U S A. 97:9514-8.
Gan L, Lee I, Smith R, Argonza-Barrett R, Lei H, McCuaig J, Moss P, Paeper B, Wang K.  2000.  Sequencing and expression analysis of the serine protease gene cluster located in chromosome 19q13 region. Gene. 257:119-30.
Katze MG, Kwieciszewski B, Goodlett DR, Blakely CM, Neddermann P, Tan SL, Aebersold R.  2000.  Ser(2194) is a highly conserved major phosphorylation site of the hepatitis C virus nonstructural protein NS5A. Virology. 278:501-13.
Raught B, Gingras AC, Gygi SP, Imataka H, Morino S, Gradi A, Aebersold R, Sonenberg N.  2000.  Serum-stimulated, rapamycin-sensitive phosphorylation sites in the eukaryotic translation initiation factor 4GI. EMBO J. 19:434-44.
Haynes PA, Aebersold R.  2000.  Simultaneous detection and identification of O-GlcNAc-modified glycoproteins using liquid chromatography-tandem mass spectrometry. Anal Chem. 72:5402-10.
Gregory KE, Oxford JT, Chen Y, Gambee JE, Gygi SP, Aebersold R, Neame PJ, Mechling DE, Bachinger HP, Morris NP.  2000.  Structural organization of distinct domains within the non-collagenous N-terminal region of collagen type XI. J Biol Chem. 275:11498-506.
Ideker T, Thorsson V, Siegel AF, Hood LE.  2000.  Testing for differentially-expressed genes by maximum-likelihood analysis of microarray data. J Comput Biol. 7:805-17.
Anderson JP, Rodrigo AG, Learn GH, Madan A, Delahunty C, Coon M, Girard M, Osmanov S, Hood L, Mullins JI.  2000.  Testing the hypothesis of a recombinant origin of human immunodeficiency virus type 1 subtype E. J Virol. 74:10752-65.
Aderem A, Ulevitch RJ.  2000.  Toll-like receptors in the induction of the innate immune response. Nature. 406:782-7.
Gygi SP, Aebersold R.  2000.  Using mass spectrometry for quantitative proteomics. Trends in Biotechnology. 18 (Supp. 1):31-36.
2001
Griffin TJ, Aebersold R.  2001.  Advances in proteome analysis by mass spectrometry. J Biol Chem. 276:45497-500.
Panigrahi AK, Gygi SP, Ernst NL, Igo, R. P. J., Palazzo SS, Schnaufer A, Weston DS, Carmean N, Salavati R, Aebersold R et al..  2001.  Association of two novel proteins, TbMP52 and TbMP48, with the Trypanosoma brucei RNA editing complex. Mol Cell Biol. 21:380-9.
Peck RF, Echavarri-Erasun C, Johnson EA, Ng WV, Kennedy SP, Hood L, DasSarma S, Krebs MP.  2001.  brp and blh are required for synthesis of the retinal cofactor of bacteriorhodopsin in Halobacterium salinarum. J Biol Chem. 276:5739-44.
Heller M, Watts J, Aebersold R.  2001.  CD28 stimulation regulates its association with N-ethylmaleimide-sensitive fusion protein and other proteins involved in vesicle sorting. Proteomics. 1:70-8.
Wang K, Gan L, Kunisada T, Lee I, Yamagishi H, Hood L.  2001.  Characterization of the Japanese pufferfish (Takifugu rubripes) T-cell receptor alpha locus reveals a unique genomic organization. Immunogenetics. 53:31-42.
Goode EL, Stanford JL, Peters MA, Janer M, Gibbs M, Kolb S, Badzioch MD, Hood L, Ostrander EA, Jarvik GP.  2001.  Clinical characteristics of prostate cancer in an analysis of linkage to four putative susceptibility loci. Clin Cancer Res. 7:2739-49.
Redl HR, Aderem A, Beutler BA, Calandra T, Mira JP, Ulevitch R.  2001.  Clinical expert round table discussion (session 1) at the Margaux Conference on Critical Illness: innate immunity: host recognition of and sensitivity to bacterial components. Crit Care Med. 29:S19-20.
Glusman G, Rowen L, Lee I, Boysen C, Roach J, Smit A, Wang K, Koop BF, Hood L.  2001.  Comparative genomics of the human and mouse T cell receptor loci. Immunity. 15:337-49.
Hood L.  2001.  Computing life: the challenge ahead. IEEE Eng Med Biol Mag. 20:20.
Pariyarath R, Wang H, Aitchison JD, Ginsberg HN, Welch WJ, Johnson AE, Fisher EA.  2001.  Co-translational interactions of apoprotein B with the ribosome and translocon during lipoprotein assembly or targeting to the proteasome. J Biol Chem. 276:541-50.
Hajjar AM, O'Mahony DS, Ozinsky A, Underhill DM, Aderem A, Klebanoff SJ, Wilson CB.  2001.  Cutting edge: functional interactions between toll-like receptor (TLR) 2 and TLR1 or TLR6 in response to phenol-soluble modulin. J Immunol. 166:15-9.
