Publications

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.

Goo YA, Yi EC, Baliga NS, Tao WA, Pan M, Aebersold R, Goodlett DR, Hood L, Ng WV.  2003.  Proteomic analysis of an extreme halophilic archaeon, Halobacterium sp. NRC-1. Mol Cell Proteomics. 2:506-24.

Utleg AG, Yi EC, Xie T, Shannon P, White JT, Goodlett DR, Hood L, Lin B.  2003.  Proteomic analysis of human prostasomes. Prostate. 56:150-61.

Guina T, Wu M, Miller SI, Purvine SO, Yi EC, Eng J, Goodlett DR, Aebersold R, Ernst RK, Lee KA.  2003.  Proteomic analysis of Pseudomonas aeruginosa grown under magnesium limitation. J Am Soc Mass Spectrom. 14:742-51.

Flory MR, Aebersold R.  2003.  Proteomic approaches for the identification of cell cycle-related drug targets. Prog Cell Cycle Res. 5:167-71.

Patterson SD, Aebersold R.  2003.  Proteomics: the first decade and beyond. Nat Genet. 33 Suppl:311-23.

Picard C, Puel A, Bonnet M, Ku CL, Bustamante J, Yang K, Soudais C, Dupuis S, Feinberg J, Fieschi C et al..  2003.  Pyogenic bacterial infections in humans with IRAK-4 deficiency. Science. 299:2076-9.

Aebersold R.  2003.  Quantitative proteome analysis: methods and applications. J Infect Dis. 187 Suppl 2:S315-20.

Guina T, Purvine SO, Yi EC, Eng J, Goodlett DR, Aebersold R, Miller SI.  2003.  Quantitative proteomic analysis indicates increased synthesis of a quinolone by Pseudomonas aeruginosa isolates from cystic fibrosis airways. Proc Natl Acad Sci U S A. 100:2771-6.

Shiio Y, Eisenman RN, Yi EC, Donohoe S, Goodlett DR, Aebersold R.  2003.  Quantitative proteomic analysis of chromatin-associated factors. J Am Soc Mass Spectrom. 14:696-703.

Davidson EH, McClay DR, Hood L.  2003.  Regulatory gene networks and the properties of the developmental process. Proc Natl Acad Sci U S A. 100:1475-80.

Auffray C, Imbeaud S, Roux-Rouquie M, Hood L.  2003.  Self-organized living systems: conjunction of a stable organization with chaotic fluctuations in biological space-time. Philos Transact A Math Phys Eng Sci. 361:1125-39.

Nesvizhskii AI, Keller A, Kolker E, Aebersold R.  2003.  A statistical model for identifying proteins by tandem mass spectrometry. Anal Chem. 75:4646-58.

Ranish JA, Yi EC, Leslie DM, Purvine SO, Goodlett DR, Eng J, Aebersold R.  2003.  The study of macromolecular complexes by quantitative proteomics. Nat Genet. 33:349-55.

Ha SA, Torabinejad J, DeWald DB, Wenk MR, Lucast L, De Camilli P, Newitt RA, Aebersold R, Nothwehr SF.  2003.  The synaptojanin-like protein Inp53/Sjl3 functions with clathrin in a yeast TGN-to-endosome pathway distinct from the GGA protein-dependent pathway. Mol Biol Cell. 14:1319-33.

Taylor CF, Paton NW, Garwood KL, Kirby PD, Stead DA, Yin Z, Deutsch EW, Selway L, Walker J, Riba-Garcia I et al..  2003.  A systematic approach to modeling, capturing, and disseminating proteomics experimental data. Nat Biotechnol. 21:247-54.

Weston AD, Baliga NS, Bonneau R, Hood L.  2003.  Systems approaches applied to the study of Saccharomyces cerevisiae and Halobacterium sp. Cold Spring Harb Symp Quant Biol. 68:345-57.

Aitchison JD.  2003.  Systems biology and elephants. Nature Cell Biology. 5:285.

Hood L.  2003.  Systems biology: integrating technology, biology, and computation. Mech Ageing Dev. 124:9-16.

Smith KD, Andersen-Nissen E, Hayashi F, Strobe K, Bergman MA, Barrett SL, Cookson BT, Aderem A.  2003.  Toll-like receptor 5 recognizes a conserved site on flagellin required for protofilament formation and bacterial motility. Nat Immunol. 4:1247-53.

Means TK, Hayashi F, Smith KD, Aderem A, Luster AD.  2003.  The Toll-like receptor 5 stimulus bacterial flagellin induces maturation and chemokine production in human dendritic cells. J Immunol. 170:5165-75.

Orellana MV, Lessard EJ, Dycus E, Chin W-C, Foy MS, Verdugo P.  2003.  Tracing the source and fate of biopolymers in seawater: application of an immunological technique.. Marine Chemistry. 83:89-99.

Orellana MV, Verdugo P.  2003.  Ultraviolet radiation inhibits the exchange between dissolved and particulate organic matter.. Luminol. Oceanogr. 48:1618-23.

Steiner-Mosonyi M, Leslie DM, Dehghani H, Aitchison JD, Mangroo D.  2003.  Utp8p is an essential intranuclear component of the nuclear tRNA export machinery of Saccharomyces cerevisiae. J Biol Chem. 278:32236-45.

Rout MP, Aitchison JD, Magnasco MO, Chait BT.  2003.  Virtual gating and nuclear transport: the hole picture. Trends Cell Biol. 13:622-8.

Vizeacoumar FJ, Torres-Guzman JC, Tam YY, Aitchison JD, Rachubinski RA.  2003.  YHR150w and YDR479c encode peroxisomal integral membrane proteins involved in the regulation of peroxisome number, size, and distribution in Saccharomyces cerevisiae. J Cell Biol. 161:321-32.

Leong KG, Hu X, Li L, Noseda M, Larrivee B, Hull C, Hood L, Wong F, Karsan A.  2002.  Activated Notch4 inhibits angiogenesis: role of beta 1-integrin activation. Mol Cell Biol. 22:2830-41.

Flory MR, Griffin TJ, Martin D, Aebersold R.  2002.  Advances in quantitative proteomics using stable isotope tags. Trends Biotechnol. 20:S23-9.

Futter, E., Wade N, Varmus H, Green E, Venter C, Hood L, Bazell R, Haseltine W, Levine A, Kreek MJ et al..  2002.  After the Genome: Where Should We Go? The Genomic Revolution: Unveiling the Unity of Life. :64-73.

Gjertsen BT, Oyan AM, Marzolf B, Hovland R, Gausdal G, Doskeland SO, Dimitrov K, Golden A, Kalland KH, Hood L et al..  2002.  Analysis of acute myelogenous leukemia: preparation of samples for genomic and proteomic analyses. J Hematother Stem Cell Res. 11:469-81.

Rowen L, Young J, Birditt B, Kaur A, Madan A, Philipps DL, Qin S, Minx P, Wilson RK, Hood L et al..  2002.  Analysis of the human neurexin genes: alternative splicing and the generation of protein diversity. Genomics. 79:587-97.

Yi EC, Marelli M, Lee H, Purvine SO, Aebersold R, Aitchison JD, Goodlett DR.  2002.  Approaching complete peroxisome characterization by gas-phase fractionation. Electrophoresis. 23:3205-16.

Foltz G, Madan A, Hood L.  2002.  Cancer Proteomics: Methodologies for the Selection of Immunotherapy Targets. Principles and Practice of Biologic Therapy of Cancer Updates, Third Edition.

Griffin TJ, Gygi SP, Ideker T, Rist B, Eng J, Hood L, Aebersold R.  2002.  Complementary profiling of gene expression at the transcriptome and proteome levels in Saccharomyces cerevisiae. Mol Cell Proteomics. 1:323-33.