Hood L.  2001.  Deciphering Heredity. The Alfred Deakin Lectures: Ideas for the Future of a Civil Society. :164-176.
Goodlett DR, Keller A, Watts J, Newitt R, Yi EC, Purvine S, Eng JK, von Haller P, Aebersold R, Kolker E.  2001.  Differential stable isotope labeling of peptides for quantitation and de novo sequence derivation. Rapid Commun Mass Spectrom. 15:1214-21.
Chen F, Rowen L, Hood L, Rothenberg EV.  2001.  Differential transcriptional regulation of individual TCR V beta segments before gene rearrangement. J Immunol. 166:1771-80.
Moore RC, Mastrangelo P, Bouzamondo E, Heinrich C, Legname G, Prusiner SB, Hood L, Westaway D, Dearmond SJ, Tremblay P.  2001.  Doppel-induced cerebellar degeneration in transgenic mice. Proc Natl Acad Sci U S A. 98:15288-93.
Marelli M, Dilworth DJ, Wozniak RW, Aitchison JD.  2001.  The dynamics of karyopherin-mediated nuclear transport. Biochem Cell Biol. 79:603-12.
Han MH, Han DK, Aebersold R, Glomset JA.  2001.  Effects of protein kinase CK2, extracellular signal-regulated kinase 2, and protein phosphatase 2A on a phosphatidic acid-preferring phospholipase A1. J Biol Chem. 276:27698-708.
Silkoff PE, Martin D, Pak J, Westcott JY, Martin RJ.  2001.  Exhaled nitric oxide correlated with induced sputum findings in COPD. Chest. 119:1049-55.
Panigrahi AK, Schnaufer A, Carmean N, Igo, R. P. J., Gygi SP, Ernst NL, Palazzo SS, Weston DS, Aebersold R, Salavati R et al..  2001.  Four related proteins of the Trypanosoma brucei RNA editing complex. Mol Cell Biol. 21:6833-40.
Martin DB, Nelson PS.  2001.  From genomics to proteomics: techniques and applications in cancer research. Trends Cell Biol. 11:S60-5.
Terskikh AV, Easterday MC, Li L, Hood L, Kornblum HI, Geschwind DH, Weissman IL.  2001.  From hematopoiesis to neuropoiesis: evidence of overlapping genetic programs. Proc Natl Acad Sci U S A. 98:7934-9.
Muthalif MM, Hefner Y, Canaan S, Harper J, Zhou H, Parmentier JH, Aebersold R, Gelb MH, Malik KU.  2001.  Functional interaction of calcium-/calmodulin-dependent protein kinase II and cytosolic phospholipase A(2). J Biol Chem. 276:39653-60.
Hamerman JA, Aderem A.  2001.  Functional transitions in macrophages during in vivo infection with Mycobacterium bovis bacillus Calmette-Guerin. J Immunol. 167:2227-33.
Peters MA, Jarvik GP, Janer M, Chakrabarti L, Kolb S, Goode EL, Gibbs M, DuBois CC, Schuster EF, Hood L et al..  2001.  Genetic linkage analysis of prostate cancer families to Xq27-28. Hum Hered. 51:107-13.
Lane RP, Cutforth T, Young J, Athanasiou M, Friedman C, Rowen L, Evans G, Axel R, Hood L, Trask BJ.  2001.  Genomic analysis of orthologous mouse and human olfactory receptor loci. Proc Natl Acad Sci U S A. 98:7390-5.
Baliga NS, Kennedy SP, Ng WV, Hood L, DasSarma S.  2001.  Genomic and genetic dissection of an archaeal regulon. Proc Natl Acad Sci U S A. 98:2521-5..
DasSarma S, Kennedy SP, Berquist B, Victor Ng W, Baliga NS, Spudich JL, Krebs MP, Eisen JA, Johnson CH, Hood L.  2001.  Genomic perspective on the photobiology of Halobacterium species NRC-1, a phototrophic, phototactic, and UV-tolerant haloarchaeon. Photosynth Res. 70:3-17.
Peters MA, Janer M, Kolb S, Jarvik GP, Ostrander EA, Stanford JL.  2001.  Germline mutations in the p73 gene do not predispose to familial prostate-brain cancer. Prostate. 48:292-6.
Gingras AC, Raught B, Gygi SP, Niedzwiecka A, Miron M, Burley SK, Polakiewicz RD, Wyslouch-Cieszynska A, Aebersold R, Sonenberg N.  2001.  Hierarchical phosphorylation of the translation inhibitor 4E-BP1. Genes Dev. 15:2852-64.
Mayer ML, Gygi SP, Aebersold R, Hieter P.  2001.  Identification of RFC(Ctf18p, Ctf8p, Dcc1p): an alternative RFC complex required for sister chromatid cohesion in S. cerevisiae. Mol Cell. 7:959-70.
Hass GM, Meyer JL, Newitt RA, Labuda T, Brown L, Aebersold R, Vessella RL.  2001.  Identification of the target of monoclonal antibody A6H as dipeptidyl peptidase IV/CD26 by LC MS\MS. Hybridoma. 20:231-6.
Aderem A, Hood L.  2001.  Immunology in the post-genomic era. Nat Immunol. 2:373-5.
Lander ES, Linton LM, Birren B, Nusbaum C, Zody MC, Baldwin J, Devon K, Dewar K, Doyle M, FitzHugh W et al..  2001.  Initial sequencing and analysis of the human genome. Nature. 409:860-921.
Hayashi F, Smith KD, Ozinsky A, Hawn TR, Yi EC, Goodlett DR, Eng JK, Akira S, Underhill DM, Aderem A.  2001.  The innate immune response to bacterial flagellin is mediated by Toll-like receptor 5. Nature. 410:1099-103.
Ideker T, Thorsson V, Ranish J, Christmas R, Buhler J, Eng JK, Bumgarner R, Goodlett DR, Aebersold R, Hood L.  2001.  Integrated genomic and proteomic analyses of a systematically perturbed metabolic network. Science. 292:929-34.
Cheung VG, Nowak N, Jang W, Kirsch IR, Zhao S, Chen XN, Furey TS, Kim UJ, Kuo WL, Olivier M et al..  2001.  Integration of cytogenetic landmarks into the draft sequence of the human genome. Nature. 409:953-8.
Werts C, Tapping RI, Mathison JC, Chuang TH, Kravchenko V, Saint Girons I, Haake DA, Godowski PJ, Hayashi F, Ozinsky A et al..  2001.  Leptospiral lipopolysaccharide activates cells through a TLR2-dependent mechanism. Nat Immunol. 2:346-52.
Marelli M, Lusk CP, Chan H, Aitchison JD, Wozniak RW.  2001.  A link between the synthesis of nucleoporins and the biogenesis of the nuclear envelope. J Cell Biol. 153:709-24.
Hume DA, Underhill DM, Sweet MJ, Ozinsky A, Liew FY, Aderem A.  2001.  Macrophages exposed continuously to lipopolysaccharide and other agonists that act via toll-like receptors exhibit a sustained and additive activation state. BMC Immunol. 2:11.
von Haller PD, Donohoe S, Goodlett DR, Aebersold R, Watts J.  2001.  Mass spectrometric characterization of proteins extracted from Jurkat T cell detergent-resistant membrane domains. Proteomics. 1:1010-21.
Aebersold R, Goodlett DR.  2001.  Mass spectrometry in proteomics. Chem Rev. 101:269-95.
Hood L.  2001.  Melanoma techniques and protocols: molecular diagnosis, treatment, and monitoring. Methods in Molecular Medicine. 61:ForwardbyHood,L.
Rabilloud T, Heller M, Rigobello MP, Bindoli A, Aebersold R, Lunardi J.  2001.  The mitochondrial antioxidant defence system and its response to oxidative stress. Proteomics. 1:1105-10.
Park IK, Klug CA, Li K, Jerabek L, Li L, Nanamori M, Neubig RR, Hood L, Weissman IL, Clarke MF.  2001.  Molecular cloning and characterization of a novel regulator of G-protein signaling from mouse hematopoietic stem cells. J Biol Chem. 276:915-23.
Ideker T, Galitski T, Hood L.  2001.  A new approach to decoding life: systems biology. Annu Rev Genomics Hum Genet. 2:343-72.
Rout MP, Aitchison JD.  2001.  The nuclear pore complex as a transport machine. J Biol Chem. 276:16593-6.
Dilworth DJ, Suprapto A, Padovan JC, Chait BT, Wozniak RW, Rout MP, Aitchison JD.  2001.  Nup2p dynamically associates with the distal regions of the yeast nuclear pore complex. J Cell Biol. 153:1465-78.
Smolka MB, Zhou H, Purkayastha S, Aebersold R.  2001.  Optimization of the isotope-coded affinity tag-labeling procedure for quantitative proteome analysis. Anal Biochem. 297:25-31.
Bruls T, Gyapay G, Petit JL, Artiguenave F, Vico V, Qin S, Tin-Wollam AM, Da Silva C, Muselet D, Mavel D et al..  2001.  A physical map of human chromosome 14. Nature. 409:947-8.
McPherson JD, Marra M, Hillier L, Waterston RH, Chinwalla A, Wallis J, Sekhon M, Wylie K, Mardis ER, Wilson RK et al..  2001.  A physical map of the human genome. Nature. 409:934-41.
Baliga NS.  2001.  Promoter analysis by saturation mutagenesis. Biol Proced Online. 3:64-69.
Lin B, White JT, Ferguson C, Wang S, Vessella R, Bumgarner R, True LD, Hood L, Nelson PS.  2001.  Prostate short-chain dehydrogenase reductase 1 (PSDR1): a new member of the short-chain steroid dehydrogenase/reductase family highly expressed in normal and neoplastic prostate epithelium. Cancer Res. 61:1611-8.
Han DK, Eng J, Zhou H, Aebersold R.  2001.  Quantitative profiling of differentiation-induced microsomal proteins using isotope-coded affinity tags and mass spectrometry. Nat Biotechnol. 19:946-51.

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