Baliga NS, Pan M, Goo YA, Yi EC, Goodlett DR, Dimitrov K, Shannon P, Aebersold R, Ng WV, Hood L.  2002.  Coordinate regulation of energy transduction modules in Halobacterium sp. analyzed by a global systems approach. Proc Natl Acad Sci U S A. 99:14913-8.

Yang T, Espenshade PJ, Wright ME, Yabe D, Gong Y, Aebersold R, Goldstein JL, Brown MS.  2002.  Crucial step in cholesterol homeostasis: sterols promote binding of SCAP to INSIG-1, a membrane protein that facilitates retention of SREBPs in ER. Cell. 110:489-500.

Spellman PT, Miller M, Stewart J, Troup C, Sarkans U, Chervitz S, Bernhart D, Sherlock G, Ball C, Lepage M et al..  2002.  Design and implementation of microarray gene expression markup language (MAGE-ML). Genome Biol. 3:RESEARCH0046.

Price ND, Papin JA, Palsson BO.  2002.  Determination of redundancy and systems properties of the metabolic network of Helicobacter pylori using genome-scale extreme pathway analysis. Genome research. 12:760-9.

Lee H, Griffin TJ, Gygi SP, Rist B, Aebersold R.  2002.  Development of a multiplexed microcapillary liquid chromatography system for high-throughput proteome analysis. Anal Chem. 74:4353-60.

Park IK, He Y, Lin F, Laerum OD, Tian Q, Bumgarner R, Klug CA, Li K, Kuhr C, Doyle MJ et al..  2002.  Differential gene expression profiling of adult murine hematopoietic stem cells. Blood. 99:488-98.

Marotti, L. A. J., Newitt R, Wang Y, Aebersold R, Dohlman HG.  2002.  Direct identification of a G protein ubiquitination site by mass spectrometry. Biochemistry. 41:5067-74.

Kabak S, Skaggs BJ, Gold MR, Affolter M, West KL, Foster MS, Siemasko K, Chan AC, Aebersold R, Clark MR.  2002.  The direct recruitment of BLNK to immunoglobulin alpha couples the B-cell antigen receptor to distal signaling pathways. Mol Cell Biol. 22:2524-35.

Yoo C, Thorsson V, Cooper GF.  2002.  Discovery of causal relationships in a gene-regulation pathway from a mixture of experimental and observational DNA microarray data. Pac Symp Biocomput. :498-509.

Keller A, Nesvizhskii AI, Kolker E, Aebersold R.  2002.  Empirical statistical model to estimate the accuracy of peptide identifications made by MS/MS and database search. Anal Chem. 74:5383-92.

Keller A, Purvine S, Nesvizhskii AI, Stolyar S, Goodlett DR, Kolker E.  2002.  Experimental protein mixture for validating tandem mass spectral analysis. OMICS. 6:207-12.

Papin JA, Price ND, Palsson BO.  2002.  Extreme pathway lengths and reaction participation in genome-scale metabolic networks. Genome research. 12:1889-900.

Price ND, Famili I., Beard D.A, Palsson BO.  2002.  Extreme pathways and Kirchhoff's second law. Biophysical journal. 83:2879-82.

Ravasi T, Wells C, Forest A, Underhill DM, Wainwright BJ, Aderem A, Grimmond S, Hume DA.  2002.  Generation of diversity in the innate immune system: macrophage heterogeneity arises from gene-autonomous transcriptional probability of individual inducible genes. J Immunol. 168:44-50.

Graham J, Hagopian WA, Kockum I, Li LS, Sanjeevi CB, Lowe RM, Schaefer JB, Zarghami M, Day HL, Landin-Olsson M et al..  2002.  Genetic effects on age-dependent onset and islet cell autoantibody markers in type 1 diabetes. Diabetes. 51:1346-55.

Papin JA, Price ND, Edwards J.S, B. Palsson B.  2002.  The genome-scale metabolic extreme pathway structure in Haemophilus influenzae shows significant network redundancy. Journal of theoretical biology. 215:67-82.

Lane RP, Roach JC, Lee I, Boysen C, Smit A, Trask BJ, Hood L.  2002.  Genomic analysis of the olfactory receptor region of the mouse and human T-cell receptor alpha/delta loci. Genome research. 12:81-7.

Gan TI, Rowen L, Nesbitt R, Roe BA, Wu H, Hu P, Yao Z, Kim UJ, O'Sickey T, Bina M.  2002.  Genomic organization of human TCF12 gene and spliced mRNA variants producing isoforms of transcription factor HTF4. Cytogenet Genome Res. 98:245-8.

Davidson EH, Rast JP, Oliveri P, Ransick A, Calestani C, Yuh CH, Minokawa T, Amore G, Hinman V, Arenas-Mena C et al..  2002.  A genomic regulatory network for development. Science. 295:1669-78.

Aderem A.  2002.  How to eat something bigger than your head. Cell. 110:5-8.

Liu AY, Nelson PS, van den Engh G, Hood L.  2002.  Human prostate epithelial cell-type cDNA libraries and prostate expression patterns. Prostate. 50:92-103.

Dramsi S, Scheid MP, Maiti A, Hojabrpour P, Chen X, Schubert K, Goodlett DR, Aebersold R, Duronio V.  2002.  Identification of a novel phosphorylation site, Ser-170, as a regulator of bad pro-apoptotic activity. J Biol Chem. 277:6399-405.

Mouse Genome Sequencing C, Waterston RH, Lindblad-Toh K, Birney E, Rogers J, Abril JF, Agarwal P, Agarwala R, Ainscough R, Alexandersson M et al..  2002.  Initial sequencing and comparative analysis of the mouse genome. Nature. 420:520-62.

Hood L.  2002.  The InTouch interview with biotech man Leroy Hood, MD, PhD. Interview by Peter Tarr. InTouch. 4:28-32.

Leslie DM, Grill B, Rout MP, Wozniak RW, Aitchison JD.  2002.  Kap121p-mediated nuclear import is required for mating and cellular differentiation in yeast. Mol Cell Biol. 22:2544-55.

Lusk CP, Makhnevych T, Marelli M, Aitchison JD, Wozniak RW.  2002.  Karyopherins in nuclear pore biogenesis: a role for Kap121p in the assembly of Nup53p into nuclear pore complexes. J Cell Biol. 159:267-78.

Hawn TR, Ozinsky A, Underhill DM, Buckner FS, Akira S, Aderem A.  2002.  Leishmania major activates IL-1 alpha expression in macrophages through a MyD88-dependent pathway. Microbes Infect. 4:763-71.

James EA, Gygi SP, Adams ML, Pierce RH, Fausto N, Aebersold R, Nelson SD, Bruschi SA.  2002.  Mitochondrial aconitase modification, functional inhibition, and evidence for a supramolecular complex of the TCA cycle by the renal toxicant S-(1,1,2,2-tetrafluoroethyl)-L-cysteine. Biochemistry. 41:6789-97.

Aebersold R, Watts J.  2002.  The need for national centers for proteomics. Nat Biotechnol. 20:651.

Guo Z, Gatterman MS, Hood L, Hansen JA, Petersdorf EW.  2002.  Oligonucleotide arrays for high-throughput SNPs detection in the MHC class I genes: HLA-B as a model system. Genome Res. 12:447-57.

Yuh CH, Brown CT, Livi CB, Rowen L, Clarke PJ, Davidson EH.  2002.  Patchy interspecific sequence similarities efficiently identify positive cis-regulatory elements in the sea urchin. Dev Biol. 246:148-61.

Hood L.  2002.  A personal view of molecular technology and how it has changed biology. J Proteome Res. 1:399-409.

Underhill DM, Ozinsky A.  2002.  Phagocytosis of microbes: complexity in action. Annu Rev Immunol. 20:825-52.

Zhang N, Aebersold R, Schwikowski B.  2002.  ProbID: a probabilistic algorithm to identify peptides through sequence database searching using tandem mass spectral data. Proteomics. 2:1406-12.

Nelson PS, Clegg N, Arnold H, Ferguson C, Bonham M, White J, Hood L, Lin B.  2002.  The program of androgen-responsive genes in neoplastic prostate epithelium. Proc Natl Acad Sci U S A. 99:11890-5.

Gygi SP, Rist B, Griffin TJ, Eng J, Aebersold R.  2002.  Proteome analysis of low-abundance proteins using multidimensional chromatography and isotope-coded affinity tags. J Proteome Res. 1:47-54.

Rabilloud T, Heller M, Gasnier F, Luche S, Rey C, Aebersold R, Benahmed M, Louisot P, Lunardi J.  2002.  Proteomics analysis of cellular response to oxidative stress. Evidence for in vivo overoxidation of peroxiredoxins at their active site. J Biol Chem. 277:19396-401.

Aebersold R, Cravatt BF.  2002.  Proteomics--advances, applications and the challenges that remain. Trends Biotechnol. 20:S1-2.

Davidson EH, Rast JP, Oliveri P, Ransick A, Calestani C, Yuh CH, Minokawa T, Amore G, Hinman V, Arenas-Mena C et al..  2002.  A provisional regulatory gene network for specification of endomesoderm in the sea urchin embryo. Dev Biol. 246:162-90.

Smolka M, Zhou H, Aebersold R.  2002.  Quantitative protein profiling using two-dimensional gel electrophoresis, isotope-coded affinity tag labeling, and mass spectrometry. Mol Cell Proteomics. 1:19-29.

Zhou H, Ranish JA, Watts J, Aebersold R.  2002.  Quantitative proteome analysis by solid-phase isotope tagging and mass spectrometry. Nat Biotechnol. 20:512-5.

Shiio Y, Donohoe S, Yi EC, Goodlett DR, Aebersold R, Eisenman RN.  2002.  Quantitative proteomic analysis of Myc oncoprotein function. EMBO J. 21:5088-96.

Kumanovics A, Madan A, Qin S, Rowen L, Hood L, Fischer Lindahl K.  2002.  QUOD ERAT FACIENDUM: sequence analysis of the H2-D and H2-Q regions of 129/SvJ mice. Immunogenetics. 54:479-89.

Lane RP, Cutforth T, Axel R, Hood L, Trask BJ.  2002.  Sequence analysis of mouse vomeronasal receptor gene clusters reveals common promoter motifs and a history of recent expansion. Proc Natl Acad Sci U S A. 99:291-6.

Hamerman JA, Hayashi F, Schroeder LA, Gygi SP, Haas AL, Hampson L, Coughlin P, Aebersold R, Aderem A.  2002.  Serpin 2a is induced in activated macrophages and conjugates to a ubiquitin homolog. J Immunol. 168:2415-23.

Aitchison JD, Rout MP.  2002.  A tense time for the nuclear envelope. Cell. 108:301-4.

Smith KD, Ozinsky A.  2002.  Toll-like receptor-5 and the innate immune response to bacterial flagellin. Curr Top Microbiol Immunol. 270:93-108.

Underhill DM, Ozinsky A.  2002.  Toll-like receptors: key mediators of microbe detection. Curr Opin Immunol. 14:103-10.

Smith JJ, Marelli M, Christmas RH, Vizeacoumar FJ, Dilworth DJ, Ideker T, Galitski T, Dimitrov K, Rachubinski RA, Aitchison JD.  2002.  Transcriptome profiling to identify genes involved in peroxisome assembly and function. J Cell Biol. 158:259-71.

Asbury CL, Diercks AH, van den Engh G.  2002.  Trapping of DNA by dielectrophoresis. Electrophoresis. 23:2658-66.

Aparicio S, Chapman J, Stupka E, Putnam N, Chia JM, Dehal P, Christoffels A, Rash S, Hoon S, Smit A et al..  2002.  Whole-genome shotgun assembly and analysis of the genome of Fugu rubripes. Science. 297:1301-10.

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.